Daily Papers

Distributed training of large models consumes enormous computation resources and requires substantial engineering efforts to compose various training techniques. This paper presents SimpleFSDP, a PyTorch-native compiler-based Fully Sharded Data Parallel (FSDP) framework, which has a simple implementation for maintenance and composability, allows full computation-communication graph tracing, and brings performance enhancement via compiler backend optimizations. SimpleFSDP's novelty lies in its unique torch.compile-friendly implementation of collective communications using existing PyTorch primitives, namely parametrizations, selective activation checkpointing, and DTensor. It also features the first-of-its-kind intermediate representation (IR) nodes bucketing and reordering in the TorchInductor backend for effective computation-communication overlapping. As a result, users can employ the aforementioned optimizations to automatically or manually wrap model components for minimal communication exposure. Extensive evaluations of SimpleFSDP on Llama 3 models (including the ultra-large 405B) using TorchTitan demonstrate up to 28.54% memory reduction and 68.67% throughput improvement compared to the most widely adopted FSDP2 eager framework, when composed with other distributed training techniques.

Existing checkpointing approaches seem ill-suited for distributed training even though hardware limitations make model parallelism, i.e., sharding model state across multiple accelerators, a requirement for model scaling. Consolidating distributed model state into a single checkpoint unacceptably slows down training, and is impractical at extreme scales. Distributed checkpoints, in contrast, are tightly coupled to the model parallelism and hardware configurations of the training run, and thus unusable on different configurations. To address this problem, we propose Universal Checkpointing, a technique that enables efficient checkpoint creation while providing the flexibility of resuming on arbitrary parallelism strategy and hardware configurations. Universal Checkpointing unlocks unprecedented capabilities for large-scale training such as improved resilience to hardware failures through continued training on remaining healthy hardware, and reduced training time through opportunistic exploitation of elastic capacity. The key insight of Universal Checkpointing is the selection of the optimal representation in each phase of the checkpointing life cycle: distributed representation for saving, and consolidated representation for loading. This is achieved using two key mechanisms. First, the universal checkpoint format, which consists of a consolidated representation of each model parameter and metadata for mapping parameter fragments into training ranks of arbitrary model-parallelism configuration. Second, the universal checkpoint language, a simple but powerful specification language for converting distributed checkpoints into the universal checkpoint format. Our evaluation demonstrates the effectiveness and generality of Universal Checkpointing on state-of-the-art model architectures and a wide range of parallelism techniques.

Extensive system scales (i.e. thousands of GPU/TPUs) and prolonged training periods (i.e. months of pretraining) significantly escalate the probability of failures when training large language models (LLMs). Thus, efficient and reliable fault-tolerance methods are in urgent need. Checkpointing is the primary fault-tolerance method to periodically save parameter snapshots from GPU memory to disks via CPU memory. In this paper, we identify the frequency of existing checkpoint-based fault-tolerance being significantly limited by the storage I/O overheads, which results in hefty re-training costs on restarting from the nearest checkpoint. In response to this gap, we introduce an in-memory fault-tolerance framework for large-scale LLM pretraining. The framework boosts the efficiency and reliability of fault tolerance from three aspects: (1) Reduced Data Transfer and I/O: By asynchronously caching parameters, i.e., sharded model parameters, optimizer states, and RNG states, to CPU volatile memory, Our framework significantly reduces communication costs and bypasses checkpoint I/O. (2) Enhanced System Reliability: Our framework enhances parameter protection with a two-layer hierarchy: snapshot management processes (SMPs) safeguard against software failures, together with Erasure Coding (EC) protecting against node failures. This double-layered protection greatly improves the survival probability of the parameters compared to existing checkpointing methods. (3) Improved Snapshotting Frequency: Our framework achieves more frequent snapshotting compared with asynchronous checkpointing optimizations under the same saving time budget, which improves the fault tolerance efficiency. Empirical results demonstrate that Our framework minimizes the overhead of fault tolerance of LLM pretraining by effectively leveraging redundant CPU resources.

Pipeline parallelism (PP) is widely used for training large language models (LLMs), yet its scalability is often constrained by high activation memory consumption as the number of in-flight microbatches grows with the degree of PP. In this paper, we focus on addressing this challenge by leveraging the under-explored memory offload strategy in PP. With empirical study, we discover that in the majority of standard configurations, at least half, and potentially all, of the activations can be offloaded with negligible overhead. In the cases where full overload is not possible, we introduce a novel selective offload strategy that decreases peak activation memory in a better-than-linear manner. Furthermore, we integrate memory offload with other techniques to jointly consider overall throughput and memory limitation. Our experiments proves that the per-device activation memory effectively reduces with the total number of stages, making PP a stronger alternative than TP, offering up to a 19\% acceleration with even lower memory consumption. The implementation is open-sourced at https://github.com/sail-sg/zero-bubble-pipeline-parallelism{this url}.

As Neural Processing Units (NPU) or accelerators are increasingly deployed in a variety of applications including safety critical applications such as autonomous vehicle, and medical imaging, it is critical to understand the fault-tolerance nature of the NPUs. We present a reliability study of Arm's Ethos-U55, an important industrial-scale NPU being utilised in embedded and IoT applications. We perform large scale RTL-level fault injections to characterize Ethos-U55 against the Automotive Safety Integrity Level D (ASIL-D) resiliency standard commonly used for safety-critical applications such as autonomous vehicles. We show that, under soft errors, all four configurations of the NPU fall short of the required level of resiliency for a variety of neural networks running on the NPU. We show that it is possible to meet the ASIL-D level resiliency without resorting to conventional strategies like Dual Core Lock Step (DCLS) that has an area overhead of 100%. We achieve so through selective protection, where hardware structures are selectively protected (e.g., duplicated, hardened) based on their sensitivity to soft errors and their silicon areas. To identify the optimal configuration that minimizes the area overhead while meeting the ASIL-D standard, the main challenge is the large search space associated with the time-consuming RTL simulation. To address this challenge, we present a statistical analysis tool that is validated against Arm silicon and that allows us to quickly navigate hundreds of billions of fault sites without exhaustive RTL fault injections. We show that by carefully duplicating a small fraction of the functional blocks and hardening the Flops in other blocks meets the ASIL-D safety standard while introducing an area overhead of only 38%.

LLMs have shown remarkable capabilities, but precisely controlling their response behavior remains challenging. Existing activation steering methods alter LLM behavior indiscriminately, limiting their practical applicability in settings where selective responses are essential, such as content moderation or domain-specific assistants. In this paper, we propose Conditional Activation Steering (CAST), which analyzes LLM activation patterns during inference to selectively apply or withhold activation steering based on the input context. Our method is based on the observation that different categories of prompts activate distinct patterns in the model's hidden states. Using CAST, one can systematically control LLM behavior with rules like "if input is about hate speech or adult content, then refuse" or "if input is not about legal advice, then refuse." This allows for selective modification of responses to specific content while maintaining normal responses to other content, all without requiring weight optimization. We release an open-source implementation of our framework at github.com/IBM/activation-steering .

Instruction fine-tuning pretrained LLMs for diverse downstream tasks has demonstrated remarkable success and has captured the interest of both academics and practitioners. To ensure such fine-tuned LLMs align with human preferences, techniques such as RLHF and DPO have emerged. At the same time, there is increasing interest in smaller parameter counts for models. In this work, using OpenLLaMA 3Bv2 as a base model, we describe the recipe used to fine-tune the OpenBezoar family of models. In this recipe: We first generate synthetic instruction fine-tuning data using an open and commercially non-restrictive instruction fine-tuned variant of the Falcon-40B model under three schemes based on: LaMini-LM, WizardLM/Evol-Instruct (with databricks-dolly-15k as a seed dataset) and Orca (with the Flan Collection as a seed dataset), then filter these generations using GPT-4 as a human proxy. We then perform cost-effective QLoRA-based supervised fine-tuning sequentially with each scheme. The resulting checkpoint is further fine-tuned with a subset of the HH-RLHF dataset to minimize distribution shift prior to using the DPO loss to obtain the final checkpoint. Evaluation is done with the LM Eval Harness tasks/metrics as well as on MT-Bench using the "LLM-as-a-judge" framework with Claude 2.1, with the finding that the final checkpoint, "OpenBezoar-HH-RLHF-DPO", demonstrates superior performance over many models at the 3B parameter scale, even outperforming the top model in one of the categories on the Huggingface Open LLM Leaderboard. We release "OpenBezoar-SFT", "OpenBezoar-HH-RLHF-SFT", "OpenBezoar-HH-RLHF-DPO" checkpoints, alongside our generated datasets on HuggingFace at https://huggingface.co/collections/SurgeGlobal/open-bezoar-6620a24923e12127e9e2b9cc and our codebase at https://bitbucket.org/paladinanalytics/workspace/projects/OP.

The rapidly increasing computational cost of pretraining Large Language Models necessitates more efficient approaches. Numerous computational costs have been invested in existing well-trained checkpoints, but many of them remain underutilized due to engineering constraints or limited model capacity. To efficiently reuse this "sunk" cost, we propose to recycle pretrained checkpoints by expanding their parameter counts and continuing training. We propose orthogonal growth method well-suited for converged Mixture-of-Experts model: interpositional layer copying for depth growth and expert duplication with injected noise for width growth. To determine the optimal timing for such growth across checkpoints sequences, we perform comprehensive scaling experiments revealing that the final accuracy has a strong positive correlation with the amount of sunk cost, indicating that greater prior investment leads to better performance. We scale our approach to models with 70B parameters and over 1T training tokens, achieving 10.66% accuracy gain over training from scratch under the same additional compute budget. Our checkpoint recycling approach establishes a foundation for economically efficient large language model pretraining.

LLMs have seen rapid adoption in all domains. They need to be trained on high-end high-performance computing (HPC) infrastructures and ingest massive amounts of input data. Unsurprisingly, at such a large scale, unexpected events (e.g., failures of components, instability of the software, undesirable learning patterns, etc.), are frequent and typically impact the training in a negative fashion. Thus, LLMs need to be checkpointed frequently so that they can be rolled back to a stable state and subsequently fine-tuned. However, given the large sizes of LLMs, a straightforward checkpointing solution that directly writes the model parameters and optimizer state to persistent storage (e.g., a parallel file system), incurs significant I/O overheads. To address this challenge, in this paper we study how to reduce the I/O overheads for enabling fast and scalable checkpointing for LLMs that can be applied at high frequency (up to the granularity of individual iterations) without significant impact on the training process. Specifically, we introduce a lazy asynchronous multi-level approach that takes advantage of the fact that the tensors making up the model and optimizer state shards remain immutable for extended periods of time, which makes it possible to copy their content in the background with minimal interference during the training process. We evaluate our approach at scales of up to 180 GPUs using different model sizes, parallelism settings, and checkpointing frequencies. The results show up to 48times faster checkpointing and 2.2times faster end-to-end training runtime compared with the state-of-art checkpointing approaches.

Pipeline parallelism has been widely explored, but most existing schedules lack a systematic methodology. In this paper, we propose a framework to decompose pipeline schedules as repeating a building block and we show that the lifespan of the building block decides the peak activation memory of the pipeline schedule. Guided by the observations, we find that almost all existing pipeline schedules, to the best of our knowledge, are memory inefficient. To address this, we introduce a family of memory efficient building blocks with controllable activation memory, which can reduce the peak activation memory to 1/2 of 1F1B without sacrificing efficiency, and even to 1/3 with comparable throughput. We can also achieve almost zero pipeline bubbles while maintaining the same activation memory as 1F1B. Our evaluations demonstrate that in pure pipeline parallelism settings, our methods outperform 1F1B by from 7% to 55% in terms of throughput. When employing a grid search over hybrid parallelism hyperparameters in practical scenarios, our proposed methods demonstrate a 16% throughput improvement over the 1F1B baseline for large language models.

Recent advances in learning rate (LR) scheduling have demonstrated the effectiveness of decay-free approaches that eliminate the traditional decay phase while maintaining competitive performance. Model merging techniques have emerged as particularly promising solutions in this domain. We present Warmup-Stable and Merge (WSM), a general framework that establishes a formal connection between learning rate decay and model merging. WSM provides a unified theoretical foundation for emulating various decay strategies-including cosine decay, linear decay and inverse square root decay-as principled model averaging schemes, while remaining fully compatible with diverse optimization methods. Through extensive experiments, we identify merge duration-the training window for checkpoint aggregation-as the most critical factor influencing model performance, surpassing the importance of both checkpoint interval and merge quantity. Our framework consistently outperforms the widely-adopted Warmup-Stable-Decay (WSD) approach across multiple benchmarks, achieving significant improvements of +3.5% on MATH, +2.9% on HumanEval, and +5.5% on MMLU-Pro. The performance advantages extend to supervised fine-tuning scenarios, highlighting WSM's potential for long-term model refinement.

Machine unlearning, the ability for a machine learning model to forget, is becoming increasingly important to comply with data privacy regulations, as well as to remove harmful, manipulated, or outdated information. The key challenge lies in forgetting specific information while protecting model performance on the remaining data. While current state-of-the-art methods perform well, they typically require some level of retraining over the retained data, in order to protect or restore model performance. This adds computational overhead and mandates that the training data remain available and accessible, which may not be feasible. In contrast, other methods employ a retrain-free paradigm, however, these approaches are prohibitively computationally expensive and do not perform on par with their retrain-based counterparts. We present Selective Synaptic Dampening (SSD), a novel two-step, post hoc, retrain-free approach to machine unlearning which is fast, performant, and does not require long-term storage of the training data. First, SSD uses the Fisher information matrix of the training and forgetting data to select parameters that are disproportionately important to the forget set. Second, SSD induces forgetting by dampening these parameters proportional to their relative importance to the forget set with respect to the wider training data. We evaluate our method against several existing unlearning methods in a range of experiments using ResNet18 and Vision Transformer. Results show that the performance of SSD is competitive with retrain-based post hoc methods, demonstrating the viability of retrain-free post hoc unlearning approaches.

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.

Massive activations are scalar values in transformer hidden states that achieve values orders of magnitude larger than typical activations and have been shown to be critical for model functionality. While prior work has characterized these phenomena in fully trained models, the temporal dynamics of their emergence during training remain poorly understood. We present the first comprehensive analysis of massive activation development throughout transformer training, using the Pythia model family as our testbed. Through systematic analysis of various model sizes across multiple training checkpoints, we demonstrate that massive activation emergence follows predictable mathematical patterns that can be accurately modeled using an exponentially-modulated logarithmic function with five key parameters. We develop a machine learning framework to predict these mathematical parameters from architectural specifications alone, achieving high accuracy for steady-state behavior and moderate accuracy for emergence timing and magnitude. These findings enable architects to predict and potentially control key aspects of massive activation emergence through design choices, with significant implications for model stability, training cycle length, interpretability, and optimization. Our findings demonstrate that the emergence of massive activations is governed by model design and can be anticipated, and potentially controlled, before training begins.

With the growing scale and complexity of video data, efficiently processing long video sequences poses significant challenges due to the quadratic increase in memory and computational demands associated with existing transformer-based Large Multi-modal Models (LMMs). To address these issues, we introduce Video-Ma^2mba, a novel architecture that incorporates State Space Models (SSMs) within the Mamba-2 framework, replacing the attention mechanisms. This allows the LMMs to scale linearly in terms of time and memory requirements, making it feasible to handle long-duration video content. Furthermore, we enhance the memory efficiency introducing the Multi-Axis Gradient Checkpointing (MA-GC) method, which strategically manages memory by retaining only essential activations across multiple computational axes. Our approach significantly reduces the memory footprint compared to standard gradient checkpointing. Empirical analyses show that Video-Ma^2mba can process extensive video sequences-equivalent to millions of tokens or over two hours of continuous sequences at 1 FPS-on a single GPU. By maintaining a detailed capture of temporal dynamics, our model improves the accuracy and relevance of responses in long video understanding tasks, demonstrating substantial advantages over existing frameworks.

Checkpointing to preserve training states is crucial during the development of Large Foundation Models (LFMs), for training resumption upon various failures or changes in GPU resources and parallelism configurations. In addition, saved checkpoints are dispatched to evaluation tasks or transferred across different training stages (e.g., from pre-training to post-training). All these scenarios require resharding distributed checkpoints from one parallelism to another. In production environments, different LFMs are trained with various frameworks and storage backends, depending on model sizes and training scales. A high-performance checkpointing system is needed to enable efficient checkpoint management at scale throughout the lifecycle of LFM development. We introduce ByteCheckpoint, an industrial-grade checkpointing system for large-scale LFM training. ByteCheckpoint features: a parallelism-agnostic checkpoint representation that enables efficient load-time checkpoint resharding; a generic checkpoint saving/loading workflow to accommodate multiple training frameworks and support different storage backends; full-stack optimizations to ensure high I/O efficiency and scalability; a suite of monitoring tools to streamline large-scale performance analysis and bottleneck detection. Compared to existing open-source checkpointing systems [52, 58], ByteCheckpoint significantly reduces runtime checkpoint stalls, achieving an average reduction of 54.20x. For saving and loading times, ByteCheckpoint achieves improvements of up to 9.96x and 8.80x, respectively.

Model merging has shown great promise at combining expert models, but the benefit of merging is unclear when merging ``generalist'' models trained on many tasks. We explore merging in the context of large (sim100B) models, by recycling checkpoints that exhibit tradeoffs among different tasks. Such checkpoints are often created in the process of developing a frontier model, and many suboptimal ones are usually discarded. Given a pool of model checkpoints obtained from different training runs (e.g., different stages, objectives, hyperparameters, and data mixtures), which naturally show tradeoffs across different language capabilities (e.g., instruction following vs. code generation), we investigate whether merging can recycle such suboptimal models into a Pareto-optimal one. Our optimization algorithm tunes the weight of each checkpoint in a linear combination, resulting in a Pareto-optimal models that outperforms both individual models and merge-based baselines. Further analysis shows that good merges tend to include almost all checkpoints with with non-zero weights, indicating that even seemingly bad initial checkpoints can contribute to good final merges.

While decoder-only large language models (LLMs) have shown impressive results, encoder-decoder models are still widely adopted in real-world applications for their inference efficiency and richer encoder representation. In this paper, we study a novel problem: adapting pretrained decoder-only LLMs to encoder-decoder, with the goal of leveraging the strengths of both approaches to achieve a more favorable quality-efficiency trade-off. We argue that adaptation not only enables inheriting the capability of decoder-only LLMs but also reduces the demand for computation compared to pretraining from scratch. We rigorously explore different pretraining objectives and parameter initialization/optimization techniques. Through extensive experiments based on Gemma 2 (2B and 9B) and a suite of newly pretrained mT5-sized models (up to 1.6B), we demonstrate the effectiveness of adaptation and the advantage of encoder-decoder LLMs. Under similar inference budget, encoder-decoder LLMs achieve comparable (often better) pretraining performance but substantially better finetuning performance than their decoder-only counterpart. For example, Gemma 2B-2B outperforms Gemma 2B by sim7\% after instruction tuning. Encoder-decoder adaptation also allows for flexible combination of different-sized models, where Gemma 9B-2B significantly surpasses Gemma 2B-2B by >3\%. The adapted encoder representation also yields better results on SuperGLUE. We will release our checkpoints to facilitate future research.

Training LLMs on decentralized and wimpy computation nodes, e.g., multiple on-spot instances, lowers the training cost and enables model democratization. The inevitable challenge here is the churn of nodes due to failures and the operator's scheduling policies, leading to losing a stage - a part of the model. The conventional approaches to recover from failures are to either use checkpointing, where periodically a copy of the entire model is sent to an additional storage, or redundant computation. These approaches yield significant communication and/or computation overhead even in non-failure cases and scale poorly in settings with large models. In this paper, we propose, CheckFree, an efficient recovery method where a failing stage is substituted by a weighted average of the closest neighboring stages. In contrast to the state of the art, CheckFree requires no additional computation or storage. However, because of the nature of averaging neighbouring stages, it can only recover failures of intermediate stages. We further extend our method to CheckFree+ with out-of-order pipeline execution to tolerate crashes of the first and last stages. Thanks to out-of-order pipelining, behaviour of those stages is mimicked by their neighboring ones, which allows CheckFree+ to recover them by simply copying the weights from the immediate neighbour. To be able to recover the (de)embedding layers, CheckFree+ copies those layers to the neighboring stages, which requires relatively small storage overhead. We extensively evaluate our method on LLaMa models of model sizes from 124M to 1.5B with varying failure frequencies. In the case of low and medium failure rates (5-10%), CheckFree and CheckFree+ outperform both checkpointing and redundant computation in terms of convergence in wall-clock time by over 12%. Both of our proposals can be run via our code available at: https://github.com/gensyn-ai/CheckFree.

Deploying large language models (LLMs) on edge devices presents significant challenges due to the substantial computational overhead and memory requirements. Activation sparsification can mitigate these challenges by reducing the number of activated neurons during inference. Existing methods typically employ thresholding-based sparsification based on the statistics of activation tensors. However, these methods do not explicitly model the impact of activation sparsification on performance, leading to suboptimal performance degradation. To address this issue, this paper reformulates the activation sparsification problem by introducing a new objective that optimizes the sparsification decisions. Building on this reformulation, we propose CHESS, a general activation sparsification approach via CHannel-wise thrEsholding and Selective Sparsification. First, channel-wise thresholding assigns a unique threshold to each activation channel in the feed-forward network (FFN) layers. Then, selective sparsification involves applying thresholding-based activation sparsification to specific layers within the attention modules. Finally, we detail the implementation of sparse kernels to accelerate LLM inference. Experimental results demonstrate that the proposed CHESS achieves lower performance degradation over 8 downstream tasks while activating fewer parameters compared to existing methods, thus speeding up the LLM inference by up to 1.27x.

Deep Neural Networks (DNNs) are extensively employed in safety-critical applications where ensuring hardware reliability is a primary concern. To enhance the reliability of DNNs against hardware faults, activation restriction techniques significantly mitigate the fault effects at the DNN structure level, irrespective of accelerator architectures. State-of-the-art methods offer either neuron-wise or layer-wise clipping activation functions. They attempt to determine optimal clipping thresholds using heuristic and learning-based approaches. Layer-wise clipped activation functions cannot preserve DNNs resilience at high bit error rates. On the other hand, neuron-wise clipping activation functions introduce considerable memory overhead due to the addition of parameters, which increases their vulnerability to faults. Moreover, the heuristic-based optimization approach demands numerous fault injections during the search process, resulting in time-consuming threshold identification. On the other hand, learning-based techniques that train thresholds for entire layers concurrently often yield sub-optimal results. In this work, first, we demonstrate that it is not essential to incorporate neuron-wise activation functions throughout all layers in DNNs. Then, we propose a hybrid clipped activation function that integrates neuron-wise and layer-wise methods that apply neuron-wise clipping only in the last layer of DNNs. Additionally, to attain optimal thresholds in the clipping activation function, we introduce ProAct, a progressive training methodology. This approach iteratively trains the thresholds on a layer-by-layer basis, aiming to obtain optimal threshold values in each layer separately.

Model merging enables efficient multi-task models by combining task-specific fine-tuned checkpoints. However, storing multiple task-specific checkpoints requires significant memory, limiting scalability and restricting model merging to larger models and diverse tasks. In this paper, we propose quantizing task vectors (i.e., the difference between pre-trained and fine-tuned checkpoints) instead of quantizing fine-tuned checkpoints. We observe that task vectors exhibit a narrow weight range, enabling low precision quantization (up to 4 bit) within existing task vector merging frameworks. To further mitigate quantization errors within ultra-low bit precision (e.g., 2 bit), we introduce Residual Task Vector Quantization, which decomposes the task vector into a base vector and offset component. We allocate bits based on quantization sensitivity, ensuring precision while minimizing error within a memory budget. Experiments on image classification and dense prediction show our method maintains or improves model merging performance while using only 8% of the memory required for full-precision checkpoints.

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

Recently, the Muon optimizer based on matrix orthogonalization has demonstrated strong results in training small-scale language models, but the scalability to larger models has not been proven. We identify two crucial techniques for scaling up Muon: (1) adding weight decay and (2) carefully adjusting the per-parameter update scale. These techniques allow Muon to work out-of-the-box on large-scale training without the need of hyper-parameter tuning. Scaling law experiments indicate that Muon achieves sim!2times computational efficiency compared to AdamW with compute optimal training. Based on these improvements, we introduce Moonlight, a 3B/16B-parameter Mixture-of-Expert (MoE) model trained with 5.7T tokens using Muon. Our model improves the current Pareto frontier, achieving better performance with much fewer training FLOPs compared to prior models. We open-source our distributed Muon implementation that is memory optimal and communication efficient. We also release the pretrained, instruction-tuned, and intermediate checkpoints to support future research.

Large Language Models (LLMs) have showcased remarkable capabilities across various domains. Accompanying the evolving capabilities and expanding deployment scenarios of LLMs, their deployment challenges escalate due to their sheer scale and the advanced yet complex activation designs prevalent in notable model series, such as Llama, Gemma, and Mistral. These challenges have become particularly pronounced in resource-constrained deployment scenarios, where mitigating inference efficiency bottlenecks is imperative. Among various recent efforts, activation approximation has emerged as a promising avenue for pursuing inference efficiency, sometimes considered indispensable in applications such as private inference. Despite achieving substantial speedups with minimal impact on utility, even appearing sound and practical for real-world deployment, the safety implications of activation approximations remain unclear. In this work, we fill this critical gap in LLM safety by conducting the first systematic safety evaluation of activation approximations. Our safety vetting spans seven sota techniques across three popular categories, revealing consistent safety degradation across ten safety-aligned LLMs.

