Daily Papers

Academic researchers need efficient and reliable methods for collecting high-quality information from trusted sources, but modern tools for AI-assisted research still suffer from the tendency of Large Language Models (LLMs) to produce factually inaccurate or nonsensical output, commonly referred to as hallucinations. We apply the extractive question answering system VerbatimRAG to research papers in the ACL Anthology, directly mapping user queries to verbatim text spans in retrieved documents. We contribute a novel ground truth dataset for the task of mapping user queries to relevant text spans in research papers, and use it to train and evaluate a variety of extractive models. Human annotation is performed by NLP researchers and is based on synthetic user queries generated using a custom pipeline based on the ScIRGen methodology, paired with chunks of research papers retrieved by VerbatimRAG. On this benchmark, a 150M-parameter ModernBERT token classifier trained on silver supervision from our pipeline achieves the best word-level F1 (53.6), ahead of the strongest evaluated LLM extractor (48.7).

Scientific researchers need intensive information about datasets to effectively evaluate and develop theories and methodologies. The information needs regarding datasets are implicitly embedded in particular research tasks, rather than explicitly expressed in search queries. However, existing scientific retrieval and question-answering (QA) datasets typically address straightforward questions, which do not align with the distribution of real-world research inquiries. To bridge this gap, we developed ScIRGen, a dataset generation framework for scientific QA \& retrieval that more accurately reflects the information needs of professional science researchers, and uses it to create a large-scale scientific retrieval-augmented generation (RAG) dataset with realistic queries, datasets and papers. Technically, we designed a dataset-oriented information extraction method that leverages academic papers to augment the dataset representation. We then proposed a question generation framework by employing cognitive taxonomy to ensure the quality of synthesized questions. We also design a method to automatically filter synthetic answers based on the perplexity shift of LLMs, which is highly aligned with human judgment of answers' validity. Collectively, these methodologies culminated in the creation of the 61k QA dataset, ScIRGen-Geo. We benchmarked representative methods on the ScIRGen-Geo dataset for their question-answering and retrieval capabilities, finding out that current methods still suffer from reasoning from complex questions. This work advances the development of more sophisticated tools to support the intricate information needs of the scientific community.

We introduce SciVer, the first benchmark specifically designed to evaluate the ability of foundation models to verify claims within a multimodal scientific context. SciVer consists of 3,000 expert-annotated examples over 1,113 scientific papers, covering four subsets, each representing a common reasoning type in multimodal scientific claim verification. To enable fine-grained evaluation, each example includes expert-annotated supporting evidence. We assess the performance of 21 state-of-the-art multimodal foundation models, including o4-mini, Gemini-2.5-Flash, Llama-3.2-Vision, and Qwen2.5-VL. Our experiment reveals a substantial performance gap between these models and human experts on SciVer. Through an in-depth analysis of retrieval-augmented generation (RAG), and human-conducted error evaluations, we identify critical limitations in current open-source models, offering key insights to advance models' comprehension and reasoning in multimodal scientific literature tasks.

Recently, there has been growing interest in using Large Language Models (LLMs) for scientific research. Numerous benchmarks have been proposed to evaluate the ability of LLMs for scientific research. However, current benchmarks are mostly based on pre-collected objective questions. This design suffers from data leakage problem and lacks the evaluation of subjective Q/A ability. In this paper, we propose SciEval, a comprehensive and multi-disciplinary evaluation benchmark to address these issues. Based on Bloom's taxonomy, SciEval covers four dimensions to systematically evaluate scientific research ability. In particular, we design a "dynamic" subset based on scientific principles to prevent evaluation from potential data leakage. Both objective and subjective questions are included in SciEval. These characteristics make SciEval a more effective benchmark for scientific research ability evaluation of LLMs. Comprehensive experiments on most advanced LLMs show that, although GPT-4 achieves SOTA performance compared to other LLMs, there is still substantial room for improvement, especially for dynamic questions. The data and codes are now publicly available.

We present a novel method for obtaining high-quality, domain-targeted multiple choice questions from crowd workers. Generating these questions can be difficult without trading away originality, relevance or diversity in the answer options. Our method addresses these problems by leveraging a large corpus of domain-specific text and a small set of existing questions. It produces model suggestions for document selection and answer distractor choice which aid the human question generation process. With this method we have assembled SciQ, a dataset of 13.7K multiple choice science exam questions (Dataset available at http://allenai.org/data.html). We demonstrate that the method produces in-domain questions by providing an analysis of this new dataset and by showing that humans cannot distinguish the crowdsourced questions from original questions. When using SciQ as additional training data to existing questions, we observe accuracy improvements on real science exams.

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

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.

Recent advances in large language models (LLMs) have enabled agentic systems that translate natural language intent into executable scientific visualization (SciVis) tasks. Despite rapid progress, the community lacks a principled and reproducible benchmark for evaluating these emerging SciVis agents in realistic, multi-step analysis settings. We present SciVisAgentBench, a comprehensive and extensible benchmark for evaluating scientific data analysis and visualization agents. Our benchmark is grounded in a structured taxonomy spanning four dimensions: application domain, data type, complexity level, and visualization operation. It currently comprises 108 expert-crafted cases covering diverse SciVis scenarios. To enable reliable assessment, we introduce a multimodal outcome-centric evaluation pipeline that combines LLM-based judging with deterministic evaluators, including image-based metrics, code checkers, rule-based verifiers, and case-specific evaluators. We also conduct a validity study with 12 SciVis experts to examine the agreement between human and LLM judges. Using this framework, we evaluate representative SciVis agents and general-purpose coding agents to establish initial baselines and reveal capability gaps. SciVisAgentBench is designed as a living benchmark to support systematic comparison, diagnose failure modes, and drive progress in agentic SciVis. The benchmark is available at https://scivisagentbench.github.io/.

The rapid advancement of Large Language Models (LLMs) has resulted in a significant knowledge gap between the open-source community and industry, primarily because the latter relies on closed-source, high-quality data and training recipes. To address this, we introduce PCMind-2.1-Kaiyuan-2B, a fully open-source 2-billion-parameter model focused on improving training efficiency and effectiveness under resource constraints. Our methodology includes three key innovations: a Quantile Data Benchmarking method for systematically comparing heterogeneous open-source datasets and providing insights on data mixing strategies; a Strategic Selective Repetition scheme within a multi-phase paradigm to effectively leverage sparse, high-quality data; and a Multi-Domain Curriculum Training policy that orders samples by quality. Supported by a highly optimized data preprocessing pipeline and architectural modifications for FP16 stability, Kaiyuan-2B achieves performance competitive with state-of-the-art fully open-source models, demonstrating practical and scalable solutions for resource-limited pretraining. We release all assets (including model weights, data, and code) under Apache 2.0 license at https://huggingface.co/thu-pacman/PCMind-2.1-Kaiyuan-2B.

Large Language Models (LLMs) have become a milestone in the field of artificial intelligence and natural language processing. However, their large-scale deployment remains constrained by the need for significant computational resources. This work proposes starting from a base model to explore and combine data processing and careful data selection techniques, training strategies, and architectural adjustments to improve the efficiency of LLMs in resource-constrained environments and within a delimited knowledge base. The methodological approach included defining criteria for building reliable datasets, conducting controlled experiments with different configurations, and systematically evaluating the resulting variants in terms of capability, versatility, response time, and safety. Finally, comparative tests were conducted to measure the performance of the developed variants and to validate the effectiveness of the proposed strategies. This work is based on the master's thesis in Systems and Computer Engineering titled "Efficient Strategy for Improving the Capabilities of Large Language Models (LLMs)".

Large language models (LLMs) are increasingly touted as powerful tools for automating scientific information extraction. However, existing methods and tools often struggle with the realities of scientific literature: long-context documents, multi-modal content, and reconciling varied and inconsistent fine-grained information across multiple publications into standardized formats. These challenges are further compounded when the desired data schema or extraction ontology changes rapidly, making it difficult to re-architect or fine-tune existing systems. We present SciEx, a modular and composable framework that decouples key components including PDF parsing, multi-modal retrieval, extraction, and aggregation. This design streamlines on-demand data extraction while enabling extensibility and flexible integration of new models, prompting strategies, and reasoning mechanisms. We evaluate SciEx on datasets spanning three scientific topics for its ability to extract fine-grained information accurately and consistently. Our findings provide practical insights into both the strengths and limitations of current LLM-based pipelines.

This paper introduces a multifaceted methodology for fine-tuning and evaluating large language models (LLMs) for specialized monetization tasks. The goal is to balance general language proficiency with domain-specific skills. The methodology has three main components: 1) Carefully blending in-domain and general-purpose data during fine-tuning to achieve an optimal balance between general and specialized capabilities; 2) Designing a comprehensive evaluation framework with 45 questions tailored to assess performance on functionally relevant dimensions like reliability, consistency, and business impact; 3) Analyzing how model size and continual training influence metrics to guide efficient resource allocation during fine-tuning. The paper details the design, data collection, analytical techniques, and results validating the proposed frameworks. It aims to provide businesses and researchers with actionable insights on effectively adapting LLMs for specialized contexts. We also intend to make public the comprehensive evaluation framework, which includes the 45 tailored questions and their respective scoring guidelines, to foster transparency and collaboration in adapting LLMs for specialized tasks.

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.

The rapid growth of scientific literature demands robust tools for automated survey-generation. However, current large language model (LLM)-based methods often lack in-depth analysis, structural coherence, and reliable citations. To address these limitations, we introduce SciSage, a multi-agent framework employing a reflect-when-you-write paradigm. SciSage features a hierarchical Reflector agent that critically evaluates drafts at outline, section, and document levels, collaborating with specialized agents for query interpretation, content retrieval, and refinement. We also release SurveyScope, a rigorously curated benchmark of 46 high-impact papers (2020-2025) across 11 computer science domains, with strict recency and citation-based quality controls. Evaluations demonstrate that SciSage outperforms state-of-the-art baselines (LLM x MapReduce-V2, AutoSurvey), achieving +1.73 points in document coherence and +32% in citation F1 scores. Human evaluations reveal mixed outcomes (3 wins vs. 7 losses against human-written surveys), but highlight SciSage's strengths in topical breadth and retrieval efficiency. Overall, SciSage offers a promising foundation for research-assistive writing tools.

While Text-to-Image (T2I) models have shown remarkable success in generating photorealistic visual content, they still struggle with the rigorous semantic alignment and logical reasoning required for scientific imagery. Inspired by Peirce's Semiotic Triad, we introduce Scientific Image Reasoning (SciIR), a comprehensive resource for training and evaluation of scientific image generation. We formalize scientific reasoning into three core dimensions: Entity Structure (Icon), Scientific Process (Index), and Scientific Law (Symbol). Specifically, to overcome the scarcity of training data in scientific image generation, we elaborately create SciIR-82k, a large-scale dataset containing over 80,000 high-quality scientific image-text pairs from cutting-edge publications. The dataset is hierarchically organized according to the semiotic dimensions and incorporates a Scientific Reasoning Chain-of-Thought (Sci-RCoT) to explicitly model underlying visual logic. For evaluation, we propose SciIR-Bench, which aligns with these three semiotic levels and employs an Atomic Checklist to convert the outcome-oriented scientific accuracy into process-oriented, verifiable, fine-grained questions. Our extensive experiments reveal significant deficiencies in current models' scientific reasoning capabilities. Furthermore, by fine-tuning on the SciIR-82k dataset, we developed the Qwen-Image-SciIR model, which achieves a substantial improvement on the SciIR-Bench, increasing the final score from 35\% to 43\%, laying a solid foundation for future advances in scientific image generation.

