Daily Papers

Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially due to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Our project page including a demonstration system and toolkit can be accessed here: https://litllm.github.io.

AI holds promise for transforming scientific processes, including hypothesis generation. Prior work on hypothesis generation can be broadly categorized into theory-driven and data-driven approaches. While both have proven effective in generating novel and plausible hypotheses, it remains an open question whether they can complement each other. To address this, we develop the first method that combines literature-based insights with data to perform LLM-powered hypothesis generation. We apply our method on five different datasets and demonstrate that integrating literature and data outperforms other baselines (8.97\% over few-shot, 15.75\% over literature-based alone, and 3.37\% over data-driven alone). Additionally, we conduct the first human evaluation to assess the utility of LLM-generated hypotheses in assisting human decision-making on two challenging tasks: deception detection and AI generated content detection. Our results show that human accuracy improves significantly by 7.44\% and 14.19\% on these tasks, respectively. These findings suggest that integrating literature-based and data-driven approaches provides a comprehensive and nuanced framework for hypothesis generation and could open new avenues for scientific inquiry.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

Literature search questions, such as "where can I find research on the evaluation of consistency in generated summaries?" pose significant challenges for modern search engines and retrieval systems. These questions often require a deep understanding of research concepts and the ability to reason over entire articles. In this work, we introduce LitSearch, a retrieval benchmark comprising 597 realistic literature search queries about recent ML and NLP papers. LitSearch is constructed using a combination of (1) questions generated by GPT-4 based on paragraphs containing inline citations from research papers and (2) questions about recently published papers, manually written by their authors. All LitSearch questions were manually examined or edited by experts to ensure high quality. We extensively benchmark state-of-the-art retrieval models and also evaluate two LLM-based reranking pipelines. We find a significant performance gap between BM25 and state-of-the-art dense retrievers, with a 24.8% difference in absolute recall@5. The LLM-based reranking strategies further improve the best-performing dense retriever by 4.4%. Additionally, commercial search engines and research tools like Google Search perform poorly on LitSearch, lagging behind the best dense retriever by 32 points. Taken together, these results show that LitSearch is an informative new testbed for retrieval systems while catering to a real-world use case.

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

The rise of generative artificial intelligence, particularly Large Language Models (LLMs), has intensified the imperative to scrutinize fairness alongside accuracy. Recent studies have begun to investigate fairness evaluations for LLMs within domains such as recommendations. Given that personalization is an intrinsic aspect of recommendation systems, its incorporation into fairness assessments is paramount. Yet, the degree to which current fairness evaluation frameworks account for personalization remains unclear. Our comprehensive literature review aims to fill this gap by examining how existing frameworks handle fairness evaluations of LLMs, with a focus on the integration of personalization factors. Despite an exhaustive collection and analysis of relevant works, we discovered that most evaluations overlook personalization, a critical facet of recommendation systems, thereby inadvertently perpetuating unfair practices. Our findings shed light on this oversight and underscore the urgent need for more nuanced fairness evaluations that acknowledge personalization. Such improvements are vital for fostering equitable development within the AI community.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

This research presents and compares multiple approaches to automate the generation of literature reviews using several Natural Language Processing (NLP) techniques and retrieval-augmented generation (RAG) with a Large Language Model (LLM). The ever-increasing number of research articles provides a huge challenge for manual literature review. It has resulted in an increased demand for automation. Developing a system capable of automatically generating the literature reviews from only the PDF files as input is the primary objective of this research work. The effectiveness of several Natural Language Processing (NLP) strategies, such as the frequency-based method (spaCy), the transformer model (Simple T5), and retrieval-augmented generation (RAG) with Large Language Model (GPT-3.5-turbo), is evaluated to meet the primary objective. The SciTLDR dataset is chosen for this research experiment and three distinct techniques are utilized to implement three different systems for auto-generating the literature reviews. The ROUGE scores are used for the evaluation of all three systems. Based on the evaluation, the Large Language Model GPT-3.5-turbo achieved the highest ROUGE-1 score, 0.364. The transformer model comes in second place and spaCy is at the last position. Finally, a graphical user interface is created for the best system based on the large language model.

With the development of data-centric AI, the focus has shifted from model-driven approaches to improving data quality. Academic literature, as one of the crucial types, is predominantly stored in PDF formats and needs to be parsed into texts before further processing. However, parsing diverse structured texts in academic literature remains challenging due to the lack of datasets that cover various text structures. In this paper, we introduce AceParse, the first comprehensive dataset designed to support the parsing of a wide range of structured texts, including formulas, tables, lists, algorithms, and sentences with embedded mathematical expressions. Based on AceParse, we fine-tuned a multimodal model, named AceParser, which accurately parses various structured texts within academic literature. This model outperforms the previous state-of-the-art by 4.1% in terms of F1 score and by 5% in Jaccard Similarity, demonstrating the potential of multimodal models in academic literature parsing. Our dataset is available at https://github.com/JHW5981/AceParse.

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

By consolidating scattered knowledge, the literature review provides a comprehensive understanding of the investigated topic. However, reading, conducting, or peer-reviewing review papers generally demands a significant investment of time and effort from researchers. To improve efficiency, this paper aims to provide a thorough review of reviews in the PAMI field from diverse perspectives. First, this paper proposes several article-level, field-normalized, and large language model-empowered bibliometric indicators to evaluate reviews. To facilitate this, a meta-data database dubbed RiPAMI, and a topic dataset are constructed. Second, based on these indicators, the study presents comparative analyses of representative reviews, unveiling the characteristics of publications across various fields, periods, and journals. The newly emerging AI-generated literature reviews are also appraised, and the observed differences suggest that most AI-generated reviews still lag behind human-authored reviews in multiple aspects. Third, we briefly provide a subjective evaluation of representative PAMI reviews and introduce a paper structure-based typology of literature reviews. This typology may improve the clarity and effectiveness for scholars in reading and writing reviews, while also serving as a guide for AI systems in generating well-organized reviews. Finally, this work offers insights into the current challenges of literature reviews and envisions future directions for their development.

Scientific literature understanding tasks have gained significant attention due to their potential to accelerate scientific discovery. Pre-trained language models (LMs) have shown effectiveness in these tasks, especially when tuned via contrastive learning. However, jointly utilizing pre-training data across multiple heterogeneous tasks (e.g., extreme classification, citation prediction, and literature search) remains largely unexplored. To bridge this gap, we propose a multi-task contrastive learning framework, SciMult, with a focus on facilitating common knowledge sharing across different scientific literature understanding tasks while preventing task-specific skills from interfering with each other. To be specific, we explore two techniques -- task-aware specialization and instruction tuning. The former adopts a Mixture-of-Experts Transformer architecture with task-aware sub-layers; the latter prepends task-specific instructions to the input text so as to produce task-aware outputs. Extensive experiments on a comprehensive collection of benchmark datasets verify the effectiveness of our task-aware specialization strategy in various tasks, where we outperform state-of-the-art scientific LMs.