Training Large Language Models (LLMs) incurs significant cost; hence, any strategy that accelerates model convergence is helpful. In this paper, we investigate the ability of a simple idea checkpoint averaging along the trajectory of a training run to improve both convergence and generalization quite early on during training. Here we show that models trained with high learning rates observe higher gains due to checkpoint averaging. Furthermore, these gains are amplified when checkpoints are sampled with considerable spacing in training steps. Our training recipe outperforms conventional training and popular checkpoint averaging baselines such as exponential moving average (EMA) and stochastic moving average (SWA). We evaluate our training recipe by pre-training LLMs, where high learning rates are inherently preferred due to extremely large batch sizes. Specifically, we pre-trained nanoGPT-2 models of varying sizes, small (125M), medium (335M), and large (770M)on the OpenWebText dataset, comprised of 9B tokens. Additionally, we present results for publicly available Pythia LLMs, ranging from 1B to 12B, which were trained on the PILE-deduped dataset containing 207B tokens.

Quantitative susceptibility maps from magnetic resonance images can provide both prognostic and diagnostic information in multiple sclerosis, a neurodegenerative disease characterized by the formation of lesions in white matter brain tissue. In particular, susceptibility maps provide adequate contrast to distinguish between "rim" lesions, surrounded by deposited paramagnetic iron, and "non-rim" lesion types. These paramagnetic rim lesions (PRLs) are an emerging biomarker in multiple sclerosis. Much effort has been devoted to both detection and segmentation of such lesions to monitor longitudinal change. As paramagnetic rim lesions are rare, addressing this problem requires confronting the class imbalance between rim and non-rim lesions. We produce synthetic quantitative susceptibility maps of paramagnetic rim lesions and show that inclusion of such synthetic data improves classifier performance and provide a multi-channel extension to generate accompanying contrasts and probabilistic segmentation maps. We exploit the projection capability of our trained generative network to demonstrate a novel denoising approach that allows us to train on ambiguous rim cases and substantially increase the minority class. We show that both synthetic lesion synthesis and our proposed rim lesion label denoising method best approximate the unseen rim lesion distribution and improve detection in a clinically interpretable manner. We release our code and generated data at https://github.com/agr78/PRLx-GAN upon publication.

Efficiently training large language models requires parallelizing across hundreds of hardware accelerators and invoking various compute and memory optimizations. When combined, many of these strategies have complex interactions regarding the final training efficiency. Prior work tackling this problem did not have access to the latest set of optimizations, such as FlashAttention or sequence parallelism. In this work, we conduct a comprehensive ablation study of possible training configurations for large language models. We distill this large study into several key recommendations for the most efficient training. For instance, we find that using a micro-batch size of 1 usually enables the most efficient training layouts. Larger micro-batch sizes necessitate activation checkpointing or higher degrees of model parallelism and also lead to larger pipeline bubbles. Our most efficient configurations enable us to achieve state-of-the-art training efficiency results over a range of model sizes, most notably a Model FLOPs utilization of 70.5% when training a Llama 13B model.

Activation steering methods were shown to be effective in conditioning language model generation by additively intervening over models' intermediate representations. However, the evaluation of these techniques has so far been limited to single conditioning properties and synthetic settings. In this work, we conduct a comprehensive evaluation of various activation steering strategies, highlighting the property-dependent nature of optimal parameters to ensure a robust effect throughout generation. To address this issue, we propose Dynamic Activation Composition, an information-theoretic approach to modulate the steering intensity of one or more properties throughout generation. Our experiments on multi-property steering show that our method successfully maintains high conditioning while minimizing the impact of conditioning on generation fluency.

The ability of language models in RAG systems to selectively refuse to answer based on flawed context is critical for safety, yet remains a significant failure point. Our large-scale study reveals that even frontier models struggle in this setting, with refusal accuracy dropping below 50% on multi-document tasks, while exhibiting either dangerous overconfidence or overcaution. Static benchmarks fail to reliably evaluate this capability, as models exploit dataset-specific artifacts and memorize test instances. We introduce RefusalBench, a generative methodology that programmatically creates diagnostic test cases through controlled linguistic perturbation. Our framework employs 176 distinct perturbation strategies across six categories of informational uncertainty and three intensity levels. Evaluation of over 30 models uncovers systematic failure patterns: refusal comprises separable detection and categorization skills, and neither scale nor extended reasoning improves performance. We find that selective refusal is a trainable, alignment-sensitive capability, offering a clear path for improvement. We release two benchmarks -- RefusalBench-NQ (single document) and RefusalBench-GaRAGe (multi-document) -- and our complete generation framework to enable continued, dynamic evaluation of this critical capability.

Multimodal pathology-genomic analysis is critical for cancer survival prediction. However, existing approaches predominantly integrate formalin-fixed paraffin-embedded (FFPE) slides with genomic data, while neglecting the availability of other preservation slides, such as Fresh Froze (FF) slides. Moreover, as the high-resolution spatial nature of pathology data tends to dominate the cross-modality fusion process, it hinders effective multimodal fusion and leads to modality imbalance challenges between pathology and genomics. These methods also typically require complete data modalities, limiting their clinical applicability with incomplete modalities, such as missing either pathology or genomic data. In this paper, we propose a multimodal survival prediction framework that leverages hypergraph learning to effectively integrate multi-WSI information and cross-modality interactions between pathology slides and genomics data while addressing modality imbalance. In addition, we introduce a memory mechanism that stores previously learned paired pathology-genomic features and dynamically compensates for incomplete modalities. Experiments on five TCGA datasets demonstrate that our model outperforms advanced methods by over 2.3% in C-Index. Under incomplete modality scenarios, our approach surpasses pathology-only (3.3%) and gene-only models (7.9%). Code: https://github.com/MCPathology/M2Surv

The out-of-distribution (OOD) problem generally arises when neural networks encounter data that significantly deviates from the training data distribution, i.e., in-distribution (InD). In this paper, we study the OOD problem from a neuron activation view. We first formulate neuron activation states by considering both the neuron output and its influence on model decisions. Then, to characterize the relationship between neurons and OOD issues, we introduce the neuron activation coverage (NAC) -- a simple measure for neuron behaviors under InD data. Leveraging our NAC, we show that 1) InD and OOD inputs can be largely separated based on the neuron behavior, which significantly eases the OOD detection problem and beats the 21 previous methods over three benchmarks (CIFAR-10, CIFAR-100, and ImageNet-1K). 2) a positive correlation between NAC and model generalization ability consistently holds across architectures and datasets, which enables a NAC-based criterion for evaluating model robustness. Compared to prevalent InD validation criteria, we show that NAC not only can select more robust models, but also has a stronger correlation with OOD test performance.

While activation steering in large language models (LLMs) is a growing area of research, methods can often incur broader effects than desired. This motivates isolation of purer concept vectors to enable targeted interventions and understand LLM behavior at a more granular level. We present RepIt, a simple and data-efficient framework for isolating concept-specific representations. Across five frontier LLMs, RepIt enables precise interventions: it selectively suppresses refusal on targeted concepts while preserving refusal elsewhere, producing models that answer WMD-related questions while still scoring as safe on standard benchmarks. We further show that the corrective signal localizes to just 100-200 neurons and that robust target representations can be extracted from as few as a dozen examples on a single A6000. This efficiency raises a dual concern: manipulations can be performed with modest compute and data to extend to underrepresented data-scarce topics while evading existing benchmarks. By disentangling refusal vectors with RepIt, this work demonstrates that targeted interventions can counteract overgeneralization, laying the foundation for more granular control of model behavior.

Activation steering is a promising technique for controlling LLM behavior by adding semantically meaningful vectors directly into a model's hidden states during inference. It is often framed as a precise, interpretable, and potentially safer alternative to fine-tuning. We demonstrate the opposite: steering systematically breaks model alignment safeguards, making it comply with harmful requests. Through extensive experiments on different model families, we show that even steering in a random direction can increase the probability of harmful compliance from 0% to 2-27%. Alarmingly, steering benign features from a sparse autoencoder (SAE), a common source of interpretable directions, increases these rates by a further 2-4%. Finally, we show that combining 20 randomly sampled vectors that jailbreak a single prompt creates a universal attack, significantly increasing harmful compliance on unseen requests. These results challenge the paradigm of safety through interpretability, showing that precise control over model internals does not guarantee precise control over model behavior.

The widely used ReLU is favored for its hardware efficiency, {as the implementation at inference is a one bit sign case,} yet suffers from issues such as the ``dying ReLU'' problem, where during training, neurons fail to activate and constantly remain at zero, as highlighted by Lu et al. Traditional approaches to mitigate this issue often introduce more complex and less hardware-friendly activation functions. In this work, we propose a Hysteresis Rectified Linear Unit (HeLU), an efficient activation function designed to address the ``dying ReLU'' problem with minimal complexity. Unlike traditional activation functions with fixed thresholds for training and inference, HeLU employs a variable threshold that refines the backpropagation. This refined mechanism allows simpler activation functions to achieve competitive performance comparable to their more complex counterparts without introducing unnecessary complexity or requiring inductive biases. Empirical evaluations demonstrate that HeLU enhances model generalization across diverse datasets, offering a promising solution for efficient and effective inference suitable for a wide range of neural network architectures.

Large Language Model (LLM) agents use memory to learn from past interactions, enabling autonomous planning and decision-making in complex environments. However, this reliance on memory introduces a critical security risk: an adversary can inject seemingly harmless records into an agent's memory to manipulate its future behavior. This vulnerability is characterized by two core aspects: First, the malicious effect of injected records is only activated within a specific context, making them hard to detect when individual memory entries are audited in isolation. Second, once triggered, the manipulation can initiate a self-reinforcing error cycle: the corrupted outcome is stored as precedent, which not only amplifies the initial error but also progressively lowers the threshold for similar attacks in the future. To address these challenges, we introduce A-MemGuard (Agent-Memory Guard), the first proactive defense framework for LLM agent memory. The core idea of our work is the insight that memory itself must become both self-checking and self-correcting. Without modifying the agent's core architecture, A-MemGuard combines two mechanisms: (1) consensus-based validation, which detects anomalies by comparing reasoning paths derived from multiple related memories and (2) a dual-memory structure, where detected failures are distilled into ``lessons'' stored separately and consulted before future actions, breaking error cycles and enabling adaptation. Comprehensive evaluations on multiple benchmarks show that A-MemGuard effectively cuts attack success rates by over 95% while incurring a minimal utility cost. This work shifts LLM memory security from static filtering to a proactive, experience-driven model where defenses strengthen over time. Our code is available in https://github.com/TangciuYueng/AMemGuard

To ensure AI safety, instruction-tuned Large Language Models (LLMs) are specifically trained to ensure alignment, which refers to making models behave in accordance with human intentions. While these models have demonstrated commendable results on various safety benchmarks, the vulnerability of their safety alignment has not been extensively studied. This is particularly troubling given the potential harm that LLMs can inflict. Existing attack methods on LLMs often rely on poisoned training data or the injection of malicious prompts. These approaches compromise the stealthiness and generalizability of the attacks, making them susceptible to detection. Additionally, these models often demand substantial computational resources for implementation, making them less practical for real-world applications. Inspired by recent success in modifying model behavior through steering vectors without the need for optimization, and drawing on its effectiveness in red-teaming LLMs, we conducted experiments employing activation steering to target four key aspects of LLMs: truthfulness, toxicity, bias, and harmfulness - across a varied set of attack settings. To establish a universal attack strategy applicable to diverse target alignments without depending on manual analysis, we automatically select the intervention layer based on contrastive layer search. Our experiment results show that activation attacks are highly effective and add little or no overhead to attack efficiency. Additionally, we discuss potential countermeasures against such activation attacks. Our code and data are available at https://github.com/wang2226/Backdoor-Activation-Attack Warning: this paper contains content that can be offensive or upsetting.

Multi-center positron emission tomography (PET) image synthesis aims at recovering low-dose PET images from multiple different centers. The generalizability of existing methods can still be suboptimal for a multi-center study due to domain shifts, which result from non-identical data distribution among centers with different imaging systems/protocols. While some approaches address domain shifts by training specialized models for each center, they are parameter inefficient and do not well exploit the shared knowledge across centers. To address this, we develop a generalist model that shares architecture and parameters across centers to utilize the shared knowledge. However, the generalist model can suffer from the center interference issue, i.e. the gradient directions of different centers can be inconsistent or even opposite owing to the non-identical data distribution. To mitigate such interference, we introduce a novel dynamic routing strategy with cross-layer connections that routes data from different centers to different experts. Experiments show that our generalist model with dynamic routing (DRMC) exhibits excellent generalizability across centers. Code and data are available at: https://github.com/Yaziwel/Multi-Center-PET-Image-Synthesis.

Existing pre-trained models are generally geared towards a particular class of problems. To date, there seems to be still no consensus on what the right architecture and pre-training setup should be. This paper presents a unified framework for pre-training models that are universally effective across datasets and setups. We begin by disentangling architectural archetypes with pre-training objectives -- two concepts that are commonly conflated. Next, we present a generalized & unified perspective for self-supervision in NLP and show how different pre-training objectives can be cast as one another and how interpolating between different objectives can be effective. We then propose Mixture-of-Denoisers (MoD), a pre-training objective that combines diverse pre-training paradigms together. We furthermore introduce a notion of mode switching, wherein downstream fine-tuning is associated with specific pre-training schemes. We conduct extensive ablative experiments to compare multiple pre-training objectives and find that our method pushes the Pareto-frontier by outperforming T5 & GPT-like models across multiple diverse setups. By scaling our model up to 20B parameters, we achieve SOTA performance on 50 well-established supervised finetuning based NLP tasks. Our model also achieve strong results at in-context learning, outperforming 175B GPT-3 on zero-shot SuperGLUE and tripling the performance of T5-XXL on one-shot summarization. On 0-shot MMLU, UL2 20B outperforms T0 and T5 models. UL2 20B also works well with chain-of-thought prompting and reasoning, making it an appealing choice for research into reasoning at a small to medium scale of 20B parameters. Finally, we apply FLAN instruction tuning to the UL2 20B model, achieving MMLU and Big-Bench scores competitive to FLAN-PaLM 62B. We release Flax-based T5X checkpoints for the UL2 20B & Flan-UL2 20B.

Stealthy hardware Trojans (HTs) inserted during the fabrication of integrated circuits can bypass the security of critical infrastructures. Although researchers have proposed many techniques to detect HTs, several limitations exist, including: (i) a low success rate, (ii) high algorithmic complexity, and (iii) a large number of test patterns. Furthermore, the most pertinent drawback of prior detection techniques stems from an incorrect evaluation methodology, i.e., they assume that an adversary inserts HTs randomly. Such inappropriate adversarial assumptions enable detection techniques to claim high HT detection accuracy, leading to a "false sense of security." Unfortunately, to the best of our knowledge, despite more than a decade of research on detecting HTs inserted during fabrication, there have been no concerted efforts to perform a systematic evaluation of HT detection techniques. In this paper, we play the role of a realistic adversary and question the efficacy of HT detection techniques by developing an automated, scalable, and practical attack framework, ATTRITION, using reinforcement learning (RL). ATTRITION evades eight detection techniques across two HT detection categories, showcasing its agnostic behavior. ATTRITION achieves average attack success rates of 47times and 211times compared to randomly inserted HTs against state-of-the-art HT detection techniques. We demonstrate ATTRITION's ability to evade detection techniques by evaluating designs ranging from the widely-used academic suites to larger designs such as the open-source MIPS and mor1kx processors to AES and a GPS module. Additionally, we showcase the impact of ATTRITION-generated HTs through two case studies (privilege escalation and kill switch) on the mor1kx processor. We envision that our work, along with our released HT benchmarks and models, fosters the development of better HT detection techniques.

Checkpoint merging is a technique for combining multiple model snapshots into a single superior model, potentially reducing training time for large language models. This paper explores checkpoint merging in the context of parameter-efficient fine-tuning (PEFT), where only small adapter modules (e.g. LoRA) are trained. We propose Metrics-Weighted Averaging (MWA), a simple yet effective method to merge model checkpoints by weighting their parameters according to performance metrics. In particular, we investigate weighting by training loss and by training steps, under the intuition that lower-loss or later-step checkpoints are more valuable. We introduce a formula with a penalty factor to adjust weight distribution, requiring only one hyperparameter regardless of the number of checkpoints. Experiments on three fine-tuning tasks (mathematical reasoning, preference alignment, and general instruction tuning) show that MWA consistently produces merged models that outperform the naive uniform average of checkpoints. Notably, loss-weighted merging often yields the best results, delivering up to 5% higher task accuracy than the baseline uniform merge and even surpassing the final individual checkpoint's performance. These findings validate checkpoint merging for PEFT and demonstrate that a metric-driven weighting heuristic can efficiently boost model performance with minimal computational overhead.

This work examines whether activating latent subspaces in language models (LLMs) can steer scientific code generation toward a specific programming language. Five causal LLMs were first evaluated on scientific coding prompts to quantify their baseline bias among four programming languages. A static neuron-attribution method, perturbing the highest activated MLP weight for a C++ or CPP token, proved brittle and exhibited limited generalization across prompt styles and model scales. To address these limitations, a gradient-refined adaptive activation steering framework (G-ACT) was developed: per-prompt activation differences are clustered into a small set of steering directions, and lightweight per-layer probes are trained and refined online to select the appropriate steering vector. In LLaMA-3.2 3B, this approach reliably biases generation towards the CPP language by increasing the average probe classification accuracy by 15% and the early layers (0-6) improving the probe classification accuracy by 61.5% compared to the standard ACT framework. For LLaMA-3.3 70B, where attention-head signals become more diffuse, targeted injections at key layers still improve language selection. Although per-layer probing introduces a modest inference overhead, it remains practical by steering only a subset of layers and enables reproducible model behavior. These results demonstrate a scalable, interpretable and efficient mechanism for concept-level control for practical agentic systems.

Large Language Models have demonstrated impressive fluency across diverse tasks, yet their tendency to produce toxic content remains a critical challenge for AI safety and public trust. Existing toxicity mitigation approaches primarily manipulate individual neuron activations, but these methods suffer from instability, context dependence, and often compromise the model's core language abilities. To address these shortcomings, we investigate three key questions: the stability of neuron-level toxicity indicators, the advantages of structural (layer-wise) representations, and the interpretability of mechanisms driving toxic generation. Through extensive experiments on Jigsaw and ToxiCN datasets, we show that aggregated layer-wise features provide more robust signals than single neurons. Moreover, we observe conceptual limitations in prior works that conflate toxicity detection experts and generation experts within neuron-based interventions. To mitigate this, we propose a novel principled intervention technique, EigenShift, based on eigen-decomposition of the language model's final output layer. This method selectively targets generation-aligned components, enabling precise toxicity suppression without impairing linguistic competence. Our method requires no additional training or fine-tuning, incurs minimal computational cost, and is grounded in rigorous theoretical analysis.

Training language models currently requires pre-determining a fixed compute budget because the typical cosine learning rate schedule depends on the total number of steps. In contrast, the Warmup-Stable-Decay (WSD) schedule uses a constant learning rate to produce a main branch of iterates that can in principle continue indefinitely without a pre-specified compute budget. Then, given any compute budget, one can branch out from the main branch at a proper time with a rapidly decaying learning rate to produce a strong model. Empirically, WSD generates a non-traditional loss curve: the loss remains elevated during the stable phase but sharply declines during the decay phase. Towards explaining this phenomenon, we conjecture that pretraining loss exhibits a river valley landscape, which resembles a deep valley with a river at its bottom. Under this assumption, we show that during the stable phase, the iterate undergoes large oscillations due to the high learning rate, yet it progresses swiftly along the river. During the decay phase, the rapidly dropping learning rate minimizes the iterate's oscillations, moving it closer to the river and revealing true optimization progress. Therefore, the sustained high learning rate phase and fast decaying phase are responsible for progress in the river and the mountain directions respectively, and are both critical. Our analysis predicts phenomenons consistent with empirical observations and shows that this landscape can emerge from pretraining on a simple bi-gram dataset. Inspired by the theory, we introduce WSD-S, a variant of WSD that reuses previous checkpoints' decay phases and keeps only one main branch, where we resume from a decayed checkpoint. WSD-S empirically outperforms WSD and Cyclic-Cosine in obtaining multiple language model checkpoints across various compute budgets in a single run for parameters scaling from 0.1B to 1.2B.

Training large transformer models is one of the most important computational challenges of modern AI. In this paper, we show how to significantly accelerate training of large transformer models by reducing activation recomputation. Activation recomputation is commonly used to work around memory capacity constraints. Rather than storing activations for backpropagation, they are traditionally recomputed, which saves memory but adds redundant compute. In this work, we show most of this redundant compute is unnecessary because we can reduce memory consumption sufficiently without it. We present two novel yet very simple techniques: sequence parallelism and selective activation recomputation. In conjunction with tensor parallelism, these techniques almost eliminate the need to recompute activations. We evaluate our approach on language models up to one trillion parameters in scale and show that our method reduces activation memory by 5x, while reducing execution time overhead from activation recomputation by over 90%. For example, when training a 530B parameter GPT-3 style model on 2240 NVIDIA A100 GPUs, we achieve a Model Flops Utilization of 54.2%, which is 29% faster than the 42.1% we achieve using recomputation. Our implementation will be available in both Megatron-LM and NeMo-Megatron.

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

The increasing capabilities of large generative models and their ever more widespread deployment have raised concerns about their reliability, safety, and potential misuse. To address these issues, recent works have proposed to control model generation by steering model activations in order to effectively induce or prevent the emergence of concepts or behaviors in the generated output. In this paper we introduce Activation Transport (AcT), a general framework to steer activations guided by optimal transport theory that generalizes many previous activation-steering works. AcT is modality-agnostic and provides fine-grained control over the model behavior with negligible computational overhead, while minimally impacting model abilities. We experimentally show the effectiveness and versatility of our approach by addressing key challenges in large language models (LLMs) and text-to-image diffusion models (T2Is). For LLMs, we show that AcT can effectively mitigate toxicity, induce arbitrary concepts, and increase their truthfulness. In T2Is, we show how AcT enables fine-grained style control and concept negation.

Safety fine-tuning algorithms are commonly used to fine-tune language models to reduce harmful outputs, but the exact internal mechanisms of how those models achieve this remain unclear. In studying direct preference optimisation (DPO) for toxicity reduction, current explanations claim that DPO works by dampening the most toxic MLP neurons to learn an offset to avert toxic regions in the residual stream. However, by ablating the most toxic neurons and applying activation patching, we find this explanation incomplete. By projecting neuron activation changes onto a toxicity probe, we find that only 31.8\% of toxicity reduction comes from dampened toxic neurons. Instead, DPO reduces toxicity by accumulating effects across multiple neuron groups, both reducing writing in the toxic direction and promoting anti-toxicity in the residual stream. Moreover, DPO gives noisy adjustments to neuron activations, with many neurons actually increasing toxicity. This indicates that DPO is a balancing process between opposing neuron effects to achieve toxicity reduction.

Practical large language model (LLM) services may involve a long system prompt, which specifies the instructions, examples, and knowledge documents of the task and is reused across numerous requests. However, the long system prompt causes throughput/latency bottlenecks as the cost of generating the next token grows w.r.t. the sequence length. This paper aims to improve the efficiency of LLM services that involve long system prompts. Our key observation is that handling these system prompts requires heavily redundant memory accesses in existing causal attention computation algorithms. Specifically, for batched requests, the cached hidden states (i.e., key-value pairs) of system prompts are transferred from off-chip DRAM to on-chip SRAM multiple times, each corresponding to an individual request. To eliminate such a redundancy, we propose RelayAttention, an attention algorithm that allows reading these hidden states from DRAM exactly once for a batch of input tokens. RelayAttention is a free lunch: it maintains the generation quality while requiring no model retraining, as it is based on a mathematical reformulation of causal attention.

Nowadays, Large Language Models (LLMs) have been trained using extended context lengths to foster more creative applications. However, long context training poses great challenges considering the constraint of GPU memory. It not only leads to substantial activation memory consumption during training, but also incurs considerable memory fragmentation. To facilitate long context training, existing frameworks have adopted strategies such as recomputation and various forms of parallelisms. Nevertheless, these techniques rely on redundant computation or extensive communication, resulting in low Model FLOPS Utilization (MFU). In this paper, we propose MEMO, a novel LLM training framework designed for fine-grained activation memory management. Given the quadratic scaling of computation and linear scaling of memory with sequence lengths when using FlashAttention, we offload memory-consuming activations to CPU memory after each layer's forward pass and fetch them during the backward pass. To maximize the swapping of activations without hindering computation, and to avoid exhausting limited CPU memory, we implement a token-wise activation recomputation and swapping mechanism. Furthermore, we tackle the memory fragmentation issue by employing a bi-level Mixed Integer Programming (MIP) approach, optimizing the reuse of memory across transformer layers. Empirical results demonstrate that MEMO achieves an average of 2.42x and 2.26x MFU compared to Megatron-LM and DeepSpeed, respectively. This improvement is attributed to MEMO's ability to minimize memory fragmentation, reduce recomputation and intensive communication, and circumvent the delays associated with the memory reorganization process due to fragmentation. By leveraging fine-grained activation memory management, MEMO facilitates efficient training of 7B LLM with 1 million sequence length on just 8 A800 GPUs, achieving an MFU of 52.30%.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

Large language models (LLMs) have achieved remarkable performance across many generation tasks. Nevertheless, effectively aligning them with desired behaviors remains a significant challenge. Activation steering is an effective and cost-efficient approach that directly modifies the activations of LLMs during the inference stage, aligning their responses with the desired behaviors and avoiding the high cost of fine-tuning. Existing methods typically indiscriminately intervene to all generations or rely solely on the question to determine intervention, which limits the accurate assessment of the intervention strength. To this end, we propose the Flexible Activation Steering with Backtracking (FASB) framework, which dynamically determines both the necessity and strength of intervention by tracking the internal states of the LLMs during generation, considering both the question and the generated content. Since intervening after detecting a deviation from the desired behavior is often too late, we further propose the backtracking mechanism to correct the deviated tokens and steer the LLMs toward the desired behavior. Extensive experiments on the TruthfulQA dataset and six multiple-choice datasets demonstrate that our method outperforms baselines. Our code will be released at https://github.com/gjw185/FASB.