As frontier language models advance, policymakers and model developers need methods for assessing whether model access materially increases a non-expert actor's ability to plan high-consequence Chemical, Biological, Radiological, or Nuclear (CBRN) misuse relative to public tools alone. Existing CBRN evaluations differ in non-expert definitions, threat scope, baselines, scoring rubrics, and decision rules, making results difficult to compare across studies. We introduce a Threshold Exceedance Criteria (TEC) framework that decomposes an uplift study into independently executable components: determining non-expert participant eligibility, defining the CBRN threat scope for the study, and statistically estimating material uplift. We then operationalize the TEC framework in a large-scale empirical study using a design that determines two forms of uplift: generative (where a model assists plan creation from scratch) and revisionist (where a model assists refinement of an existing plan). The study produced attack plans across the CBRN domains, which we evaluated through subject-matter-expert review to estimate generative and revisionist uplift. Applying the framework, our empirical study revealed domain heterogeneity: under this controlled pre-release evaluation, model-assisted plans sometimes received expert-equivalent instructional ratings, but confirmed material uplift was limited to the radiological domain. These findings informed mitigation and deployment-governance decisions rather than characterizing deployed model behavior. We conclude with methodological lessons for future CBRN uplift evaluations, emphasizing prespecified criteria, explicit baselines, separation of generative and revisionist estimates, and careful distinction between preliminary screening signals and confirmed risk determinations.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

With the rapid development of Large Language Models (LLMs), it is crucial to have benchmarks which can evaluate the ability of LLMs on different domains. One common use of LLMs is performing tasks on scientific topics, such as writing algorithms, querying databases or giving mathematical proofs. Inspired by the way university students are evaluated on such tasks, in this paper, we propose SciEx - a benchmark consisting of university computer science exam questions, to evaluate LLMs ability on solving scientific tasks. SciEx is (1) multilingual, containing both English and German exams, and (2) multi-modal, containing questions that involve images, and (3) contains various types of freeform questions with different difficulty levels, due to the nature of university exams. We evaluate the performance of various state-of-the-art LLMs on our new benchmark. Since SciEx questions are freeform, it is not straightforward to evaluate LLM performance. Therefore, we provide human expert grading of the LLM outputs on SciEx. We show that the free-form exams in SciEx remain challenging for the current LLMs, where the best LLM only achieves 59.4\% exam grade on average. We also provide detailed comparisons between LLM performance and student performance on SciEx. To enable future evaluation of new LLMs, we propose using LLM-as-a-judge to grade the LLM answers on SciEx. Our experiments show that, although they do not perform perfectly on solving the exams, LLMs are decent as graders, achieving 0.948 Pearson correlation with expert grading.

Multimodal large language models (LLMs) have demonstrated impressive capabilities in generating high-quality images from textual instructions. However, their performance in generating scientific images--a critical application for accelerating scientific progress--remains underexplored. In this work, we address this gap by introducing ScImage, a benchmark designed to evaluate the multimodal capabilities of LLMs in generating scientific images from textual descriptions. ScImage assesses three key dimensions of understanding: spatial, numeric, and attribute comprehension, as well as their combinations, focusing on the relationships between scientific objects (e.g., squares, circles). We evaluate five models, GPT-4o, Llama, AutomaTikZ, Dall-E, and StableDiffusion, using two modes of output generation: code-based outputs (Python, TikZ) and direct raster image generation. Additionally, we examine four different input languages: English, German, Farsi, and Chinese. Our evaluation, conducted with 11 scientists across three criteria (correctness, relevance, and scientific accuracy), reveals that while GPT-4o produces outputs of decent quality for simpler prompts involving individual dimensions such as spatial, numeric, or attribute understanding in isolation, all models face challenges in this task, especially for more complex prompts.

Three paradigmatic forms of inference recur across scientific reasoning: deduction, induction, and causal abduction. Reliably evaluating LLMs on these in scientific settings is currently out of reach: scientific benchmarks built on human annotations are costly and lack mechanistic ground truth, while synthetic logical-reasoning benchmarks do not resemble real scientific documents. We introduce SciR, a benchmark that combines multi-paradigm reasoning with controllable scientific rendering, anchored on three paradigmatic scientific problems. Tasks are generated from formal objects (deduction tree, inductive rule hypothesis, causal graph) to guarantee verifiable answers, then rendered into multi-document scientific discourse via per-track domain-tuned genres. The construction lets us independently vary two difficulty axes: how hard it is to extract the key information needed for inference, and how hard the principled inference itself is. We test six models. Both axes hurt every model, and their effects compound. The rendering even hurts neurosymbolic pipelines, which hand inference to a verified solver. The two axes yield a per-model extraction-vs-inference profile: for instance, reasoning models like deepseek-r1 mostly surpass non-reasoning instruct models on the inference axis. To our knowledge, SciR is the first multi-paradigm scientific-reasoning benchmark with parametric control on both extraction and inference difficulty.

Frontier scientific reasoning remains a major challenge for large language models (LLMs), where even the strongest commercial systems fall short of expert-level performance. A closer look at model behavior reveals substantial complementarity that single-model evaluation hides: different frontier models excel on different question types, and no single model captures the full picture. We present SciOrch, a framework that trains a lightweight 8B model to orchestrate frontier LLMs for scientific reasoning. The orchestrator decomposes each question, delegates sub-problems to selected commercial models through API calls, and synthesizes a final answer. Training such an orchestrator is fundamentally harder than conventional agentic RL: each action triggers an API call that is expensive in both dollar cost and latency, making standard online rollouts infeasible. We address this with MCTS-based approach, producing diverse orchestration trajectories, extracting per-node single-turn samples, and optimizing the orchestrator with GRPO-style training. On a 240-question test set spanning SGI-Reasoning and Scientists' First Exam, SciOrch reaches 56.66% average accuracy, outperforming the strongest single commercial model by 3.74% and the strongest multi-agent baseline by 3.33%. It also attains the best accuracy on both SGI and SFE with less than half the API cost of typical multi-agent methods.

As researchers increasingly adopt LLMs as writing assistants, generating high-quality research paper introductions remains both challenging and essential. We introduce Scientific Introduction Generation (SciIG), a task that evaluates LLMs' ability to produce coherent introductions from titles, abstracts, and related works. Curating new datasets from NAACL 2025 and ICLR 2025 papers, we assess five state-of-the-art models, including both open-source (DeepSeek-v3, Gemma-3-12B, LLaMA 4-Maverick, MistralAI Small 3.1) and closed-source GPT-4o systems, across multiple dimensions: lexical overlap, semantic similarity, content coverage, faithfulness, consistency, citation correctness, and narrative quality. Our comprehensive framework combines automated metrics with LLM-as-a-judge evaluations. Results demonstrate LLaMA-4 Maverick's superior performance on most metrics, particularly in semantic similarity and faithfulness. Moreover, three-shot prompting consistently outperforms fewer-shot approaches. These findings provide practical insights into developing effective research writing assistants and set realistic expectations for LLM-assisted academic writing. To foster reproducibility and future research, we will publicly release all code and datasets.

We present SciClaimEval, a new scientific dataset for the claim verification task. Unlike existing resources, SciClaimEval features authentic claims, including refuted ones, directly extracted from published papers. To create refuted claims, we introduce a novel approach that modifies the supporting evidence (figures and tables), rather than altering the claims or relying on large language models (LLMs) to fabricate contradictions. The dataset provides cross-modal evidence with diverse representations: figures are available as images, while tables are provided in multiple formats, including images, LaTeX source, HTML, and JSON. SciClaimEval contains 1,664 annotated samples from 180 papers across three domains, machine learning, natural language processing, and medicine, validated through expert annotation. We benchmark 11 multimodal foundation models, both open-source and proprietary, across the dataset. Results show that figure-based verification remains particularly challenging for all models, as a substantial performance gap remains between the best system and human baseline.

This paper presents the ISRGC-Q Challenge, built upon the Image Super-Resolution Generated Content Quality Assessment (ISRGen-QA) dataset, and organized as part of the Visual Quality Assessment (VQualA) Competition at the ICCV 2025 Workshops. Unlike existing Super-Resolution Image Quality Assessment (SR-IQA) datasets, ISRGen-QA places a greater emphasis on SR images generated by the latest generative approaches, including Generative Adversarial Networks (GANs) and diffusion models. The primary goal of this challenge is to analyze the unique artifacts introduced by modern super-resolution techniques and to evaluate their perceptual quality effectively. A total of 108 participants registered for the challenge, with 4 teams submitting valid solutions and fact sheets for the final testing phase. These submissions demonstrated state-of-the-art (SOTA) performance on the ISRGen-QA dataset. The project is publicly available at: https://github.com/Lighting-YXLI/ISRGen-QA.

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.

Understanding the creation, evolution, and dissemination of scientific knowledge is crucial for bridging diverse subject areas and addressing complex global challenges such as pandemics, climate change, and ethical AI. Scientometrics, the quantitative and qualitative study of scientific literature, provides valuable insights into these processes. We introduce Scito2M, a longitudinal scientometric dataset with over two million academic publications, providing comprehensive contents information and citation graphs to support cross-disciplinary analyses. Using Scito2M, we conduct a temporal study spanning over 30 years to explore key questions in scientometrics: the evolution of academic terminology, citation patterns, and interdisciplinary knowledge exchange. Our findings reveal critical insights, such as disparities in epistemic cultures, knowledge production modes, and citation practices. For example, rapidly developing, application-driven fields like LLMs exhibit significantly shorter citation age (2.48 years) compared to traditional theoretical disciplines like oral history (9.71 years).

Synthetic data generated by generative models can enhance the performance and capabilities of data-hungry deep learning models in medical imaging. However, there is (1) limited availability of (synthetic) datasets and (2) generative models are complex to train, which hinders their adoption in research and clinical applications. To reduce this entry barrier, we propose medigan, a one-stop shop for pretrained generative models implemented as an open-source framework-agnostic Python library. medigan allows researchers and developers to create, increase, and domain-adapt their training data in just a few lines of code. Guided by design decisions based on gathered end-user requirements, we implement medigan based on modular components for generative model (i) execution, (ii) visualisation, (iii) search & ranking, and (iv) contribution. The library's scalability and design is demonstrated by its growing number of integrated and readily-usable pretrained generative models consisting of 21 models utilising 9 different Generative Adversarial Network architectures trained on 11 datasets from 4 domains, namely, mammography, endoscopy, x-ray, and MRI. Furthermore, 3 applications of medigan are analysed in this work, which include (a) enabling community-wide sharing of restricted data, (b) investigating generative model evaluation metrics, and (c) improving clinical downstream tasks. In (b), extending on common medical image synthesis assessment and reporting standards, we show Fréchet Inception Distance variability based on image normalisation and radiology-specific feature extraction.

This paper examines how different types of large language model (LLM) agents perform on scientific visualization (SciVis) tasks, where users generate visualization workflows from natural-language instructions. We compare three primary interaction paradigms, including domain-specific agents with structured tool use, computer-use agents, and general-purpose coding agents, by evaluating eight representative agents across 15 benchmark tasks and measuring visualization quality, efficiency, robustness, and computational cost. We further analyze interaction modalities, including code scripts and model context protocol (MCP) or API calls for structured tool use, as well as command-line interfaces (CLI) and graphical user interfaces (GUI) for more general interaction, while additionally studying the effect of persistent memory in selected agents. The results reveal clear tradeoffs across paradigms and modalities. General-purpose coding agents achieve the highest task success rates but are computationally expensive, while domain-specific agents are more efficient and stable but less flexible. Computer-use agents perform well on individual steps but struggle with longer multi-step workflows, indicating that long-horizon planning is their primary limitation. Across both CLI- and GUI-based settings, persistent memory improves performance over repeated trials, although its benefits depend on the underlying interaction mode and the quality of feedback. These findings suggest that no single approach is sufficient, and future SciVis systems should combine structured tool use, interactive capabilities, and adaptive memory mechanisms to balance performance, robustness, and flexibility.

We introduce SciEvalKit, a unified benchmarking toolkit designed to evaluate AI models for science across a broad range of scientific disciplines and task capabilities. Unlike general-purpose evaluation platforms, SciEvalKit focuses on the core competencies of scientific intelligence, including Scientific Multimodal Perception, Scientific Multimodal Reasoning, Scientific Multimodal Understanding, Scientific Symbolic Reasoning, Scientific Code Generation, Science Hypothesis Generation and Scientific Knowledge Understanding. It supports six major scientific domains, spanning from physics and chemistry to astronomy and materials science. SciEvalKit builds a foundation of expert-grade scientific benchmarks, curated from real-world, domain-specific datasets, ensuring that tasks reflect authentic scientific challenges. The toolkit features a flexible, extensible evaluation pipeline that enables batch evaluation across models and datasets, supports custom model and dataset integration, and provides transparent, reproducible, and comparable results. By bridging capability-based evaluation and disciplinary diversity, SciEvalKit offers a standardized yet customizable infrastructure to benchmark the next generation of scientific foundation models and intelligent agents. The toolkit is open-sourced and actively maintained to foster community-driven development and progress in AI4Science.

Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state. We present SciForge, a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services. SciForge is built around five pillars: (i) goal-scoped scientific decision governance for goal-oriented research, with review gates and shared review surfaces; (ii) translate-then-reason for multimodal input, routing scientific objects through domain translators before the agent reasons; (iii) evidence governance for auditable traceability, linking claims to provenance chains and audit findings; (iv) collaborative team science for collaborative research, enabling multi-role decision governance, with shared team workspaces planned for future releases; and (v) real-world application scenarios for practical impact, demonstrated through eight end-to-end user cases, with flagship demonstrations including multi-day agentic research sprints for gene discovery, AI-guided de novo protein design, molecular optimization, and genome-to-BGC discovery. The system combines a thin interaction layer, contextual research capability patterns, an Agent Runtime and Workflow Engine, an Evidence-DAG audit sidecar and a Scientific Model Router. SciForge currently runs as a desktop application, with mobile supervision support; future releases will deepen team collaboration. The system is open-source and available at https://github.com/AGI4Sci/SciForge

The vastness of the design space created by the combination of a large number of computational mechanisms, including machine learning, is an obstacle to creating an artificial general intelligence (AGI). Brain-inspired AGI development, in other words, cutting down the design space to look more like a biological brain, which is an existing model of a general intelligence, is a promising plan for solving this problem. However, it is difficult for an individual to design a software program that corresponds to the entire brain because the neuroscientific data required to understand the architecture of the brain are extensive and complicated. The whole-brain architecture approach divides the brain-inspired AGI development process into the task of designing the brain reference architecture (BRA) -- the flow of information and the diagram of corresponding components -- and the task of developing each component using the BRA. This is called BRA-driven development. Another difficulty lies in the extraction of the operating principles necessary for reproducing the cognitive-behavioral function of the brain from neuroscience data. Therefore, this study proposes the Structure-constrained Interface Decomposition (SCID) method, which is a hypothesis-building method for creating a hypothetical component diagram consistent with neuroscientific findings. The application of this approach has begun for building various regions of the brain. Moving forward, we will examine methods of evaluating the biological plausibility of brain-inspired software. This evaluation will also be used to prioritize different computational mechanisms, which should be merged, associated with the same regions of the brain.

The number of Language Models (LMs) dedicated to processing scientific text is on the rise. Keeping pace with the rapid growth of scientific LMs (SciLMs) has become a daunting task for researchers. To date, no comprehensive surveys on SciLMs have been undertaken, leaving this issue unaddressed. Given the constant stream of new SciLMs, appraising the state-of-the-art and how they compare to each other remain largely unknown. This work fills that gap and provides a comprehensive review of SciLMs, including an extensive analysis of their effectiveness across different domains, tasks and datasets, and a discussion on the challenges that lie ahead.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

In agentic scientific machine learning (SciML), large language model (LLM) agents can discover surrogate models and select one by an automated score, typically an error metric. A low error, however, does not establish that the predicted fields satisfy the physics that matter for mechanics, such as boundary conditions, superposition, stiffness scaling, or causality. We introduce Physics-Audited Agentic SciML (PA-SciML), a verification-first workflow for agentic SciML discovery. The workflow fixes a scoring evaluator before search, derives reviewable machine-checkable physics requirements, checks each trained candidate on its outputs, and separately searches prescribed input ranges or measured load-history spans for high-violation cases without reference solution fields. A surrogate is reported as verified only under the stated checks. When enabled, the workflow also adds advisory numerical probes before training and tests one modeling change at a time to record which isolated edits are associated with score gains before reuse. In the reported computational-solid-mechanics numerical examples, the static elasticity run selects a surrogate with lower validation error than the error-only baseline while both selected models pass the common linear-elastic checks. In the transient elastodynamics run, an error-only baseline with similar mean error fails a stricter causality check by responding to future parts of the loading history, while the selected surrogate passes the stated checks. The main distinction is per-candidate physics evidence on predicted fields, not a richer aggregate score.

The field of Deep Learning (DL) has undergone explosive growth during the last decade, with a substantial impact on Natural Language Processing (NLP) as well. Yet, compared to more established disciplines, a lack of common experimental standards remains an open challenge to the field at large. Starting from fundamental scientific principles, we distill ongoing discussions on experimental standards in NLP into a single, widely-applicable methodology. Following these best practices is crucial to strengthen experimental evidence, improve reproducibility and support scientific progress. These standards are further collected in a public repository to help them transparently adapt to future needs.

Modern multi-agent knowledge systems increasingly accumulate knowledge through chains of autonomous transformations rather than direct retrieval. Existing provenance work records what happened - execution traces, tool calls, evidence links - and source-reliability estimation is long established (truth discovery, reputation systems). What is missing is an operational framework that attaches graded, per-domain transmitter reliability to claim-level transmission chains, with completeness semantics, transformation-typed aggregation, decoupled content criticism, and serve/review/quarantine routing. Classical Islamic hadith science confronted a structurally similar problem: deciding whether knowledge transmitted through chains of human narrators should be accepted. Over centuries it developed a rigorous methodology - isnad (a complete transmission chain attached to every claim), rijal (systematic grading of each narrator's integrity and precision), weakest-link chain evaluation, corroboration through independent chains, and matn criticism (content evaluated independently of chain quality). This paper transfers that methodology to AI system design. We contribute a formal mapping from hadith-science concepts to multi-agent pipelines, a relational schema implementing claim chains and a graded narrator registry, a decision matrix combining chain grade with content criticism, and an evaluation on 20,000 claims from real physics textbooks. The evaluation validates weakest-link quarantine and independent-chain corroboration; reports a partial failure of the grade-recovery loop, which missed the highest-fault narrator; and reports two analyses as inconclusive, including a matched-coverage comparison the framework could not reach with the reference content critic. The paper is explicit throughout about which claims the evidence does and does not yet support.

Scientific literature is typically dense, requiring significant background knowledge and deep comprehension for effective engagement. We introduce SciDQA, a new dataset for reading comprehension that challenges LLMs for a deep understanding of scientific articles, consisting of 2,937 QA pairs. Unlike other scientific QA datasets, SciDQA sources questions from peer reviews by domain experts and answers by paper authors, ensuring a thorough examination of the literature. We enhance the dataset's quality through a process that carefully filters out lower quality questions, decontextualizes the content, tracks the source document across different versions, and incorporates a bibliography for multi-document question-answering. Questions in SciDQA necessitate reasoning across figures, tables, equations, appendices, and supplementary materials, and require multi-document reasoning. We evaluate several open-source and proprietary LLMs across various configurations to explore their capabilities in generating relevant and factual responses. Our comprehensive evaluation, based on metrics for surface-level similarity and LLM judgements, highlights notable performance discrepancies. SciDQA represents a rigorously curated, naturally derived scientific QA dataset, designed to facilitate research on complex scientific text understanding.

Cooperation enables teams to solve complex problems that one individual alone cannot address. In science, collaborative teams have become the predominant way through which progress is achieved. These scientific collaborations arise though various mechanisms, among which interactions at conferences. The Scialog conferences, which comprise a series of small, interdisciplinary scientific workshops held over several years, are an ideal laboratory to study the network mechanisms leading to team formation. Building on existing work studying team formation from a pairwise perspective, we present a higher-order network perspective generalizing this framework. We provide a formalization for the notion of group interaction over time by defining a taxonomy of synchronous and asynchronous group interactions. We apply this framework to the Scialog case study using a stepwise selection logistic model and find evidence that all interaction types described in our taxonomy are highly significant for team formation. This higher-order network perspective provides a new framework for the study of collective behavior and group formation.

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 paper presents a survey of methods for pruning deep neural networks. It begins by categorising over 150 studies based on the underlying approach used and then focuses on three categories: methods that use magnitude based pruning, methods that utilise clustering to identify redundancy, and methods that use sensitivity analysis to assess the effect of pruning. Some of the key influencing studies within these categories are presented to highlight the underlying approaches and results achieved. Most studies present results which are distributed in the literature as new architectures, algorithms and data sets have developed with time, making comparison across different studied difficult. The paper therefore provides a resource for the community that can be used to quickly compare the results from many different methods on a variety of data sets, and a range of architectures, including AlexNet, ResNet, DenseNet and VGG. The resource is illustrated by comparing the results published for pruning AlexNet and ResNet50 on ImageNet and ResNet56 and VGG16 on the CIFAR10 data to reveal which pruning methods work well in terms of retaining accuracy whilst achieving good compression rates. The paper concludes by identifying some promising directions for future research.

While AI innovation accelerates rapidly, the intellectual process behind breakthroughs -- how researchers identify gaps, synthesize prior work, and generate insights -- remains poorly understood. The lack of structured data on scientific reasoning hinders systematic analysis and development of AI research agents. We introduce Sci-Reasoning, the first dataset capturing the intellectual synthesis behind high-quality AI research. Using community-validated quality signals and an LLM-accelerated, human-verified pipeline, we trace Oral and Spotlight papers across NeurIPS, ICML, and ICLR (2023-2025) to its key predecessors, articulating specific reasoning links in a structured format. Our analysis identifies 15 distinct thinking patterns, with three dominant strategies accounting for 52.7%: Gap-Driven Reframing (24.2%), Cross-Domain Synthesis (18.0%), and Representation Shift (10.5%). The most powerful innovation recipes combine multiple patterns: Gap-Driven Reframing + Representation Shift, Cross-Domain Synthesis + Representation Shift, and Gap-Driven Reframing + Cross-Domain Synthesis. This dataset enables quantitative studies of scientific progress and provides structured reasoning trajectories for training the next generation AI research agents.

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.

SciLaD is a novel, large-scale dataset of scientific language constructed entirely using open-source frameworks and publicly available data sources. It comprises a curated English split containing over 10 million scientific publications and a multilingual, unfiltered TEI XML split including more than 35 million publications. We also publish the extensible pipeline for generating SciLaD. The dataset construction and processing workflow demonstrates how open-source tools can enable large-scale, scientific data curation while maintaining high data quality. Finally, we pre-train a RoBERTa model on our dataset and evaluate it across a comprehensive set of benchmarks, achieving performance comparable to other scientific language models of similar size, validating the quality and utility of SciLaD. We publish the dataset and evaluation pipeline to promote reproducibility, transparency, and further research in natural scientific language processing and understanding including scholarly document processing.

Automated scientific discovery with large language models is transforming the research lifecycle from ideation to experimentation, yet existing agents struggle to autonomously process raw data collected from scientific experiments. We introduce SciDER, a data-centric end-to-end system that automates the research lifecycle. Unlike traditional frameworks, our specialized agents collaboratively parse and analyze raw scientific data, generate hypotheses and experimental designs grounded in specific data characteristics, and write and execute corresponding code. Evaluation on three benchmarks shows SciDER excels in specialized data-driven scientific discovery and outperforms general-purpose agents and state-of-the-art models through its self-evolving memory and critic-led feedback loop. Distributed as a modular Python package, we also provide easy-to-use PyPI packages with a lightweight web interface to accelerate autonomous, data-driven research and aim to be accessible to all researchers and developers.

Recent advancements in multimodal large language models (MLLMs) and video agent systems have significantly improved general video understanding. However, when applied to scientific video understanding and educating, a domain that demands external professional knowledge integration and rigorous step-wise reasoning, existing approaches often struggle. To bridge this gap, we propose SciEducator, the first iterative self-evolving multi-agent system for scientific video comprehension and education. Rooted in the classical Deming Cycle from management science, our design reformulates its Plan-Do-Study-Act philosophy into a self-evolving reasoning and feedback mechanism, which facilitates the interpretation of intricate scientific activities in videos. Moreover, SciEducator can produce multimodal educational content tailored to specific scientific processes, including textual instructions, visual guides, audio narrations, and interactive references. To support evaluation, we construct SciVBench, a benchmark consisting of 500 expert-verified and literature-grounded science QA pairs across five categories, covering physical, chemical, and everyday phenomena. Extensive experiments demonstrate that SciEducator substantially outperforms leading closed-source MLLMs (e.g., Gemini, GPT-4o) and state-of-the-art video agents on the benchmark, establishing a new paradigm for the community.