Scientific literature review generation aims to extract and organize important information from an abundant collection of reference papers and produces corresponding reviews while lacking a clear and logical hierarchy. We observe that a high-quality catalogue-guided generation process can effectively alleviate this problem. Therefore, we present an atomic and challenging task named Hierarchical Catalogue Generation for Literature Review as the first step for review generation, which aims to produce a hierarchical catalogue of a review paper given various references. We construct a novel English Hierarchical Catalogues of Literature Reviews Dataset with 7.6k literature review catalogues and 389k reference papers. To accurately assess the model performance, we design two evaluation metrics for informativeness and similarity to ground truth from semantics and structure.Our extensive analyses verify the high quality of our dataset and the effectiveness of our evaluation metrics. We further benchmark diverse experiments on state-of-the-art summarization models like BART and large language models like ChatGPT to evaluate their capabilities. We further discuss potential directions for this task to motivate future research.

Scientific literature serves as a high-quality corpus, supporting a lot of Natural Language Processing (NLP) research. However, existing datasets are centered around the English language, which restricts the development of Chinese scientific NLP. In this work, we present CSL, a large-scale Chinese Scientific Literature dataset, which contains the titles, abstracts, keywords and academic fields of 396k papers. To our knowledge, CSL is the first scientific document dataset in Chinese. The CSL can serve as a Chinese corpus. Also, this semi-structured data is a natural annotation that can constitute many supervised NLP tasks. Based on CSL, we present a benchmark to evaluate the performance of models across scientific domain tasks, i.e., summarization, keyword generation and text classification. We analyze the behavior of existing text-to-text models on the evaluation tasks and reveal the challenges for Chinese scientific NLP tasks, which provides a valuable reference for future research. Data and code are available at https://github.com/ydli-ai/CSL

Chatbots are intelligent conversational computer systems designed to mimic human conversation to enable automated online guidance and support. The increased benefits of chatbots led to their wide adoption by many industries in order to provide virtual assistance to customers. Chatbots utilise methods and algorithms from two Artificial Intelligence domains: Natural Language Processing and Machine Learning. However, there are many challenges and limitations in their application. In this survey we review recent advances on chatbots, where Artificial Intelligence and Natural Language processing are used. We highlight the main challenges and limitations of current work and make recommendations for future research investigation.

Employees of early childhood education and care (ECEC) organisations may experience a wide range of barriers as they attempt to integrate information technology (IT) into their work practices. However, studies within the ECEC organisational literature which attempt to identify and understand these barriers are scant. This literature review is the first to present consolidated findings from the body of knowledge on barriers to the integration of IT within ECEC organisations. In addition to highlighting limitations and gaps in the literature, it proposes a tri-perspective framework to provide for future research to develop a deeper understanding of not only what barriers exist but also how they interrelate and shape the IT integration process and the work practices of ECEC organisational employees.

Scientific progress depends on researchers' ability to synthesize the growing body of literature. Can large language models (LMs) assist scientists in this task? We introduce OpenScholar, a specialized retrieval-augmented LM that answers scientific queries by identifying relevant passages from 45 million open-access papers and synthesizing citation-backed responses. To evaluate OpenScholar, we develop ScholarQABench, the first large-scale multi-domain benchmark for literature search, comprising 2,967 expert-written queries and 208 long-form answers across computer science, physics, neuroscience, and biomedicine. On ScholarQABench, OpenScholar-8B outperforms GPT-4o by 5% and PaperQA2 by 7% in correctness, despite being a smaller, open model. While GPT4o hallucinates citations 78 to 90% of the time, OpenScholar achieves citation accuracy on par with human experts. OpenScholar's datastore, retriever, and self-feedback inference loop also improves off-the-shelf LMs: for instance, OpenScholar-GPT4o improves GPT-4o's correctness by 12%. In human evaluations, experts preferred OpenScholar-8B and OpenScholar-GPT4o responses over expert-written ones 51% and 70% of the time, respectively, compared to GPT4o's 32%. We open-source all of our code, models, datastore, data and a public demo.

Text generation has become more accessible than ever, and the increasing interest in these systems, especially those using large language models, has spurred an increasing number of related publications. We provide a systematic literature review comprising 244 selected papers between 2017 and 2024. This review categorizes works in text generation into five main tasks: open-ended text generation, summarization, translation, paraphrasing, and question answering. For each task, we review their relevant characteristics, sub-tasks, and specific challenges (e.g., missing datasets for multi-document summarization, coherence in story generation, and complex reasoning for question answering). Additionally, we assess current approaches for evaluating text generation systems and ascertain problems with current metrics. Our investigation shows nine prominent challenges common to all tasks and sub-tasks in recent text generation publications: bias, reasoning, hallucinations, misuse, privacy, interpretability, transparency, datasets, and computing. We provide a detailed analysis of these challenges, their potential solutions, and which gaps still require further engagement from the community. This systematic literature review targets two main audiences: early career researchers in natural language processing looking for an overview of the field and promising research directions, as well as experienced researchers seeking a detailed view of tasks, evaluation methodologies, open challenges, and recent mitigation strategies.

As Distributed Ledger Technologies (DLTs) rapidly evolve, their impacts extend beyond technology, influencing environmental and societal aspects. This evolution has increased publications, making manual literature analysis increasingly challenging. We address this with a Natural Language Processing (NLP)-based systematic literature review method to explore the intersection of Distributed Ledger Technology (DLT) with its Environmental, Social, and Governance (ESG) aspects. Our approach involves building and refining a directed citation network from 107 seed papers to a corpus of 24,539 publications and fine-tuning a transformer-based language model for Named Entity Recognition (NER) on DLT and ESG domains. Applying this model, we distilled the corpus to 505 key publications, enabling an inaugural literature review and temporal graph analysis of DLT's evolution in ESG contexts. Our contributions include an adaptable and scalable NLP-driven systematic literature review methodology and a unique NER dataset of 54,808 entities, tailored for DLT and ESG research. Our inaugural literature review demonstrates their applicability and effectiveness in analyzing DLT's evolution and impacts, proving invaluable for stakeholders in the DLT domain.

Large Language Models (LLMs) have significantly impacted numerous domains, including Software Engineering (SE). Many recent publications have explored LLMs applied to various SE tasks. Nevertheless, a comprehensive understanding of the application, effects, and possible limitations of LLMs on SE is still in its early stages. To bridge this gap, we conducted a systematic literature review on LLM4SE, with a particular focus on understanding how LLMs can be exploited to optimize processes and outcomes. We collect and analyze 229 research papers from 2017 to 2023 to answer four key research questions (RQs). In RQ1, we categorize different LLMs that have been employed in SE tasks, characterizing their distinctive features and uses. In RQ2, we analyze the methods used in data collection, preprocessing, and application highlighting the role of well-curated datasets for successful LLM for SE implementation. RQ3 investigates the strategies employed to optimize and evaluate the performance of LLMs in SE. Finally, RQ4 examines the specific SE tasks where LLMs have shown success to date, illustrating their practical contributions to the field. From the answers to these RQs, we discuss the current state-of-the-art and trends, identifying gaps in existing research, and flagging promising areas for future study.