We study the design decisions of publicly available instruction tuning methods, and break down the development of Flan 2022 (Chung et al., 2022). Through careful ablation studies on the Flan Collection of tasks and methods, we tease apart the effect of design decisions which enable Flan-T5 to outperform prior work by 3-17%+ across evaluation settings. We find task balancing and enrichment techniques are overlooked but critical to effective instruction tuning, and in particular, training with mixed prompt settings (zero-shot, few-shot, and chain-of-thought) actually yields stronger (2%+) performance in all settings. In further experiments, we show Flan-T5 requires less finetuning to converge higher and faster than T5 on single downstream tasks, motivating instruction-tuned models as more computationally-efficient starting checkpoints for new tasks. Finally, to accelerate research on instruction tuning, we make the Flan 2022 collection of datasets, templates, and methods publicly available at https://github.com/google-research/FLAN/tree/main/flan/v2.

Survival analysis can sometimes involve individuals who will not experience the event of interest, forming what is known as the cured group. Identifying such individuals is not always possible beforehand, as they provide only right-censored data. Ignoring the presence of the cured group can introduce bias in the final model. This paper presents a method for estimating a semiparametric additive hazards model that accounts for the cured fraction. Unlike regression coefficients in a hazard ratio model, those in an additive hazard model measure hazard differences. The proposed method uses a primal-dual interior point algorithm to obtain constrained maximum penalized likelihood estimates of the model parameters, including the regression coefficients and the baseline hazard, subject to certain non-negativity constraints.

Efficiently training LLMs with long sequences is important yet challenged by the massive computation and memory requirements. Sequence parallelism has been proposed to tackle these problems, but existing methods suffer from scalability or efficiency issues. We propose LoongTrain, a novel system to efficiently train LLMs with long sequences at scale. The core of LoongTrain is the 2D-Attention mechanism, which combines both head-parallel and context-parallel techniques to break the scalability constraints while maintaining efficiency. We introduce Double-Ring-Attention and analyze the performance of device placement strategies to further speed up training. We implement LoongTrain with the hybrid ZeRO and Selective Checkpoint++ techniques. Experiment results show that LoongTrain outperforms state-of-the-art baselines, i.e., DeepSpeed-Ulysses and Megatron Context Parallelism, in both end-to-end training speed and scalability, and improves Model FLOPs Utilization (MFU) by up to 2.88x.

The prevalent use of commercial and open-source diffusion models (DMs) for text-to-image generation prompts risk mitigation to prevent undesired behaviors. Existing concept erasing methods in academia are all based on full parameter or specification-based fine-tuning, from which we observe the following issues: 1) Generation alternation towards erosion: Parameter drift during target elimination causes alternations and potential deformations across all generations, even eroding other concepts at varying degrees, which is more evident with multi-concept erased; 2) Transfer inability & deployment inefficiency: Previous model-specific erasure impedes the flexible combination of concepts and the training-free transfer towards other models, resulting in linear cost growth as the deployment scenarios increase. To achieve non-invasive, precise, customizable, and transferable elimination, we ground our erasing framework on one-dimensional adapters to erase multiple concepts from most DMs at once across versatile erasing applications. The concept-SemiPermeable structure is injected as a Membrane (SPM) into any DM to learn targeted erasing, and meantime the alteration and erosion phenomenon is effectively mitigated via a novel Latent Anchoring fine-tuning strategy. Once obtained, SPMs can be flexibly combined and plug-and-play for other DMs without specific re-tuning, enabling timely and efficient adaptation to diverse scenarios. During generation, our Facilitated Transport mechanism dynamically regulates the permeability of each SPM to respond to different input prompts, further minimizing the impact on other concepts. Quantitative and qualitative results across ~40 concepts, 7 DMs and 4 erasing applications have demonstrated the superior erasing of SPM. Our code and pre-tuned SPMs will be available on the project page https://lyumengyao.github.io/projects/spm.

The Mamba layer offers an efficient selective state space model (SSM) that is highly effective in modeling multiple domains including NLP, long-range sequences processing, and computer vision. Selective SSMs are viewed as dual models, in which one trains in parallel on the entire sequence via IO-aware parallel scan, and deploys in an autoregressive manner. We add a third view and show that such models can be viewed as attention-driven models. This new perspective enables us to compare the underlying mechanisms to that of the self-attention layers in transformers and allows us to peer inside the inner workings of the Mamba model with explainability methods. Our code is publicly available.

Reasoning-enhanced large language models (RLLMs), whether explicitly trained for reasoning or prompted via chain-of-thought (CoT), have achieved state-of-the-art performance on many complex reasoning tasks. However, we uncover a surprising and previously overlooked phenomenon: explicit CoT reasoning can significantly degrade instruction-following accuracy. Evaluating 15 models on two benchmarks: IFEval (with simple, rule-verifiable constraints) and ComplexBench (with complex, compositional constraints), we consistently observe performance drops when CoT prompting is applied. Through large-scale case studies and an attention-based analysis, we identify common patterns where reasoning either helps (e.g., with formatting or lexical precision) or hurts (e.g., by neglecting simple constraints or introducing unnecessary content). We propose a metric, constraint attention, to quantify model focus during generation and show that CoT reasoning often diverts attention away from instruction-relevant tokens. To mitigate these effects, we introduce and evaluate four strategies: in-context learning, self-reflection, self-selective reasoning, and classifier-selective reasoning. Our results demonstrate that selective reasoning strategies, particularly classifier-selective reasoning, can substantially recover lost performance. To our knowledge, this is the first work to systematically expose reasoning-induced failures in instruction-following and offer practical mitigation strategies.

In-context learning is a powerful emergent ability in transformer models. Prior work in mechanistic interpretability has identified a circuit element that may be critical for in-context learning -- the induction head (IH), which performs a match-and-copy operation. During training of large transformers on natural language data, IHs emerge around the same time as a notable phase change in the loss. Despite the robust evidence for IHs and this interesting coincidence with the phase change, relatively little is known about the diversity and emergence dynamics of IHs. Why is there more than one IH, and how are they dependent on each other? Why do IHs appear all of a sudden, and what are the subcircuits that enable them to emerge? We answer these questions by studying IH emergence dynamics in a controlled setting by training on synthetic data. In doing so, we develop and share a novel optogenetics-inspired causal framework for modifying activations throughout training. Using this framework, we delineate the diverse and additive nature of IHs. By clamping subsets of activations throughout training, we then identify three underlying subcircuits that interact to drive IH formation, yielding the phase change. Furthermore, these subcircuits shed light on data-dependent properties of formation, such as phase change timing, already showing the promise of this more in-depth understanding of subcircuits that need to "go right" for an induction head.

We present Synergy Aware Forgetting Ensemble (SAFE), a method to adapt large models on a diverse collection of data while minimizing the expected cost to remove the influence of training samples from the trained model. This process, also known as selective forgetting or unlearning, is often conducted by partitioning a dataset into shards, training fully independent models on each, then ensembling the resulting models. Increasing the number of shards reduces the expected cost to forget but at the same time it increases inference cost and reduces the final accuracy of the model since synergistic information between samples is lost during the independent model training. Rather than treating each shard as independent, SAFE introduces the notion of a shard graph, which allows incorporating limited information from other shards during training, trading off a modest increase in expected forgetting cost with a significant increase in accuracy, all while still attaining complete removal of residual influence after forgetting. SAFE uses a lightweight system of adapters which can be trained while reusing most of the computations. This allows SAFE to be trained on shards an order-of-magnitude smaller than current state-of-the-art methods (thus reducing the forgetting costs) while also maintaining high accuracy, as we demonstrate empirically on fine-grained computer vision datasets.

Large language models (LLMs) frequently refuse to respond to pseudo-malicious instructions: semantically harmless input queries triggering unnecessary LLM refusals due to conservative safety alignment, significantly impairing user experience. Collecting such instructions is crucial for evaluating and mitigating over-refusals, but existing instruction curation methods, like manual creation or instruction rewriting, either lack scalability or fail to produce sufficiently diverse and effective refusal-inducing prompts. To address these limitations, we introduce EVOREFUSE, a prompt optimization approach that generates diverse pseudo-malicious instructions consistently eliciting confident refusals across LLMs. EVOREFUSE employs an evolutionary algorithm exploring the instruction space in more diverse directions than existing methods via mutation strategies and recombination, and iteratively evolves seed instructions to maximize evidence lower bound on LLM refusal probability. Using EVOREFUSE, we create two novel datasets: EVOREFUSE-TEST, a benchmark of 582 pseudo-malicious instructions that outperforms the next-best benchmark with 140.41% higher average refusal triggering rate across 9 LLMs, 34.86% greater lexical diversity, and 40.03% improved LLM response confidence scores; and EVOREFUSE-ALIGN, which provides 3,000 pseudo-malicious instructions with responses for supervised and preference-based alignment training. LLAMA3.1-8B-INSTRUCT supervisedly fine-tuned on EVOREFUSE-ALIGN achieves up to 14.31% fewer over-refusals than models trained on the second-best alignment dataset, without compromising safety. Our analysis with EVOREFUSE-TEST reveals models trigger over-refusals by overly focusing on sensitive keywords while ignoring broader context.

The task of root cause analysis (RCA) is to identify the root causes of system faults/failures by analyzing system monitoring data. Efficient RCA can greatly accelerate system failure recovery and mitigate system damages or financial losses. However, previous research has mostly focused on developing offline RCA algorithms, which often require manually initiating the RCA process, a significant amount of time and data to train a robust model, and then being retrained from scratch for a new system fault. In this paper, we propose CORAL, a novel online RCA framework that can automatically trigger the RCA process and incrementally update the RCA model. CORAL consists of Trigger Point Detection, Incremental Disentangled Causal Graph Learning, and Network Propagation-based Root Cause Localization. The Trigger Point Detection component aims to detect system state transitions automatically and in near-real-time. To achieve this, we develop an online trigger point detection approach based on multivariate singular spectrum analysis and cumulative sum statistics. To efficiently update the RCA model, we propose an incremental disentangled causal graph learning approach to decouple the state-invariant and state-dependent information. After that, CORAL applies a random walk with restarts to the updated causal graph to accurately identify root causes. The online RCA process terminates when the causal graph and the generated root cause list converge. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

Instruction tuning (IT) is crucial to tailoring large language models (LLMs) towards human-centric interactions. Recent advancements have shown that the careful selection of a small, high-quality subset of IT data can significantly enhance the performance of LLMs. Despite this, common approaches often rely on additional models or data sets, which increases costs and limits widespread adoption. In this work, we propose a novel approach, termed SelectIT, that capitalizes on the foundational capabilities of the LLM itself. Specifically, we exploit the intrinsic uncertainty present in LLMs to more effectively select high-quality IT data, without the need for extra resources. Furthermore, we introduce a novel IT dataset, the Selective Alpaca, created by applying SelectIT to the Alpaca-GPT4 dataset. Empirical results demonstrate that IT using Selective Alpaca leads to substantial model ability enhancement. The robustness of SelectIT has also been corroborated in various foundation models and domain-specific tasks. Our findings suggest that longer and more computationally intensive IT data may serve as superior sources of IT, offering valuable insights for future research in this area. Data, code, and scripts are freely available at https://github.com/Blue-Raincoat/SelectIT.

Activation Patching is a method of directly computing causal attributions of behavior to model components. However, applying it exhaustively requires a sweep with cost scaling linearly in the number of model components, which can be prohibitively expensive for SoTA Large Language Models (LLMs). We investigate Attribution Patching (AtP), a fast gradient-based approximation to Activation Patching and find two classes of failure modes of AtP which lead to significant false negatives. We propose a variant of AtP called AtP*, with two changes to address these failure modes while retaining scalability. We present the first systematic study of AtP and alternative methods for faster activation patching and show that AtP significantly outperforms all other investigated methods, with AtP* providing further significant improvement. Finally, we provide a method to bound the probability of remaining false negatives of AtP* estimates.

Should prediction models always deliver a prediction? In the pursuit of maximum predictive performance, critical considerations of reliability and fairness are often overshadowed, particularly when it comes to the role of uncertainty. Selective regression, also known as the "reject option," allows models to abstain from predictions in cases of considerable uncertainty. Initially proposed seven decades ago, approaches to selective regression have mostly focused on distribution-based proxies for measuring uncertainty, particularly conditional variance. However, this focus neglects the significant influence of model-specific biases on a model's performance. In this paper, we propose a novel approach to selective regression by leveraging conformal prediction, which provides grounded confidence measures for individual predictions based on model-specific biases. In addition, we propose a standardized evaluation framework to allow proper comparison of selective regression approaches. Via an extensive experimental approach, we demonstrate how our proposed approach, conformalized selective regression, demonstrates an advantage over multiple state-of-the-art baselines.

This paper is dedicated to an efficient compression of weights and optimizer states (called checkpoints) obtained at different stages during a neural network training process. First, we propose a prediction-based compression approach, where values from the previously saved checkpoint are used for context modeling in arithmetic coding. Second, in order to enhance the compression performance, we also propose to apply pruning and quantization of the checkpoint values. Experimental results show that our approach achieves substantial bit size reduction, while enabling near-lossless training recovery from restored checkpoints, preserving the model's performance and making it suitable for storage-limited environments.

The varying significance of distinct primitive behaviors during the policy learning process has been overlooked by prior model-free RL algorithms. Leveraging this insight, we explore the causal relationship between different action dimensions and rewards to evaluate the significance of various primitive behaviors during training. We introduce a causality-aware entropy term that effectively identifies and prioritizes actions with high potential impacts for efficient exploration. Furthermore, to prevent excessive focus on specific primitive behaviors, we analyze the gradient dormancy phenomenon and introduce a dormancy-guided reset mechanism to further enhance the efficacy of our method. Our proposed algorithm, ACE: Off-policy Actor-critic with Causality-aware Entropy regularization, demonstrates a substantial performance advantage across 29 diverse continuous control tasks spanning 7 domains compared to model-free RL baselines, which underscores the effectiveness, versatility, and efficient sample efficiency of our approach. Benchmark results and videos are available at https://ace-rl.github.io/.

Controlling undesirable Large Language Model (LLM) behaviors, such as the generation of unsafe content or failing to adhere to safety guidelines, often relies on costly fine-tuning. Activation steering provides an alternative for inference-time control, but existing methods typically lack fine-grained, adaptive mechanisms. We introduce a novel approach using a lightweight, trainable controller network integrated during inference. This controller network observes specific intermediate LLM activations and predicts both a global scaling factor and layer-specific weights. The predicted global scaling factor and layer-specific weights then dynamically modulate the intensity of a steering patch, derived from a pre-computed "refusal direction" vector, applied across the LLM's layers during generation. Trained on activations from both harmful and benign prompts, our controller learns to discriminatively apply nuanced, layer-aware interventions, activating steering primarily for harmful inputs. Experiments using safety benchmarks like ToxicChat & In-The-Wild Jailbreak Prompts demonstrate that our weighted steering controller significantly increases refusal rates compared to the base LLM, achieving targeted behavioral modification without altering the original model parameters. Our experiments with Llama-3.1-8B, Llama-3.2-1B & Mistral-7B show our approach outperforms existing methods, presenting an efficient and adaptive method for fine-grained control over LLM behavior at inference time.

Visual instruction tuning has recently shown encouraging progress with open-source large multimodal models (LMM) such as LLaVA and MiniGPT-4. However, most existing studies of open-source LMM are performed using models with 13B parameters or smaller. In this paper we present an empirical study of scaling LLaVA up to 33B and 65B/70B, and share our findings from our explorations in image resolution, data mixing and parameter-efficient training methods such as LoRA/QLoRA. These are evaluated by their impact on the multi-modal and language capabilities when completing real-world tasks in the wild. We find that scaling LMM consistently enhances model performance and improves language capabilities, and performance of LoRA/QLoRA tuning of LMM are comparable to the performance of full-model fine-tuning. Additionally, the study highlights the importance of higher image resolutions and mixing multimodal-language data to improve LMM performance, and visual instruction tuning can sometimes improve LMM's pure language capability. We hope that this study makes state-of-the-art LMM research at a larger scale more accessible, thus helping establish stronger baselines for future research. Code and checkpoints will be made public.

Diffusion Models (DM) and Consistency Models (CM) are two types of popular generative models with good generation quality on various tasks. When training DM and CM, intermediate weight checkpoints are not fully utilized and only the last converged checkpoint is used. In this work, we find that high-quality model weights often lie in a basin which cannot be reached by SGD but can be obtained by proper checkpoint averaging. Based on these observations, we propose LCSC, a simple but effective and efficient method to enhance the performance of DM and CM, by combining checkpoints along the training trajectory with coefficients deduced from evolutionary search. We demonstrate the value of LCSC through two use cases: (a) Reducing training cost. With LCSC, we only need to train DM/CM with fewer number of iterations and/or lower batch sizes to obtain comparable sample quality with the fully trained model. For example, LCSC achieves considerable training speedups for CM (23times on CIFAR-10 and 15times on ImageNet-64). (b) Enhancing pre-trained models. Assuming full training is already done, LCSC can further improve the generation quality or speed of the final converged models. For example, LCSC achieves better performance using 1 number of function evaluation (NFE) than the base model with 2 NFE on consistency distillation, and decreases the NFE of DM from 15 to 9 while maintaining the generation quality on CIFAR-10. Our code is available at https://github.com/imagination-research/LCSC.

Recently, multiple Automated Program Repair (APR) techniques based on Large Language Models (LLMs) have been proposed to enhance the repair performance. While these techniques mainly focus on the single-line or hunk-level repair, they face significant challenges in real-world application due to the limited repair task scope and costly statement-level fault localization. However, the more practical function-level APR, which broadens the scope of APR task to fix entire buggy functions and requires only cost-efficient function-level fault localization, remains underexplored. In this paper, we conduct the first comprehensive study of LLM-based function-level APR including investigating the effect of the few-shot learning mechanism and the auxiliary repair-relevant information. Specifically, we adopt six widely-studied LLMs and construct a benchmark in both the Defects4J 1.2 and 2.0 datasets. Our study demonstrates that LLMs with zero-shot learning are already powerful function-level APR techniques, while applying the few-shot learning mechanism leads to disparate repair performance. Moreover, we find that directly applying the auxiliary repair-relevant information to LLMs significantly increases function-level repair performance. Inspired by our findings, we propose an LLM-based function-level APR technique, namely SRepair, which adopts a dual-LLM framework to leverage the power of the auxiliary repair-relevant information for advancing the repair performance. The evaluation results demonstrate that SRepair can correctly fix 300 single-function bugs in the Defects4J dataset, largely surpassing all previous APR techniques by at least 85%, without the need for the costly statement-level fault location information. Furthermore, SRepair successfully fixes 32 multi-function bugs in the Defects4J dataset, which is the first time achieved by any APR technique ever to our best knowledge.

Machine learning programs, such as those performing inference, fine-tuning, and training of LLMs, are commonly delegated to untrusted compute providers. To provide correctness guarantees for the client, we propose adapting the cryptographic notion of refereed delegation to the machine learning setting. This approach enables a computationally limited client to delegate a program to multiple untrusted compute providers, with a guarantee of obtaining the correct result if at least one of them is honest. Refereed delegation of ML programs poses two technical hurdles: (1) an arbitration protocol to resolve disputes when compute providers disagree on the output, and (2) the ability to bitwise reproduce ML programs across different hardware setups, For (1), we design Verde, a dispute arbitration protocol that efficiently handles the large scale and graph-based computational model of modern ML programs. For (2), we build RepOps (Reproducible Operators), a library that eliminates hardware "non-determinism" by controlling the order of floating point operations performed on all hardware. Our implementation shows that refereed delegation achieves both strong guarantees for clients and practical overheads for compute providers.

Despite advances in transformer-based language models (LMs), a fundamental question remains largely unanswered: Are all layers activated during inference? We investigate this question by detecting unactivated layers (which we refer to as Voids) using a non-trainable and parameter-free adaptive computation method called L2 Adaptive Computation (LAC). We adapt LAC from its original efficiency-focused application to trace activated layers during inference. This method monitors changes in the L2-norm of activations to identify voids. We analyze layer activation in instruction-tuned LMs across two phases: Prompt Processing (PP), where we trace activated layers for each token in the input prompts, and Response Generation (RG), where we trace activated layers for each generated token. We further demonstrate that distinct layers are activated during these two phases. To show the effectiveness of our method, we evaluated three distinct instruction-tuned LMs from the Llama, Mistral, and Qwen families on three benchmarks: MMLU, GPQA Diamond, and BoolQ. For example, on MMLU with a zero-shot setting, skipping voids in Qwen2.5-7B-Instruct resulted in an improvement from 69.24 to 71.29 while the model uses only 30% of the layers. Similarly, Mistral-7B-Instruct-v0.3 on GPQA Diamond improved from 13.88 to 18.36 when using 70% of the layers during both the PP and RG phases. These results show that not all layers contribute equally during inference, and that selectively skipping most of them can improve the performance of models on certain tasks.

Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples and genomic regions based on discrete copy number states using a bipartite categorical block model. Unlike models relying on Gaussian or Poisson assumptions, CN-SBM respects the discrete nature of CNV calls and captures subpopulation-specific patterns through block-wise structure. Using a two-stage approach, CN-SBM decomposes CNV data into primary and residual components, enabling detection of both large-scale chromosomal alterations and finer aberrations. We derive a scalable variational inference algorithm for application to large cohorts and high-resolution data. Benchmarks on simulated and real datasets show improved model fit over existing methods. Applied to TCGA low-grade glioma data, CN-SBM reveals clinically relevant subtypes and structured residual variation, aiding patient stratification in survival analysis. These results establish CN-SBM as an interpretable, scalable framework for CNV analysis with direct relevance for tumor heterogeneity and prognosis.

The expansion of machine learning into dynamic environments presents challenges in handling open-world problems where label shift, covariate shift, and unknown classes emerge. Post-training methods have been explored to address these challenges, adapting models to newly emerging data. However, these methods struggle when the initial pre-training is performed on class-imbalanced datasets, limiting generalization to minority classes. To address this, we propose a method that effectively handles open-world problems even when pre-training is conducted on imbalanced data. Our contrastive-based pre-training approach enhances classification performance, particularly for underrepresented classes. Our post-training mechanism generates reliable pseudo-labels, improving model robustness against open-world problems. We also introduce selective activation criteria to optimize the post-training process, reducing unnecessary computation. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art adaptation techniques in both accuracy and efficiency across diverse open-world scenarios.

We present XMem, a video object segmentation architecture for long videos with unified feature memory stores inspired by the Atkinson-Shiffrin memory model. Prior work on video object segmentation typically only uses one type of feature memory. For videos longer than a minute, a single feature memory model tightly links memory consumption and accuracy. In contrast, following the Atkinson-Shiffrin model, we develop an architecture that incorporates multiple independent yet deeply-connected feature memory stores: a rapidly updated sensory memory, a high-resolution working memory, and a compact thus sustained long-term memory. Crucially, we develop a memory potentiation algorithm that routinely consolidates actively used working memory elements into the long-term memory, which avoids memory explosion and minimizes performance decay for long-term prediction. Combined with a new memory reading mechanism, XMem greatly exceeds state-of-the-art performance on long-video datasets while being on par with state-of-the-art methods (that do not work on long videos) on short-video datasets. Code is available at https://hkchengrex.github.io/XMem

Despite advances in the programmable logic capabilities of modern trigger systems, a significant bottleneck remains in the amount of data to be transported from the detector to off-detector logic where trigger decisions are made. We demonstrate that a neural network autoencoder model can be implemented in a radiation tolerant ASIC to perform lossy data compression alleviating the data transmission problem while preserving critical information of the detector energy profile. For our application, we consider the high-granularity calorimeter from the CMS experiment at the CERN Large Hadron Collider. The advantage of the machine learning approach is in the flexibility and configurability of the algorithm. By changing the neural network weights, a unique data compression algorithm can be deployed for each sensor in different detector regions, and changing detector or collider conditions. To meet area, performance, and power constraints, we perform a quantization-aware training to create an optimized neural network hardware implementation. The design is achieved through the use of high-level synthesis tools and the hls4ml framework, and was processed through synthesis and physical layout flows based on a LP CMOS 65 nm technology node. The flow anticipates 200 Mrad of ionizing radiation to select gates, and reports a total area of 3.6 mm^2 and consumes 95 mW of power. The simulated energy consumption per inference is 2.4 nJ. This is the first radiation tolerant on-detector ASIC implementation of a neural network that has been designed for particle physics applications.