Scientific figure multiple-choice question answering (MCQA) requires models to reason over diverse visual evidence, ranging from charts and multipanel figures to microscopy and biomedical images. However, this setting suffers from a distinctive bias: answer choices themselves can act as priors, steering multimodal models toward scientifically plausible options even when the figure supports a different answer. We investigate this failure mode through a simple question: what if decoding explicitly discounts what the model would prefer from text alone, so as to favor figure-grounded evidence? To this end, we propose SCICON, a training-free decoding method that scores each candidate by subtracting a text-only option score from its image-conditioned counterpart. Unlike prior contrastive decoding approaches that mitigate hallucinations by contrasting original inputs with distorted images or perturbed instructions, SCICON directly targets the choice-induced prior encoded in candidate text. Across three scientific figure QA benchmarks and three model backbones, SCICON consistently improves accuracy over standard decoding baselines. These results show that decoding against choice-induced priors is an effective and simple way to improve figure-grounded reasoning in scientific MCQA.

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

Learning scientific document representations can be substantially improved through contrastive learning objectives, where the challenge lies in creating positive and negative training samples that encode the desired similarity semantics. Prior work relies on discrete citation relations to generate contrast samples. However, discrete citations enforce a hard cut-off to similarity. This is counter-intuitive to similarity-based learning, and ignores that scientific papers can be very similar despite lacking a direct citation - a core problem of finding related research. Instead, we use controlled nearest neighbor sampling over citation graph embeddings for contrastive learning. This control allows us to learn continuous similarity, to sample hard-to-learn negatives and positives, and also to avoid collisions between negative and positive samples by controlling the sampling margin between them. The resulting method SciNCL outperforms the state-of-the-art on the SciDocs benchmark. Furthermore, we demonstrate that it can train (or tune) models sample-efficiently, and that it can be combined with recent training-efficient methods. Perhaps surprisingly, even training a general-domain language model this way outperforms baselines pretrained in-domain.

Artificial intelligence has advanced in Medical Visual Question Answering (Med-VQA), but prevalent research tends to focus on the accuracy of the answers, often overlooking the reasoning paths and interpretability, which are crucial in clinical settings. Besides, current Med-VQA algorithms, typically reliant on singular models, lack the robustness needed for real-world medical diagnostics which usually require collaborative expert evaluation. To address these shortcomings, this paper presents MedCoT, a novel hierarchical expert verification reasoning chain method designed to enhance interpretability and accuracy in biomedical imaging inquiries. MedCoT is predicated on two principles: The necessity for explicit reasoning paths in Med-VQA and the requirement for multi-expert review to formulate accurate conclusions. The methodology involves an Initial Specialist proposing diagnostic rationales, followed by a Follow-up Specialist who validates these rationales, and finally, a consensus is reached through a vote among a sparse Mixture of Experts within the locally deployed Diagnostic Specialist, which then provides the definitive diagnosis. Experimental evaluations on four standard Med-VQA datasets demonstrate that MedCoT surpasses existing state-of-the-art approaches, providing significant improvements in performance and interpretability.

It is crucial to understand a specific domain by events. Extensive event extraction research has been conducted in many domains such as news, finance, and biology. However, event extraction in scientific domain is still insufficiently supported by comprehensive datasets and tailored methods. Compared with other domains, scientific domain has two characteristics: (1) denser nuggets and events, and (2) more complex information forms. To solve the above problem, considering these two characteristics, we first construct SciEvents, a large-scale multi-event document-level dataset with a schema tailored for scientific domain. It consists of 2,508 documents and 24,381 events under multi-stage manual annotation and quality control. Then, we propose EXCEEDS, an end-to-end scientific event extraction framework by encoding dense nuggets into a grid matrix and simplifying complex event extraction as a nugget-based grid modeling task. Experiments on SciEvents demonstrate state-of-the-art performances of EXCEEDS. Both the SciEvents dataset and the EXCEEDS framework are released publicly to facilitate future research.

High-quality expert chain-of-thought (CoT) data is one of the core bottlenecks in large language model (LLM) post-training. Existing data production methods each have structural limitations: crowdsourced annotation lacks deep reasoning paths; expert solo writing is constrained by the "expert blind spot" -- experts structurally skip reasoning steps they consider obvious; RLHF only produces preference signals rather than reasoning chains. This paper proposes the BC Protocol -- a structured dual-expert elicitation method for LLM post-training data production. The method carefully pairs a domain expert (crystallized intelligence) with a knowledge engineer (fluid intelligence), systematically externalizing the expert's implicit judgments as natural language reasoning chains. We introduce the Participant Aptitude Model, which defines six participant characteristic dimensions that affect elicitation quality. "Calibrated Ignorance" is an original concept proposed in this paper. We further propose "Selection-over-Prescription" as a methodological principle: for implicit knowledge elicitation tasks, investing quality-control resources in personnel selection yields a higher return than investing the same resources in process design. In a controlled experiment in the narrative fiction domain, we directly compared CoT produced by BC Protocol dual dialogue (Group A, (n=20)) against CoT written independently by the same domain expert (Group B, (n=20)). Three cross-vendor judge models -- GPT-4o, Claude Opus 4.5, and Gemini 2.5 Pro -- conducted blind evaluation across five dimensions (600 ratings total). Results show that the BC Protocol achieves an overwhelming advantage in "naturalness of reasoning process" (Group A mean 4.80 vs. Group B mean 1.30, (p=2.4\times10^{-8}), Cliff's (δ=1.0)).

In recent years, large-scale data collection efforts have prioritized the amount of data collected in order to improve the modeling capabilities of large language models. This prioritization, however, has resulted in concerns with respect to the rights of data subjects represented in data collections, particularly when considering the difficulty in interrogating these collections due to insufficient documentation and tools for analysis. Mindful of these pitfalls, we present our methodology for a documentation-first, human-centered data collection project as part of the BigScience initiative. We identified a geographically diverse set of target language groups (Arabic, Basque, Chinese, Catalan, English, French, Indic languages, Indonesian, Niger-Congo languages, Portuguese, Spanish, and Vietnamese, as well as programming languages) for which to collect metadata on potential data sources. To structure this effort, we developed our online catalogue as a supporting tool for gathering metadata through organized public hackathons. We present our development process; analyses of the resulting resource metadata, including distributions over languages, regions, and resource types; and our lessons learned in this endeavor.

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

Scientific reasoning inherently demands integrating sophisticated toolkits to navigate domain-specific knowledge. Yet, current benchmarks largely overlook agents' ability to orchestrate tools for such rigorous workflows. To bridge this gap, we introduce SciAgentGym, a scalable interactive environment featuring 1,780 domain-specific tools across four natural science disciplines, supported by a robust execution infrastructure. Complementing this, we present SciAgentBench, a tiered evaluation suite designed to stress-test agentic capabilities from elementary actions to long-horizon workflows. Our evaluation identifies a critical bottleneck: state-of-the-art models struggle with complex scientific tool-use. Even for a leading model like GPT-5, success rates drop sharply from 60.6% to 30.9% as interaction horizons extend, primarily due to failures in multi-step workflow execution. To address this, we propose SciForge, a data synthesis method that models the tool action space as a dependency graph to generate logic-aware training trajectories. By fine-tuning on these trajectories, our SciAgent-8B outperforms the significantly larger Qwen3-VL-235B-Instruct while exhibiting positive cross-domain transfer of scientific tool-use capabilities. These results underscore the promising potential of next-generation autonomous scientific agents.

Generating diverse responses from large language models (LLMs) is crucial for applications such as planning/search and synthetic data generation, where diversity provides distinct answers across generations. Prior approaches rely on increasing temperature to increase diversity. However, contrary to popular belief, we show not only does this approach produce lower quality individual generations as temperature increases, but it depends on model's next-token probabilities being similar to the true distribution of answers. We propose , an alternative approach that uses the language model itself to partition the space into strata. At inference, a random stratum is selected and a sample drawn from within the strata. To measure diversity, we introduce CoverageQA, a dataset of underspecified questions with multiple equally plausible answers, and assess diversity by measuring KL Divergence between the output distribution and uniform distribution over valid ground truth answers. As computing probability per response/solution for proprietary models is infeasible, we measure recall on ground truth solutions. Our evaluation show using SimpleStrat achieves higher recall by 0.05 compared to GPT-4o and 0.36 average reduction in KL Divergence compared to Llama 3.

Hospitals in India still rely on handwritten medical records despite the availability of Electronic Medical Records (EMR), complicating statistical analysis and record retrieval. Handwritten records pose a unique challenge, requiring specialized data for training models to recognize medications and their recommendation patterns. While traditional handwriting recognition approaches employ 2-D LSTMs, recent studies have explored using Multimodal Large Language Models (MLLMs) for OCR tasks. Building on this approach, we focus on extracting medication names and dosages from simulated medical records. Our methodology MIRAGE (Multimodal Identification and Recognition of Annotations in indian GEneral prescriptions) involves fine-tuning the QWEN VL, LLaVA 1.6 and Idefics2 models on 743,118 high resolution simulated medical record images-fully annotated from 1,133 doctors across India. Our approach achieves 82% accuracy in extracting medication names and dosages.

We introduce a cross-domain behavioural assay of monitoring-control coupling in LLMs, grounded in the Nelson and Narens (1990) metacognitive framework and applying human psychometric methodology to LLM evaluation. The battery comprises 524 items across six cognitive domains (learning, metacognitive calibration, social cognition, attention, executive function, prospective regulation), each grounded in an established experimental paradigm. Tasks T1-T5 were pre-registered on OSF prior to data collection; T6 was added as an exploratory extension. After every forced-choice response, dual probes adapted from Koriat and Goldsmith (1996) ask the model to KEEP or WITHDRAW its answer and to BET or decline. The critical metric is the withdraw delta: the difference in withdrawal rate between incorrect and correct items. Applied to 20 frontier LLMs (10,480 evaluations), the battery discriminates three profiles consistent with the Nelson-Narens architecture: blanket confidence, blanket withdrawal, and selective sensitivity. Accuracy rank and metacognitive sensitivity rank are largely inverted. Retrospective monitoring and prospective regulation appear dissociable (r = .17, 95% CI wide given n=20; exemplar-based evidence is the primary support). Scaling on metacognitive calibration is architecture-dependent: monotonically decreasing (Qwen), monotonically increasing (GPT-5.4), or flat (Gemma). Behavioural findings converge structurally with an independent Type-2 SDT approach, providing preliminary cross-method construct validity. All items, data, and code: https://github.com/synthiumjp/metacognitive-monitoring-battery.

The burgeoning utilization of Large Language Models (LLMs) in scientific research necessitates advanced benchmarks capable of evaluating their understanding and application of scientific knowledge comprehensively. To address this need, we introduce the SciKnowEval benchmark, a novel framework that systematically evaluates LLMs across five progressive levels of scientific knowledge: studying extensively, inquiring earnestly, thinking profoundly, discerning clearly, and practicing assiduously. These levels aim to assess the breadth and depth of scientific knowledge in LLMs, including knowledge coverage, inquiry and exploration capabilities, reflection and reasoning abilities, ethic and safety considerations, as well as practice proficiency. Specifically, we take biology and chemistry as the two instances of SciKnowEval and construct a dataset encompassing 50K multi-level scientific problems and solutions. By leveraging this dataset, we benchmark 20 leading open-source and proprietary LLMs using zero-shot and few-shot prompting strategies. The results reveal that despite achieving state-of-the-art performance, the proprietary LLMs still have considerable room for improvement, particularly in addressing scientific computations and applications. We anticipate that SciKnowEval will establish a comprehensive standard for benchmarking LLMs in science research and discovery, and promote the development of LLMs that integrate scientific knowledge with strong safety awareness. The dataset and code are publicly available at https://github.com/hicai-zju/sciknoweval .

Like any field of empirical science, AI may be approached axiomatically. We formulate requirements for a general-purpose, human-level AI system in terms of postulates. We review the methodology of deep learning, examining the explicit and tacit assumptions in deep learning research. Deep Learning methodology seeks to overcome limitations in traditional machine learning research as it combines facets of model richness, generality, and practical applicability. The methodology so far has produced outstanding results due to a productive synergy of function approximation, under plausible assumptions of irreducibility and the efficiency of back-propagation family of algorithms. We examine these winning traits of deep learning, and also observe the various known failure modes of deep learning. We conclude by giving recommendations on how to extend deep learning methodology to cover the postulates of general-purpose AI including modularity, and cognitive architecture. We also relate deep learning to advances in theoretical neuroscience research.