We utilize a recently developed topic modeling method called SeNMFk, extending the standard Non-negative Matrix Factorization (NMF) methods by incorporating the semantic structure of the text, and adding a robust system for determining the number of topics. With SeNMFk, we were able to extract coherent topics validated by human experts. From these topics, a few are relatively general and cover broad concepts, while the majority can be precisely mapped to specific scientific effects or measurement techniques. The topics also differ by ubiquity, with only three topics prevalent in almost 40 percent of the abstract, while each specific topic tends to dominate a small subset of the abstracts. These results demonstrate the ability of SeNMFk to produce a layered and nuanced analysis of large scientific corpora.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Context: Jupyter Notebook has emerged as a versatile tool that transforms how researchers, developers, and data scientists conduct and communicate their work. As the adoption of Jupyter notebooks continues to rise, so does the interest from the software engineering research community in improving the software engineering practices for Jupyter notebooks. Objective: The purpose of this study is to analyze trends, gaps, and methodologies used in software engineering research on Jupyter notebooks. Method: We selected 146 relevant publications from the DBLP Computer Science Bibliography up to the end of 2024, following established systematic literature review guidelines. We explored publication trends, categorized them based on software engineering topics, and reported findings based on those topics. Results: The most popular venues for publishing software engineering research on Jupyter notebooks are related to human-computer interaction instead of traditional software engineering venues. Researchers have addressed a wide range of software engineering topics on notebooks, such as code reuse, readability, and execution environment. Although reusability is one of the research topics for Jupyter notebooks, only 64 of the 146 studies can be reused based on their provided URLs. Additionally, most replication packages are not hosted on permanent repositories for long-term availability and adherence to open science principles. Conclusion: Solutions specific to notebooks for software engineering issues, including testing, refactoring, and documentation, are underexplored. Future research opportunities exist in automatic testing frameworks, refactoring clones between notebooks, and generating group documentation for coherent code cells.

Leading vision-language models (VLMs) are trained on general Internet content, overlooking scientific journals' rich, domain-specific knowledge. Training on specialty-specific literature could yield high-performance, task-specific tools, enabling generative AI to match generalist models in specialty publishing, educational, and clinical tasks. We created NeuroPubs, a multimodal dataset of 23,000 Neurosurgery Publications articles (134M words, 78K image-caption pairs). Using NeuroPubs, VLMs generated publication-ready graphical abstracts (70% of 100 abstracts) and board-style questions indistinguishable from human-written ones (54% of 89,587 questions). We used these questions to train CNS-Obsidian, a 34B-parameter VLM. In a blinded, randomized controlled trial, our model demonstrated non-inferiority to then state-of-the-art GPT-4o in neurosurgical differential diagnosis (clinical utility, 40.62% upvotes vs. 57.89%, p=0.1150; accuracy, 59.38% vs. 65.79%, p=0.3797). Our pilot study demonstrates how training generative AI models on specialty-specific journal content - without large-scale internet data - results in high-performance academic and clinical tools, enabling domain-tailored AI across diverse fields.

Natural Language Processing (NLP) is widely used to supply summarization ability from long context to structured information. However, extracting structured knowledge from scientific text by NLP models remains a challenge because of its domain-specific nature to complex data preprocessing and the granularity of multi-layered device-level information. To address this, we introduce ByteScience, a non-profit cloud-based auto fine-tuned Large Language Model (LLM) platform, which is designed to extract structured scientific data and synthesize new scientific knowledge from vast scientific corpora. The platform capitalizes on DARWIN, an open-source, fine-tuned LLM dedicated to natural science. The platform was built on Amazon Web Services (AWS) and provides an automated, user-friendly workflow for custom model development and data extraction. The platform achieves remarkable accuracy with only a small amount of well-annotated articles. This innovative tool streamlines the transition from the science literature to structured knowledge and data and benefits the advancements in natural informatics.

When conducting literature reviews, scientists often create literature review tables - tables whose rows are publications and whose columns constitute a schema, a set of aspects used to compare and contrast the papers. Can we automatically generate these tables using language models (LMs)? In this work, we introduce a framework that leverages LMs to perform this task by decomposing it into separate schema and value generation steps. To enable experimentation, we address two main challenges: First, we overcome a lack of high-quality datasets to benchmark table generation by curating and releasing arxivDIGESTables, a new dataset of 2,228 literature review tables extracted from ArXiv papers that synthesize a total of 7,542 research papers. Second, to support scalable evaluation of model generations against human-authored reference tables, we develop DecontextEval, an automatic evaluation method that aligns elements of tables with the same underlying aspects despite differing surface forms. Given these tools, we evaluate LMs' abilities to reconstruct reference tables, finding this task benefits from additional context to ground the generation (e.g. table captions, in-text references). Finally, through a human evaluation study we find that even when LMs fail to fully reconstruct a reference table, their generated novel aspects can still be useful.

This paper presents a systematic literature review in Computer Science that provide an overview of the initiatives related to digital misinformation. This is an exploratory study that covers research from 1993 to 2020, focusing on the investigation of the phenomenon of misinformation. The review consists of 788 studies from SCOPUS, IEEE, and ACM digital libraries, synthesizing the primary research directions and sociotechnical challenges. These challenges are classified into Physical, Empirical, Syntactic, Semantic, Pragmatic, and Social dimensions, drawing from Organizational Semiotics. The mapping identifies issues related to the concept of misinformation, highlights deficiencies in mitigation strategies, discusses challenges in approaching stakeholders, and unveils various sociotechnical aspects relevant to understanding and mitigating the harmful effects of digital misinformation. As contributions, this study present a novel categorization of mitigation strategies, a sociotechnical taxonomy for classifying types of false information and elaborate on the inter-relation of sociotechnical aspects and their impacts.

Our research endeavors to advance the concept of responsible artificial intelligence (AI), a topic of increasing importance within EU policy discussions. The EU has recently issued several publications emphasizing the necessity of trust in AI, underscoring the dual nature of AI as both a beneficial tool and a potential weapon. This dichotomy highlights the urgent need for international regulation. Concurrently, there is a need for frameworks that guide companies in AI development, ensuring compliance with such regulations. Our research aims to assist lawmakers and machine learning practitioners in navigating the evolving landscape of AI regulation, identifying focal areas for future attention. This paper introduces a comprehensive and, to our knowledge, the first unified definition of responsible AI. Through a structured literature review, we elucidate the current understanding of responsible AI. Drawing from this analysis, we propose an approach for developing a future framework centered around this concept. Our findings advocate for a human-centric approach to Responsible AI. This approach encompasses the implementation of AI methods with a strong emphasis on ethics, model explainability, and the pillars of privacy, security, and trust.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