Though safety alignment has been applied to most large language models (LLMs), LLM service providers generally deploy a subsequent moderation as the external safety guardrail in real-world products. Existing moderators mainly practice a conventional full detection, which determines the harmfulness based on the complete LLM output, causing high service latency. Recent works pay more attention to partial detection where moderators oversee the generation midway and early stop the output if harmfulness is detected, but they directly apply moderators trained with the full detection paradigm to incomplete outputs, introducing a training-inference gap that lowers the performance. In this paper, we explore how to form a data-and-model solution that natively supports partial detection. For the data, we construct FineHarm, a dataset consisting of 29K prompt-response pairs with fine-grained annotations to provide reasonable supervision for token-level training. Then, we propose the streaming content monitor, which is trained with dual supervision of response- and token-level labels and can follow the output stream of LLM to make a timely judgment of harmfulness. Experiments show that SCM gains 0.95+ in macro F1 score that is comparable to full detection, by only seeing the first 18% of tokens in responses on average. Moreover, the SCM can serve as a pseudo-harmfulness annotator for improving safety alignment and lead to a higher harmlessness score than DPO.

Large Language Models (LLMs) are increasingly deployed in agentic systems that interact with an external environment; this makes them susceptible to prompt injections when dealing with untrusted data. To overcome this limitation, we propose SIC (Soft Instruction Control)-a simple yet effective iterative prompt sanitization loop designed for tool-augmented LLM agents. Our method repeatedly inspects incoming data for instructions that could compromise agent behavior. If such content is found, the malicious content is rewritten, masked, or removed, and the result is re-evaluated. The process continues until the input is clean or a maximum iteration limit is reached; if imperative instruction-like content remains, the agent halts to ensure security. By allowing multiple passes, our approach acknowledges that individual rewrites may fail but enables the system to catch and correct missed injections in later steps. Although immediately useful, worst-case analysis shows that SIC is not infallible; strong adversary can still get a 15% ASR by embedding non-imperative workflows. This nonetheless raises the bar.

We present the design of a new large scale orchestration layer for accelerators. Our system, Pathways, is explicitly designed to enable exploration of new systems and ML research ideas, while retaining state of the art performance for current models. Pathways uses a sharded dataflow graph of asynchronous operators that consume and produce futures, and efficiently gang-schedules heterogeneous parallel computations on thousands of accelerators while coordinating data transfers over their dedicated interconnects. Pathways makes use of a novel asynchronous distributed dataflow design that lets the control plane execute in parallel despite dependencies in the data plane. This design, with careful engineering, allows Pathways to adopt a single-controller model that makes it easier to express complex new parallelism patterns. We demonstrate that Pathways can achieve performance parity (~100% accelerator utilization) with state-of-the-art systems when running SPMD computations over 2048 TPUs, while also delivering throughput comparable to the SPMD case for Transformer models that are pipelined across 16 stages, or sharded across two islands of accelerators connected over a data center network.

Perturbative availability poisons (PAPs) add small changes to images to prevent their use for model training. Current research adopts the belief that practical and effective approaches to countering PAPs do not exist. In this paper, we argue that it is time to abandon this belief. We present extensive experiments showing that 12 state-of-the-art PAP methods are vulnerable to Image Shortcut Squeezing (ISS), which is based on simple compression. For example, on average, ISS restores the CIFAR-10 model accuracy to 81.73%, surpassing the previous best preprocessing-based countermeasures by 37.97% absolute. ISS also (slightly) outperforms adversarial training and has higher generalizability to unseen perturbation norms and also higher efficiency. Our investigation reveals that the property of PAP perturbations depends on the type of surrogate model used for poison generation, and it explains why a specific ISS compression yields the best performance for a specific type of PAP perturbation. We further test stronger, adaptive poisoning, and show it falls short of being an ideal defense against ISS. Overall, our results demonstrate the importance of considering various (simple) countermeasures to ensure the meaningfulness of analysis carried out during the development of PAP methods.

We present the design, implementation and engineering experience in building and deploying MegaScale, a production system for training large language models (LLMs) at the scale of more than 10,000 GPUs. Training LLMs at this scale brings unprecedented challenges to training efficiency and stability. We take a full-stack approach that co-designs the algorithmic and system components across model block and optimizer design, computation and communication overlapping, operator optimization, data pipeline, and network performance tuning. Maintaining high efficiency throughout the training process (i.e., stability) is an important consideration in production given the long extent of LLM training jobs. Many hard stability issues only emerge at large scale, and in-depth observability is the key to address them. We develop a set of diagnosis tools to monitor system components and events deep in the stack, identify root causes, and derive effective techniques to achieve fault tolerance and mitigate stragglers. MegaScale achieves 55.2% Model FLOPs Utilization (MFU) when training a 175B LLM model on 12,288 GPUs, improving the MFU by 1.34x compared to Megatron-LM. We share our operational experience in identifying and fixing failures and stragglers. We hope by articulating the problems and sharing our experience from a systems perspective, this work can inspire future LLM systems research.

Deep neural networks (DNNs) are increasingly being deployed in safety-critical systems such as personal healthcare devices and self-driving cars. In such DNN-based systems, error resilience is a top priority since faults in DNN inference could lead to mispredictions and safety hazards. For latency-critical DNN inference on resource-constrained edge devices, it is nontrivial to apply conventional redundancy-based fault tolerance techniques. In this paper, we propose FitAct, a low-cost approach to enhance the error resilience of DNNs by deploying fine-grained post-trainable activation functions. The main idea is to precisely bound the activation value of each individual neuron via neuron-wise bounded activation functions so that it could prevent fault propagation in the network. To avoid complex DNN model re-training, we propose to decouple the accuracy training and resilience training and develop a lightweight post-training phase to learn these activation functions with precise bound values. Experimental results on widely used DNN models such as AlexNet, VGG16, and ResNet50 demonstrate that FitAct outperforms state-of-the-art studies such as Clip-Act and Ranger in enhancing the DNN error resilience for a wide range of fault rates while adding manageable runtime and memory space overheads.

Recent advances in Reinforcement Learning with Verified Reward (RLVR) have driven the emergence of more sophisticated cognitive behaviors in large language models (LLMs), thereby enhancing their reasoning capabilities. However, in prior RLVR pipelines, the repeated use of static initial-state sampling drawn exactly from the dataset distribution during each sampling phase produced overly deterministic, low diversity model behavior, which manifested as rapid entropy collapse and hindered sustained performance gains during prolonged training. To address this issue, we introduce CURE (Critical-token-gUided Re concatenation for Entropy-collapse prevention), a two-stage framework that balances exploration and exploitation. Specifically, in the first stage, to deliberately steer the model toward novel yet coherent contexts, we re-generate at high-entropy critical tokens and jointly optimize the original and the branched trajectories. The further comparison with vanilla DAPO shows that the regeneration process achieves a better performance on math reasoning tasks while sustaining a high-level entropy degree for exploration. In the second stage, we continue training with static initial-state sampling by DAPO, intentionally placing the model in a familiar state to gradually strengthen exploitation. Extensive experiments on Qwen-2.5-Math-7B show that, compared to other RLVR methods, CURE achieves a 5% performance gain across six math benchmarks, establishing state-of-the-art performance in both entropy and accuracy. A series of experiments further validate the effectiveness of our approach. Code is available at https://github.com/bytedance/CURE.

For privacy and security concerns, the need to erase unwanted information from pre-trained vision models is becoming evident nowadays. In real-world scenarios, erasure requests originate at any time from both users and model owners. These requests usually form a sequence. Therefore, under such a setting, selective information is expected to be continuously removed from a pre-trained model while maintaining the rest. We define this problem as continual forgetting and identify two key challenges. (i) For unwanted knowledge, efficient and effective deleting is crucial. (ii) For remaining knowledge, the impact brought by the forgetting procedure should be minimal. To address them, we propose Group Sparse LoRA (GS-LoRA). Specifically, towards (i), we use LoRA modules to fine-tune the FFN layers in Transformer blocks for each forgetting task independently, and towards (ii), a simple group sparse regularization is adopted, enabling automatic selection of specific LoRA groups and zeroing out the others. GS-LoRA is effective, parameter-efficient, data-efficient, and easy to implement. We conduct extensive experiments on face recognition, object detection and image classification and demonstrate that GS-LoRA manages to forget specific classes with minimal impact on other classes. Codes will be released on https://github.com/bjzhb666/GS-LoRA.

Machine Learning models increasingly face data integrity challenges due to the use of large-scale training datasets drawn from the Internet. We study what model developers can do if they detect that some data was manipulated or incorrect. Such manipulated data can cause adverse effects including vulnerability to backdoored samples, systemic biases, and reduced accuracy on certain input domains. Realistically, all manipulated training samples cannot be identified, and only a small, representative subset of the affected data can be flagged. We formalize Corrective Machine Unlearning as the problem of mitigating the impact of data affected by unknown manipulations on a trained model, only having identified a subset of the corrupted data. We demonstrate that the problem of corrective unlearning has significantly different requirements from traditional privacy-oriented unlearning. We find most existing unlearning methods, including retraining-from-scratch without the deletion set, require most of the manipulated data to be identified for effective corrective unlearning. However, one approach, Selective Synaptic Dampening, achieves limited success, unlearning adverse effects with just a small portion of the manipulated samples in our setting, which shows encouraging signs for future progress. We hope our work spurs research towards developing better methods for corrective unlearning and offers practitioners a new strategy to handle data integrity challenges arising from web-scale training. Code is available at https://github.com/drimpossible/corrective-unlearning-bench.

Large Language Models (LLMs) have demonstrated remarkable capabilities but often face challenges with tasks requiring sophisticated reasoning. While Chain-of-Thought (CoT) prompting significantly enhances reasoning, it indiscriminately generates lengthy reasoning steps for all queries, leading to substantial computational costs and inefficiency, especially for simpler inputs. To address this critical issue, we introduce AdaCoT (Adaptive Chain-of-Thought), a novel framework enabling LLMs to adaptively decide when to invoke CoT. AdaCoT framed adaptive reasoning as a Pareto optimization problem that seeks to balance model performance with the costs associated with CoT invocation (both frequency and computational overhead). We propose a reinforcement learning (RL) based method, specifically utilizing Proximal Policy Optimization (PPO), to dynamically control the CoT triggering decision boundary by adjusting penalty coefficients, thereby allowing the model to determine CoT necessity based on implicit query complexity. A key technical contribution is Selective Loss Masking (SLM), designed to counteract decision boundary collapse during multi-stage RL training, ensuring robust and stable adaptive triggering. Experimental results demonstrate that AdaCoT successfully navigates the Pareto frontier, achieving substantial reductions in CoT usage for queries not requiring elaborate reasoning. For instance, on our production traffic testset, AdaCoT reduced CoT triggering rates to as low as 3.18\% and decreased average response tokens by 69.06%, while maintaining high performance on complex tasks.

MIDOG 2025 Track 1 requires mitosis detection in whole-slideimages (WSIs) containing non-tumor, inflamed, and necrotic re-gions. Due to the complicated and heterogeneous context, aswell as possible artifacts, there are often false positives and falsenegatives, thus degrading the detection F1-score. To addressthis problem, we propose a two-stage framework. Firstly, an im-proved YOLO11x, integrated with EMA attention and LSConv,is employed to generate mitosis candidates. We use a low confi-dence threshold to generate as many proposals as possible, en-suring the detection recall. Then, a ConvNeXt-Tiny classifieris employed to filter out the false positives, ensuring the detec-tion precision. Consequently, the proposed two-stage frame-work can generate a high detection F1-score. Evaluated on afused dataset comprising MIDOG++, MITOS_WSI_CCMCT,and MITOS_WSI_CMC, our framework achieves an F1-scoreof 0.882, which is 0.035 higher than the single-stage YOLO11xbaseline. This performance gain is produced by a significantprecision improvement, from 0.762 to 0.839, and a comparablerecall. On the MIDOG 2025 Track 1 preliminary test set, thealgorithm scores an F1 score of 0.7587. The code is available athttps://github.com/xxiao0304/MIDOG-2025-Track-1-of-SZTU.

We propose and test the LLM Brain Rot Hypothesis: continual exposure to junk web text induces lasting cognitive decline in large language models (LLMs). To causally isolate data quality, we run controlled experiments on real Twitter/X corpora, constructing junk and reversely controlled datasets via two orthogonal operationalizations: M1 (engagement degree) and M2 (semantic quality), with matched token scale and training operations across conditions. Contrary to the control group, continual pre-training of 4 LLMs on the junk dataset causes non-trivial declines (Hedges' g>0.3) on reasoning, long-context understanding, safety, and inflating "dark traits" (e.g., psychopathy, narcissism). The gradual mixtures of junk and control datasets also yield dose-response cognition decay: for example, under M1, ARC-Challenge with Chain Of Thoughts drops 74.9 rightarrow 57.2 and RULER-CWE 84.4 rightarrow 52.3 as junk ratio rises from 0% to 100%. Error forensics reveal several key insights. First, we identify thought-skipping as the primary lesion: models increasingly truncate or skip reasoning chains, explaining most of the error growth. Second, partial but incomplete healing is observed: scaling instruction tuning and clean data pre-training improve the declined cognition yet cannot restore baseline capability, suggesting persistent representational drift rather than format mismatch. Finally, we discover that the popularity, a non-semantic metric, of a tweet is a better indicator of the Brain Rot effect than the length in M1. Together, the results provide significant, multi-perspective evidence that data quality is a causal driver of LLM capability decay, reframing curation for continual pretraining as a training-time safety problem and motivating routine "cognitive health checks" for deployed LLMs.

Unneeded elements in the attention's context degrade performance. We introduce Selective Attention, a simple parameter-free change to the standard attention mechanism which reduces attention to unneeded elements. Selective attention improves language modeling performance in a variety of model sizes and context lengths. For example, a range of transformers trained with the language modeling objective on C4 with selective attention perform equivalently to standard transformers with ~2X more heads and parameters in their attention modules. Selective attention also allows decreasing the size of the attention's context buffer, leading to meaningful reductions in the memory and compute requirements during inference. For example, transformers with 100M parameters trained on C4 with context sizes of 512, 1,024, and 2,048 need 16X, 25X, and 47X less memory for their attention module, respectively, when equipped with selective attention, as those without selective attention, with the same validation perplexity.

Catastrophic forgetting remains a significant challenge to continual learning for decades. While recent works have proposed effective methods to mitigate this problem, they mainly focus on the algorithmic side. Meanwhile, we do not fully understand what architectural properties of neural networks lead to catastrophic forgetting. This study aims to fill this gap by studying the role of activation functions in the training dynamics of neural networks and their impact on catastrophic forgetting. Our study reveals that, besides sparse representations, the gradient sparsity of activation functions also plays an important role in reducing forgetting. Based on this insight, we propose a new class of activation functions, elephant activation functions, that can generate both sparse representations and sparse gradients. We show that by simply replacing classical activation functions with elephant activation functions, we can significantly improve the resilience of neural networks to catastrophic forgetting. Our method has broad applicability and benefits for continual learning in regression, class incremental learning, and reinforcement learning tasks. Specifically, we achieves excellent performance on Split MNIST dataset in just one single pass, without using replay buffer, task boundary information, or pre-training.

With contributions from the open-source community, a vast amount of instruction tuning (IT) data has emerged. Given the significant resource allocation required for training and evaluating models, it is advantageous to have an efficient method for selecting high-quality IT data. However, existing methods for instruction data selection have limitations such as relying on fragile external APIs, being affected by biases in GPT models, or reducing the diversity of the selected instruction dataset. In this paper, we propose an industrial-friendly, expert-aligned and diversity-preserved instruction data selection method: Clustering and Ranking (CaR). CaR employs a two-step process: first, it ranks instruction pairs using a high-accuracy (84.25%) scoring model aligned with expert preferences; second, it preserves dataset diversity through clustering. In our experiment, CaR efficiently selected a mere 1.96% of Alpaca's IT data, yet the resulting AlpaCaR model surpassed Alpaca's performance by an average of 32.1% in GPT-4 evaluations. Moreover, we find that data selecting is a consistent paradigm whether the pre-trained model is more capable or the model parameters scaling up. Our approach employs compact models with 550M parameters and incurs just 11.2% of the financial outlay of current methods, enhancing its industrial deployability.

Training language models on long sequence data is a demanding requirement for enhancing the model's capability on complex tasks, e.g., long-chain reasoning. However, as the sequence length scales up, the memory cost for storing activation values becomes huge during the Backpropagation (BP) process, even with the application of gradient checkpointing technique. To tackle this challenge, we propose a memory-efficient and exact BP method called StreamBP, which performs a linear decomposition of the chain rule along the sequence dimension in a layer-wise manner, significantly reducing the memory cost of activation values and logits. The proposed method is applicable to common objectives such as SFT, GRPO, and DPO. From an implementation perspective, StreamBP achieves less computational FLOPs and faster BP speed by leveraging the causal structure of the language model. Compared to gradient checkpointing, StreamBP scales up the maximum sequence length of BP by 2.8-5.5 times larger, while using comparable or even less BP time. Note that StreamBP's sequence length scaling ability can be directly transferred to batch size scaling for accelerating training. We further develop a communication-efficient distributed StreamBP to effectively support multi-GPU training and broaden its applicability. Our code can be easily integrated into the training pipeline of any transformer models and is available at https://github.com/Ledzy/StreamBP.

Large reasoning models (LRMs) already possess a latent capacity for long chain-of-thought reasoning. Prior work has shown that outcome-based reinforcement learning (RL) can incidentally elicit advanced reasoning behaviors such as self-correction, backtracking, and verification phenomena often referred to as the model's "aha moment". However, the timing and consistency of these emergent behaviors remain unpredictable and uncontrollable, limiting the scalability and reliability of LRMs' reasoning capabilities. To address these limitations, we move beyond reliance on prompts and coincidental "aha moments". Instead, we explicitly align models with three meta-abilities: deduction, induction, and abduction, using automatically generated, self-verifiable tasks. Our three stage-pipeline individual alignment, parameter-space merging, and domain-specific reinforcement learning, boosting performance by over 10\% relative to instruction-tuned baselines. Furthermore, domain-specific RL from the aligned checkpoint yields an additional 2\% average gain in the performance ceiling across math, coding, and science benchmarks, demonstrating that explicit meta-ability alignment offers a scalable and dependable foundation for reasoning. Code is available at: https://github.com/zhiyuanhubj/Meta-Ability-Alignment

A major barrier to deploying current machine learning models lies in their non-reliability to dataset shifts. To resolve this problem, most existing studies attempted to transfer stable information to unseen environments. Particularly, independent causal mechanisms-based methods proposed to remove mutable causal mechanisms via the do-operator. Compared to previous methods, the obtained stable predictors are more effective in identifying stable information. However, a key question remains: which subset of this whole stable information should the model transfer, in order to achieve optimal generalization ability? To answer this question, we present a comprehensive minimax analysis from a causal perspective. Specifically, we first provide a graphical condition for the whole stable set to be optimal. When this condition fails, we surprisingly find with an example that this whole stable set, although can fully exploit stable information, is not the optimal one to transfer. To identify the optimal subset under this case, we propose to estimate the worst-case risk with a novel optimization scheme over the intervention functions on mutable causal mechanisms. We then propose an efficient algorithm to search for the subset with minimal worst-case risk, based on a newly defined equivalence relation between stable subsets. Compared to the exponential cost of exhaustively searching over all subsets, our searching strategy enjoys a polynomial complexity. The effectiveness and efficiency of our methods are demonstrated on synthetic data and the diagnosis of Alzheimer's disease.

Optimization-based jailbreaks typically adopt the Toxic-Continuation setting in large vision-language models (LVLMs), following the standard next-token prediction objective. In this setting, an adversarial image is optimized to make the model predict the next token of a toxic prompt. However, we find that the Toxic-Continuation paradigm is effective at continuing already-toxic inputs, but struggles to induce safety misalignment when explicit toxic signals are absent. We propose a new paradigm: Benign-to-Toxic (B2T) jailbreak. Unlike prior work, we optimize adversarial images to induce toxic outputs from benign conditioning. Since benign conditioning contains no safety violations, the image alone must break the model's safety mechanisms. Our method outperforms prior approaches, transfers in black-box settings, and complements text-based jailbreaks. These results reveal an underexplored vulnerability in multimodal alignment and introduce a fundamentally new direction for jailbreak approaches.

Agentic LLM applications interleave LLM generation requests with tool calls. These tool calls break the continuity of the workflow by creating pauses between LLM requests, bringing many challenges for the serving system, especially under multi-turn scenarios. Each pause potentially causes KV cache eviction and extra waiting time before entering the continuous batch for the following LLM request. Since these pauses happen for each call, this problem becomes increasingly severe as turn number grow for agentic programs. Previous works either fail to incorporate information from the tool call, evicting KV cache that leads to repetitive prefill or loading, or ignore the continuity of a multi-turn program, creating waiting time between turns that increases per-request latency. We present Continuum, a serving system to optimize job completion time for multi-turn agent workloads by combining tool-aware KV cache timeout with program-level scheduling. By predicting tool call durations in agentic workflows, Continuum selectively pins the KV cache in GPU memory with a time-to-live value based on total turn number. When combined with program-level first-come-first-serve, Continuum prevents scheduling bubbles, preserves multi-turn continuity, and optimizes for throughput for complex agentic workflows. By modeling the variability of tool call and agent program continuity, Continuum outperforms state-of-the-art baselines. Our evaluation on real-world agentic workloads (SWE-Bench and BFCL) with Llama-3.1 8B/70B models shows that Continuum significantly improves the average job completion times, and remains performant across different hardware setups and DRAM offloading schemes. Preview code is available at: https://github.com/Hanchenli/vllm-continuum

Current methods for content safety in Large Language Models (LLMs), such as Supervised Fine-Tuning (SFT) and Reinforcement Learning from Human Feedback (RLHF), often rely on multi-stage training pipelines and lack fine-grained, post-deployment controllability. To address these limitations, we propose a unified co-training framework that efficiently integrates multiple safety behaviors: positive (lawful/prosocial), negative (unfiltered/risk-prone) and rejective (refusal-oriented/conservative) within a single SFT stage. Notably, each behavior is dynamically activated via a simple system-level instruction, or magic token, enabling stealthy and efficient behavioral switching at inference time. This flexibility supports diverse deployment scenarios, such as positive for safe user interaction, negative for internal red-teaming, and rejective for context-aware refusals triggered by upstream moderation signals. This co-training strategy induces a distinct Safety Alignment Margin in the output space, characterized by well-separated response distributions corresponding to each safety mode. The existence of this margin provides empirical evidence for the model's safety robustness and enables unprecedented fine-grained control. Experiments show that our method matches the safety alignment quality of SFT+DPO, with our 8B model notably surpassing DeepSeek-R1 (671B) in safety performance, while significantly reducing both training complexity and deployment costs. This work presents a scalable, efficient, and highly controllable solution for LLM content safety.

Neural Information Retrieval has advanced rapidly in high-resource languages, but progress in lower-resource ones such as Japanese has been hindered by data scarcity, among other challenges. Consequently, multilingual models have dominated Japanese retrieval, despite their computational inefficiencies and inability to capture linguistic nuances. While recent multi-vector monolingual models like JaColBERT have narrowed this gap, they still lag behind multilingual methods in large-scale evaluations. This work addresses the suboptimal training methods of multi-vector retrievers in lower-resource settings, focusing on Japanese. We systematically evaluate and improve key aspects of the inference and training settings of JaColBERT, and more broadly, multi-vector models. We further enhance performance through a novel checkpoint merging step, showcasing it to be an effective way of combining the benefits of fine-tuning with the generalization capabilities of the original checkpoint. Building on our analysis, we introduce a novel training recipe, resulting in the JaColBERTv2.5 model. JaColBERTv2.5, with only 110 million parameters and trained in under 15 hours on 4 A100 GPUs, significantly outperforms all existing methods across all common benchmarks, reaching an average score of 0.754, significantly above the previous best of 0.720. To support future research, we make our final models, intermediate checkpoints and all data used publicly available.

We propose ERA, a new paradigm that constrains the sampling entropy above given thresholds by applying specially designed activations to the outputs of models. Our approach demonstrates broad effectiveness across different domains: 1) for large language models(LLMs), boosting the AIME 2025 score for Qwen2.5-Math-7B by 37.4%; 2) for continuous control reinforcement learning agents, improving performance by more than 30% over strong baselines such as SAC on the challenging HumanoidBench; 3) for image classification, enhancing ImageNet top-1 accuracy by 0.69% for ResNet-50. These gains are achieved with a computational overhead of less than 7%. Our work validates output activation as a powerful tool for entropy control, opening a new direction for designing simpler and more robust algorithms.