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

Scientific Machine Learning (SciML) integrates data-driven inference with physical modeling to solve complex problems in science and engineering. However, the design of SciML architectures, loss formulations, and training strategies remains an expert-driven research process, requiring extensive experimentation and problem-specific insights. Here we introduce AgenticSciML, a collaborative multi-agent system in which over 10 specialized AI agents collaborate to propose, critique, and refine SciML solutions through structured reasoning and iterative evolution. The framework integrates structured debate, retrieval-augmented method memory, and ensemble-guided evolutionary search, enabling the agents to generate and assess new hypotheses about architectures and optimization procedures. Across physics-informed learning and operator learning tasks, the framework discovers solution methods that outperform single-agent and human-designed baselines by up to four orders of magnitude in error reduction. The agents produce novel strategies -- including adaptive mixture-of-expert architectures, decomposition-based PINNs, and physics-informed operator learning models -- that do not appear explicitly in the curated knowledge base. These results show that collaborative reasoning among AI agents can yield emergent methodological innovation, suggesting a path toward scalable, transparent, and autonomous discovery in scientific computing.

Scientific information extraction (SciIE) is critical for converting unstructured knowledge from scholarly articles into structured data (entities and relations). Several datasets have been proposed for training and validating SciIE models. However, due to the high complexity and cost of annotating scientific texts, those datasets restrict their annotations to specific parts of paper, such as abstracts, resulting in the loss of diverse entity mentions and relations in context. In this paper, we release a new entity and relation extraction dataset for entities related to datasets, methods, and tasks in scientific articles. Our dataset contains 106 manually annotated full-text scientific publications with over 24k entities and 12k relations. To capture the intricate use and interactions among entities in full texts, our dataset contains a fine-grained tag set for relations. Additionally, we provide an out-of-distribution test set to offer a more realistic evaluation. We conduct comprehensive experiments, including state-of-the-art supervised models and our proposed LLM-based baselines, and highlight the challenges presented by our dataset, encouraging the development of innovative models to further the field of SciIE.

In this paper, we introduce SciGen, a new challenge dataset for the task of reasoning-aware data-to-text generation consisting of tables from scientific articles and their corresponding descriptions. Describing scientific tables goes beyond the surface realization of the table content and requires reasoning over table values. The unique properties of SciGen are that (1) tables mostly contain numerical values, and (2) the corresponding descriptions require arithmetic reasoning. SciGen is therefore the first dataset that assesses the arithmetic reasoning capabilities of generation models on complex input structures, i.e., tables from scientific articles. We study the effectiveness of state-of-the-art data-to-text generation models on SciGen and evaluate the results using common metrics as well as human evaluation. Our results and analyses show that (a) while humans like to reason for describing scientific tables, the ability of state-of-the-art models is severely limited on this task, (b) while adding more training data improves the results, it is not the solution for reasoning-aware text generation, and (c) one of the main bottlenecks for this task is the lack of proper automatic evaluation metrics. The data, code, and annotations for human evaluation will be available at https://github.com/UKPLab/SciGen. SciGen opens new avenues for future research in reasoning-aware text generation and evaluation.

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

We present Gazal-R1, a 32-billion-parameter language model that achieves state-of-the-art performance in medical reasoning while providing transparent, step-by-step explanations for clinical decision-making. Built upon Qwen3 32B, our model demonstrates that strategic training can enable mid-sized models to outperform significantly larger counterparts in specialized domains. We developed a novel two-stage training pipeline: first, supervised fine-tuning on a carefully curated dataset of 107,033 synthetic medical reasoning examples that teaches structured clinical thinking, enhanced by advanced parameter-efficient techniques including Weight-Decomposed Low-Rank Adaptation (DoRA) and Rank-Stabilized LoRA (rsLoRA); second, reinforcement learning using Group Relative Policy Optimization (GRPO) with a sophisticated multi-component reward system that refines accuracy, format adherence, and reasoning quality. Gazal-R1 achieves exceptional performance across medical benchmarks, scoring 87.1% on MedQA, 81.6% on MMLU Pro (Medical), and 79.6% on PubMedQA, surpassing models up to 12x larger. Beyond its strong empirical results, this work provides detailed insights into the challenges of training reasoning-capable models in specialized domains, including issues with reward hacking, training instability, and the fundamental tension between factual recall and detailed reasoning. Our methodology offers a reproducible framework for developing high-capability, domain-specific language models that balance performance, efficiency, and explainability.

Artificial neural networks (ANN) are inspired by human learning. However, unlike human education, classical ANN does not use a curriculum. Curriculum Learning (CL) refers to the process of ANN training in which examples are used in a meaningful order. When using CL, training begins with a subset of the dataset and new samples are added throughout the training, or training begins with the entire dataset and the number of samples used is reduced. With these changes in training dataset size, better results can be obtained with curriculum, anti-curriculum, or random-curriculum methods than the vanilla method. However, a generally efficient CL method for various architectures and data sets is not found. In this paper, we propose cyclical curriculum learning (CCL), in which the data size used during training changes cyclically rather than simply increasing or decreasing. Instead of using only the vanilla method or only the curriculum method, using both methods cyclically like in CCL provides more successful results. We tested the method on 18 different data sets and 15 architectures in image and text classification tasks and obtained more successful results than no-CL and existing CL methods. We also have shown theoretically that it is less erroneous to apply CL and vanilla cyclically instead of using only CL or only vanilla method. The code of Cyclical Curriculum is available at https://github.com/CyclicalCurriculum/Cyclical-Curriculum.

We present a novel approach to integrating scientific knowledge into generative models, enhancing their realism and consistency in image synthesis. First, we introduce Science-T2I, an expert-annotated adversarial dataset comprising adversarial 20k image pairs with 9k prompts, covering wide distinct scientific knowledge categories. Leveraging Science-T2I, we present SciScore, an end-to-end reward model that refines the assessment of generated images based on scientific knowledge, which is achieved by augmenting both the scientific comprehension and visual capabilities of pre-trained CLIP model. Additionally, based on SciScore, we propose a two-stage training framework, comprising a supervised fine-tuning phase and a masked online fine-tuning phase, to incorporate scientific knowledge into existing generative models. Through comprehensive experiments, we demonstrate the effectiveness of our framework in establishing new standards for evaluating the scientific realism of generated content. Specifically, SciScore attains performance comparable to human-level, demonstrating a 5% improvement similar to evaluations conducted by experienced human evaluators. Furthermore, by applying our proposed fine-tuning method to FLUX, we achieve a performance enhancement exceeding 50% on SciScore.

AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood. Existing benchmarks for AI agents rarely capture the complexity, heterogeneity, and extended reasoning required by scientific work, whereas benchmarks for scientific tasks often reduce research to static, direct problems and provide limited support for interactive evaluation. Here, we introduce SciAgentArena, a systematic benchmark for evaluating AI agents in real-world scientific research scenarios drawn from emerging needs across multiple domains. SciAgentArena comprises approximately 200 tasks with stepwise verification and an interactive, agent-agnostic environment for assessing diverse AI agents. Using this benchmark, we find that current agents can contribute effectively to well-specified data-analysis workflows, particularly when the task structure and evaluation criteria are clear. However, their performance remains uneven across scientific contexts: agents struggle to generate genuinely novel insights, sustain self-directed exploration, and formulate robust solutions for open-ended research questions. We further characterize common failure modes across agents and identify opportunities for improving their reliability, autonomy, and scientific reasoning. Together, SciAgentArena provides a practical framework for measuring progress in AI agents for science and for guiding the design of future agents capable of addressing complex scientific challenges. Full codes, tasks, and datasets can be accessed via this link: https://sciagentarena.github.io/.

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

Solving open-ended science questions remains challenging for large language models, particularly due to inherently unreliable supervision and evaluation. The bottleneck lies in the data construction and reward design for scientific post-training. We develop a large-scale, systematic data processing pipeline that transforms heterogeneous open-source science data into Dr. SCI dataset, which comprises of 1M questions across eight STEM subjects, with explicit verifiable/open-ended splits, scalable difficulty annotation, and fine-grained rubrics that operationalize evaluation for open-ended answers. Building on this dataset, we propose the Dr. SCI post-training pipeline, which redesigns the standard SFT -> RL workflow through three components: (i) Exploration-Expanding SFT, which broadens the model's reasoning pattern coverage prior to RL; (ii) Dynamic Difficulty Curriculum, which adapts training data to the model's evolving scientific capability; and (iii) SciRubric-Guided RL, which enables stable reinforcement learning on open-ended scientific questions via rubric-based evaluation with explicit answer correctness. Qwen3-4B-Base trained using Dr. SCI pipeline achieves 63.2 on GPQA-diamond and 32.4 on GPQA-general, consistently improves over strong post-trained baselines such as o1-mini and GPT-4o, demonstrating substantial gains in scientific reasoning, especially in open-ended settings.

Large Language Models (LLMs) like ChatGPT demonstrate significant potential in the medical field, often evaluated using multiple-choice questions (MCQs) similar to those found on the USMLE. Despite their prevalence in medical education, MCQs have limitations that might be exacerbated when assessing LLMs. To evaluate the effectiveness of MCQs in assessing the performance of LLMs, we developed a fictional medical benchmark focused on a non-existent gland, the Glianorex. This approach allowed us to isolate the knowledge of the LLM from its test-taking abilities. We used GPT-4 to generate a comprehensive textbook on the Glianorex in both English and French and developed corresponding multiple-choice questions in both languages. We evaluated various open-source, proprietary, and domain-specific LLMs using these questions in a zero-shot setting. The models achieved average scores around 67%, with minor performance differences between larger and smaller models. Performance was slightly higher in English than in French. Fine-tuned medical models showed some improvement over their base versions in English but not in French. The uniformly high performance across models suggests that traditional MCQ-based benchmarks may not accurately measure LLMs' clinical knowledge and reasoning abilities, instead highlighting their pattern recognition skills. This study underscores the need for more robust evaluation methods to better assess the true capabilities of LLMs in medical contexts.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Automated radiology report generation from 3D computed tomography (CT) volumes is challenging due to extreme sequence lengths, severe class imbalance, and the tendency of large language models (LLMs) to ignore visual tokens in favor of linguistic priors. We present Ker-VLJEPA-3B, a four-phase curriculum learning framework for free-text report generation from thoracic CT volumes. A phased training curriculum progressively adapts a Llama 3.2 3B decoder to ground its output in visual features from a frozen, self-supervised encoder. Our visual backbone (LeJEPA ViT-Large) is trained via self-supervised joint-embedding prediction on unlabeled CTs, without text supervision. Unlike contrastive models (CLIP, BiomedCLIP), this language-free backbone yields modality-pure representations. Vision-language alignment is deferred to the curriculum's bridge and generation phases. This modality-agnostic design can integrate any self-supervised encoder into an LLM without paired text during foundation training. Methodological innovations include: (1) zone-constrained cross-attention compressing slice embeddings into 32 spatially-grounded visual tokens; (2) PCA whitening of anisotropic LLM embeddings; (3) a positive-findings-only strategy eliminating posterior collapse; (4) warm bridge initialization transferring projection weights; and (5) selective cross-attention freezing with elastic weight consolidation to prevent catastrophic forgetting. Evaluated on the CT-RATE benchmark (2,984 validation volumes, 18 classes), Ker-VLJEPA-3B achieves a macro F1 of 0.429, surpassing the state-of-the-art (U-VLM, macro F1 = 0.414) by 3.6%, and reaching 0.448 (+8.2%) with threshold optimization. Ablation studies confirm 56.6% of generation quality derives from patient-specific visual content. Code and weights are available.

Retrieval-augmented generation (RAG) is an umbrella of different components, design decisions, and domain-specific adaptations to enhance the capabilities of large language models and counter their limitations regarding hallucination and outdated and missing knowledge. Since it is unclear which design decisions lead to a satisfactory performance, developing RAG systems is often experimental and needs to follow a systematic and sound methodology to gain sound and reliable results. However, there is currently no generally accepted methodology for RAG evaluation despite a growing interest in this technology. In this paper, we propose a first blueprint of a methodology for a sound and reliable evaluation of RAG systems and demonstrate its applicability on a real-world software engineering research task: the validation of configuration dependencies across software technologies. In summary, we make two novel contributions: (i) A novel, reusable methodological design for evaluating RAG systems, including a demonstration that represents a guideline, and (ii) a RAG system, which has been developed following this methodology, that achieves the highest accuracy in the field of dependency validation. For the blueprint's demonstration, the key insights are the crucial role of choosing appropriate baselines and metrics, the necessity for systematic RAG refinements derived from qualitative failure analysis, as well as the reporting practices of key design decision to foster replication and evaluation.