Large language models trained on source code can support a variety of software development tasks, such as code recommendation and program repair. Large amounts of data for training such models benefit the models' performance. However, the size of the data and models results in long training times and high energy consumption. While publishing source code allows for replicability, users need to repeat the expensive training process if models are not shared. The main goal of the study is to investigate if publications that trained language models for software engineering (SE) tasks share source code and trained artifacts. The second goal is to analyze the transparency on training energy usage. We perform a snowballing-based literature search to find publications on language models for source code, and analyze their reusability from a sustainability standpoint. From 494 unique publications, we identified 293 relevant publications that use language models to address code-related tasks. Among them, 27% (79 out of 293) make artifacts available for reuse. This can be in the form of tools or IDE plugins designed for specific tasks or task-agnostic models that can be fine-tuned for a variety of downstream tasks. Moreover, we collect insights on the hardware used for model training, as well as training time, which together determine the energy consumption of the development process. We find that there are deficiencies in the sharing of information and artifacts for current studies on source code models for software engineering tasks, with 40% of the surveyed papers not sharing source code or trained artifacts. We recommend the sharing of source code as well as trained artifacts, to enable sustainable reproducibility. Moreover, comprehensive information on training times and hardware configurations should be shared for transparency on a model's carbon footprint.

Codification of free-text clinical narratives have long been recognised to be beneficial for secondary uses such as funding, insurance claim processing and research. The current scenario of assigning codes is a manual process which is very expensive, time-consuming and error prone. In recent years, many researchers have studied the use of Natural Language Processing (NLP), related Machine Learning (ML) and Deep Learning (DL) methods and techniques to resolve the problem of manual coding of clinical narratives and to assist human coders to assign clinical codes more accurately and efficiently. This systematic literature review provides a comprehensive overview of automated clinical coding systems that utilises appropriate NLP, ML and DL methods and techniques to assign ICD codes to discharge summaries. We have followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA) guidelines and conducted a comprehensive search of publications from January, 2010 to December 2020 in four academic databases- PubMed, ScienceDirect, Association for Computing Machinery(ACM) Digital Library, and the Association for Computational Linguistics(ACL) Anthology. We reviewed 7,556 publications; 38 met the inclusion criteria. This review identified: datasets having discharge summaries; NLP techniques along with some other data extraction processes, different feature extraction and embedding techniques. To measure the performance of classification methods, different evaluation metrics are used. Lastly, future research directions are provided to scholars who are interested in automated ICD code assignment. Efforts are still required to improve ICD code prediction accuracy, availability of large-scale de-identified clinical corpora with the latest version of the classification system. This can be a platform to guide and share knowledge with the less experienced coders and researchers.

Internet is one of the important inventions and a large number of persons are its users. These persons use this for different purposes. There are different social media platforms that are accessible to these users. Any user can make a post or spread the news through the online platforms. These platforms do not verify the users or their posts. So some of the users try to spread fake news through these platforms. These news can be propaganda against an individual, society, organization or political party. A human being is unable to detect all these fake news. So there is a need for machine learning classifiers that can detect these fake news automatically. Use of machine learning classifiers for detecting fake news is described in this systematic literature review.

Characters are the smallest unit of text that can extract stylometric signals to determine the author of a text. In this paper, we investigate the effectiveness of character-level signals in Authorship Attribution of Bangla Literature and show that the results are promising but improvable. The time and memory efficiency of the proposed model is much higher than the word level counterparts but accuracy is 2-5% less than the best performing word-level models. Comparison of various word-based models is performed and shown that the proposed model performs increasingly better with larger datasets. We also analyze the effect of pre-training character embedding of diverse Bangla character set in authorship attribution. It is seen that the performance is improved by up to 10% on pre-training. We used 2 datasets from 6 to 14 authors, balancing them before training and compare the results.

The development of Artificial General Intelligence (AGI) promises to be a major event. Along with its many potential benefits, it also raises serious safety concerns (Bostrom, 2014). The intention of this paper is to provide an easily accessible and up-to-date collection of references for the emerging field of AGI safety. A significant number of safety problems for AGI have been identified. We list these, and survey recent research on solving them. We also cover works on how best to think of AGI from the limited knowledge we have today, predictions for when AGI will first be created, and what will happen after its creation. Finally, we review the current public policy on AGI.

We present SciArena, an open and collaborative platform for evaluating foundation models on scientific literature tasks. Unlike traditional benchmarks for scientific literature understanding and synthesis, SciArena engages the research community directly, following the Chatbot Arena evaluation approach of community voting on model comparisons. By leveraging collective intelligence, SciArena offers a community-driven evaluation of model performance on open-ended scientific tasks that demand literature-grounded, long-form responses. The platform currently supports 23 open-source and proprietary foundation models and has collected over 13,000 votes from trusted researchers across diverse scientific domains. We analyze the data collected so far and confirm that the submitted questions are diverse, aligned with real-world literature needs, and that participating researchers demonstrate strong self-consistency and inter-annotator agreement in their evaluations. We discuss the results and insights based on the model ranking leaderboard. To further promote research in building model-based automated evaluation systems for literature tasks, we release SciArena-Eval, a meta-evaluation benchmark based on our collected preference data. The benchmark measures the accuracy of models in judging answer quality by comparing their pairwise assessments with human votes. Our experiments highlight the benchmark's challenges and emphasize the need for more reliable automated evaluation methods.

The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep learning framework that unifies molecule detection, reaction diagram parsing, and optical chemical structure recognition (OCSR) into a single pipeline for automating the extraction of chemical data directly from page-level documents. Recognizing the lack of a standard page-level benchmark and evaluation metric, we also present a testset of 550 pages annotated with molecule bounding boxes, reaction labels, and MOLfiles, along with a novel evaluation metric. Experimental results demonstrate that MolMole outperforms existing toolkits on both our benchmark and public datasets. The benchmark testset will be publicly available, and the MolMole toolkit will be accessible soon through an interactive demo on the LG AI Research website. For commercial inquiries, please contact us at mailto:contact_ddu@lgresearch.ai{contact\_ddu@lgresearch.ai}.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

Recent breakthroughs in Large Language Models (LLMs) have revolutionized natural language understanding and generation, igniting a surge of interest in leveraging these technologies in the field of scientific literature analysis. Existing benchmarks, however, inadequately evaluate the proficiency of LLMs in scientific literature analysis, especially in scenarios involving complex comprehension and multimodal data. In response, we introduced SciAssess, a benchmark tailored for the in-depth analysis of scientific literature, crafted to provide a thorough assessment of LLMs' efficacy. SciAssess focuses on evaluating LLMs' abilities in memorization, comprehension, and analysis within the context of scientific literature analysis. It includes representative tasks from diverse scientific fields, such as general chemistry, organic materials, and alloy materials. And rigorous quality control measures ensure its reliability in terms of correctness, anonymization, and copyright compliance. SciAssess evaluates leading LLMs, including GPT-4, GPT-3.5, and Gemini, identifying their strengths and aspects for improvement and supporting the ongoing development of LLM applications in scientific literature analysis. SciAssess and its resources are made available at https://sci-assess.github.io, offering a valuable tool for advancing LLM capabilities in scientific literature analysis.