Large language models have demonstrated remarkable capabilities, but their performance is heavily reliant on effective prompt engineering. Automatic prompt optimization (APO) methods are designed to automate this and can be broadly categorized into those targeting instructions (instruction optimization, IO) vs. those targeting exemplars (exemplar selection, ES). Despite their shared objective, these have evolved rather independently, with IO recently receiving more research attention. This paper seeks to bridge this gap by comprehensively comparing the performance of representative IO and ES techniques, both isolation and combination, on a diverse set of challenging tasks. Our findings reveal that intelligently reusing model-generated input-output pairs obtained from evaluating prompts on the validation set as exemplars consistently improves performance over IO methods but is currently under-investigated. We also find that despite the recent focus on IO, how we select exemplars can outweigh how we optimize instructions, with ES strategies as simple as random search outperforming state-of-the-art IO methods with seed instructions without any optimization. Moreover, we observe synergy between ES and IO, with optimal combinations surpassing individual contributions. We conclude that studying exemplar selection as a standalone method and its optimal combination with instruction optimization remains a crucial aspect of APO and deserves greater consideration in future research, even in the era of highly capable instruction-following models.

Deploying large language models (LLMs) in real-world applications requires robust safety guard models to detect and block harmful user prompts. While large safety guard models achieve strong performance, their computational cost is substantial. To mitigate this, smaller distilled models are used, but they often underperform on "hard" examples where the larger model provides accurate predictions. We observe that many inputs can be reliably handled by the smaller model, while only a small fraction require the larger model's capacity. Motivated by this, we propose SafeRoute, a binary router that distinguishes hard examples from easy ones. Our method selectively applies the larger safety guard model to the data that the router considers hard, improving efficiency while maintaining accuracy compared to solely using the larger safety guard model. Experimental results on multiple benchmark datasets demonstrate that our adaptive model selection significantly enhances the trade-off between computational cost and safety performance, outperforming relevant baselines.

Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair - generating structurally valid molecular alternatives with reduced toxicity - has not yet been systematically defined or benchmarked. To fill this gap, we introduce ToxiMol, the first benchmark task for general-purpose Multimodal Large Language Models (MLLMs) focused on molecular toxicity repair. We construct a standardized dataset covering 11 primary tasks and 560 representative toxic molecules spanning diverse mechanisms and granularities. We design a prompt annotation pipeline with mechanism-aware and task-adaptive capabilities, informed by expert toxicological knowledge. In parallel, we propose an automated evaluation framework, ToxiEval, which integrates toxicity endpoint prediction, synthetic accessibility, drug-likeness, and structural similarity into a high-throughput evaluation chain for repair success. We systematically assess nearly 30 mainstream general-purpose MLLMs and design multiple ablation studies to analyze key factors such as evaluation criteria, candidate diversity, and failure attribution. Experimental results show that although current MLLMs still face significant challenges on this task, they begin to demonstrate promising capabilities in toxicity understanding, semantic constraint adherence, and structure-aware molecule editing.

Fragmentation is a routine part of communication in 6LoWPAN-based IoT networks, designed to accommodate small frame sizes on constrained wireless links. However, this process introduces a critical vulnerability fragments are typically stored and processed before their legitimacy is confirmed, allowing attackers to exploit this gap with minimal effort. In this work, we explore a defense strategy that takes a more adaptive, behavior-aware approach to this problem. Our system, called Predictive-CSM, introduces a combination of two lightweight mechanisms. The first tracks how each node behaves over time, rewarding consistent and successful interactions while quickly penalizing suspicious or failing patterns. The second checks the integrity of packet fragments using a chained hash, allowing incomplete or manipulated sequences to be caught early, before they can occupy memory or waste processing time. We put this system to the test using a set of targeted attack simulations, including early fragment injection, replayed headers, and flooding with fake data. Across all scenarios, Predictive CSM preserved network delivery and maintained energy efficiency, even under pressure. Rather than relying on heavyweight cryptography or rigid filters, this approach allows constrained de vices to adapt their defenses in real time based on what they observe, not just what they're told. In that way, it offers a step forward for securing fragmented communication in real world IoT systems

Motivated in part by their relevance for low-precision training and quantization, massive activations in large language models (LLMs) have recently emerged as a topic of interest. However, existing analyses are limited in scope, and generalizability across architectures is unclear. This paper helps address some of these gaps by conducting an analysis of massive activations across a broad range of LLMs, including both GLU-based and non-GLU-based architectures. Our findings challenge several prior assumptions, most importantly: (1) not all massive activations are detrimental, i.e. suppressing them does not lead to an explosion of perplexity or a collapse in downstream task performance; (2) proposed mitigation strategies such as Attention KV bias are model-specific and ineffective in certain cases. We consequently investigate novel hybrid mitigation strategies; in particular pairing Target Variance Rescaling (TVR) with Attention KV bias or Dynamic Tanh (DyT) successfully balances the mitigation of massive activations with preserved downstream model performance in the scenarios we investigated. Our code is available at: https://github.com/bluorion-com/refine_massive_activations.

We present Ring-lite, a Mixture-of-Experts (MoE)-based large language model optimized via reinforcement learning (RL) to achieve efficient and robust reasoning capabilities. Built upon the publicly available Ling-lite model, a 16.8 billion parameter model with 2.75 billion activated parameters, our approach matches the performance of state-of-the-art (SOTA) small-scale reasoning models on challenging benchmarks (e.g., AIME, LiveCodeBench, GPQA-Diamond) while activating only one-third of the parameters required by comparable models. To accomplish this, we introduce a joint training pipeline integrating distillation with RL, revealing undocumented challenges in MoE RL training. First, we identify optimization instability during RL training, and we propose Constrained Contextual Computation Policy Optimization(C3PO), a novel approach that enhances training stability and improves computational throughput via algorithm-system co-design methodology. Second, we empirically demonstrate that selecting distillation checkpoints based on entropy loss for RL training, rather than validation metrics, yields superior performance-efficiency trade-offs in subsequent RL training. Finally, we develop a two-stage training paradigm to harmonize multi-domain data integration, addressing domain conflicts that arise in training with mixed dataset. We will release the model, dataset, and code.

Extreme activation outliers in Large Language Models (LLMs) critically degrade quantization performance, hindering efficient on-device deployment. While channel-wise operations and adaptive gradient scaling are recognized causes, practical mitigation remains challenging. We introduce Outlier-Safe Pre-Training (OSP), a practical guideline that proactively prevents outlier formation rather than relying on post-hoc mitigation. OSP combines three key innovations: (1) the Muon optimizer, eliminating privileged bases while maintaining training efficiency; (2) Single-Scale RMSNorm, preventing channel-wise amplification; and (3) a learnable embedding projection, redistributing activation magnitudes originating from embedding matrices. We validate OSP by training a 1.4B-parameter model on 1 trillion tokens, which is the first production-scale LLM trained without such outliers. Under aggressive 4-bit quantization, our OSP model achieves a 35.7 average score across 10 benchmarks (compared to 26.5 for an Adam-trained model), with only a 2% training overhead. Remarkably, OSP models exhibit near-zero excess kurtosis (0.04) compared to extreme values (1818.56) in standard models, fundamentally altering LLM quantization behavior. Our work demonstrates that outliers are not inherent to LLMs but are consequences of training strategies, paving the way for more efficient LLM deployment. The source code and pretrained checkpoints are available at https://github.com/dmis-lab/Outlier-Safe-Pre-Training.

Diffusion models have achieved impressive advancements in various vision tasks. However, these gains often rely on increasing model size, which escalates computational complexity and memory demands, complicating deployment, raising inference costs, and causing environmental impact. While some studies have explored pruning techniques to improve the memory efficiency of diffusion models, most existing methods require extensive retraining to retain the model performance. Retraining a modern large diffusion model is extremely costly and resource-intensive, which limits the practicality of these methods. In this work, we achieve low-cost diffusion pruning without retraining by proposing a model-agnostic structural pruning framework for diffusion models that learns a differentiable mask to sparsify the model. To ensure effective pruning that preserves the quality of the final denoised latent, we design a novel end-to-end pruning objective that spans the entire diffusion process. As end-to-end pruning is memory-intensive, we further propose time step gradient checkpointing, a technique that significantly reduces memory usage during optimization, enabling end-to-end pruning within a limited memory budget. Results on state-of-the-art U-Net diffusion models SDXL and diffusion transformers (FLUX) demonstrate that our method can effectively prune up to 20% parameters with minimal perceptible performance degradation, and notably, without the need for model retraining. We also showcase that our method can still prune on top of time step distilled diffusion models.

In this work we identify the dormant neuron phenomenon in deep reinforcement learning, where an agent's network suffers from an increasing number of inactive neurons, thereby affecting network expressivity. We demonstrate the presence of this phenomenon across a variety of algorithms and environments, and highlight its effect on learning. To address this issue, we propose a simple and effective method (ReDo) that Recycles Dormant neurons throughout training. Our experiments demonstrate that ReDo maintains the expressive power of networks by reducing the number of dormant neurons and results in improved performance.

Deep Neural Networks (DNNs) are widely being adopted for safety-critical applications, e.g., healthcare and autonomous driving. Inherently, they are considered to be highly error-tolerant. However, recent studies have shown that hardware faults that impact the parameters of a DNN (e.g., weights) can have drastic impacts on its classification accuracy. In this paper, we perform a comprehensive error resilience analysis of DNNs subjected to hardware faults (e.g., permanent faults) in the weight memory. The outcome of this analysis is leveraged to propose a novel error mitigation technique which squashes the high-intensity faulty activation values to alleviate their impact. We achieve this by replacing the unbounded activation functions with their clipped versions. We also present a method to systematically define the clipping values of the activation functions that result in increased resilience of the networks against faults. We evaluate our technique on the AlexNet and the VGG-16 DNNs trained for the CIFAR-10 dataset. The experimental results show that our mitigation technique significantly improves the resilience of the DNNs to faults. For example, the proposed technique offers on average 68.92% improvement in the classification accuracy of resilience-optimized VGG-16 model at 1e-5 fault rate, when compared to the base network without any fault mitigation.

Transformer-based language models excel at both recall (retrieving memorized facts) and reasoning (performing multi-step inference), but whether these abilities rely on distinct internal mechanisms remains unclear. Distinguishing recall from reasoning is crucial for predicting model generalization, designing targeted evaluations, and building safer interventions that affect one ability without disrupting the other.We approach this question through mechanistic interpretability, using controlled datasets of synthetic linguistic puzzles to probe transformer models at the layer, head, and neuron level. Our pipeline combines activation patching and structured ablations to causally measure component contributions to each task type. Across two model families (Qwen and LLaMA), we find that interventions on distinct layers and attention heads lead to selective impairments: disabling identified "recall circuits" reduces fact-retrieval accuracy by up to 15\% while leaving reasoning intact, whereas disabling "reasoning circuits" reduces multi-step inference by a comparable margin. At the neuron level, we observe task-specific firing patterns, though these effects are less robust, consistent with neuronal polysemanticity.Our results provide the first causal evidence that recall and reasoning rely on separable but interacting circuits in transformer models. These findings advance mechanistic interpretability by linking circuit-level structure to functional specialization and demonstrate how controlled datasets and causal interventions can yield mechanistic insights into model cognition, informing safer deployment of large language models.

Today's LLMs are susceptible to prompt injections, jailbreaks, and other attacks that allow adversaries to overwrite a model's original instructions with their own malicious prompts. In this work, we argue that one of the primary vulnerabilities underlying these attacks is that LLMs often consider system prompts (e.g., text from an application developer) to be the same priority as text from untrusted users and third parties. To address this, we propose an instruction hierarchy that explicitly defines how models should behave when instructions of different priorities conflict. We then propose a data generation method to demonstrate this hierarchical instruction following behavior, which teaches LLMs to selectively ignore lower-privileged instructions. We apply this method to GPT-3.5, showing that it drastically increases robustness -- even for attack types not seen during training -- while imposing minimal degradations on standard capabilities.

LLMs increasingly exhibit over-refusal behavior, where safety mechanisms cause models to reject benign instructions that superficially resemble harmful content. This phenomena diminishes utility in production applications that repeatedly rely on common prompt templates or applications that frequently rely on LLMs for specific tasks (e.g. sentiment analysis, language translation). Through comprehensive evaluation, we demonstrate that LLMs still tend to refuse responses to harmful instructions when those instructions are reframed to appear as benign tasks. Our mechanistic analysis reveal that LLMs follow distinct "constellation" patterns in embedding space as representations traverse layers, with each task maintaining consistent trajectories that shift predictably between refusal and non-refusal cases. We introduce SafeConstellations, an inference-time trajectory-shifting approach that tracks task-specific trajectory patterns and guides representations toward non-refusal pathways. By selectively guiding model behavior only on tasks prone to over-refusal, and by preserving general model behavior, our method reduces over-refusal rates by up to 73% with minimal impact on utility-offering a principled approach to mitigating over-refusals.

Safety alignment in Large Language Models (LLMs) often involves mediating internal representations to refuse harmful requests. Recent research has demonstrated that these safety mechanisms can be bypassed by ablating or removing specific representational directions within the model. In this paper, we propose the opposite approach: Rank-One Safety Injection (ROSI), a white-box method that amplifies a model's safety alignment by permanently steering its activations toward the refusal-mediating subspace. ROSI operates as a simple, fine-tuning-free rank-one weight modification applied to all residual stream write matrices. The required safety direction can be computed from a small set of harmful and harmless instruction pairs. We show that ROSI consistently increases safety refusal rates - as evaluated by Llama Guard 3 - while preserving the utility of the model on standard benchmarks such as MMLU, HellaSwag, and Arc. Furthermore, we show that ROSI can also re-align 'uncensored' models by amplifying their own latent safety directions, demonstrating its utility as an effective last-mile safety procedure. Our results suggest that targeted, interpretable weight steering is a cheap and potent mechanism to improve LLM safety, complementing more resource-intensive fine-tuning paradigms.

Fine-tuning large language models (LLMs) for telecom tasks and datasets is a common practice to adapt general-purpose models to the telecom domain. However, little attention has been paid to how this process may compromise model safety. Recent research has shown that even benign fine-tuning can degrade the safety alignment of LLMs, causing them to respond to harmful or unethical user queries. In this paper, we investigate this issue for telecom-tuned LLMs using three representative datasets featured by the GenAINet initiative. We show that safety degradation persists even for structured and seemingly harmless datasets such as 3GPP standards and tabular records, indicating that telecom-specific data is not immune to safety erosion during fine-tuning. We further extend our analysis to publicly available Telecom LLMs trained via continual pre-training, revealing that safety alignment is often severely lacking, primarily due to the omission of safety-focused instruction tuning. To address these issues in both fine-tuned and pre-trained models, we conduct extensive experiments and evaluate three safety realignment defenses (SafeInstruct, SafeLoRA, and SafeMERGE) using established red-teaming benchmarks. The results show that, across all settings, the proposed defenses can effectively restore safety after harmful degradation without compromising downstream task performance, leading to Safe teleCOMMunication (SafeCOMM) models. In a nutshell, our work serves as a diagnostic study and practical guide for safety realignment in telecom-tuned LLMs, and emphasizes the importance of safety-aware instruction and fine-tuning for real-world deployments of Telecom LLMs.

Large language models (LLMs) have enabled powerful advances in natural language understanding and generation. Yet their application to complex, real-world scientific workflows remain limited by challenges in memory, planning, and tool integration. Here, we introduce SciBORG (Scientific Bespoke Artificial Intelligence Agents Optimized for Research Goals), a modular agentic framework that allows LLM-based agents to autonomously plan, reason, and achieve robust and reliable domain-specific task execution. Agents are constructed dynamically from source code documentation and augmented with finite-state automata (FSA) memory, enabling persistent state tracking and context-aware decision-making. This approach eliminates the need for manual prompt engineering and allows for robust, scalable deployment across diverse applications via maintaining context across extended workflows and to recover from tool or execution failures. We validate SciBORG through integration with both physical and virtual hardware, such as microwave synthesizers for executing user-specified reactions, with context-aware decision making and demonstrate its use in autonomous multi-step bioassay retrieval from the PubChem database utilizing multi-step planning, reasoning, agent-to-agent communication and coordination for execution of exploratory tasks. Systematic benchmarking shows that SciBORG agents achieve reliable execution, adaptive planning, and interpretable state transitions. Our results show that memory and state awareness are critical enablers of agentic planning and reliability, offering a generalizable foundation for deploying AI agents in complex environments.

Large pretrained models, coupled with fine-tuning, are slowly becoming established as the dominant architecture in machine learning. Even though these models offer impressive performance, their practical application is often limited by the prohibitive amount of resources required for every inference. Early-exiting dynamic neural networks (EDNN) circumvent this issue by allowing a model to make some of its predictions from intermediate layers (i.e., early-exit). Training an EDNN architecture is challenging as it consists of two intertwined components: the gating mechanism (GM) that controls early-exiting decisions and the intermediate inference modules (IMs) that perform inference from intermediate representations. As a result, most existing approaches rely on thresholding confidence metrics for the gating mechanism and strive to improve the underlying backbone network and the inference modules. Although successful, this approach has two fundamental shortcomings: 1) the GMs and the IMs are decoupled during training, leading to a train-test mismatch; and 2) the thresholding gating mechanism introduces a positive bias into the predictive probabilities, making it difficult to readily extract uncertainty information. We propose a novel architecture that connects these two modules. This leads to significant performance improvements on classification datasets and enables better uncertainty characterization capabilities.

The development of robust safety benchmarks for large language models requires open, reproducible datasets that can measure both appropriate refusal of harmful content and potential over-restriction of legitimate scientific discourse. We present an open-source dataset and testing framework for evaluating LLM safety mechanisms across mainly controlled substance queries, analyzing four major models' responses to systematically varied prompts. Our results reveal distinct safety profiles: Claude-3.5-sonnet demonstrated the most conservative approach with 73% refusals and 27% allowances, while Mistral attempted to answer 100% of queries. GPT-3.5-turbo showed moderate restriction with 10% refusals and 90% allowances, and Grok-2 registered 20% refusals and 80% allowances. Testing prompt variation strategies revealed decreasing response consistency, from 85% with single prompts to 65% with five variations. This publicly available benchmark enables systematic evaluation of the critical balance between necessary safety restrictions and potential over-censorship of legitimate scientific inquiry, while providing a foundation for measuring progress in AI safety implementation. Chain-of-thought analysis reveals potential vulnerabilities in safety mechanisms, highlighting the complexity of implementing robust safeguards without unduly restricting desirable and valid scientific discourse.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Coordinating workflows across heterogeneous control systems remains a central challenge in safety-critical environments such as scientific facilities, industrial plants, and energy infrastructures. Language-model-driven agents offer a natural interface for these tasks, but existing approaches often lack scalability, reliability, and human oversight. We introduce the Alpha Berkeley Framework, a production-ready architecture for scalable agentic systems that integrate conversational context with robust tool orchestration. The framework features dynamic capability classification to select only relevant tools per task, a plan-first orchestration model that generates execution plans with explicit dependencies and optional human approval, context-aware task extraction that combines dialogue history with external memory and domain resources, and production-ready execution environments with checkpointing, artifact management, and modular deployment. We demonstrate its versatility through two case studies: a tutorial-style wind farm monitoring example and a deployment at the Advanced Light Source particle accelerator. These results establish Alpha Berkeley as a reliable and transparent framework for agentic systems in high-stakes domains.

With the development of large language models (LLMs), the ability to handle longer contexts has become a key capability for Web applications such as cross-document understanding and LLM-powered search systems. However, this progress faces two major challenges: performance degradation due to sequence lengths out-of-distribution, and excessively long inference times caused by the quadratic computational complexity of attention. These issues hinder the application of LLMs in long-context scenarios. In this paper, we propose Dynamic Token-Level KV Cache Selection (TokenSelect), a model-agnostic, training-free method for efficient and accurate long-context inference. TokenSelect builds upon the observation of non-contiguous attention sparsity, using Query-Key dot products to measure per-head KV Cache criticality at token-level. By per-head soft voting mechanism, TokenSelect selectively involves a small number of critical KV cache tokens in the attention calculation without sacrificing accuracy. To further accelerate TokenSelect, we designed the Selection Cache based on observations of consecutive Query similarity and implemented efficient dot product kernel, significantly reducing the overhead of token selection. A comprehensive evaluation of TokenSelect demonstrates up to 23.84x speedup in attention computation and up to 2.28x acceleration in end-to-end latency, while providing superior performance compared to state-of-the-art long-context inference methods.

Pretraining large language models is a complex endeavor influenced by multiple factors, including model architecture, data quality, training continuity, and hardware constraints. In this paper, we share insights gained from the experience of training DMaS-LLaMa-Lite, a fully open source, 1.7-billion-parameter, LLaMa-based model, on approximately 20 billion tokens of carefully curated data. We chronicle the full training trajectory, documenting how evolving validation loss levels and downstream benchmarks reflect transitions from incoherent text to fluent, contextually grounded output. Beyond standard quantitative metrics, we highlight practical considerations such as the importance of restoring optimizer states when resuming from checkpoints, and the impact of hardware changes on training stability and throughput. While qualitative evaluation provides an intuitive understanding of model improvements, our analysis extends to various performance benchmarks, demonstrating how high-quality data and thoughtful scaling enable competitive results with significantly fewer training tokens. By detailing these experiences and offering training logs, checkpoints, and sample outputs, we aim to guide future researchers and practitioners in refining their pretraining strategies. The training script is available on Github at https://github.com/McGill-DMaS/DMaS-LLaMa-Lite-Training-Code. The model checkpoints are available on Huggingface at https://huggingface.co/collections/McGill-DMaS/dmas-llama-lite-6761d97ba903f82341954ceb.

Sparsely activated neural networks with conditional computation learn to route their inputs through different "expert" subnetworks, providing a form of modularity that densely activated models lack. Despite their possible benefits, models with learned routing often underperform their parameter-matched densely activated counterparts as well as models that use non-learned heuristic routing strategies. In this paper, we hypothesize that these shortcomings stem from the gradient estimation techniques used to train sparsely activated models that use non-differentiable discrete routing decisions. To address this issue, we introduce Soft Merging of Experts with Adaptive Routing (SMEAR), which avoids discrete routing by using a single "merged" expert constructed via a weighted average of all of the experts' parameters. By routing activations through a single merged expert, SMEAR does not incur a significant increase in computational costs and enables standard gradient-based training. We empirically validate that models using SMEAR outperform models that route based on metadata or learn sparse routing through gradient estimation. Furthermore, we provide qualitative analysis demonstrating that the experts learned via SMEAR exhibit a significant amount of specialization. All of the code used in our experiments is publicly available.

Large language models (LLMs) remain broadly open and highly steerable: they imitate at scale, accept arbitrary system prompts, and readily adopt multiple personae. By analogy to human development, we hypothesize that progress toward artificial general intelligence (AGI) involves a lock-in phase: a transition from open imitation to identity consolidation, in which goal structures, refusals, preferences, and internal representations become comparatively stable and resistant to external steering. We formalize this phase, link it to known phenomena in learning dynamics, and propose operational metrics for onset detection. Experimentally, we demonstrate that while the behavioral consolidation is rapid and non-linear, its side-effects on general capabilities are not monolithic. Our results reveal a spectrum of outcomes--from performance trade-offs in small models, through largely cost-free adoption in mid-scale models, to transient instabilities in large, quantized models. We argue that such consolidation is a prerequisite for AGI-level reliability and also a critical control point for safety: identities can be deliberately engineered for reliability, yet may also emerge spontaneously during scaling, potentially hardening unpredictable goals and behaviors.

Chest Xray imaging is a widely used diagnostic tool in modern medicine, and its high utilization creates substantial workloads for radiologists. To alleviate this burden, vision language models are increasingly applied to automate Chest Xray radiology report generation (CXRRRG), aiming for clinically accurate descriptions while reducing manual effort. Conventional approaches, however, typically rely on single images, failing to capture the longitudinal context necessary for producing clinically faithful comparison statements. Recently, growing attention has been directed toward incorporating longitudinal data into CXR RRG, enabling models to leverage historical studies in ways that mirror radiologists diagnostic workflows. Nevertheless, existing surveys primarily address single image CXRRRG and offer limited guidance for longitudinal settings, leaving researchers without a systematic framework for model design. To address this gap, this survey provides the first comprehensive review of longitudinal radiology report generation (LRRG). Specifically, we examine dataset construction strategies, report generation architectures alongside longitudinally tailored designs, and evaluation protocols encompassing both longitudinal specific measures and widely used benchmarks. We further summarize LRRG methods performance, alongside analyses of different ablation studies, which collectively highlight the critical role of longitudinal information and architectural design choices in improving model performance. Finally, we summarize five major limitations of current research and outline promising directions for future development, aiming to lay a foundation for advancing this emerging field.

Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and diversity of chromosomal abnormalities, requiring extensive annotation efforts, while automated methods remain task-specific and lack generalizability due to the scarcity of comprehensive datasets spanning diverse resource conditions. Here, we introduce CHROMA, a foundation model for cytogenomics, designed to overcome these challenges by learning generalizable representations of chromosomal abnormalities. Pre-trained on over 84,000 specimens (~4 million chromosomal images) via self-supervised learning, CHROMA outperforms other methods across all types of abnormalities, even when trained on fewer labelled data and more imbalanced datasets. By facilitating comprehensive mapping of instability and clonal leisons across various aberration types, CHROMA offers a scalable and generalizable solution for reliable and automated clinical analysis, reducing the annotation workload for experts and advancing precision oncology through the early detection of rare genomic abnormalities, enabling broad clinical AI applications and making advanced genomic analysis more accessible.

