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Nov 19

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

  • 9 authors
·
Jun 20, 2022

Introducing L2M3, A Multilingual Medical Large Language Model to Advance Health Equity in Low-Resource Regions

Addressing the imminent shortfall of 10 million health workers by 2030, predominantly in Low- and Middle-Income Countries (LMICs), this paper introduces an innovative approach that harnesses the power of Large Language Models (LLMs) integrated with machine translation models. This solution is engineered to meet the unique needs of Community Health Workers (CHWs), overcoming language barriers, cultural sensitivities, and the limited availability of medical dialog datasets. I have crafted a model that not only boasts superior translation capabilities but also undergoes rigorous fine-tuning on open-source datasets to ensure medical accuracy and is equipped with comprehensive safety features to counteract the risks of misinformation. Featuring a modular design, this approach is specifically structured for swift adaptation across various linguistic and cultural contexts, utilizing open-source components to significantly reduce healthcare operational costs. This strategic innovation markedly improves the accessibility and quality of healthcare services by providing CHWs with contextually appropriate medical knowledge and diagnostic tools. This paper highlights the transformative impact of this context-aware LLM, underscoring its crucial role in addressing the global healthcare workforce deficit and propelling forward healthcare outcomes in LMICs.

  • 1 authors
·
Apr 11, 2024

SAM-I2V: Upgrading SAM to Support Promptable Video Segmentation with Less than 0.2% Training Cost

Foundation models like the Segment Anything Model (SAM) have significantly advanced promptable image segmentation in computer vision. However, extending these capabilities to videos presents substantial challenges, particularly in ensuring precise and temporally consistent mask propagation in dynamic scenes. SAM 2 attempts to address this by training a model on massive image and video data from scratch to learn complex spatiotemporal associations, resulting in huge training costs that hinder research and practical deployment. In this paper, we introduce SAM-I2V, an effective image-to-video upgradation method for cultivating a promptable video segmentation (PVS) model. Our approach strategically upgrades the pre-trained SAM to support PVS, significantly reducing training complexity and resource requirements. To achieve this, we introduce three key innovations: (i) an image-to-video feature extraction upgrader built upon SAM's static image encoder to enable spatiotemporal video perception, (ii) a memory filtering strategy that selects the most relevant past frames for more effective utilization of historical information, and (iii) a memory-as-prompt mechanism leveraging object memory to ensure temporally consistent mask propagation in dynamic scenes. Comprehensive experiments demonstrate that our method achieves over 90% of SAM 2's performance while using only 0.2% of its training cost. Our work presents a resource-efficient pathway to PVS, lowering barriers for further research in PVS model design and enabling broader applications and advancements in the field. Code and model are available at: https://github.com/showlab/SAM-I2V.

  • 3 authors
·
Jun 2

Preserving Privacy, Increasing Accessibility, and Reducing Cost: An On-Device Artificial Intelligence Model for Medical Transcription and Note Generation

Background: Clinical documentation represents a significant burden for healthcare providers, with physicians spending up to 2 hours daily on administrative tasks. Recent advances in large language models (LLMs) offer promising solutions, but privacy concerns and computational requirements limit their adoption in healthcare settings. Objective: To develop and evaluate a privacy-preserving, on-device medical transcription system using a fine-tuned Llama 3.2 1B model capable of generating structured medical notes from medical transcriptions while maintaining complete data sovereignty entirely in the browser. Methods: We fine-tuned a Llama 3.2 1B model using Parameter-Efficient Fine-Tuning (PEFT) with LoRA on 1,500 synthetic medical transcription-to-structured note pairs. The model was evaluated against the base Llama 3.2 1B on two datasets: 100 endocrinology transcripts and 140 modified ACI benchmark cases. Evaluation employed both statistical metrics (ROUGE, BERTScore, BLEURT) and LLM-as-judge assessments across multiple clinical quality dimensions. Results: The fine-tuned OnDevice model demonstrated substantial improvements over the base model. On the ACI benchmark, ROUGE-1 scores increased from 0.346 to 0.496, while BERTScore F1 improved from 0.832 to 0.866. Clinical quality assessments showed marked reduction in major hallucinations (from 85 to 35 cases) and enhanced factual correctness (2.81 to 3.54 on 5-point scale). Similar improvements were observed on the internal evaluation dataset, with composite scores increasing from 3.13 to 4.43 (+41.5%). Conclusions: Fine-tuning compact LLMs for medical transcription yields clinically meaningful improvements while enabling complete on-device browser deployment. This approach addresses key barriers to AI adoption in healthcare: privacy preservation, cost reduction, and accessibility for resource-constrained environments.