Scientific Research, vital for improving human life, is hindered by its inherent complexity, slow pace, and the need for specialized experts. To enhance its productivity, we propose a ResearchAgent, a large language model-powered research idea writing agent, which automatically generates problems, methods, and experiment designs while iteratively refining them based on scientific literature. Specifically, starting with a core paper as the primary focus to generate ideas, our ResearchAgent is augmented not only with relevant publications through connecting information over an academic graph but also entities retrieved from an entity-centric knowledge store based on their underlying concepts, mined and shared across numerous papers. In addition, mirroring the human approach to iteratively improving ideas with peer discussions, we leverage multiple ReviewingAgents that provide reviews and feedback iteratively. Further, they are instantiated with human preference-aligned large language models whose criteria for evaluation are derived from actual human judgments. We experimentally validate our ResearchAgent on scientific publications across multiple disciplines, showcasing its effectiveness in generating novel, clear, and valid research ideas based on human and model-based evaluation results.

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases, and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

As AI tools become increasingly common for research ideation, robust evaluation is critical to ensure the validity and usefulness of generated ideas. We introduce ScholarEval, a retrieval augmented evaluation framework that assesses research ideas based on two fundamental criteria: soundness - the empirical validity of proposed methods based on existing literature, and contribution - the degree of advancement made by the idea across different dimensions relative to prior research. To evaluate ScholarEval, we introduce ScholarIdeas, the first expert-annotated dataset of multi-domain research ideas and reviews, comprised of 117 ideas across four disciplines: artificial intelligence, neuroscience, biochemistry, and ecology. Our evaluation shows that ScholarEval achieves significantly higher coverage of points mentioned in the human expert annotated rubrics in ScholarIdeas compared to all baselines. Furthermore, ScholarEval is consistently preferred over our strongest baseline o4-mini-deep-research, a reasoning and search-enabled agentic system by OpenAI, in terms of evaluation actionability, depth, and evidence support. Our large-scale user study also shows that ScholarEval significantly outperforms deep research in literature engagement, idea refinement, and usefulness. We openly release our code, dataset, and ScholarEval tool for the community to use and build on.

Extraction and synthesis of structured knowledge from extensive scientific literature are crucial for advancing and disseminating scientific progress. Although many existing systems facilitate literature review and digest, they struggle to process multimodal, varied, and inconsistent information within and across the literature into structured data. We introduce SciDaSynth, a novel interactive system powered by large language models (LLMs) that enables researchers to efficiently build structured knowledge bases from scientific literature at scale. The system automatically creates data tables to organize and summarize users' interested knowledge in literature via question-answering. Furthermore, it provides multi-level and multi-faceted exploration of the generated data tables, facilitating iterative validation, correction, and refinement. Our within-subjects study with researchers demonstrates the effectiveness and efficiency of SciDaSynth in constructing quality scientific knowledge bases. We further discuss the design implications for human-AI interaction tools for data extraction and structuring.

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated method for connecting scientific literature to synthesis insights. Starting from natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for arbitrary materials. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties, and that the model's behavior complements existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.

We introduce LibriConvo, a simulated multi-speaker conversational dataset based on speaker-aware conversation simulation (SASC), designed to support training and evaluation of speaker diarization and automatic speech recognition (ASR) systems. Unlike prior resources that mostly rely on semantically disconnected utterances and implausible temporal gaps, LibriConvo ensures semantic coherence and realistic conversational timing. Our pipeline leverages CallHome with external VAD for reliable boundaries, applies compression to reduce unnaturally long silences, and organizes LibriTTS utterances by book to maintain contextual consistency. Acoustic realism is enhanced via a novel room impulse response selection procedure that ranks speaker-microphone configurations by spatial plausibility, balancing realism and diversity. The dataset comprises 240.1 hours across 1,496 dialogues with 830 unique speakers, split in a speaker-disjoint manner for robust evaluation. Baselines show that the sortformer model outperforms the pyannote pipeline in diarization, while a fine-tuned Fast Conformer-CTC XLarge with Serialized Output Training achieves 7.29\% WER for ASR, surpassing zero-shot Whisper-large-v3. LibriConvo provides a valuable resource for advancing multi-speaker speech processing research with realistic conversational dynamics and controlled experimental conditions.

Data-driven materials discovery requires large-scale experimental datasets, yet most of the information remains trapped in unstructured literature. Existing extraction efforts often focus on a limited set of features and have not addressed the integrated composition-processing-microstructure-property relationships essential for understanding materials behavior, thereby posing challenges for building comprehensive databases. To address this gap, we propose a multi-stage information extraction pipeline powered by large language models, which captures 47 features spanning composition, processing, microstructure, and properties exclusively from experimentally reported materials. The pipeline integrates iterative extraction with source tracking to enhance both accuracy and reliability. Evaluations at the feature level (independent attributes) and tuple level (interdependent features) yielded F1 scores around 0.96. Compared with single-pass extraction without source tracking, our approach improved F1 scores of microstructure category by 10.0% (feature level) and 13.7% (tuple level), and reduced missed materials from 49 to 13 out of 396 materials in 100 articles on precipitate-containing multi-principal element alloys (miss rate reduced from 12.4% to 3.3%). The pipeline enables scalable and efficient literature mining, producing databases with high precision, minimal omissions, and zero false positives. These datasets provide trustworthy inputs for machine learning and materials informatics, while the modular design generalizes to diverse material classes, enabling comprehensive materials information extraction.

The emergence of advanced reasoning capabilities in Large Language Models (LLMs) marks a transformative development in healthcare applications. Beyond merely expanding functional capabilities, these reasoning mechanisms enhance decision transparency and explainability-critical requirements in medical contexts. This survey examines the transformation of medical LLMs from basic information retrieval tools to sophisticated clinical reasoning systems capable of supporting complex healthcare decisions. We provide a thorough analysis of the enabling technological foundations, with a particular focus on specialized prompting techniques like Chain-of-Thought and recent breakthroughs in Reinforcement Learning exemplified by DeepSeek-R1. Our investigation evaluates purpose-built medical frameworks while also examining emerging paradigms such as multi-agent collaborative systems and innovative prompting architectures. The survey critically assesses current evaluation methodologies for medical validation and addresses persistent challenges in field interpretation limitations, bias mitigation strategies, patient safety frameworks, and integration of multimodal clinical data. Through this survey, we seek to establish a roadmap for developing reliable LLMs that can serve as effective partners in clinical practice and medical research.