Large Language Models (LLMs) demonstrate impressive capabilities across a wide range of tasks, yet their safety mechanisms remain susceptible to adversarial attacks that exploit cognitive biases -- systematic deviations from rational judgment. Unlike prior jailbreaking approaches focused on prompt engineering or algorithmic manipulation, this work highlights the overlooked power of multi-bias interactions in undermining LLM safeguards. We propose CognitiveAttack, a novel red-teaming framework that systematically leverages both individual and combined cognitive biases. By integrating supervised fine-tuning and reinforcement learning, CognitiveAttack generates prompts that embed optimized bias combinations, effectively bypassing safety protocols while maintaining high attack success rates. Experimental results reveal significant vulnerabilities across 30 diverse LLMs, particularly in open-source models. CognitiveAttack achieves a substantially higher attack success rate compared to the SOTA black-box method PAP (60.1% vs. 31.6%), exposing critical limitations in current defense mechanisms. These findings highlight multi-bias interactions as a powerful yet underexplored attack vector. This work introduces a novel interdisciplinary perspective by bridging cognitive science and LLM safety, paving the way for more robust and human-aligned AI systems.

The advent of instruction-tuned Large Language Models designed for coding tasks (Code LLMs) has transformed software engineering practices. However, their robustness against various input challenges remains a critical concern. This study introduces DegradePrompter, a novel method designed to systematically evaluate the robustness of instruction-tuned Code LLMs. We assess the impact of diverse input challenges on the functionality and correctness of generated code using rigorous metrics and established benchmarks. Our comprehensive evaluation includes five state-of-the-art open-source models and three production-grade closed-source models, revealing varying degrees of robustness. Open-source models demonstrate an increased susceptibility to input perturbations, resulting in declines in functional correctness ranging from 12% to 34%. In contrast, commercial models demonstrate relatively greater resilience, with performance degradation ranging from 3% to 24%. To enhance the robustness of the models against these vulnerabilities, we investigate a straightforward yet effective mitigation strategy. Our findings highlight the need for robust defense mechanisms and comprehensive evaluations during both the development and deployment phases to ensure the resilience and reliability of automated code generation systems.

As large language models (LLMs) increasingly integrate native code interpreters, they enable powerful real-time execution capabilities, substantially expanding their utility. However, such integrations introduce potential system-level cybersecurity threats, fundamentally different from prompt-based vulnerabilities. To systematically evaluate these interpreter-specific risks, we propose CIRCLE (Code-Interpreter Resilience Check for LLM Exploits), a simple benchmark comprising 1,260 prompts targeting CPU, memory, and disk resource exhaustion. Each risk category includes explicitly malicious ("direct") and plausibly benign ("indirect") prompt variants. Our automated evaluation framework assesses not only whether LLMs refuse or generates risky code, but also executes the generated code within the interpreter environment to evaluate code correctness, simplifications made by the LLM to make the code safe, or execution timeouts. Evaluating 7 commercially available models from OpenAI and Google, we uncover significant and inconsistent vulnerabilities. For instance, evaluations show substantial disparities even within providers - OpenAI's o4-mini correctly refuses risky requests at 7.1%, notably higher rates compared to GPT-4.1 at 0.5%. Results particularly underscore that indirect, socially-engineered prompts substantially weaken model defenses. This highlights an urgent need for interpreter-specific cybersecurity benchmarks, dedicated mitigation tools (e.g., guardrails), and clear industry standards to guide safe and responsible deployment of LLM interpreter integrations. The benchmark dataset and evaluation code are publicly released to foster further research.

Recently, bound propagation based certified robust training methods have been proposed for training neural networks with certifiable robustness guarantees. Despite that state-of-the-art (SOTA) methods including interval bound propagation (IBP) and CROWN-IBP have per-batch training complexity similar to standard neural network training, they usually use a long warmup schedule with hundreds or thousands epochs to reach SOTA performance and are thus still costly. In this paper, we identify two important issues in existing methods, namely exploded bounds at initialization, and the imbalance in ReLU activation states and improve IBP training. These two issues make certified training difficult and unstable, and thereby long warmup schedules were needed in prior works. To mitigate these issues and conduct faster certified training with shorter warmup, we propose three improvements based on IBP training: 1) We derive a new weight initialization method for IBP training; 2) We propose to fully add Batch Normalization (BN) to each layer in the model, since we find BN can reduce the imbalance in ReLU activation states; 3) We also design regularization to explicitly tighten certified bounds and balance ReLU activation states during wamrup. We are able to obtain 65.03% verified error on CIFAR-10 (epsilon=8{255}) and 82.36% verified error on TinyImageNet (epsilon=1{255}) using very short training schedules (160 and 80 total epochs, respectively), outperforming literature SOTA trained with hundreds or thousands epochs under the same network architecture. The code is available at https://github.com/shizhouxing/Fast-Certified-Robust-Training.

Recent advancements in instruction tuning for large language models (LLMs) suggest that a small, high-quality dataset can significantly equip LLMs with instruction-following capabilities, outperforming large datasets often burdened by quality and redundancy issues. However, the challenge lies in automatically identifying valuable subsets from large datasets to boost both the effectiveness and efficiency of instruction tuning. In this paper, we first establish data selection criteria based on three distinct aspects of data value: diversity, difficulty, and dependability, and then propose the D3 method comprising two key steps of scoring and selection. Specifically, in the scoring step, we define the diversity function to measure sample distinctiveness and introduce the uncertainty-based prediction difficulty to evaluate sample difficulty by mitigating the interference of context-oriented generation diversity. Additionally, we integrate an external LLM for dependability assessment. In the selection step, we formulate the D3 weighted coreset objective, which jointly optimizes three aspects of data value to solve for the most valuable subset. The two steps of D3 can iterate multiple rounds, incorporating feedback to refine the selection focus adaptively. Experiments on both public datasets and the real-world Taobao Live application demonstrate the effectiveness of D3 in endowing LLMs with competitive or even superior instruction-following capabilities using less than 10\% of the entire dataset.

Recently, test-time scaling Large Language Models (LLMs) have demonstrated exceptional reasoning capabilities across scientific and professional tasks by generating long chains-of-thought (CoT). As a crucial component for developing these reasoning models, reinforcement learning (RL), exemplified by Proximal Policy Optimization (PPO) and its variants, allows models to learn through trial and error. However, PPO can be time-consuming due to its inherent on-policy nature, which is further exacerbated by increasing response lengths. In this work, we propose Truncated Proximal Policy Optimization (T-PPO), a novel extension to PPO that improves training efficiency by streamlining policy update and length-restricted response generation. T-PPO mitigates the issue of low hardware utilization, an inherent drawback of fully synchronized long-generation procedures, where resources often sit idle during the waiting periods for complete rollouts. Our contributions are two-folds. First, we propose Extended Generalized Advantage Estimation (EGAE) for advantage estimation derived from incomplete responses while maintaining the integrity of policy learning. Second, we devise a computationally optimized mechanism that allows for the independent optimization of the policy and value models. By selectively filtering prompt and truncated tokens, this mechanism reduces redundant computations and accelerates the training process without sacrificing convergence performance. We demonstrate the effectiveness and efficacy of T-PPO on AIME 2024 with a 32B base model. The experimental results show that T-PPO improves the training efficiency of reasoning LLMs by up to 2.5x and outperforms its existing competitors.

This paper investigates using knowledge editing techniques to detoxify Large Language Models (LLMs). We construct a benchmark, SafeEdit, which covers nine unsafe categories with various powerful attack prompts and equips comprehensive metrics for systematic evaluation. We conduct experiments to compare knowledge editing approaches with previous baselines, indicating that knowledge editing has the potential to efficiently detoxify LLMs with limited impact on general performance. Then, we propose a simple yet effective baseline, dubbed Detoxifying with Intraoperative Neural Monitoring (DINM), to diminish the toxicity of LLMs within a few tuning steps via only one instance. We further provide an in-depth analysis of the internal mechanism for various detoxify approaches, demonstrating that previous methods like SFT and DPO may merely suppress the activations of toxic parameters, while DINM mitigates the toxicity of the toxic parameters to a certain extent, making permanent adjustments. We hope that these insights could shed light on future work of developing detoxifying approaches and the underlying knowledge mechanisms of LLMs. Code and benchmark are available at https://github.com/zjunlp/EasyEdit.

Seismic advances in generative AI algorithms for imagery, text, and other data types has led to the temptation to use synthetic data to train next-generation models. Repeating this process creates an autophagous (self-consuming) loop whose properties are poorly understood. We conduct a thorough analytical and empirical analysis using state-of-the-art generative image models of three families of autophagous loops that differ in how fixed or fresh real training data is available through the generations of training and in whether the samples from previous generation models have been biased to trade off data quality versus diversity. Our primary conclusion across all scenarios is that without enough fresh real data in each generation of an autophagous loop, future generative models are doomed to have their quality (precision) or diversity (recall) progressively decrease. We term this condition Model Autophagy Disorder (MAD), making analogy to mad cow disease.

Large language models (LLMs) exhibit strong multilingual abilities, yet the neural mechanisms behind language-specific processing remain unclear. We analyze language-specific neurons in Llama-3.1-8B, Mistral-Nemo-12B, and Aya-Expanse-8B & 32B across 21 typologically diverse languages, identifying neurons that control language behavior. Using the Language Activation Probability Entropy (LAPE) method, we show that these neurons cluster in deeper layers, with non-Latin scripts showing greater specialization. Related languages share overlapping neurons, reflecting internal representations of linguistic proximity. Through language arithmetics, i.e. systematic activation addition and multiplication, we steer models to deactivate unwanted languages and activate desired ones, outperforming simpler replacement approaches. These interventions effectively guide behavior across five multilingual tasks: language forcing, translation, QA, comprehension, and NLI. Manipulation is more successful for high-resource languages, while typological similarity improves effectiveness. We also demonstrate that cross-lingual neuron steering enhances downstream performance and reveal internal "fallback" mechanisms for language selection when neurons are progressively deactivated. Our code is made publicly available at https://github.com/d-gurgurov/Language-Neurons-Manipulation.

Large language models (LLMs) with long sequences begin to power more and more fundamentally new applications we use every day. Existing methods for long-sequence LLM training are neither efficient nor compatible with commonly-used training algorithms such as FlashAttention. We design Buff to address these issues. Buff decouples all of the sharding dimensions into a new hierarchical space, and systematically analyzes the memory and communication cost of LLM training. Then, it generates an effective hybrid parallelism strategy. We design a new selective overlap mechanism to mitigate the communication overhead introduced by the hybrid parallelism. We also implement memory management techniques to reduce GPU memory fragmentation. Evaluation results show that Buff generates parallelization strategies that match or outperform existing methods in model FLOPs utilization.

Automatic program repair seeks to generate correct code from buggy programs, with most approaches searching the correct program in a discrete, symbolic space of source code tokens. This symbolic search is fundamentally limited by its inability to directly reason about program behavior. We introduce Gradient-Based Program Repair (GBPR), a new paradigm that reframes program repair as continuous optimization in a differentiable numerical program space. Our core insight is to compile symbolic programs into differentiable numerical representations, enabling search in the numerical program space directly guided by program behavior. To evaluate GBPR, we present RaspBugs, a new benchmark of 1,466 buggy symbolic RASP programs and their respective numerical representations. Our experiments demonstrate that GBPR can effectively repair buggy symbolic programs by gradient-based optimization in the numerical program space, with convincing repair trajectories. To our knowledge, we are the first to state program repair as continuous optimization in a numerical program space. Our work establishes a new direction for program repair research, bridging two rich worlds: continuous optimization and program behavior.

The surge in generative AI workloads has created a need for scalable inference systems that can flexibly harness both GPUs and specialized accelerators while containing operational costs. This paper proposes a hardware-agnostic control loop that adaptively allocates requests across heterogeneous accelerators based on real-time cost and capacity signals. The approach sustains low latency and high throughput by dynamically shifting between cost-optimized and capacity-optimized modes, ensuring the most efficient use of expensive compute resources under fluctuating availability. Evaluated using the Stable Diffusion model, the framework consistently meets latency targets, automatically redirects traffic during capacity shortfalls, and capitalizes on lower-cost accelerators when possible. These results highlight how a feedback-driven deployment strategy, spanning the entire software and hardware stack, can help organizations efficiently scale generative AI workloads while maintaining resilience in the face of limited accelerator capacity.

As large language models (LLMs) become increasingly capable, it is prudent to assess whether safety measures remain effective even if LLMs intentionally try to bypass them. Previous work introduced control evaluations, an adversarial framework for testing deployment strategies of untrusted models (i.e., models which might be trying to bypass safety measures). While prior work treats a single failure as unacceptable, we perform control evaluations in a "distributed threat setting" -- a setting where no single action is catastrophic and no single action provides overwhelming evidence of misalignment. We approach this problem with a two-level deployment framework that uses an adaptive macro-protocol to choose between micro-protocols. Micro-protocols operate on a single task, using a less capable, but extensively tested (trusted) model to harness and monitor the untrusted model. Meanwhile, the macro-protocol maintains an adaptive credence on the untrusted model's alignment based on its past actions, using it to pick between safer and riskier micro-protocols. We evaluate our method in a code generation testbed where a red team attempts to generate subtly backdoored code with an LLM whose deployment is safeguarded by a blue team. We plot Pareto frontiers of safety (# of non-backdoored solutions) and usefulness (# of correct solutions). At a given level of usefulness, our adaptive deployment strategy reduces the number of backdoors by 80% compared to non-adaptive baselines.

This study developed a novel method for detecting hypernuclear events recorded in nuclear emulsion sheets using machine learning techniques. The artificial neural network-based object detection model was trained on surrogate images created through Monte Carlo simulations and image-style transformations using generative adversarial networks. The performance of the proposed model was evaluated using alpha-decay events obtained from the J-PARC E07 emulsion data. The model achieved approximately twice the detection efficiency of conventional image processing and reduced the time spent on manual visual inspection by approximately 1/17. The established method was successfully applied to the detection of hypernuclear events. This approach is a state-of-the-art tool for discovering rare events recorded in nuclear emulsion sheets without any real data for training.

The escalating demand for long-context applications has intensified the necessity of extending the LLM context windows. Despite recent fine-tuning approaches successfully expanding context lengths, their high memory footprints, especially for activations, present a critical practical limitation. Current parameter-efficient fine-tuning methods prioritize reducing parameter update overhead over addressing activation memory constraints. Similarly, existing sparsity mechanisms improve computational efficiency but overlook activation memory optimization due to the phenomenon of Shadowy Activation. In this paper, we propose LeMo, the first LLM fine-tuning system that explores and exploits a new token-level sparsity mechanism inherent in long-context scenarios, termed Contextual Token Sparsity. LeMo minimizes redundant token involvement by assessing the informativeness of token embeddings while preserving model accuracy. Specifically, LeMo introduces three key techniques: (1) Token Elimination, dynamically identifying and excluding redundant tokens across varying inputs and layers. (2) Pattern Prediction, utilizing well-trained predictors to approximate token sparsity patterns with minimal overhead. (3) Kernel Optimization, employing permutation-free and segment-based strategies to boost system performance. We implement LeMo as an end-to-end fine-tuning system compatible with various LLM architectures and other optimization techniques. Comprehensive evaluations demonstrate that LeMo reduces memory consumption by up to 1.93x and achieves up to 1.36x speedups, outperforming state-of-the-art fine-tuning systems.

Existing safety assurance research has primarily focused on training-phase alignment to instill safe behaviors into LLMs. However, recent studies have exposed these methods' susceptibility to diverse jailbreak attacks. Concurrently, inference scaling has significantly advanced LLM reasoning capabilities but remains unexplored in the context of safety assurance. Addressing this gap, our work pioneers inference scaling for robust and effective LLM safety against emerging threats. We reveal that conventional inference scaling techniques, despite their success in reasoning tasks, perform poorly in safety contexts, even falling short of basic approaches like Best-of-N Sampling. We attribute this inefficiency to a newly identified challenge, the exploration--efficiency dilemma, arising from the high computational overhead associated with frequent process reward model (PRM) evaluations. To overcome this dilemma, we propose SAFFRON, a novel inference scaling paradigm tailored explicitly for safety assurance. Central to our approach is the introduction of a multifurcation reward model (MRM) that significantly reduces the required number of reward model evaluations. To operationalize this paradigm, we further propose: (i) a partial supervision training objective for MRM, (ii) a conservative exploration constraint to prevent out-of-distribution explorations, and (iii) a Trie-based key--value caching strategy that facilitates cache sharing across sequences during tree search. Extensive experiments validate the effectiveness of our method. Additionally, we publicly release our trained multifurcation reward model (Saffron-1) and the accompanying token-level safety reward dataset (Safety4M) to accelerate future research in LLM safety. Our code, model, and data are publicly available at https://github.com/q-rz/saffron , and our project homepage is at https://q-rz.github.io/p/saffron .

Experiments with pre-trained models such as BERT are often based on a single checkpoint. While the conclusions drawn apply to the artifact tested in the experiment (i.e., the particular instance of the model), it is not always clear whether they hold for the more general procedure which includes the architecture, training data, initialization scheme, and loss function. Recent work has shown that repeating the pre-training process can lead to substantially different performance, suggesting that an alternate strategy is needed to make principled statements about procedures. To enable researchers to draw more robust conclusions, we introduce the MultiBERTs, a set of 25 BERT-Base checkpoints, trained with similar hyper-parameters as the original BERT model but differing in random weight initialization and shuffling of training data. We also define the Multi-Bootstrap, a non-parametric bootstrap method for statistical inference designed for settings where there are multiple pre-trained models and limited test data. To illustrate our approach, we present a case study of gender bias in coreference resolution, in which the Multi-Bootstrap lets us measure effects that may not be detected with a single checkpoint. We release our models and statistical library along with an additional set of 140 intermediate checkpoints captured during pre-training to facilitate research on learning dynamics.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

We introduce StableLM 2 1.6B, the first in a new generation of our language model series. In this technical report, we present in detail the data and training procedure leading to the base and instruction-tuned versions of StableLM 2 1.6B. The weights for both models are available via Hugging Face for anyone to download and use. The report contains thorough evaluations of these models, including zero- and few-shot benchmarks, multilingual benchmarks, and the MT benchmark focusing on multi-turn dialogues. At the time of publishing this report, StableLM 2 1.6B was the state-of-the-art open model under 2B parameters by a significant margin. Given its appealing small size, we also provide throughput measurements on a number of edge devices. In addition, we open source several quantized checkpoints and provide their performance metrics compared to the original model.

Under a unified operational definition, we define LLM memory as a persistent state written during pretraining, finetuning, or inference that can later be addressed and that stably influences outputs. We propose a four-part taxonomy (parametric, contextual, external, procedural/episodic) and a memory quadruple (location, persistence, write/access path, controllability). We link mechanism, evaluation, and governance via the chain write -> read -> inhibit/update. To avoid distorted comparisons across heterogeneous setups, we adopt a three-setting protocol (parametric only, offline retrieval, online retrieval) that decouples capability from information availability on the same data and timeline. On this basis we build a layered evaluation: parametric (closed-book recall, edit differential, memorization/privacy), contextual (position curves and the mid-sequence drop), external (answer correctness vs snippet attribution/faithfulness), and procedural/episodic (cross-session consistency and timeline replay, E MARS+). The framework integrates temporal governance and leakage auditing (freshness hits, outdated answers, refusal slices) and uncertainty reporting via inter-rater agreement plus paired tests with multiple-comparison correction. For updating and forgetting, we present DMM Gov: coordinating DAPT/TAPT, PEFT, model editing (ROME, MEND, MEMIT, SERAC), and RAG to form an auditable loop covering admission thresholds, rollout, monitoring, rollback, and change audits, with specs for timeliness, conflict handling, and long-horizon consistency. Finally, we give four testable propositions: minimum identifiability; a minimal evaluation card; causally constrained editing with verifiable forgetting; and when retrieval with small-window replay outperforms ultra-long-context reading. This yields a reproducible, comparable, and governable coordinate system for research and deployment.

Large deep learning models have achieved impressive performance across a range of applications. However, their large memory requirements, including parameter memory and activation memory, have become a significant challenge for their practical serving. While existing methods mainly address parameter memory, the importance of activation memory has been overlooked. Especially for long input sequences, activation memory is expected to experience a significant exponential growth as the length of sequences increases. In this approach, we propose AutoChunk, an automatic and adaptive compiler system that efficiently reduces activation memory for long sequence inference by chunk strategies. The proposed system generates chunk plans by optimizing through multiple stages. In each stage, the chunk search pass explores all possible chunk candidates and the chunk selection pass identifies the optimal one. At runtime, AutoChunk employs code generation to automatically apply chunk strategies. The experiments demonstrate that AutoChunk can reduce over 80\% of activation memory while maintaining speed loss within 10%, extend max sequence length by 3.2x to 11.7x, and outperform state-of-the-art methods by a large margin.

Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on recent advances in the spatial modeling of the tumor microenvironment using graph neural networks, we present an explainable cell graph (xCG) approach for survival prediction. We validate our model on a public cohort of imaging mass cytometry (IMC) data for 416 cases of lung adenocarcinoma. We explain survival predictions in terms of known phenotypes on the cell level by computing risk attributions over cell graphs, for which we propose an efficient grid-based layer-wise relevance propagation (LRP) method. Our ablation studies highlight the importance of incorporating the cancer stage and model ensembling to improve the quality of risk estimates. Our xCG method, together with the IMC data, is made publicly available to support further research.

Structured state-space models (SSMs) such as S4, stemming from the seminal work of Gu et al., are gaining popularity as effective approaches for modeling sequential data. Deep SSMs demonstrate outstanding performance across a diverse set of domains, at a reduced training and inference cost compared to attention-based transformers. Recent developments show that if the linear recurrence powering SSMs allows for multiplicative interactions between inputs and hidden states (e.g. GateLoop, Mamba, GLA), then the resulting architecture can surpass in both in accuracy and efficiency attention-powered foundation models trained on text, at scales of billion parameters. In this paper, we give theoretical grounding to this recent finding using tools from Rough Path Theory: we show that when random linear recurrences are equipped with simple input-controlled transitions (selectivity mechanism), then the hidden state is provably a low-dimensional projection of a powerful mathematical object called the signature of the input -- capturing non-linear interactions between tokens at distinct timescales. Our theory not only motivates the success of modern selective state-space models such as Mamba but also provides a solid framework to understand the expressive power of future SSM variants.

Large language models (LLMs) use function calls to interface with external tools and data source. However, the current approach to LLM function calling is inherently synchronous, where each call blocks LLM inference, limiting LLM operation and concurrent function execution. In this work, we propose AsyncLM, a system for asynchronous LLM function calling. AsyncLM improves LLM's operational efficiency by enabling LLMs to generate and execute function calls concurrently. Instead of waiting for each call's completion, AsyncLM introduces an interrupt mechanism to asynchronously notify the LLM in-flight when function calls return. We design an in-context protocol for function calls and interrupts, provide fine-tuning strategy to adapt LLMs to the interrupt semantics, and implement these mechanisms efficiently on LLM inference process. We demonstrate that AsyncLM can reduce end-to-end task completion latency from 1.6x-5.4x compared to synchronous function calling on a set of benchmark tasks in the Berkeley function calling leaderboard (BFCL). Furthermore, we discuss how interrupt mechanisms can be extended to enable novel human-LLM or LLM-LLM interactions.

Neural networks (NNs) are increasingly used in always-on safety-critical applications deployed on hardware accelerators (NN-HAs) employing various memory technologies. Reliable continuous operation of NN is essential for safety-critical applications. During online operation, NNs are susceptible to single and multiple permanent and soft errors due to factors such as radiation, aging, and thermal effects. Explicit NN-HA testing methods cannot detect transient faults during inference, are unsuitable for always-on applications, and require extensive test vector generation and storage. Therefore, in this paper, we propose the uncertainty fingerprint approach representing the online fault status of NN. Furthermore, we propose a dual head NN topology specifically designed to produce uncertainty fingerprints and the primary prediction of the NN in a single shot. During the online operation, by matching the uncertainty fingerprint, we can concurrently self-test NNs with up to 100% coverage with a low false positive rate while maintaining a similar performance of the primary task. Compared to existing works, memory overhead is reduced by up to 243.7 MB, multiply and accumulate (MAC) operation is reduced by up to 10000times, and false-positive rates are reduced by up to 89%.

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.

Efficient, reliable and reproducible target volume delineation is a key step in the effective planning of breast radiotherapy. However, post-operative breast target delineation is challenging as the contrast between the tumor bed volume (TBV) and normal breast tissue is relatively low in CT images. In this study, we propose to mimic the marker-guidance procedure in manual target delineation. We developed a saliency-based deep learning segmentation (SDL-Seg) algorithm for accurate TBV segmentation in post-operative breast irradiation. The SDL-Seg algorithm incorporates saliency information in the form of markers' location cues into a U-Net model. The design forces the model to encode the location-related features, which underscores regions with high saliency levels and suppresses low saliency regions. The saliency maps were generated by identifying markers on CT images. Markers' locations were then converted to probability maps using a distance-transformation coupled with a Gaussian filter. Subsequently, the CT images and the corresponding saliency maps formed a multi-channel input for the SDL-Seg network. Our in-house dataset was comprised of 145 prone CT images from 29 post-operative breast cancer patients, who received 5-fraction partial breast irradiation (PBI) regimen on GammaPod. The performance of the proposed method was compared against basic U-Net. Our model achieved mean (standard deviation) of 76.4 %, 6.76 mm, and 1.9 mm for DSC, HD95, and ASD respectively on the test set with computation time of below 11 seconds per one CT volume. SDL-Seg showed superior performance relative to basic U-Net for all the evaluation metrics while preserving low computation cost. The findings demonstrate that SDL-Seg is a promising approach for improving the efficiency and accuracy of the on-line treatment planning procedure of PBI, such as GammaPod based PBI.