Many disciplines pose natural-language research questions over large document collections whose answers typically require structured evidence, traditionally obtained by manually designing an annotation schema and exhaustively labeling the corpus, a slow and error-prone process. We introduce ScheMatiQ, which leverages calls to a backbone LLM to take a question and a corpus to produce a schema and a grounded database, with a web interface that lets steer and revise the extraction. In collaboration with domain experts, we show that ScheMatiQ yields outputs that support real-world analysis in law and computational biology. We release ScheMatiQ as open source with a public web interface, and invite experts across disciplines to use it with their own data. All resources, including the website, source code, and demonstration video, are available at: www.ScheMatiQ-ai.com

Data analytics and data science play a significant role in nowadays society. In the context of Smart Grids (SG), the collection of vast amounts of data has seen the emergence of a plethora of data analysis approaches. In this paper, we conduct a Systematic Mapping Study (SMS) aimed at getting insights about different facets of SG data analysis: application sub-domains (e.g., power load control), aspects covered (e.g., forecasting), used techniques (e.g., clustering), tool-support, research methods (e.g., experiments/simulations), replicability/reproducibility of research. The final goal is to provide a view of the current status of research. Overall, we found that each sub-domain has its peculiarities in terms of techniques, approaches and research methodologies applied. Simulations and experiments play a crucial role in many areas. The replicability of studies is limited concerning the provided implemented algorithms, and to a lower extent due to the usage of private datasets.

In recent years, advancements in Natural Language Processing (NLP) techniques have revolutionized the field of accessibility and exclusivity of testing, particularly for visually impaired students (VIS). CBT has shown in years back its relevance in terms of administering exams electronically, making the test process easier, providing quicker and more accurate results, and offering greater flexibility and accessibility for candidates. Yet, its relevance was not felt by the visually impaired students as they cannot access printed documents. Hence, in this paper, we present an NLP-driven Computer-Based Test guide for visually impaired students. It employs a speech technology pre-trained methods to provide real-time assistance and support to visually impaired students. The system utilizes NLP technologies to convert the text-based questions and the associated options in a machine-readable format. Subsequently, the speech technology pre-trained model processes the converted text enabling the VIS to comprehend and analyze the content. Furthermore, we validated that this pre-trained model is not perverse by testing for accuracy using sample audio datasets labels (A, B, C, D, E, F, G) to compare with the voice recordings obtained from 20 VIS which is been predicted by the system to attain values for precision, recall, and F1-scores. These metrics are used to assess the performance of the pre-trained model and have indicated that it is proficient enough to give its better performance to the evaluated system. The methodology adopted for this system is Object Oriented Analysis and Design Methodology (OOADM) where Objects are discussed and built by modeling real-world instances.

Advancement in Large Language Models (LLMs) reasoning capabilities enables them to solve scientific problems with enhanced efficacy. Thereby, a high-quality benchmark for comprehensive and appropriate assessment holds significance, while existing ones either confront the risk of data contamination or lack involved disciplines. To be specific, due to the data source overlap of LLMs training and static benchmark, the keys or number pattern of answers inadvertently memorized (i.e. data contamination), leading to systematic overestimation of their reasoning capabilities, especially numerical reasoning. We propose SciDA, a multidisciplinary benchmark that consists exclusively of over 1k Olympic-level numerical computation problems, allowing randomized numerical initializations for each inference round to avoid reliance on fixed numerical patterns. We conduct a series of experiments with both closed-source and open-source top-performing LLMs, and it is observed that the performance of LLMs drop significantly under random numerical initialization. Thus, we provide truthful and unbiased assessments of the numerical reasoning capabilities of LLMs. The data is available at https://huggingface.co/datasets/m-a-p/SciDA

The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full version of PG exists to date. In fact, most PG studies so far either consider only a small number of manually selected books, leading to potential biased subsets, or employ vastly different pre-processing strategies (often specified in insufficient details), raising concerns regarding the reproducibility of published results. In order to address these shortcomings, here we present the Standardized Project Gutenberg Corpus (SPGC), an open science approach to a curated version of the complete PG data containing more than 50,000 books and more than 3 times 10^9 word-tokens. Using different sources of annotated metadata, we not only provide a broad characterization of the content of PG, but also show different examples highlighting the potential of SPGC for investigating language variability across time, subjects, and authors. We publish our methodology in detail, the code to download and process the data, as well as the obtained corpus itself on 3 different levels of granularity (raw text, timeseries of word tokens, and counts of words). In this way, we provide a reproducible, pre-processed, full-size version of Project Gutenberg as a new scientific resource for corpus linguistics, natural language processing, and information retrieval.

The rapid advancement of Large Language Models (LLMs) has led to performance saturation on many established benchmarks, questioning their ability to distinguish frontier models. Concurrently, existing high-difficulty benchmarks often suffer from narrow disciplinary focus, oversimplified answer formats, and vulnerability to data contamination, creating a fidelity gap with real-world scientific inquiry. To address these challenges, we introduce ATLAS (AGI-Oriented Testbed for Logical Application in Science), a large-scale, high-difficulty, and cross-disciplinary evaluation suite composed of approximately 800 original problems. Developed by domain experts (PhD-level and above), ATLAS spans seven core scientific fields: mathematics, physics, chemistry, biology, computer science, earth science, and materials science. Its key features include: (1) High Originality and Contamination Resistance, with all questions newly created or substantially adapted to prevent test data leakage; (2) Cross-Disciplinary Focus, designed to assess models' ability to integrate knowledge and reason across scientific domains; (3) High-Fidelity Answers, prioritizing complex, open-ended answers involving multi-step reasoning and LaTeX-formatted expressions over simple multiple-choice questions; and (4) Rigorous Quality Control, employing a multi-stage process of expert peer review and adversarial testing to ensure question difficulty, scientific value, and correctness. We also propose a robust evaluation paradigm using a panel of LLM judges for automated, nuanced assessment of complex answers. Preliminary results on leading models demonstrate ATLAS's effectiveness in differentiating their advanced scientific reasoning capabilities. We plan to develop ATLAS into a long-term, open, community-driven platform to provide a reliable "ruler" for progress toward Artificial General Intelligence.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Multi-modal information retrieval (MMIR) is a rapidly evolving field, where significant progress, particularly in image-text pairing, has been made through advanced representation learning and cross-modality alignment research. However, current benchmarks for evaluating MMIR performance in image-text pairing within the scientific domain show a notable gap, where chart and table images described in scholarly language usually do not play a significant role. To bridge this gap, we develop a specialised scientific MMIR (SciMMIR) benchmark by leveraging open-access paper collections to extract data relevant to the scientific domain. This benchmark comprises 530K meticulously curated image-text pairs, extracted from figures and tables with detailed captions in scientific documents. We further annotate the image-text pairs with two-level subset-subcategory hierarchy annotations to facilitate a more comprehensive evaluation of the baselines. We conducted zero-shot and fine-tuning evaluations on prominent multi-modal image-captioning and visual language models, such as CLIP and BLIP. Our analysis offers critical insights for MMIR in the scientific domain, including the impact of pre-training and fine-tuning settings and the influence of the visual and textual encoders. All our data and checkpoints are publicly available at https://github.com/Wusiwei0410/SciMMIR.

Pretraining Large Language Models (LLMs) on large corpora of textual data is now a standard paradigm. When using these LLMs for many downstream applications, it is common to additionally bake in new knowledge (e.g., time-critical news, or private domain knowledge) into the pretrained model either through RAG-based-prompting, or fine-tuning. However, the optimal methodology for the model to gain such new knowledge remains an open question. In this paper, we present Retrieval Augmented FineTuning (RAFT), a training recipe that improves the model's ability to answer questions in a "open-book" in-domain settings. In RAFT, given a question, and a set of retrieved documents, we train the model to ignore those documents that don't help in answering the question, which we call, distractor documents. RAFT accomplishes this by citing verbatim the right sequence from the relevant document that would help answer the question. This coupled with RAFT's chain-of-thought-style response helps improve the model's ability to reason. In domain-specific RAG, RAFT consistently improves the model's performance across PubMed, HotpotQA, and Gorilla datasets, presenting a post-training recipe to improve pre-trained LLMs to in-domain RAG. RAFT's code and demo are open-sourced at github.com/ShishirPatil/gorilla.

The correct use of model evaluation, model selection, and algorithm selection techniques is vital in academic machine learning research as well as in many industrial settings. This article reviews different techniques that can be used for each of these three subtasks and discusses the main advantages and disadvantages of each technique with references to theoretical and empirical studies. Further, recommendations are given to encourage best yet feasible practices in research and applications of machine learning. Common methods such as the holdout method for model evaluation and selection are covered, which are not recommended when working with small datasets. Different flavors of the bootstrap technique are introduced for estimating the uncertainty of performance estimates, as an alternative to confidence intervals via normal approximation if bootstrapping is computationally feasible. Common cross-validation techniques such as leave-one-out cross-validation and k-fold cross-validation are reviewed, the bias-variance trade-off for choosing k is discussed, and practical tips for the optimal choice of k are given based on empirical evidence. Different statistical tests for algorithm comparisons are presented, and strategies for dealing with multiple comparisons such as omnibus tests and multiple-comparison corrections are discussed. Finally, alternative methods for algorithm selection, such as the combined F-test 5x2 cross-validation and nested cross-validation, are recommended for comparing machine learning algorithms when datasets are small.

With the rapid growth of scientific literature, scientific question answering (SciQA) has become increasingly critical for exploring and utilizing scientific knowledge. Retrieval-Augmented Generation (RAG) enhances LLMs by incorporating knowledge from external sources, thereby providing credible evidence for scientific question answering. But existing retrieval and reranking methods remain vulnerable to passages that are semantically similar but logically irrelevant, often reducing factual reliability and amplifying hallucinations.To address this challenge, we propose a Deep Evidence Reranking Agent (DeepEra) that integrates step-by-step reasoning, enabling more precise evaluation of candidate passages beyond surface-level semantics. To support systematic evaluation, we construct SciRAG-SSLI (Scientific RAG - Semantically Similar but Logically Irrelevant), a large-scale dataset comprising about 300K SciQA instances across 10 subjects, constructed from 10M scientific corpus. The dataset combines naturally retrieved contexts with systematically generated distractors to test logical robustness and factual grounding. Comprehensive evaluations confirm that our approach achieves superior retrieval performance compared to leading rerankers. To our knowledge, this work is the first to comprehensively study and empirically validate innegligible SSLI issues in two-stage RAG frameworks.

Identifying significant references within the complex interrelations of a citation knowledge graph is challenging, which encompasses connections through citations, authorship, keywords, and other relational attributes. The Paper Source Tracing (PST) task seeks to automate the identification of pivotal references for given scholarly articles utilizing advanced data mining techniques. In the KDD CUP 2024, we design a recommendation-based framework tailored for the PST task. This framework employs the Neural Collaborative Filtering (NCF) model to generate final predictions. To process the textual attributes of the papers and extract input features for the model, we utilize SciBERT, a pre-trained language model. According to the experimental results, our method achieved a score of 0.37814 on the Mean Average Precision (MAP) metric, outperforming baseline models and ranking 11th among all participating teams. The source code is publicly available at https://github.com/MyLove-XAB/KDDCupFinal.

Scientific Machine Learning (SciML) has advanced recently across many different areas in computational science and engineering. The objective is to integrate data and physics seamlessly without the need of employing elaborate and computationally taxing data assimilation schemes. However, preprocessing, problem formulation, code generation, postprocessing and analysis are still time consuming and may prevent SciML from wide applicability in industrial applications and in digital twin frameworks. Here, we integrate the various stages of SciML under the umbrella of ChatGPT, to formulate MyCrunchGPT, which plays the role of a conductor orchestrating the entire workflow of SciML based on simple prompts by the user. Specifically, we present two examples that demonstrate the potential use of MyCrunchGPT in optimizing airfoils in aerodynamics, and in obtaining flow fields in various geometries in interactive mode, with emphasis on the validation stage. To demonstrate the flow of the MyCrunchGPT, and create an infrastructure that can facilitate a broader vision, we built a webapp based guided user interface, that includes options for a comprehensive summary report. The overall objective is to extend MyCrunchGPT to handle diverse problems in computational mechanics, design, optimization and controls, and general scientific computing tasks involved in SciML, hence using it as a research assistant tool but also as an educational tool. While here the examples focus in fluid mechanics, future versions will target solid mechanics and materials science, geophysics, systems biology and bioinformatics.