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

The rapid expansion of enzyme kinetics literature has outpaced the curation capabilities of major biochemical databases, creating a substantial barrier to AI-driven modeling and knowledge discovery. We present zERExtractor, an automated and extensible platform for comprehensive extraction of enzyme-catalyzed reaction and activity data from scientific literature. zERExtractor features a unified, modular architecture that supports plug-and-play integration of state-of-the-art models, including large language models (LLMs), as interchangeable components, enabling continuous system evolution alongside advances in AI. Our pipeline combines domain-adapted deep learning, advanced OCR, semantic entity recognition, and prompt-driven LLM modules, together with human expert corrections, to extract kinetic parameters (e.g., kcat, Km), enzyme sequences, substrate SMILES, experimental conditions, and molecular diagrams from heterogeneous document formats. Through active learning strategies integrating AI-assisted annotation, expert validation, and iterative refinement, the system adapts rapidly to new data sources. We also release a large benchmark dataset comprising over 1,000 annotated tables and 5,000 biological fields from 270 P450-related enzymology publications. Benchmarking demonstrates that zERExtractor consistently outperforms existing baselines in table recognition (Acc 89.9%), molecular image interpretation (up to 99.1%), and relation extraction (accuracy 94.2%). zERExtractor bridges the longstanding data gap in enzyme kinetics with a flexible, plugin-ready framework and high-fidelity extraction, laying the groundwork for future AI-powered enzyme modeling and biochemical knowledge discovery.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Climate change poses an urgent global threat, needing the rapid identification and deployment of innovative solutions. We hypothesise that many of these solutions already exist within scientific literature but remain underutilised. To address this gap, this study employs a curated dataset sourced from OpenAlex, a comprehensive repository of scientific papers. Utilising Large Language Models (LLMs), such as GPT4-o from OpenAI, we evaluate title-abstract pairs from scientific papers on seven dimensions, covering climate change mitigation potential, stage of technological development, and readiness for deployment. The outputs of the language models are then compared with human evaluations to assess their effectiveness in identifying promising yet overlooked climate innovations. Our findings suggest that these LLM-based models can effectively augment human expertise, uncovering climate solutions that are potentially impactful but with far greater speed, throughput and consistency. Here, we focused on UK-based solutions, but the workflow is region-agnostic. This work contributes to the discovery of neglected innovations in scientific literature and demonstrates the potential of AI in enhancing climate action strategies.

Large language models (LLMs) are becoming increasingly better at a wide range of Natural Language Processing tasks (NLP), such as text generation and understanding. Recently, these models have extended their capabilities to coding tasks, bridging the gap between natural languages (NL) and programming languages (PL). Foundational models such as the Generative Pre-trained Transformer (GPT) and LLaMA series have set strong baseline performances in various NL and PL tasks. Additionally, several models have been fine-tuned specifically for code generation, showing significant improvements in code-related applications. Both foundational and fine-tuned models are increasingly used in education, helping students write, debug, and understand code. We present a comprehensive systematic literature review to examine the impact of LLMs in computer science and computer engineering education. We analyze their effectiveness in enhancing the learning experience, supporting personalized education, and aiding educators in curriculum development. We address five research questions to uncover insights into how LLMs contribute to educational outcomes, identify challenges, and suggest directions for future research.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Identifying effective interventions from the scientific literature is challenging due to the high volume of publications, specialized terminology, and inconsistent reporting formats, making manual curation laborious and prone to oversight. To address this challenge, this paper proposes a novel framework leveraging large language models (LLMs), which integrates a progressive ontology prompting (POP) algorithm with a dual-agent system, named LLM-Duo. On the one hand, the POP algorithm conducts a prioritized breadth-first search (BFS) across a predefined ontology, generating structured prompt templates and action sequences to guide the automatic annotation process. On the other hand, the LLM-Duo system features two specialized LLM agents, an explorer and an evaluator, working collaboratively and adversarially to continuously refine annotation quality. We showcase the real-world applicability of our framework through a case study focused on speech-language intervention discovery. Experimental results show that our approach surpasses advanced baselines, achieving more accurate and comprehensive annotations through a fully automated process. Our approach successfully identified 2,421 interventions from a corpus of 64,177 research articles in the speech-language pathology domain, culminating in the creation of a publicly accessible intervention knowledge base with great potential to benefit the speech-language pathology community.

The field of conlang has evidenced an important growth in the last decades. This has been the product of a wide interest in the use and study of conlangs for artistic purposes. However, one important question is what it is happening with conlang in the academic world. This paper aims to have an overall understanding of the literature on conlang research. With this we aim to give a realistic picture of the field in present days. We have implemented a computational linguistic approach, combining bibliometrics and network analysis to examine all publications available in the Scopus database. Analysing over 2300 academic publications since 1927 until 2022, we have found that Esperanto is by far the most documented conlang. Three main authors have contributed to this: Garv\'ia R., Fiedler S., and Blanke D. The 1970s and 1980s have been the decades where the foundations of current research have been built. In terms of methodologies, language learning and experimental linguistics are the ones contributing to most to the preferred approaches of study in the field. We present the results and discuss our limitations and future work.

Background: Collaborative Software Package Registries (SPRs) are an integral part of the software supply chain. Much engineering work synthesizes SPR package into applications. Prior research has examined SPRs for traditional software, such as NPM (JavaScript) and PyPI (Python). Pre-Trained Model (PTM) Registries are an emerging class of SPR of increasing importance, because they support the deep learning supply chain. Aims: Recent empirical research has examined PTM registries in ways such as vulnerabilities, reuse processes, and evolution. However, no existing research synthesizes them to provide a systematic understanding of the current knowledge. Some of the existing research includes qualitative claims lacking quantitative analysis. Our research fills these gaps by providing a knowledge synthesis and quantitative analyses. Methods: We first conduct a systematic literature review (SLR). We then observe that some of the claims are qualitative. We identify quantifiable metrics associated with those claims, and measure in order to substantiate these claims. Results: From our SLR, we identify 12 claims about PTM reuse on the HuggingFace platform, 4 of which lack quantitative validation. We successfully test 3 of these claims through a quantitative analysis, and directly compare one with traditional software. Our findings corroborate qualitative claims with quantitative measurements. Our findings are: (1) PTMs have a much higher turnover rate than traditional software, indicating a dynamic and rapidly evolving reuse environment within the PTM ecosystem; and (2) There is a strong correlation between documentation quality and PTM popularity. Conclusions: We confirm qualitative research claims with concrete metrics, supporting prior qualitative and case study research. Our measures show further dynamics of PTM reuse, inspiring research infrastructure and new measures.

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

In recent decades, several assistive technologies have been developed for visually impaired and blind (VIB) individuals to improve their ability to navigate independently and safely. At the same time, simultaneous localization and mapping (SLAM) techniques have become sufficiently robust and efficient to be adopted in the development of these assistive technologies. In this paper, we first report the results of an anonymous worldwide survey conducted with VIB people to understand their experiences, needs, and challenges in navigation, differentiating our approach from prior work that often has a limited geographic scope and focuses on specific challenges. We then present a systematic literature review of recent studies on SLAM-based solutions for VIB people. This review explores various SLAM techniques employed in this context. We discuss the advantages and limitations of these techniques for VIB navigation. Moreover, we examined a range of challenging situations addressed in the studies included in this review. We explain how SLAM-based solutions offer potential to improve the ability of visually impaired individuals to navigate effectively. Finally, we present future opportunities and challenges in this domain.