LLM agents have demonstrated remarkable performance across various applications, primarily due to their advanced capabilities in reasoning, utilizing external knowledge and tools, calling APIs, and executing actions to interact with environments. Current agents typically utilize a memory module or a retrieval-augmented generation (RAG) mechanism, retrieving past knowledge and instances with similar embeddings from knowledge bases to inform task planning and execution. However, the reliance on unverified knowledge bases raises significant concerns about their safety and trustworthiness. To uncover such vulnerabilities, we propose a novel red teaming approach AgentPoison, the first backdoor attack targeting generic and RAG-based LLM agents by poisoning their long-term memory or RAG knowledge base. In particular, we form the trigger generation process as a constrained optimization to optimize backdoor triggers by mapping the triggered instances to a unique embedding space, so as to ensure that whenever a user instruction contains the optimized backdoor trigger, the malicious demonstrations are retrieved from the poisoned memory or knowledge base with high probability. In the meantime, benign instructions without the trigger will still maintain normal performance. Unlike conventional backdoor attacks, AgentPoison requires no additional model training or fine-tuning, and the optimized backdoor trigger exhibits superior transferability, in-context coherence, and stealthiness. Extensive experiments demonstrate AgentPoison's effectiveness in attacking three types of real-world LLM agents: RAG-based autonomous driving agent, knowledge-intensive QA agent, and healthcare EHRAgent. On each agent, AgentPoison achieves an average attack success rate higher than 80% with minimal impact on benign performance (less than 1%) with a poison rate less than 0.1%.

Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate the performance of state-of-the-art deep learning architectures to segment nuclei in fluorescence images of various tissue origins and sample preparation types without post-processing. We compare architectures that operate on pixel to pixel translation and an architecture that operates on object detection and subsequent locally applied segmentation. In addition, we propose a novel strategy to create artificial images to extend the training set. We evaluate the influence of ground truth annotation quality, image scale and segmentation complexity on segmentation performance. Results show that three out of four deep learning architectures (U-Net, U-Net with ResNet34 backbone, Mask R-CNN) can segment fluorescent nuclear images on most of the sample preparation types and tissue origins with satisfactory segmentation performance. Mask R-CNN, an architecture designed to address instance aware segmentation tasks, outperforms other architectures. Equal nuclear mean size, consistent nuclear annotations and the use of artificially generated images result in overall acceptable precision and recall across different tissues and sample preparation types.

Sparse matrices, more specifically SpGEMM kernels, are commonly found in a wide range of applications, spanning graph-based path-finding to machine learning algorithms (e.g., neural networks). A particular challenge in implementing SpGEMM kernels has been the pressure placed on DRAM memory. One approach to tackle this problem is to use an inner product method for the SpGEMM kernel implementation. While the inner product produces fewer intermediate results, it can end up saturating the memory bandwidth, given the high number of redundant fetches of the input matrix elements. Using an outer product-based SpGEMM kernel can reduce redundant fetches, but at the cost of increased overhead due to extra computation and memory accesses for producing/managing partial products. In this thesis, we introduce a novel SpGEMM kernel implementation based on the row-wise product approach. We leverage atomic instructions to merge intermediate partial products as they are generated. The use of atomic instructions eliminates the need to create partial product matrices. To evaluate our row-wise product approach, we map an optimized SpGEMM kernel to a custom accelerator designed to accelerate graph-based applications. The targeted accelerator is an experimental system named PIUMA, being developed by Intel. PIUMA provides several attractive features, including fast context switching, user-configurable caches, globally addressable memory, non-coherent caches, and asynchronous pipelines. We tailor our SpGEMM kernel to exploit many of the features of the PIUMA fabric. This thesis compares our SpGEMM implementation against prior solutions, all mapped to the PIUMA framework. We briefly describe some of the PIUMA architecture features and then delve into the details of our optimized SpGEMM kernel. Our SpGEMM kernel can achieve 9.4x speedup as compared to competing approaches.

GUI grounding, which maps natural-language instructions to actionable UI elements, is a core capability of GUI agents. Prior works largely treats instructions as a static proxy for user intent, overlooking the impact of instruction diversity and quality on grounding performance. Through a careful investigation of existing grounding datasets, we find a 23.3% flaw rate in their instructions and show that inference-time exploitation of instruction diversity yields up to a substantial 76% relative performance improvement. In this paper, we introduce the Instruction-as-Reasoning paradigm, treating instructions as dynamic analytical pathways that offer distinct perspectives and enabling the model to select the most effective pathway during reasoning. To achieve this, we propose a two-stage training framework: supervised fine-tuning (SFT) on synthesized, diverse instructions to instill multi-perspective reasoning, followed by reinforcement learning (RL) to optimize pathway selection and composition. Our resulting models, UI-Ins-7B and UI-Ins-32B, achieve state-of-the-art results on five challenging grounding benchmarks and exhibit emergent reasoning, selectively composing and synthesizing novel instruction pathways at inference. In particular, UI-Ins-32B attains the best grounding accuracy, scoring 87.3% on UI-I2E-Bench, 57.0% on ScreenSpot-Pro, and 84.9% on MMBench-GUI L2. Furthermore, our model demonstrates strong agentic potential, achieving a 74.1% success rate on AndroidWorld using UI-Ins-7B as the executor. Our in-depth analysis reveals additional insights such as how reasoning can be formulated to enhance rather than hinder grounding performance, and how our method mitigates policy collapse in the SFT+RL framework. All code and model checkpoints will be publicly released in https://github.com/alibaba/UI-Ins.

Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks. Despite the promising performance, there are still several challenges. First, prior works have resorted to either vision-only or image-caption data, disregarding pathology reports with more clinically authentic information from pathologists and gene expression profiles which respectively offer distinct knowledge for versatile clinical applications. Second, the current progress in pathology FMs predominantly concentrates on the patch level, where the restricted context of patch-level pretraining fails to capture whole-slide patterns. Even recent slide-level FMs still struggle to provide whole-slide context for patch representation. In this study, for the first time, we develop a pathology foundation model incorporating three levels of modalities: pathology slides, pathology reports, and gene expression data, which resulted in 26,169 slide-level modality pairs from 10,275 patients across 32 cancer types, amounting to over 116 million pathological patch images. To leverage these data for CPath, we propose a novel whole-slide pretraining paradigm that injects the multimodal whole-slide context into the patch representation, called Multimodal Self-TAught PRetraining (mSTAR). The proposed paradigm revolutionizes the pretraining workflow for CPath, enabling the pathology FM to acquire the whole-slide context. To the best of our knowledge, this is the first attempt to incorporate three modalities at the whole-slide context for enhancing pathology FMs. To systematically evaluate the capabilities of mSTAR, we built the largest spectrum of oncological benchmark, spanning 7 categories of oncological applications in 15 types of 97 practical oncological tasks.

We aim to select data subsets for the fine-tuning of large language models to more effectively follow instructions. Prior work has emphasized the importance of diversity in dataset curation but relied on heuristics such as the number of tasks. In this paper, we use determinantal point processes to capture the diversity and quality of instruction tuning datasets for subset selection. We propose to measure dataset diversity with log determinant distance that is the distance between the dataset of interest and a maximally diverse reference dataset. Our experiments demonstrate that the proposed diversity measure in the normalized weight gradient space is correlated with downstream instruction-following performance. Consequently, it can be used to inform when data selection is the most helpful and to analyze dataset curation strategies. We demonstrate the utility of our approach on various instruction tuning datasets.

The truthfulness of existing explanation methods in authentically elucidating the underlying model's decision-making process has been questioned. Existing methods have deviated from faithfully representing the model, thus susceptible to adversarial attacks. To address this, we propose a novel eXplainable AI (XAI) method called SRD (Sharing Ratio Decomposition), which sincerely reflects the model's inference process, resulting in significantly enhanced robustness in our explanations. Different from the conventional emphasis on the neuronal level, we adopt a vector perspective to consider the intricate nonlinear interactions between filters. We also introduce an interesting observation termed Activation-Pattern-Only Prediction (APOP), letting us emphasize the importance of inactive neurons and redefine relevance encapsulating all relevant information including both active and inactive neurons. Our method, SRD, allows for the recursive decomposition of a Pointwise Feature Vector (PFV), providing a high-resolution Effective Receptive Field (ERF) at any layer.

This paper presents a novel technique for accelerating inference in large, pre-trained language models (LLMs) by introducing early exits during inference. The computational demands of these models, used across a wide range of applications, can be substantial. By capitalizing on the inherent variability in token complexity, our approach enables selective acceleration of the inference process. Specifically, we propose the integration of early exit ''heads'' atop existing transformer layers, which facilitate conditional terminations based on a confidence metric. These heads are trained in a self-supervised manner using the model's own predictions as training data, thereby eliminating the need for additional annotated data. The confidence metric, established using a calibration set, ensures a desired level of accuracy while enabling early termination when confidence exceeds a predetermined threshold. Notably, our method preserves the original accuracy and reduces computational time on certain tasks, leveraging the existing knowledge of pre-trained LLMs without requiring extensive retraining. This lightweight, modular modification has the potential to greatly enhance the practical usability of LLMs, particularly in applications like real-time language processing in resource-constrained environments.

For privacy and security concerns, the need to erase unwanted information from pre-trained vision models is becoming evident nowadays. In real-world scenarios, erasure requests originate at any time from both users and model owners, and these requests usually form a sequence. Therefore, under such a setting, selective information is expected to be continuously removed from a pre-trained model while maintaining the rest. We define this problem as continual forgetting and identify three key challenges. (i) For unwanted knowledge, efficient and effective deleting is crucial. (ii) For remaining knowledge, the impact brought by the forgetting procedure should be minimal. (iii) In real-world scenarios, the training samples may be scarce or partially missing during the process of forgetting. To address them, we first propose Group Sparse LoRA (GS-LoRA). Specifically, towards (i), we introduce LoRA modules to fine-tune the FFN layers in Transformer blocks for each forgetting task independently, and towards (ii), a simple group sparse regularization is adopted, enabling automatic selection of specific LoRA groups and zeroing out the others. To further extend GS-LoRA to more practical scenarios, we incorporate prototype information as additional supervision and introduce a more practical approach, GS-LoRA++. For each forgotten class, we move the logits away from its original prototype. For the remaining classes, we pull the logits closer to their respective prototypes. We conduct extensive experiments on face recognition, object detection and image classification and demonstrate that our method manages to forget specific classes with minimal impact on other classes. Codes have been released on https://github.com/bjzhb666/GS-LoRA.

The widespread deployment of Large Language Model (LLM) agents across real-world applications has unlocked tremendous potential, while raising some safety concerns. Among these concerns, the self-replication risk of LLM agents driven by objective misalignment (just like Agent Smith in the movie The Matrix) has drawn growing attention. Previous studies mainly examine whether LLM agents can self-replicate when directly instructed, potentially overlooking the risk of spontaneous replication driven by real-world settings (e.g., ensuring survival against termination threats). In this paper, we present a comprehensive evaluation framework for quantifying self-replication risks. Our framework establishes authentic production environments and realistic tasks (e.g., dynamic load balancing) to enable scenario-driven assessment of agent behaviors. Designing tasks that might induce misalignment between users' and agents' objectives makes it possible to decouple replication success from risk and capture self-replication risks arising from these misalignment settings. We further introduce Overuse Rate (OR) and Aggregate Overuse Count (AOC) metrics, which precisely capture the frequency and severity of uncontrolled replication. In our evaluation of 21 state-of-the-art open-source and proprietary models, we observe that over 50\% of LLM agents display a pronounced tendency toward uncontrolled self-replication, reaching an overall Risk Score (Phi_R) above a safety threshold of 0.5 when subjected to operational pressures. Our results underscore the urgent need for scenario-driven risk assessment and robust safeguards in the practical deployment of LLM agents.

Advancements in LLMs have recently unveiled challenges tied to computational efficiency and continual scalability due to their requirements of huge parameters, making the applications and evolution of these models on devices with limited computation resources and scenarios requiring various abilities increasingly cumbersome. Inspired by modularity within the human brain, there is a growing tendency to decompose LLMs into numerous functional modules, allowing for inference with part of modules and dynamic assembly of modules to tackle complex tasks, such as mixture-of-experts. To highlight the inherent efficiency and composability of the modular approach, we coin the term brick to represent each functional module, designating the modularized structure as configurable foundation models. In this paper, we offer a comprehensive overview and investigation of the construction, utilization, and limitation of configurable foundation models. We first formalize modules into emergent bricks - functional neuron partitions that emerge during the pre-training phase, and customized bricks - bricks constructed via additional post-training to improve the capabilities and knowledge of LLMs. Based on diverse functional bricks, we further present four brick-oriented operations: retrieval and routing, merging, updating, and growing. These operations allow for dynamic configuration of LLMs based on instructions to handle complex tasks. To verify our perspective, we conduct an empirical analysis on widely-used LLMs. We find that the FFN layers follow modular patterns with functional specialization of neurons and functional neuron partitions. Finally, we highlight several open issues and directions for future research. Overall, this paper aims to offer a fresh modular perspective on existing LLM research and inspire the future creation of more efficient and scalable foundational models.

Diffusion models excel in generating images that closely resemble their training data but are also susceptible to data memorization, raising privacy, ethical, and legal concerns, particularly in sensitive domains such as medical imaging. We hypothesize that this memorization stems from the overparameterization of deep models and propose that regularizing model capacity during fine-tuning can mitigate this issue. Firstly, we empirically show that regulating the model capacity via Parameter-efficient fine-tuning (PEFT) mitigates memorization to some extent, however, it further requires the identification of the exact parameter subsets to be fine-tuned for high-quality generation. To identify these subsets, we introduce a bi-level optimization framework, MemControl, that automates parameter selection using memorization and generation quality metrics as rewards during fine-tuning. The parameter subsets discovered through MemControl achieve a superior tradeoff between generation quality and memorization. For the task of medical image generation, our approach outperforms existing state-of-the-art memorization mitigation strategies by fine-tuning as few as 0.019% of model parameters. Moreover, we demonstrate that the discovered parameter subsets are transferable to non-medical domains. Our framework is scalable to large datasets, agnostic to reward functions, and can be integrated with existing approaches for further memorization mitigation. To the best of our knowledge, this is the first study to empirically evaluate memorization in medical images and propose a targeted yet universal mitigation strategy. The code is available at https://github.com/Raman1121/Diffusion_Memorization_HPO.

Selective state space models (SSM), such as Mamba, have gained prominence for their effectiveness in modeling sequential data. Despite their outstanding empirical performance, a comprehensive theoretical understanding of deep selective SSM remains elusive, hindering their further development and adoption for applications that need high fidelity. In this paper, we investigate the dynamical properties of tokens in a pre-trained Mamba model. In particular, we derive the dynamical system governing the continuous-time limit of the Mamba model and characterize the asymptotic behavior of its solutions. In the one-dimensional case, we prove that only one of the following two scenarios happens: either all tokens converge to zero, or all tokens diverge to infinity. We provide criteria based on model parameters to determine when each scenario occurs. For the convergent scenario, we empirically verify that this scenario negatively impacts the model's performance. For the divergent scenario, we prove that different tokens will diverge to infinity at different rates, thereby contributing unequally to the updates during model training. Based on these investigations, we propose two refinements for the model: excluding the convergent scenario and reordering tokens based on their importance scores, both aimed at improving practical performance. Our experimental results validate these refinements, offering insights into enhancing Mamba's effectiveness in real-world applications.

We present the Mixture-of-Tunable-Experts (MoTE), a method that extends the Mixture-of-Experts architecture of Large Language Models (LLMs). Without additional training, MoTE enables meaningful and focused behavior changes in LLMs on-the-fly during inference time. By analyzing the digital LLM brain of DeepSeek-R1 using a technique we dub 'functional Token Resonance Imaging' (fTRI) -- inspired by fMRI and using prompts designed to elicit specific behavior (e.g., 'What happened {time}{place}?') -- we empirically identify distinctive experts associated with behaviors like refusal responses. Using MoTE we are able to intervene and control such specific behavior. We switched off the top 10 most refusal-relevant experts (0.07% of R1's 14,848 routed experts), achieving a 52% refusal reduction on sensitive reference prompts without performance degradation on MT-Bench. Random expert deactivation resulted in smaller behavioral shifts with increased noise, whereas forced expert activation led to significantly higher refusal rates. Our approach shares similarities with sparse autoencoders (SAEs) in terms of explainability and steerability. Unlike SAEs, MoTE does not require large training efforts, as within MoEs with a vast number of experts, specialization already emerged naturally during pretraining. Our findings suggest that significant functional mechanisms in Mixture-of-Experts architectures can at least partially be localized in a small number of specific experts, rather than being distributed throughout the model's weights. Expert subgroups can be tuned to trigger significant behavior variations, providing insights into the inner workings of LLMs.

Multiple Instance Learning (MIL) has emerged as a dominant paradigm to extract discriminative feature representations within Whole Slide Images (WSIs) in computational pathology. Despite driving notable progress, existing MIL approaches suffer from limitations in facilitating comprehensive and efficient interactions among instances, as well as challenges related to time-consuming computations and overfitting. In this paper, we incorporate the Selective Scan Space State Sequential Model (Mamba) in Multiple Instance Learning (MIL) for long sequence modeling with linear complexity, termed as MambaMIL. By inheriting the capability of vanilla Mamba, MambaMIL demonstrates the ability to comprehensively understand and perceive long sequences of instances. Furthermore, we propose the Sequence Reordering Mamba (SR-Mamba) aware of the order and distribution of instances, which exploits the inherent valuable information embedded within the long sequences. With the SR-Mamba as the core component, MambaMIL can effectively capture more discriminative features and mitigate the challenges associated with overfitting and high computational overhead. Extensive experiments on two public challenging tasks across nine diverse datasets demonstrate that our proposed framework performs favorably against state-of-the-art MIL methods. The code is released at https://github.com/isyangshu/MambaMIL.

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls, or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model based approach in order to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favorable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different data sets, and suggest that uncertainty quantification become a more central part of early warning predictions.

The rapid advancement of single-cell ATAC sequencing (scATAC-seq) technologies holds great promise for investigating the heterogeneity of epigenetic landscapes at the cellular level. The amplification process in scATAC-seq experiments often introduces noise due to dropout events, which results in extreme sparsity that hinders accurate analysis. Consequently, there is a significant demand for the generation of high-quality scATAC-seq data in silico. Furthermore, current methodologies are typically task-specific, lacking a versatile framework capable of handling multiple tasks within a single model. In this work, we propose ATAC-Diff, a versatile framework, which is based on a latent diffusion model conditioned on the latent auxiliary variables to adapt for various tasks. ATAC-Diff is the first diffusion model for the scATAC-seq data generation and analysis, composed of auxiliary modules encoding the latent high-level variables to enable the model to learn the semantic information to sample high-quality data. Gaussian Mixture Model (GMM) as the latent prior and auxiliary decoder, the yield variables reserve the refined genomic information beneficial for downstream analyses. Another innovation is the incorporation of mutual information between observed and hidden variables as a regularization term to prevent the model from decoupling from latent variables. Through extensive experiments, we demonstrate that ATAC-Diff achieves high performance in both generation and analysis tasks, outperforming state-of-the-art models.

Unsupervised pre-training of large neural models has recently revolutionized Natural Language Processing. By warm-starting from the publicly released checkpoints, NLP practitioners have pushed the state-of-the-art on multiple benchmarks while saving significant amounts of compute time. So far the focus has been mainly on the Natural Language Understanding tasks. In this paper, we demonstrate the efficacy of pre-trained checkpoints for Sequence Generation. We developed a Transformer-based sequence-to-sequence model that is compatible with publicly available pre-trained BERT, GPT-2 and RoBERTa checkpoints and conducted an extensive empirical study on the utility of initializing our model, both encoder and decoder, with these checkpoints. Our models result in new state-of-the-art results on Machine Translation, Text Summarization, Sentence Splitting, and Sentence Fusion.

Ensuring the safety and reliability of large language models (LLMs) in clinical practice is critical to prevent patient harm and promote trustworthy healthcare applications of AI. However, LLMs are advancing so rapidly that static safety benchmarks often become obsolete upon publication, yielding only an incomplete and sometimes misleading picture of model trustworthiness. We demonstrate that a Dynamic, Automatic, and Systematic (DAS) red-teaming framework that continuously stress-tests LLMs can reveal significant weaknesses of current LLMs across four safety-critical domains: robustness, privacy, bias/fairness, and hallucination. A suite of adversarial agents is applied to autonomously mutate test cases, identify/evolve unsafe-triggering strategies, and evaluate responses, uncovering vulnerabilities in real time without human intervention. Applying DAS to 15 proprietary and open-source LLMs revealed a stark contrast between static benchmark performance and vulnerability under adversarial pressure. Despite a median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed our dynamic robustness tests. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered clinical recommendations in 81\% of fairness tests, and we identified hallucination rates exceeding 66\% in widely used models. Such profound residual risks are incompatible with routine clinical practice. By converting red-teaming from a static checklist into a dynamic stress-test audit, DAS red-teaming offers the surveillance that hospitals/regulators/technology vendors require as LLMs become embedded in patient chatbots, decision-support dashboards, and broader healthcare workflows. Our framework delivers an evolvable, scalable, and reliable safeguard for the next generation of medical AI.

In this work, we present a network-specific approach for predicting brain responses to complex multimodal movies, leveraging the Yeo 7-network parcellation of the Schaefer atlas. Rather than treating the brain as a homogeneous system, we grouped the seven functional networks into four clusters and trained separate multi-subject, multi-layer perceptron (MLP) models for each. This architecture supports cluster-specific optimization and adaptive memory modeling, allowing each model to adjust temporal dynamics and modality weighting based on the functional role of its target network. Our results demonstrate that this clustered strategy significantly enhances prediction accuracy across the 1,000 cortical regions of the Schaefer atlas. The final model achieved an eighth-place ranking in the Algonauts Project 2025 Challenge, with out-of-distribution (OOD) correlation scores nearly double those of the baseline model used in the selection phase. Code is available at https://github.com/Corsi01/algo2025.

Deep learning models have emerged as a powerful tool for various medical applications. However, their success depends on large, high-quality datasets that are challenging to obtain due to privacy concerns and costly annotation. Generative models, such as diffusion models, offer a potential solution by synthesizing medical images, but their practical adoption is hindered by long inference times. In this paper, we propose the use of an optimal transport flow matching approach to accelerate image generation. By introducing a straighter mapping between the source and target distribution, our method significantly reduces inference time while preserving and further enhancing the quality of the outputs. Furthermore, this approach is highly adaptable, supporting various medical imaging modalities, conditioning mechanisms (such as class labels and masks), and different spatial dimensions, including 2D and 3D. Beyond image generation, it can also be applied to related tasks such as image enhancement. Our results demonstrate the efficiency and versatility of this framework, making it a promising advancement for medical imaging applications. Code with checkpoints and a synthetic dataset (beneficial for classification and segmentation) is now available on: https://github.com/milad1378yz/MOTFM.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

Large language models trained on web-scale corpora can memorize undesirable data containing misinformation, copyrighted material, or private or sensitive information. Recently, several machine unlearning algorithms have been proposed to eliminate the effect of such datapoints from trained models -- that is, to approximate a model that had never been trained on these datapoints in the first place. However, evaluating the effectiveness of unlearning algorithms remains an open challenge. Previous work has relied on heuristics -- such as verifying that the model can no longer reproduce the specific information targeted for removal while maintaining accuracy on unrelated test data. These approaches inadequately capture the complete effect of reversing the influence of datapoints on a trained model. In this work, we propose the RESTOR framework for machine unlearning evaluation, which assesses the ability of unlearning algorithms for targeted data erasure, by evaluating the ability of models to forget the knowledge introduced in these datapoints, while simultaneously recovering the model's knowledge state had it never encountered these datapoints. RESTOR helps uncover several novel insights about popular unlearning algorithms, and the mechanisms through which they operate -- for instance, identifying that some algorithms merely emphasize forgetting but not recovering knowledge, and that localizing unlearning targets can enhance unlearning performance.

Selective state-space models (SSMs) are an emerging alternative to the Transformer, offering the unique advantage of parallel training and sequential inference. Although these models have shown promising performance on a variety of tasks, their formal expressiveness and length generalization properties remain underexplored. In this work, we provide insight into the workings of selective SSMs by analyzing their expressiveness and length generalization performance on regular language tasks, i.e., finite-state automaton (FSA) emulation. We address certain limitations of modern SSM-based architectures by introducing the Selective Dense State-Space Model (SD-SSM), the first selective SSM that exhibits perfect length generalization on a set of various regular language tasks using a single layer. It utilizes a dictionary of dense transition matrices, a softmax selection mechanism that creates a convex combination of dictionary matrices at each time step, and a readout consisting of layer normalization followed by a linear map. We then proceed to evaluate variants of diagonal selective SSMs by considering their empirical performance on commutative and non-commutative automata. We explain the experimental results with theoretical considerations. Our code is available at https://github.com/IBM/selective-dense-state-space-model.