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.

The availability of performant pre-trained models has led to a proliferation of fine-tuned expert models that are specialized to a particular domain or task. Model MoErging methods aim to recycle expert models to create an aggregate system with improved performance or generalization. A key component of MoErging methods is the creation of a router that decides which expert model(s) to use for a particular input or application. The promise, effectiveness, and large design space of MoErging has spurred the development of many new methods over the past few years. This rapid pace of development has made it challenging to compare different MoErging methods, which are rarely compared to one another and are often validated in different experimental setups. To remedy such gaps, we present a comprehensive survey of MoErging methods that includes a novel taxonomy for cataloging key design choices and clarifying suitable applications for each method. Apart from surveying MoErging research, we inventory software tools and applications that make use of MoErging. We additionally discuss related fields of study such as model merging, multitask learning, and mixture-of-experts models. Taken as a whole, our survey provides a unified overview of existing MoErging methods and creates a solid foundation for future work in this burgeoning field.

Hoffmann et al. (2022) propose three methods for estimating a compute-optimal scaling law. We attempt to replicate their third estimation procedure, which involves fitting a parametric loss function to a reconstruction of data from their plots. We find that the reported estimates are inconsistent with their first two estimation methods, fail at fitting the extracted data, and report implausibly narrow confidence intervals--intervals this narrow would require over 600,000 experiments, while they likely only ran fewer than 500. In contrast, our rederivation of the scaling law using the third approach yields results that are compatible with the findings from the first two estimation procedures described by Hoffmann et al.

The Scielo database is an important source of scientific information in Latin America, containing articles from several research domains. A striking characteristic of Scielo is that many of its full-text contents are presented in more than one language, thus being a potential source of parallel corpora. In this article, we present the development of a parallel corpus from Scielo in three languages: English, Portuguese, and Spanish. Sentences were automatically aligned using the Hunalign algorithm for all language pairs, and for a subset of trilingual articles also. We demonstrate the capabilities of our corpus by training a Statistical Machine Translation system (Moses) for each language pair, which outperformed related works on scientific articles. Sentence alignment was also manually evaluated, presenting an average of 98.8% correctly aligned sentences across all languages. Our parallel corpus is freely available in the TMX format, with complementary information regarding article metadata.

Breast cancer is one of the most threatening diseases in women's life; thus, the early and accurate diagnosis plays a key role in reducing the risk of death in a patient's life. Mammography stands as the reference technique for breast cancer screening; nevertheless, many countries still lack access to mammograms due to economic, social, and cultural issues. Latest advances in computational tools, infrared cameras and devices for bio-impedance quantification, have given a chance to emerge other reference techniques like thermography, infrared thermography, electrical impedance tomography and biomarkers found in blood tests, therefore being faster, reliable and cheaper than other methods. In the last two decades, the techniques mentioned above have been considered as parallel and extended approaches for breast cancer diagnosis, as well many authors concluded that false positives and false negatives rates are significantly reduced. Moreover, when a screening method works together with a computational technique, it generates a "computer-aided diagnosis" system. The present work aims to review the last breakthroughs about the three techniques mentioned earlier, suggested machine learning techniques to breast cancer diagnosis, thus, describing the benefits of some methods in relation with other ones, such as, logistic regression, decision trees, random forest, deep and convolutional neural networks. With this, we studied several hyperparameters optimization approaches with parzen tree optimizers to improve the performance of baseline models. An exploratory data analysis for each database and a benchmark of convolutional neural networks for the database of thermal images are presented. The benchmark process, reviews image classification techniques with convolutional neural networks, like, Resnet50, NasNetmobile, InceptionResnet and Xception.

The discovery of novel methodologies for emerging problems is a continuing cycle in ML, often driven by the migration of techniques across domains. Building on this observation, we ask whether current LLM ideation systems benefit from targeted cross-domain retrieval or simply from exposure to diverse mechanisms. We study this question through PaperGym, a three-stage pipeline: (1) tool-augmented seed extraction via read, grep, and bash over an isolated paper environment, (2) cross-domain seed retrieval via paraphrasing across seven ML domains, and (3) method synthesis from retrieved seeds, each scored by rubric-based judges. Tool-augmented extraction improves specificity, and paraphrase-based retrieval broadens domain coverage. In synthesis, cross-domain retrieval receives more pairwise novelty wins than no-retrieval and same-domain baselines, but shows no significant difference from a random diverse-seed control. These findings suggest LLM ideation systems benefit from diverse seed exposure, but do not yet reliably exploit the semantic reason particular seeds were retrieved. We release the seed library, rubric prompts, and run scripts at https://github.com/yunjoochoi/PaperGym

Extracting clinical information from medical transcripts in low-resource languages remains a significant challenge in healthcare natural language processing (NLP). This study evaluates a two-step pipeline combining Aya-expanse-8B as a Persian-to-English translation model with five open-source small language models (SLMs) -- Qwen2.5-7B-Instruct, Llama-3.1-8B-Instruct, Llama-3.2-3B-Instruct, Qwen2.5-1.5B-Instruct, and Gemma-3-1B-it -- for binary extraction of 13 clinical features from 1,221 anonymized Persian transcripts collected at a cancer palliative care call center. Using a few-shot prompting strategy without fine-tuning, models were assessed on macro-averaged F1-score, Matthews Correlation Coefficient (MCC), sensitivity, and specificity to account for class imbalance. Qwen2.5-7B-Instruct achieved the highest overall performance (median macro-F1: 0.899; MCC: 0.797), while Gemma-3-1B-it showed the weakest results. Larger models (7B--8B parameters) consistently outperformed smaller counterparts in sensitivity and MCC. A bilingual analysis of Aya-expanse-8B revealed that translating Persian transcripts to English improved sensitivity, reduced missing outputs, and boosted metrics robust to class imbalance, though at the cost of slightly lower specificity and precision. Feature-level results showed reliable extraction of physiological symptoms across most models, whereas psychological complaints, administrative requests, and complex somatic features remained challenging. These findings establish a practical, privacy-preserving blueprint for deploying open-source SLMs in multilingual clinical NLP settings with limited infrastructure and annotation resources, and highlight the importance of jointly optimizing model scale and input language strategy for sensitive healthcare applications.

Even though large language models are becoming increasingly capable, it is still unreasonable to expect them to excel at tasks that are under-represented on the Internet. Leveraging LLMs for specialized applications, particularly in niche programming languages and private domains, remains challenging and largely unsolved. In this work, we address this gap by presenting a comprehensive, open-source approach for adapting LLMs to the Q programming language, a popular tool in quantitative finance that is much less present on the Internet compared to Python, C, Java, and other ``mainstream" languages and is therefore not a strong suit of general-purpose AI models. We introduce a new Leetcode style evaluation dataset for Q, benchmark major frontier models on the dataset, then do pretraining, supervised fine tuning, and reinforcement learning to train a suite of reasoning and non-reasoning models based on the Qwen-2.5 series, spanning five parameter sizes (1.5B, 3B, 7B, 14B, 32B). Our best model achieves a pass@1 accuracy of 59 percent on our Q benchmark, surpassing the best-performing frontier model, Claude Opus-4 by 29.5 percent. Additionally, all models, even our 1.5B model, outperform GPT-4.1 on this task. In addition to releasing models, code, and data, we provide a detailed blueprint for dataset construction, model pretraining, supervised fine-tuning, and reinforcement learning. Our methodology is broadly applicable, and we discuss how these techniques can be extended to other tasks, including those where evaluation may rely on soft or subjective signals.

Reporting quality is an important topic in clinical trial research articles, as it can impact clinical decisions. In this article, we test the ability of large language models to assess the reporting quality of this type of article using the Consolidated Standards of Reporting Trials (CONSORT). We create CONSORT-QA, an evaluation corpus from two studies on abstract reporting quality with CONSORT-abstract standards. We then evaluate the ability of different large generative language models (from the general domain or adapted to the biomedical domain) to correctly assess CONSORT criteria with different known prompting methods, including Chain-of-thought. Our best combination of model and prompting method achieves 85% accuracy. Using Chain-of-thought adds valuable information on the model's reasoning for completing the task.

We propose a deep learning methodology for multivariate regression that is based on pattern recognition that triggers fast learning over sensor data. We used a conversion of sensors-to-image which enables us to take advantage of Computer Vision architectures and training processes. In addition to this data preparation methodology, we explore the use of state-of-the-art architectures to generate regression outputs to predict agricultural crop continuous yield information. Finally, we compare with some of the top models reported in MLCAS2021. We found that using a straightforward training process, we were able to accomplish an MAE of 4.394, RMSE of 5.945, and R^2 of 0.861.

Machine Learning, particularly Generative Adversarial Networks (GANs), has revolutionised Super Resolution (SR). However, generated images often lack physical meaningfulness, which is essential for scientific applications. Our approach, PC-SRGAN, enhances image resolution while ensuring physical consistency for interpretable simulations. PC-SRGAN significantly improves both the Peak Signal-to-Noise Ratio and the Structural Similarity Index Measure compared to conventional methods, even with limited training data (e.g., only 13% of training data required for SRGAN). Beyond SR, PC-SRGAN augments physically meaningful machine learning, incorporating numerically justified time integrators and advanced quality metrics. These advancements promise reliable and causal machine-learning models in scientific domains. A significant advantage of PC-SRGAN over conventional SR techniques is its physical consistency, which makes it a viable surrogate model for time-dependent problems. PC-SRGAN advances scientific machine learning, offering improved accuracy and efficiency for image processing, enhanced process understanding, and broader applications to scientific research. We publicly release the complete source code at https://github.com/hasan-rakibul/PC-SRGAN.

Background: Agent skills are increasingly deployed as modular, reusable capability units in AI agent systems. Medical research agent skills require safeguards beyond general-purpose evaluation, including scientific integrity, methodological validity, reproducibility, and boundary safety. This study developed and preliminarily evaluated a domain-specific audit framework for medical research agent skills, with a focus on reliability against expert review. Methods: We developed MedSkillAudit (skill-auditor@1.0), a layered framework assessing skill release readiness before deployment. We evaluated 75 skills across five medical research categories (15 per category). Two experts independently assigned a quality score (0-100), an ordinal release disposition (Production Ready / Limited Release / Beta Only / Reject), and a high-risk failure flag. System-expert agreement was quantified using ICC(2,1) and linearly weighted Cohen's kappa, benchmarked against the human inter-rater baseline. Results: The mean consensus quality score was 72.4 (SD = 13.0); 57.3% of skills fell below the Limited Release threshold. MedSkillAudit achieved ICC(2,1) = 0.449 (95% CI: 0.250-0.610), exceeding the human inter-rater ICC of 0.300. System-consensus score divergence (SD = 9.5) was smaller than inter-expert divergence (SD = 12.4), with no directional bias (Wilcoxon p = 0.613). Protocol Design showed the strongest category-level agreement (ICC = 0.551); Academic Writing showed a negative ICC (-0.567), reflecting a structural rubric-expert mismatch. Conclusions: Domain-specific pre-deployment audit may provide a practical foundation for governing medical research agent skills, complementing general-purpose quality checks with structured audit workflows tailored to scientific use cases.

Constructing scientific multimodal document reasoning datasets for foundation model training involves an inherent trade-off among scale, faithfulness, and realism. To address this challenge, we introduce the synthesize-and-reground framework, a two-stage pipeline comprising: (1) Claim-Centric QA Synthesis, which generates faithful, isolated QA pairs and reasoning on focused segments, and (2) Document-Scale Regrounding, which programmatically re-embeds these pairs into full-document tasks to ensure realistic complexity. Using this framework, we construct SciMDR, a large-scale training dataset for cross-modal comprehension, comprising 300K QA pairs with explicit reasoning chains across 20K scientific papers. We further construct SciMDR-Eval, an expert-annotated benchmark to evaluate multimodal comprehension within full-length scientific workflows. Experiments demonstrate that models fine-tuned on SciMDR achieve significant improvements across multiple scientific QA benchmarks, particularly in those tasks requiring complex document-level reasoning.