The growing importance of understanding and addressing algorithmic bias in artificial intelligence (AI) has led to a surge in research on AI fairness, which often assumes that the underlying data is independent and identically distributed (IID). However, real-world data frequently exists in non-IID graph structures that capture connections among individual units. To effectively mitigate bias in AI systems, it is essential to bridge the gap between traditional fairness literature, designed for IID data, and the prevalence of non-IID graph data. This survey reviews recent advancements in fairness amidst non-IID graph data, including the newly introduced fair graph generation and the commonly studied fair graph classification. In addition, available datasets and evaluation metrics for future research are identified, the limitations of existing work are highlighted, and promising future directions are proposed.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

We present in this work a new dataset of coreference annotations for works of literature in English, covering 29,103 mentions in 210,532 tokens from 100 works of fiction. This dataset differs from previous coreference datasets in containing documents whose average length (2,105.3 words) is four times longer than other benchmark datasets (463.7 for OntoNotes), and contains examples of difficult coreference problems common in literature. This dataset allows for an evaluation of cross-domain performance for the task of coreference resolution, and analysis into the characteristics of long-distance within-document coreference.

As Natural Language Processing (NLP) and Machine Learning (ML) tools rise in popularity, it becomes increasingly vital to recognize the role they play in shaping societal biases and stereotypes. Although NLP models have shown success in modeling various applications, they propagate and may even amplify gender bias found in text corpora. While the study of bias in artificial intelligence is not new, methods to mitigate gender bias in NLP are relatively nascent. In this paper, we review contemporary studies on recognizing and mitigating gender bias in NLP. We discuss gender bias based on four forms of representation bias and analyze methods recognizing gender bias. Furthermore, we discuss the advantages and drawbacks of existing gender debiasing methods. Finally, we discuss future studies for recognizing and mitigating gender bias in NLP.

Much of machine learning research focuses on producing models which perform well on benchmark tasks, in turn improving our understanding of the challenges associated with those tasks. From the perspective of ML researchers, the content of the task itself is largely irrelevant, and thus there have increasingly been calls for benchmark tasks to more heavily focus on problems which are of social or cultural relevance. In this work, we introduce Kuzushiji-MNIST, a dataset which focuses on Kuzushiji (cursive Japanese), as well as two larger, more challenging datasets, Kuzushiji-49 and Kuzushiji-Kanji. Through these datasets, we wish to engage the machine learning community into the world of classical Japanese literature. Dataset available at https://github.com/rois-codh/kmnist

Within the past few decades we have witnessed digital revolution, which moved scholarly communication to electronic media and also resulted in a substantial increase in its volume. Nowadays keeping track with the latest scientific achievements poses a major challenge for the researchers. Scientific information overload is a severe problem that slows down scholarly communication and knowledge propagation across the academia. Modern research infrastructures facilitate studying scientific literature by providing intelligent search tools, proposing similar and related documents, visualizing citation and author networks, assessing the quality and impact of the articles, and so on. In order to provide such high quality services the system requires the access not only to the text content of stored documents, but also to their machine-readable metadata. Since in practice good quality metadata is not always available, there is a strong demand for a reliable automatic method of extracting machine-readable metadata directly from source documents. This research addresses these problems by proposing an automatic, accurate and flexible algorithm for extracting wide range of metadata directly from scientific articles in born-digital form. Extracted information includes basic document metadata, structured full text and bibliography section. Designed as a universal solution, proposed algorithm is able to handle a vast variety of publication layouts with high precision and thus is well-suited for analyzing heterogeneous document collections. This was achieved by employing supervised and unsupervised machine-learning algorithms trained on large, diverse datasets. The evaluation we conducted showed good performance of proposed metadata extraction algorithm. The comparison with other similar solutions also proved our algorithm performs better than competition for most metadata types.

The specialized language and complex concepts in physics pose significant challenges for information extraction through Natural Language Processing (NLP). Central to effective NLP applications is the text embedding model, which converts text into dense vector representations for efficient information retrieval and semantic analysis. In this work, we introduce PhysBERT, the first physics-specific text embedding model. Pre-trained on a curated corpus of 1.2 million arXiv physics papers and fine-tuned with supervised data, PhysBERT outperforms leading general-purpose models on physics-specific tasks including the effectiveness in fine-tuning for specific physics subdomains.

The automatic extraction of materials and related properties from the scientific literature is gaining attention in data-driven materials science (Materials Informatics). In this paper, we discuss Grobid-superconductors, our solution for automatically extracting superconductor material names and respective properties from text. Built as a Grobid module, it combines machine learning and heuristic approaches in a multi-step architecture that supports input data as raw text or PDF documents. Using Grobid-superconductors, we built SuperCon2, a database of 40324 materials and properties records from 37700 papers. The material (or sample) information is represented by name, chemical formula, and material class, and is characterized by shape, doping, substitution variables for components, and substrate as adjoined information. The properties include the Tc superconducting critical temperature and, when available, applied pressure with the Tc measurement method.

We present SciRIFF (Scientific Resource for Instruction-Following and Finetuning), a dataset of 137K instruction-following demonstrations for 54 tasks covering five essential scientific literature understanding capabilities: information extraction, summarization, question answering, claim verification, and classification. SciRIFF demonstrations are notable for their long input contexts, detailed task specifications, and complex structured outputs. While instruction-following resources are available in specific domains such as clinical medicine and chemistry, SciRIFF is the first dataset focused on extracting and synthesizing information from research literature across a wide range of scientific fields. To demonstrate the utility of SciRIFF, we develop a sample-efficient strategy to adapt a general instruction-following model for science by performing additional finetuning on a mix of general-domain and SciRIFF demonstrations. In evaluations on nine held-out scientific tasks, our model -- called SciTulu -- improves over a strong LLM baseline by 28.1% and 6.5% at the 7B and 70B scales respectively, while maintaining general instruction-following performance within 2% of the baseline. We are optimistic that SciRIFF will facilitate the development and evaluation of LLMs to help researchers navigate the ever-growing body of scientific literature. We release our dataset, model checkpoints, and data processing and evaluation code to enable further research.

The rapid advancement of Large Language Models (LLMs) has opened up new opportunities for leveraging artificial intelligence in various domains, including cybersecurity. As the volume and sophistication of cyber threats continue to grow, there is an increasing need for intelligent systems that can automatically detect vulnerabilities, analyze malware, and respond to attacks. In this survey, we conduct a comprehensive review of the literature on the application of LLMs in cybersecurity (LLM4Security). By comprehensively collecting over 30K relevant papers and systematically analyzing 127 papers from top security and software engineering venues, we aim to provide a holistic view of how LLMs are being used to solve diverse problems across the cybersecurity domain. Through our analysis, we identify several key findings. First, we observe that LLMs are being applied to a wide range of cybersecurity tasks, including vulnerability detection, malware analysis, network intrusion detection, and phishing detection. Second, we find that the datasets used for training and evaluating LLMs in these tasks are often limited in size and diversity, highlighting the need for more comprehensive and representative datasets. Third, we identify several promising techniques for adapting LLMs to specific cybersecurity domains, such as fine-tuning, transfer learning, and domain-specific pre-training. Finally, we discuss the main challenges and opportunities for future research in LLM4Security, including the need for more interpretable and explainable models, the importance of addressing data privacy and security concerns, and the potential for leveraging LLMs for proactive defense and threat hunting. Overall, our survey provides a comprehensive overview of the current state-of-the-art in LLM4Security and identifies several promising directions for future research.