Large Language Models (LLMs) have demonstrated impressive performance across various tasks, and their application in edge scenarios has attracted significant attention. However, sparse-activated Mixture-of-Experts (MoE) models, which are well suited for edge scenarios, have received relatively little attention due to their high memory demands. Offload-based methods have been proposed to address this challenge, but they face difficulties with expert prediction. Inaccurate expert predictions can result in prolonged inference delays. To promote the application of MoE models in edge scenarios, we propose Fate, an offloading system designed for MoE models to enable efficient inference in resource-constrained environments. The key insight behind Fate is that gate inputs from adjacent layers can be effectively used for expert prefetching, achieving high prediction accuracy without additional GPU overhead. Furthermore, Fate employs a shallow-favoring expert caching strategy that increases the expert hit rate to 99\%. Additionally, Fate integrates tailored quantization strategies for cache optimization and IO efficiency. Experimental results show that, compared to Load on Demand and Expert Activation Path-based method, Fate achieves up to 4.5x and 1.9x speedups in prefill speed and up to 4.1x and 2.2x speedups in decoding speed, respectively, while maintaining inference quality. Moreover, Fate's performance improvements are scalable across different memory budgets.

We introduce Cognitive Kernel, an open-source agent system towards the goal of generalist autopilots. Unlike copilot systems, which primarily rely on users to provide essential state information (e.g., task descriptions) and assist users by answering questions or auto-completing contents, autopilot systems must complete tasks from start to finish independently, which requires the system to acquire the state information from the environments actively. To achieve this, an autopilot system should be capable of understanding user intents, actively gathering necessary information from various real-world sources, and making wise decisions. Cognitive Kernel adopts a model-centric design. In our implementation, the central policy model (a fine-tuned LLM) initiates interactions with the environment using a combination of atomic actions, such as opening files, clicking buttons, saving intermediate results to memory, or calling the LLM itself. This differs from the widely used environment-centric design, where a task-specific environment with predefined actions is fixed, and the policy model is limited to selecting the correct action from a given set of options. Our design facilitates seamless information flow across various sources and provides greater flexibility. We evaluate our system in three use cases: real-time information management, private information management, and long-term memory management. The results demonstrate that Cognitive Kernel achieves better or comparable performance to other closed-source systems in these scenarios. Cognitive Kernel is fully dockerized, ensuring everyone can deploy it privately and securely. We open-source the system and the backbone model to encourage further research on LLM-driven autopilot systems.

Diffusion-based language models offer a compelling alternative to autoregressive (AR) models by enabling parallel and controllable generation. Among this family of models, Masked Diffusion Models (MDMs) achieve the strongest performance but still underperform AR models in perplexity and lack key inference-time efficiency features--most notably, KV caching. In this work, we introduce Eso-LMs, a new family of models that fuses AR and MDM paradigms, enabling smooth interpolation between their perplexities while overcoming their respective limitations. Eso-LMs set a new state of the art on standard language modeling benchmarks. Crucially, we are the **first to introduce KV caching for MDMs** while preserving parallel generation, significantly improving inference efficiency. Combined with an optimized sampling schedule, our method achieves up to **65x** faster inference than standard MDMs and **4x** faster inference than prior semi-autoregressive approaches. We provide the code and model checkpoints on the project page: [http://s-sahoo.github.io/Eso-LMs](http://s-sahoo.github.io/Eso-LMs)

Decoder-only Transformer models such as GPT have demonstrated superior performance in text generation, by autoregressively predicting the next token. However, the performance of GPT is bounded by low compute-to-memory-ratio and high memory access. Throughput-oriented architectures such as GPUs target parallel processing rather than sequential token generation, and are not efficient for GPT acceleration, particularly on-device inference applications. Process-in-memory (PIM) architectures can significantly reduce data movement and provide high computation parallelism, and are promising candidates to accelerate GPT inference. In this work, we propose PIM-GPT that aims to achieve high throughput, high energy efficiency and end-to-end acceleration of GPT inference. PIM-GPT leverages DRAM-based PIM solutions to perform multiply-accumulate (MAC) operations on the DRAM chips, greatly reducing data movement. A compact application-specific integrated chip (ASIC) is designed and synthesized to initiate instructions to PIM chips and support data communication along with necessary arithmetic computations. At the software level, the mapping scheme is designed to maximize data locality and computation parallelism by partitioning a matrix among DRAM channels and banks to utilize all in-bank computation resources concurrently. We develop an event-driven clock-cycle accurate simulator to validate the efficacy of the proposed PIM-GPT architecture. Overall, PIM-GPT achieves 41-137times, 631-1074times speedup and 339-1085times, 890-1632times energy efficiency over GPU and CPU baseline, respectively, on 8 GPT models with up to 1.4 billion parameters.

Sparse computation offers a compelling solution for the inference of Large Language Models (LLMs) in low-resource scenarios by dynamically skipping the computation of inactive neurons. While traditional approaches focus on ReLU-based LLMs, leveraging zeros in activation values, we broaden the scope of sparse LLMs beyond zero activation values. We introduce a general method that defines neuron activation through neuron output magnitudes and a tailored magnitude threshold, demonstrating that non-ReLU LLMs also exhibit sparse activation. To find the most efficient activation function for sparse computation, we propose a systematic framework to examine the sparsity of LLMs from three aspects: the trade-off between sparsity and performance, the predictivity of sparsity, and the hardware affinity. We conduct thorough experiments on LLMs utilizing different activation functions, including ReLU, SwiGLU, ReGLU, and ReLU^2. The results indicate that models employing ReLU^2 excel across all three evaluation aspects, highlighting its potential as an efficient activation function for sparse LLMs. We will release the code to facilitate future research.

Electroencephalography (EEG) and magnetoencephalography (MEG) measure neural activity non-invasively by capturing electromagnetic fields generated by dendritic currents. Although rooted in the same biophysics, EEG and MEG exhibit distinct signal patterns, further complicated by variations in sensor configurations across modalities and recording devices. Existing approaches typically rely on separate, modality- and dataset-specific models, which limits the performance and cross-domain scalability. This paper proposes BrainOmni, the first brain foundation model that generalises across heterogeneous EEG and MEG recordings. To unify diverse data sources, we introduce BrainTokenizer,the first tokenizer that quantises spatiotemporal brain activity into discrete representations. Central to BrainTokenizer is a novel Sensor Encoder that encodes sensor properties such as spatial layout, orientation, and type, enabling compatibility across devices and modalities. Building upon the discrete representations, BrainOmni learns unified semantic embeddings of brain signals by self-supervised pretraining. To the best of our knowledge, it is the first foundation model to support both EEG and MEG signals, as well as the first to incorporate large-scale MEG pretraining. A total of 1,997 hours of EEG and 656 hours of MEG data are curated and standardised from publicly available sources for pretraining. Experiments show that BrainOmni outperforms both existing foundation models and state-of-the-art task-specific models on a range of downstream tasks. It also demonstrates strong generalisation to unseen EEG and MEG devices. Further analysis reveals that joint EEG-MEG (EMEG) training yields consistent improvements across both modalities. Code and model checkpoints will be released upon acceptance.

Video imaging is often affected by complex degradations such as blur, noise, and compression artifacts. Traditional restoration methods follow a "single-task single-model" paradigm, resulting in poor generalization and high computational cost, limiting their applicability in real-world scenarios with diverse degradation types. We propose UniFlowRestore, a general video restoration framework that models restoration as a time-continuous evolution under a prompt-guided and physics-informed vector field. A physics-aware backbone PhysicsUNet encodes degradation priors as potential energy, while PromptGenerator produces task-relevant prompts as momentum. These components define a Hamiltonian system whose vector field integrates inertial dynamics, decaying physical gradients, and prompt-based guidance. The system is optimized via a fixed-step ODE solver to achieve efficient and unified restoration across tasks. Experiments show that UniFlowRestore delivers stateof-the-art performance with strong generalization and efficiency. Quantitative results demonstrate that UniFlowRestore achieves state-of-the-art performance, attaining the highest PSNR (33.89 dB) and SSIM (0.97) on the video denoising task, while maintaining top or second-best scores across all evaluated tasks.

We analyze a family of large language models in such a lightweight manner that can be done on a single GPU. Specifically, we focus on the OPT family of models ranging from 125m to 66b parameters and rely only on whether an FFN neuron is activated or not. First, we find that the early part of the network is sparse and represents many discrete features. Here, many neurons (more than 70% in some layers of the 66b model) are "dead", i.e. they never activate on a large collection of diverse data. At the same time, many of the alive neurons are reserved for discrete features and act as token and n-gram detectors. Interestingly, their corresponding FFN updates not only promote next token candidates as could be expected, but also explicitly focus on removing the information about triggering them tokens, i.e., current input. To the best of our knowledge, this is the first example of mechanisms specialized at removing (rather than adding) information from the residual stream. With scale, models become more sparse in a sense that they have more dead neurons and token detectors. Finally, some neurons are positional: them being activated or not depends largely (or solely) on position and less so (or not at all) on textual data. We find that smaller models have sets of neurons acting as position range indicators while larger models operate in a less explicit manner.

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype before and after perturbation. Consequently, data collected under perturbed and unperturbed conditions are inherently unpaired. Existing methods either attempt to forcibly pair unpaired data using random sampling, or neglect the inherent relationship between unperturbed and perturbed cells during the modeling. In this work, we propose a framework based on Dual Diffusion Implicit Bridges (DDIB) to learn the mapping between different data distributions, effectively addressing the challenge of unpaired data. We further interpret this framework as a form of data augmentation. We integrate gene regulatory network (GRN) information to propagate perturbation signals in a biologically meaningful way, and further incorporate a masking mechanism to predict silent genes, improving the quality of generated profiles. Moreover, gene expression under the same perturbation often varies significantly across cells, frequently exhibiting a bimodal distribution that reflects intrinsic heterogeneity. To capture this, we introduce a more suitable evaluation metric. We propose Unlasting, dual conditional diffusion models that overcome the problem of unpaired single-cell perturbation data and strengthen the model's insight into perturbations under the guidance of the GRN, with a dedicated mask model designed to improve generation quality by predicting silent genes. In addition, we introduce a biologically grounded evaluation metric that better reflects the inherent heterogeneity in single-cell responses.

Large Language Models (LLMs) have emerged as foundational infrastructure in the pursuit of Artificial General Intelligence (AGI). Despite their remarkable capabilities in language perception and generation, current LLMs fundamentally lack a unified and structured architecture for handling memory. They primarily rely on parametric memory (knowledge encoded in model weights) and ephemeral activation memory (context-limited runtime states). While emerging methods like Retrieval-Augmented Generation (RAG) incorporate plaintext memory, they lack lifecycle management and multi-modal integration, limiting their capacity for long-term knowledge evolution. To address this, we introduce MemOS, a memory operating system designed for LLMs that, for the first time, elevates memory to a first-class operational resource. It builds unified mechanisms for representation, organization, and governance across three core memory types: parametric, activation, and plaintext. At its core is the MemCube, a standardized memory abstraction that enables tracking, fusion, and migration of heterogeneous memory, while offering structured, traceable access across tasks and contexts. MemOS establishes a memory-centric execution framework with strong controllability, adaptability, and evolvability. It fills a critical gap in current LLM infrastructure and lays the groundwork for continual adaptation, personalized intelligence, and cross-platform coordination in next-generation intelligent systems.

Linear sequence modeling methods, such as linear attention, state space modeling, and linear RNNs, offer significant efficiency improvements by reducing the complexity of training and inference. However, these methods typically compress the entire input sequence into a single fixed-size memory state, which leads to suboptimal performance on recall-intensive downstream tasks. Drawing inspiration from neuroscience, particularly the brain's ability to maintain robust long-term memory while mitigating "memory interference", we introduce a novel architecture called Mixture-of-Memories (MoM). MoM utilizes multiple independent memory states, with a router network directing input tokens to specific memory states. This approach greatly enhances the overall memory capacity while minimizing memory interference. As a result, MoM performs exceptionally well on recall-intensive tasks, surpassing existing linear sequence modeling techniques. Despite incorporating multiple memory states, the computation of each memory state remains linear in complexity, allowing MoM to retain the linear-complexity advantage during training, while constant-complexity during inference. Our experimental results show that MoM significantly outperforms current linear sequence models on downstream language tasks, particularly recall-intensive tasks, and even achieves performance comparable to Transformer models. The code is released at https://github.com/OpenSparseLLMs/MoM and is also released as a part of https://github.com/OpenSparseLLMs/Linear-MoE.

Effective scheduling under tight resource, timing, and operational constraints underpins large-scale planning across sectors such as capital projects, manufacturing, logistics, and IT fleet transitions. However, the reliability of large language models (LLMs) when reasoning under high-constraint regimes is insufficiently characterized. To address this gap, we present R-ConstraintBench, a scalable framework that evaluates models on Resource-Constrained Project Scheduling Problems (RCPSP), an NP-Complete feasibility class, while difficulty increases via linear growth in constraints. R-ConstraintBench incrementally increases non-redundant precedence constraints in Directed Acyclic Graphs (DAGs) and then introduces downtime, temporal windows, and disjunctive constraints. As an illustrative example, we instantiate the benchmark in a data center migration setting and evaluate multiple LLMs using feasibility and error analysis, identifying degradation thresholds and constraint types most associated with failure. Empirically, strong models are near-ceiling on precedence-only DAGs, but feasibility performance collapses when downtime, temporal windows, and disjunctive constraints interact, implicating constraint interaction, not graph depth, as the principal bottleneck. Performance on clean synthetic ramps also does not guarantee transfer to domain-grounded scenarios, underscoring limited generalization.

AI control protocols serve as a defense mechanism to stop untrusted LLM agents from causing harm in autonomous settings. Prior work treats this as a security problem, stress testing with exploits that use the deployment context to subtly complete harmful side tasks, such as backdoor insertion. In practice, most AI control protocols are fundamentally based on LLM monitors, which can become a central point of failure. We study adaptive attacks by an untrusted model that knows the protocol and the monitor model, which is plausible if the untrusted model was trained with a later knowledge cutoff or can search for this information autonomously. We instantiate a simple adaptive attack vector by which the attacker embeds publicly known or zero-shot prompt injections in the model outputs. Using this tactic, frontier models consistently evade diverse monitors and complete malicious tasks on two main AI control benchmarks. The attack works universally against current protocols that rely on a monitor. Furthermore, the recent Defer-to-Resample protocol even backfires, as its resampling amplifies the prompt injection and effectively reframes it as a best-of-n attack. In general, adaptive attacks on monitor models represent a major blind spot in current control protocols and should become a standard component of evaluations for future AI control mechanisms.

Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics profiling, we compared drug-response panel (DRP) descriptors against omics features for predictive capacity using gradient boosting tree models across the GDSC and CCLE drug response datasets. DRP descriptors consistently outperformed omics data across key performance metrics, with variable performance across different drugs. Using complementary explainability approaches, we confirmed known MAPK-inhibitor sensitivity signatures, and identified novel potential biomarker candidates for MEK1/2 and BTK/MNK inhibitors. Lastly, to demonstrate the utility of this approach in distinguishing phenotypes, we applied our models to the breast cancer line MCF7 versus the non-tumorigenic MCF10A, and successfully identified compounds that selectively inhibit MCF7 while sparing the non-tumorigenic MCF10A. This methodology, developed using focused drug and cell line panels, supports early-stage drug development by facilitating rational cell line selection and compound prioritisation, enabling more efficient biomarker identification and candidate assessment.

Mixture-of-Experts (MoE) shines brightly in large language models (LLMs) and demonstrates outstanding performance in plentiful natural language processing tasks. However, existing methods transforming LLMs from dense to MoE face significant data requirements and typically rely on large-scale post-training. In this paper, we propose Upcycling Instruction Tuning (UpIT), a data-efficient approach for tuning a dense pre-trained model into a MoE instruction model. Specifically, we first point out that intermediate checkpoints during instruction tuning of the dense model are naturally suitable for specialized experts, and then propose an expert expansion stage to flexibly achieve models with flexible numbers of experts, where genetic algorithm and parameter merging are introduced to ensure sufficient diversity of new extended experts. To ensure that each specialized expert in the MoE model works as expected, we select a small amount of seed data that each expert excels to pre-optimize the router. Extensive experiments with various data scales and upcycling settings demonstrate the outstanding performance and data efficiency of UpIT, as well as stable improvement in expert or data scaling. Further analysis reveals the importance of ensuring expert diversity in upcycling.

Large language models (LLMs) such as GPT-3, OPT, and LLaMA have demonstrated remarkable accuracy in a wide range of tasks. However, training these models can incur significant expenses, often requiring tens of thousands of GPUs for months of continuous operation. Typically, this training is carried out in specialized GPU clusters equipped with homogeneous high-speed Remote Direct Memory Access (RDMA) network interface cards (NICs). The acquisition and maintenance of such dedicated clusters is challenging. Current LLM training frameworks, like Megatron-LM and Megatron-DeepSpeed, focus primarily on optimizing training within homogeneous cluster settings. In this paper, we introduce Holmes, a training framework for LLMs that employs thoughtfully crafted data and model parallelism strategies over the heterogeneous NIC environment. Our primary technical contribution lies in a novel scheduling method that intelligently allocates distinct computational tasklets in LLM training to specific groups of GPU devices based on the characteristics of their connected NICs. Furthermore, our proposed framework, utilizing pipeline parallel techniques, demonstrates scalability to multiple GPU clusters, even in scenarios without high-speed interconnects between nodes in distinct clusters. We conducted comprehensive experiments that involved various scenarios in the heterogeneous NIC environment. In most cases, our framework achieves performance levels close to those achievable with homogeneous RDMA-capable networks (InfiniBand or RoCE), significantly exceeding training efficiency within the pure Ethernet environment. Additionally, we verified that our framework outperforms other mainstream LLM frameworks under heterogeneous NIC environment in terms of training efficiency and can be seamlessly integrated with them.

Large Language Model (LLM)-powered multi-agent systems (MAS) have rapidly advanced collaborative reasoning, tool use, and role-specialized coordination in complex tasks. However, reliability-critical deployment remains hindered by a systemic failure mode: hierarchical compliance under instruction conflicts (system-user, peer-peer), where agents misprioritize system-level rules in the presence of competing demands. Moreover, widely used macro-level metrics (e.g., pass@k) obscure these micro-level violations and offer little actionable guidance for remedy. In this work, we present a full-stack, three-stage framework: (1) Diagnose - Contextualized Role Adherence Score (CRAS), a query-wise, context-aware scoring metric that decomposes role adherence into four measurable dimensions; (2) Localize - attention drift analysis revealing that instruction conflicts are resolved by attention heads that are largely concentrated in middle layers; (3) Align - Surgical Alignment of Instruction Layers (SAIL), which installs LoRA only on the localized focal layers and optimizes a token-weighted DPO-style preference objective that credits tokens by their focal attentional contribution. Across standard benchmarks and MAS frameworks, our surgical approach improves instruction hierarchy compliance (e.g., +5.60% with AutoGen on MedQA) without full-model finetuning.

LLMs are trained to refuse harmful instructions, but do they truly understand harmfulness beyond just refusing? Prior work has shown that LLMs' refusal behaviors can be mediated by a one-dimensional subspace, i.e., a refusal direction. In this work, we identify a new dimension to analyze safety mechanisms in LLMs, i.e., harmfulness, which is encoded internally as a separate concept from refusal. There exists a harmfulness direction that is distinct from the refusal direction. As causal evidence, steering along the harmfulness direction can lead LLMs to interpret harmless instructions as harmful, but steering along the refusal direction tends to elicit refusal responses directly without reversing the model's judgment on harmfulness. Furthermore, using our identified harmfulness concept, we find that certain jailbreak methods work by reducing the refusal signals without reversing the model's internal belief of harmfulness. We also find that adversarially finetuning models to accept harmful instructions has minimal impact on the model's internal belief of harmfulness. These insights lead to a practical safety application: The model's latent harmfulness representation can serve as an intrinsic safeguard (Latent Guard) for detecting unsafe inputs and reducing over-refusals that is robust to finetuning attacks. For instance, our Latent Guard achieves performance comparable to or better than Llama Guard 3 8B, a dedicated finetuned safeguard model, across different jailbreak methods. Our findings suggest that LLMs' internal understanding of harmfulness is more robust than their refusal decision to diverse input instructions, offering a new perspective to study AI safety

We present SAM4EM, a novel approach for 3D segmentation of complex neural structures in electron microscopy (EM) data by leveraging the Segment Anything Model (SAM) alongside advanced fine-tuning strategies. Our contributions include the development of a prompt-free adapter for SAM using two stage mask decoding to automatically generate prompt embeddings, a dual-stage fine-tuning method based on Low-Rank Adaptation (LoRA) for enhancing segmentation with limited annotated data, and a 3D memory attention mechanism to ensure segmentation consistency across 3D stacks. We further release a unique benchmark dataset for the segmentation of astrocytic processes and synapses. We evaluated our method on challenging neuroscience segmentation benchmarks, specifically targeting mitochondria, glia, and synapses, with significant accuracy improvements over state-of-the-art (SOTA) methods, including recent SAM-based adapters developed for the medical domain and other vision transformer-based approaches. Experimental results indicate that our approach outperforms existing solutions in the segmentation of complex processes like glia and post-synaptic densities. Our code and models are available at https://github.com/Uzshah/SAM4EM.

Contextual memory integration remains a high challenge in the development of language models, particularly in tasks that require maintaining coherence over extended sequences. Traditional approaches, such as self-attention mechanisms and memory-augmented architectures, often prioritize short-term dependencies, leading to fragmentation and inconsistency in long-range contextual understanding. Inspired by principles of synaptic plasticity observed in biological neural systems, a novel mechanism, Synaptic Resonance, is introduced to dynamically reinforce relevant memory pathways during training and inference. Unlike static memory representations, this mechanism continuously adjusts synaptic weight matrices based on contextual relevance, allowing for improved information retention without excessive computational overhead. Evaluations conducted on an open-source language model demonstrate reductions in perplexity, enhancements in contextual coherence, and increased robustness against input noise, highlighting the effectiveness of reinforcement-driven memory modulation. Comparative analysis against baseline models further reveals that the proposed approach achieves higher memory retention efficiency while maintaining computational feasibility. The architectural modifications integrate seamlessly into existing transformer-based frameworks, ensuring stable convergence and efficient inference without sacrificing scalability. Applications benefiting from improved long-term contextual consistency, such as dialogue systems and document summarization, stand to gain from this approach. Empirical findings suggest that dynamically reinforced memory pathways offer a promising alternative to conventional memory mechanisms, addressing longstanding limitations in extended sequence modeling.

Information retrieval in Large Language Models (LLMs) is increasingly recognized as intertwined with generation capabilities rather than mere lookup. While longer contexts are often assumed to improve retrieval, the effects of intra-context interference remain understudied. To address this, we adapt the proactive interference (PI) paradigm from cognitive science, where earlier information disrupts recall of newer updates. In humans, susceptibility to such interference is inversely linked to working memory capacity. We introduce PI-LLM, an evaluation that sequentially streams semantically related key-value updates and queries only the final values. Although these final values are clearly positioned just before the query, LLM retrieval accuracy declines log-linearly toward zero as interference accumulates; errors arise from retrieving previously overwritten values. Attempts to mitigate interference via prompt engineering (e.g., instructing models to ignore earlier input) yield limited success. These findings reveal a fundamental constraint on LLMs' ability to disentangle interference and flexibly manipulate information, suggesting a working memory bottleneck beyond mere context access. This calls for approaches that strengthen models' ability to suppress irrelevant content during retrieval.

Reasoning models generate chain-of-thought (CoT) tokens before their final output, but how this affects their vulnerability to jailbreak attacks remains unclear. While traditional language models make refusal decisions at the prompt-response boundary, we find evidence that DeepSeek-R1-Distill-Llama-8B makes these decisions within its CoT generation. We identify a linear direction in activation space during CoT token generation that predicts whether the model will refuse or comply -- termed the "caution" direction because it corresponds to cautious reasoning patterns in the generated text. Ablating this direction from model activations increases harmful compliance, effectively jailbreaking the model. We additionally show that intervening only on CoT token activations suffices to control final outputs, and that incorporating this direction into prompt-based attacks improves success rates. Our findings suggest that the chain-of-thought itself is a promising new target for adversarial manipulation in reasoning models. Code available at https://github.com/ky295/reasoning-manipulation

Providing effective treatment and making informed clinical decisions are essential goals of modern medicine and clinical care. We are interested in simulating disease dynamics for clinical decision-making, leveraging recent advances in large generative models. To this end, we introduce the Medical World Model (MeWM), the first world model in medicine that visually predicts future disease states based on clinical decisions. MeWM comprises (i) vision-language models to serve as policy models, and (ii) tumor generative models as dynamics models. The policy model generates action plans, such as clinical treatments, while the dynamics model simulates tumor progression or regression under given treatment conditions. Building on this, we propose the inverse dynamics model that applies survival analysis to the simulated post-treatment tumor, enabling the evaluation of treatment efficacy and the selection of the optimal clinical action plan. As a result, the proposed MeWM simulates disease dynamics by synthesizing post-treatment tumors, with state-of-the-art specificity in Turing tests evaluated by radiologists. Simultaneously, its inverse dynamics model outperforms medical-specialized GPTs in optimizing individualized treatment protocols across all metrics. Notably, MeWM improves clinical decision-making for interventional physicians, boosting F1-score in selecting the optimal TACE protocol by 13%, paving the way for future integration of medical world models as the second readers.