  • 6 authors
·
Jul 2 1

Efficiently Democratizing Medical LLMs for 50 Languages via a Mixture of Language Family Experts

Adapting medical Large Language Models to local languages can reduce barriers to accessing healthcare services, but data scarcity remains a significant challenge, particularly for low-resource languages. To address this, we first construct a high-quality medical dataset and conduct analysis to ensure its quality. In order to leverage the generalization capability of multilingual LLMs to efficiently scale to more resource-constrained languages, we explore the internal information flow of LLMs from a multilingual perspective using Mixture of Experts (MoE) modularity. Technically, we propose a novel MoE routing method that employs language-specific experts and cross-lingual routing. Inspired by circuit theory, our routing analysis revealed a Spread Out in the End information flow mechanism: while earlier layers concentrate cross-lingual information flow, the later layers exhibit language-specific divergence. This insight directly led to the development of the Post-MoE architecture, which applies sparse routing only in the later layers while maintaining dense others. Experimental results demonstrate that this approach enhances the generalization of multilingual models to other languages while preserving interpretability. Finally, to efficiently scale the model to 50 languages, we introduce the concept of language family experts, drawing on linguistic priors, which enables scaling the number of languages without adding additional parameters.

  • 6 authors
·
Oct 14, 2024 2

Bailong: Bilingual Transfer Learning based on QLoRA and Zip-tie Embedding

Large language models (LLMs) have demonstrated exceptional performance in various NLP applications. However, the majority of existing open-source LLMs are pre-trained primarily on English data and little part of other languages. This deficiency in multilingual training data results in suboptimal performance when applied to languages with fewer available resources. Furthermore, enhancing the performance of LLMs on low-resource languages by full-parameter fine-tuning with additional data requires substantial computational resources, posing computational barriers for research organizations and individual researchers. Consequently, several techniques such as parameter-efficient tuning and advanced embedding initialization have been proposed to address these challenges. In this work, we combine them to facilitate cross-lingual transfer on English-dominated open-source LLM. To effectively enhance the model's proficiency in Traditional Chinese, we conduct secondary pre-training on Llama 2 7B with Traditional Chinese data by leveraging QLoRA and our proposed zip-tie embedding initialization. The resulting model called Bailong, which stands for Bilingual trAnsfer learnIng based on qLOra and zip-tie embeddiNG. We present Bailong-instruct 7B, a fine-tuned version of Bailong 7B optimized for multi-turn dialogue scenarios. Recognizing the inadequacy of benchmark datasets in Traditional Chinese, we further introduce Bailong-bench to assess the alignment of models with human preferences and the capability to follow instructions in both Traditional Chinese and English tasks. In our evaluation, Bailong-instruct 7B exhibits competitive performance on Bailong-bench and other benchmark datasets when compared to other open-source models of similar or even larger parameter sizes. Bailong-instruct 7B and Bailong-bench are publicly available with the aim of empowering the community to build upon our efforts.

  • 2 authors
·
Mar 31, 2024

PIKA: Expert-Level Synthetic Datasets for Post-Training Alignment from Scratch

Reinforcement Learning from Human Feedback (RLHF) has become a cornerstone for aligning large language models (LLMs). However, its effectiveness depends on high-quality instruction data. Most existing alignment datasets are either private or require costly human annotation, which limits reproducibility and scalability. Even with Reinforcement Learning from AI Feedback (RLAIF), concerns about data quality remain. Moreover, it is unclear how much data is actually required to fine-tune a base model into a strong instruction-following model. Current approaches often rely on over 300k examples even at the supervised fine-tuning (SFT) stage, yet they still underperform compared to proprietary models, creating barriers for academic and resource-limited communities. To address this gap, we introduce PiKa, a data-efficient family of expert-level alignment datasets. In particular, the PiKa-SFT dataset uses only 30k SFT examples, far fewer than state-of-the-art datasets like Magpie. Through evaluations by fine-tuning Llama-3-8B-Base on PiKa and other public datasets, we show that PiKa-SFT outperforms models trained on much larger data. On AlpacaEval 2.0 and Arena-Hard benchmarks, PiKa-SFT fine-tuning even surpasses the official Llama-3-8B-Instruct model trained on over 10 million proprietary examples. We further extend our study by training the Qwen2.5 series (0.5B to 7B) on PiKa-SFT, achieving consistent gains. These findings demonstrate that high-quality alignment can be achieved with significantly less data, offering a scalable path for open-source LLM alignment. Code and data: https://github.com/SJY8460/PiKa.

  • 7 authors
·
Oct 8