With the proliferation of open-sourced Large Language Models (LLMs) and efficient finetuning techniques, we are on the cusp of the emergence of numerous domain-specific LLMs that have been finetuned for expertise across specialized fields and applications for which the current general-purpose LLMs are unsuitable. In academia, this technology has the potential to revolutionize the way we conduct systematic literature reviews (SLRs), access knowledge and generate new insights. This paper proposes an AI-enabled methodological framework that combines the power of LLMs with the rigorous reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). By finetuning LLMs on domain-specific academic papers that have been selected as a result of a rigorous SLR process, the proposed PRISMA-DFLLM (for Domain-specific Finetuned LLMs) reporting guidelines offer the potential to achieve greater efficiency, reusability and scalability, while also opening the potential for conducting incremental living systematic reviews with the aid of LLMs. Additionally, the proposed approach for leveraging LLMs for SLRs enables the dissemination of finetuned models, empowering researchers to accelerate advancements and democratize cutting-edge research. This paper presents the case for the feasibility of finetuned LLMs to support rigorous SLRs and the technical requirements for realizing this. This work then proposes the extended PRISMA-DFLLM checklist of reporting guidelines as well as the advantages, challenges, and potential implications of implementing PRISMA-DFLLM. Finally, a future research roadmap to develop this line of AI-enabled SLRs is presented, paving the way for a new era of evidence synthesis and knowledge discovery.

The cybersecurity landscape evolves rapidly and poses threats to organizations. To enhance resilience, one needs to track the latest developments and trends in the domain. It has been demonstrated that standard bibliometrics approaches show their limits in such a fast-evolving domain. For this purpose, we use large language models (LLMs) to extract relevant knowledge entities from cybersecurity-related texts. We use a subset of arXiv preprints on cybersecurity as our data and compare different LLMs in terms of entity recognition (ER) and relevance. The results suggest that LLMs do not produce good knowledge entities that reflect the cybersecurity context, but our results show some potential for noun extractors. For this reason, we developed a noun extractor boosted with some statistical analysis to extract specific and relevant compound nouns from the domain. Later, we tested our model to identify trends in the LLM domain. We observe some limitations, but it offers promising results to monitor the evolution of emergent trends.

Scientific information extraction (SciIE), which aims to automatically extract information from scientific literature, is becoming more important than ever. However, there are no existing SciIE datasets for polymer materials, which is an important class of materials used ubiquitously in our daily lives. To bridge this gap, we introduce POLYIE, a new SciIE dataset for polymer materials. POLYIE is curated from 146 full-length polymer scholarly articles, which are annotated with different named entities (i.e., materials, properties, values, conditions) as well as their N-ary relations by domain experts. POLYIE presents several unique challenges due to diverse lexical formats of entities, ambiguity between entities, and variable-length relations. We evaluate state-of-the-art named entity extraction and relation extraction models on POLYIE, analyze their strengths and weaknesses, and highlight some difficult cases for these models. To the best of our knowledge, POLYIE is the first SciIE benchmark for polymer materials, and we hope it will lead to more research efforts from the community on this challenging task. Our code and data are available on: https://github.com/jerry3027/PolyIE.

Creating an abridged version of a text involves shortening it while maintaining its linguistic qualities. In this paper, we examine this task from an NLP perspective for the first time. We present a new resource, AbLit, which is derived from abridged versions of English literature books. The dataset captures passage-level alignments between the original and abridged texts. We characterize the linguistic relations of these alignments, and create automated models to predict these relations as well as to generate abridgements for new texts. Our findings establish abridgement as a challenging task, motivating future resources and research. The dataset is available at github.com/roemmele/AbLit.

Medical systematic reviews typically require assessing all the documents retrieved by a search. The reason is two-fold: the task aims for ``total recall''; and documents retrieved using Boolean search are an unordered set, and thus it is unclear how an assessor could examine only a subset. Screening prioritisation is the process of ranking the (unordered) set of retrieved documents, allowing assessors to begin the downstream processes of the systematic review creation earlier, leading to earlier completion of the review, or even avoiding screening documents ranked least relevant. Screening prioritisation requires highly effective ranking methods. Pre-trained language models are state-of-the-art on many IR tasks but have yet to be applied to systematic review screening prioritisation. In this paper, we apply several pre-trained language models to the systematic review document ranking task, both directly and fine-tuned. An empirical analysis compares how effective neural methods compare to traditional methods for this task. We also investigate different types of document representations for neural methods and their impact on ranking performance. Our results show that BERT-based rankers outperform the current state-of-the-art screening prioritisation methods. However, BERT rankers and existing methods can actually be complementary, and thus, further improvements may be achieved if used in conjunction.

Lay summarisation aims to jointly summarise and simplify a given text, thus making its content more comprehensible to non-experts. Automatic approaches for lay summarisation can provide significant value in broadening access to scientific literature, enabling a greater degree of both interdisciplinary knowledge sharing and public understanding when it comes to research findings. However, current corpora for this task are limited in their size and scope, hindering the development of broadly applicable data-driven approaches. Aiming to rectify these issues, we present two novel lay summarisation datasets, PLOS (large-scale) and eLife (medium-scale), each of which contains biomedical journal articles alongside expert-written lay summaries. We provide a thorough characterisation of our lay summaries, highlighting differing levels of readability and abstractiveness between datasets that can be leveraged to support the needs of different applications. Finally, we benchmark our datasets using mainstream summarisation approaches and perform a manual evaluation with domain experts, demonstrating their utility and casting light on the key challenges of this task.

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area

With worldwide concerns surrounding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is a rapidly growing body of scientific literature on the virus. Clinicians, researchers, and policy-makers need to be able to search these articles effectively. In this work, we present a zero-shot ranking algorithm that adapts to COVID-related scientific literature. Our approach filters training data from another collection down to medical-related queries, uses a neural re-ranking model pre-trained on scientific text (SciBERT), and filters the target document collection. This approach ranks top among zero-shot methods on the TREC COVID Round 1 leaderboard, and exhibits a P@5 of 0.80 and an nDCG@10 of 0.68 when evaluated on both Round 1 and 2 judgments. Despite not relying on TREC-COVID data, our method outperforms models that do. As one of the first search methods to thoroughly evaluate COVID-19 search, we hope that this serves as a strong baseline and helps in the global crisis.