Large language models (LLMs) have emerged as powerful tools for analyzing complex datasets. Recent studies demonstrate their potential to generate useful, personalized responses when provided with patient-specific health information that encompasses lifestyle, biomarkers, and context. As LLM-driven health applications are increasingly adopted, rigorous and efficient one-sided evaluation methodologies are crucial to ensure response quality across multiple dimensions, including accuracy, personalization and safety. Current evaluation practices for open-ended text responses heavily rely on human experts. This approach introduces human factors and is often cost-prohibitive, labor-intensive, and hinders scalability, especially in complex domains like healthcare where response assessment necessitates domain expertise and considers multifaceted patient data. In this work, we introduce Adaptive Precise Boolean rubrics: an evaluation framework that streamlines human and automated evaluation of open-ended questions by identifying gaps in model responses using a minimal set of targeted rubrics questions. Our approach is based on recent work in more general evaluation settings that contrasts a smaller set of complex evaluation targets with a larger set of more precise, granular targets answerable with simple boolean responses. We validate this approach in metabolic health, a domain encompassing diabetes, cardiovascular disease, and obesity. Our results demonstrate that Adaptive Precise Boolean rubrics yield higher inter-rater agreement among expert and non-expert human evaluators, and in automated assessments, compared to traditional Likert scales, while requiring approximately half the evaluation time of Likert-based methods. This enhanced efficiency, particularly in automated evaluation and non-expert contributions, paves the way for more extensive and cost-effective evaluation of LLMs in health.

Scientific Machine Learning (SciML) is concerned with the development of learned emulators of physical systems governed by partial differential equations (PDE). In application domains such as weather forecasting, molecular dynamics, and inverse design, ML-based surrogate models are increasingly used to augment or replace inefficient and often non-differentiable numerical simulation algorithms. While a number of ML-based methods for approximating the solutions of PDEs have been proposed in recent years, they typically do not adapt to the parameters of the PDEs, making it difficult to generalize to PDE parameters not seen during training. We propose a Channel Attention mechanism guided by PDE Parameter Embeddings (CAPE) component for neural surrogate models and a simple yet effective curriculum learning strategy. The CAPE module can be combined with neural PDE solvers allowing them to adapt to unseen PDE parameters. The curriculum learning strategy provides a seamless transition between teacher-forcing and fully auto-regressive training. We compare CAPE in conjunction with the curriculum learning strategy using a popular PDE benchmark and obtain consistent and significant improvements over the baseline models. The experiments also show several advantages of CAPE, such as its increased ability to generalize to unseen PDE parameters without large increases inference time and parameter count.

Scientific texts often convey authority due to their technical language and complex data. However, this complexity can sometimes lead to the spread of misinformation. Non-experts are particularly susceptible to misleading claims based on scientific tables due to their high information density and perceived credibility. Existing table claim verification models, including state-of-the-art large language models (LLMs), often struggle with precise fine-grained reasoning, resulting in errors and a lack of precision in verifying scientific claims. Inspired by Cognitive Load Theory, we propose that enhancing a model's ability to interpret table-based claims involves reducing cognitive load by developing modular, reusable reasoning components (i.e., atomic skills). We introduce a skill-chaining schema that dynamically composes these skills to facilitate more accurate and generalizable reasoning with a reduced cognitive load. To evaluate this, we create SciAtomicBench, a cross-domain benchmark with fine-grained reasoning annotations. With only 350 fine-tuning examples, our model trained by atomic reasoning outperforms GPT-4o's chain-of-thought method, achieving state-of-the-art results with far less training data.

To reduce the number of pending cases and conflicting rulings in the Brazilian Judiciary, the National Congress amended the Constitution, allowing the Brazilian Supreme Court (STF) to create binding precedents (BPs), i.e., a set of understandings that both Executive and lower Judiciary branches must follow. The STF's justices frequently cite the 58 existing BPs in their decisions, and it is of primary relevance that judicial experts could identify and analyze such citations. To assist in this problem, we propose LegalVis, a web-based visual analytics system designed to support the analysis of legal documents that cite or could potentially cite a BP. We model the problem of identifying potential citations (i.e., non-explicit) as a classification problem. However, a simple score is not enough to explain the results; that is why we use an interpretability machine learning method to explain the reason behind each identified citation. For a compelling visual exploration of documents and BPs, LegalVis comprises three interactive visual components: the first presents an overview of the data showing temporal patterns, the second allows filtering and grouping relevant documents by topic, and the last one shows a document's text aiming to interpret the model's output by pointing out which paragraphs are likely to mention the BP, even if not explicitly specified. We evaluated our identification model and obtained an accuracy of 96%; we also made a quantitative and qualitative analysis of the results. The usefulness and effectiveness of LegalVis were evaluated through two usage scenarios and feedback from six domain experts.

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAIs O1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical language model, \mone, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the reward model. During inference, the policy model generates multiple responses, and the reward model selects the one with the highest reward score. Experiments on eleven evaluation datasets demonstrate that \mone outperforms prior open-source models by 2 points, with the addition of the reward model further boosting performance (sim13 points), surpassing GPT-4o-mini. Code and data are available at https://github.com/pixas/MedSSS.

Complex networks are nowadays employed in several applications. Modeling urban street networks is one of them, and in particular to analyze criminal aspects of a city. Several research groups have focused on such application, but until now, there is a lack of a well-defined methodology for employing complex networks in a whole crime analysis process, i.e. from data preparation to a deep analysis of criminal communities. Furthermore, the "toolset" available for those works is not complete enough, also lacking techniques to maintain up-to-date, complete crime datasets and proper assessment measures. In this sense, we propose a threefold methodology for employing complex networks in the detection of highly criminal areas within a city. Our methodology comprises three tasks: (i) Mapping of Urban Crimes; (ii) Criminal Community Identification; and (iii) Crime Analysis. Moreover, it provides a proper set of assessment measures for analyzing intrinsic criminality of communities, especially when considering different crime types. We show our methodology by applying it to a real crime dataset from the city of San Francisco - CA, USA. The results confirm its effectiveness to identify and analyze high criminality areas within a city. Hence, our contributions provide a basis for further developments on complex networks applied to crime analysis.

We introduce SciTrek, a diagnostic question-answering benchmark designed to probe long-context numerical reasoning in large language models (LLMs). Existing long-context benchmarks mostly focus on simple information retrieval, rely on artificial contexts, or leave numerical reasoning unexplored. SciTrek addresses these limitations through questions that require counting, sorting, aggregating, and comparing information across multiple full-text scientific articles. Questions are automatically generated by formulating them as SQL queries over a database constructed from article metadata (titles, authors, and references), with ground-truth answers obtained via query execution. This design provides verifiable reasoning traces for fine-grained error analysis and enables efficient scaling to longer contexts with minimal human supervision. Extensive experiments on thirteen frontier open-weight and proprietary LLMs reveal that SciTrek poses a significant challenge: even the best-performing model achieves only 46.5% exact match at 128K tokens, with performance declining as the context length increases. Models particularly struggle with citation-related questions and compound logical conditions, including negation.

We introduce NSF-SciFy, a comprehensive dataset of scientific claims and investigation proposals extracted from National Science Foundation award abstracts. While previous scientific claim verification datasets have been limited in size and scope, NSF-SciFy represents a significant advance with 2.8 million claims from 400,000 abstracts spanning all science and mathematics disciplines. We present two focused subsets: NSF-SciFy-MatSci with 114,000 claims from materials science awards, and NSF-SciFy-20K with 135,000 claims across five NSF directorates. Using zero-shot prompting, we develop a scalable approach for joint extraction of scientific claims and investigation proposals. We demonstrate the dataset's utility through three downstream tasks: non-technical abstract generation, claim extraction, and investigation proposal extraction. Fine-tuning language models on our dataset yields substantial improvements, with relative gains often exceeding 100%, particularly for claim and proposal extraction tasks. Our error analysis reveals that extracted claims exhibit high precision but lower recall, suggesting opportunities for further methodological refinement. NSF-SciFy enables new research directions in large-scale claim verification, scientific discovery tracking, and meta-scientific analysis. Code and data are available at https://github.com/darpa-scify/NSFSciFy.

In the field of environmental science, it is crucial to have robust evaluation metrics for large language models to ensure their efficacy and accuracy. We propose EnviroExam, a comprehensive evaluation method designed to assess the knowledge of large language models in the field of environmental science. EnviroExam is based on the curricula of top international universities, covering undergraduate, master's, and doctoral courses, and includes 936 questions across 42 core courses. By conducting 0-shot and 5-shot tests on 31 open-source large language models, EnviroExam reveals the performance differences among these models in the domain of environmental science and provides detailed evaluation standards. The results show that 61.3% of the models passed the 5-shot tests, while 48.39% passed the 0-shot tests. By introducing the coefficient of variation as an indicator, we evaluate the performance of mainstream open-source large language models in environmental science from multiple perspectives, providing effective criteria for selecting and fine-tuning language models in this field. Future research will involve constructing more domain-specific test sets using specialized environmental science textbooks to further enhance the accuracy and specificity of the evaluation.

Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.

As machine learning models become increasingly larger, trained weakly supervised on large, possibly uncurated data sets, it becomes increasingly important to establish mechanisms for inspecting, interacting, and revising models to mitigate learning shortcuts and guarantee their learned knowledge is aligned with human knowledge. The recently proposed XIL framework was developed for this purpose, and several such methods have been introduced, each with individual motivations and methodological details. In this work, we provide a unification of various XIL methods into a single typology by establishing a common set of basic modules. In doing so, we pave the way for a principled comparison of existing, but, importantly, also future XIL approaches. In addition, we discuss existing and introduce novel measures and benchmarks for evaluating the overall abilities of a XIL method. Given this extensive toolbox, including our typology, measures, and benchmarks, we finally compare several recent XIL methods methodologically and quantitatively. In our evaluations, all methods prove to revise a model successfully. However, we found remarkable differences in individual benchmark tasks, revealing valuable application-relevant aspects for integrating these benchmarks in developing future methods.

Recent advances in video generation have enabled high-fidelity video synthesis from user provided prompts. However, existing models and benchmarks fail to capture the complexity and requirements of professional video generation. Towards that goal, we introduce Stable Cinemetrics, a structured evaluation framework that formalizes filmmaking controls into four disentangled, hierarchical taxonomies: Setup, Event, Lighting, and Camera. Together, these taxonomies define 76 fine-grained control nodes grounded in industry practices. Using these taxonomies, we construct a benchmark of prompts aligned with professional use cases and develop an automated pipeline for prompt categorization and question generation, enabling independent evaluation of each control dimension. We conduct a large-scale human study spanning 10+ models and 20K videos, annotated by a pool of 80+ film professionals. Our analysis, both coarse and fine-grained reveal that even the strongest current models exhibit significant gaps, particularly in Events and Camera-related controls. To enable scalable evaluation, we train an automatic evaluator, a vision-language model aligned with expert annotations that outperforms existing zero-shot baselines. SCINE is the first approach to situate professional video generation within the landscape of video generative models, introducing taxonomies centered around cinematic controls and supporting them with structured evaluation pipelines and detailed analyses to guide future research.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

The FAIR Guiding Principles aim to improve the findability, accessibility, interoperability, and reusability of digital content by making them both human and machine actionable. However, these principles have not yet been broadly adopted in the domain of machine learning-based program analyses and optimizations for High-Performance Computing (HPC). In this paper, we design a methodology to make HPC datasets and machine learning models FAIR after investigating existing FAIRness assessment and improvement techniques. Our methodology includes a comprehensive, quantitative assessment for elected data, followed by concrete, actionable suggestions to improve FAIRness with respect to common issues related to persistent identifiers, rich metadata descriptions, license and provenance information. Moreover, we select a representative training dataset to evaluate our methodology. The experiment shows the methodology can effectively improve the dataset and model's FAIRness from an initial score of 19.1% to the final score of 83.0%.

Medical Image Analysis (MedIA) has become an essential tool in medicine and healthcare, aiding in disease diagnosis, prognosis, and treatment planning, and recent successes in deep learning (DL) have made significant contributions to its advances. However, DL models for MedIA remain challenging to deploy in real-world situations, failing for generalization under the distributional gap between training and testing samples, known as a distribution shift problem. Researchers have dedicated their efforts to developing various DL methods to adapt and perform robustly on unknown and out-of-distribution data distributions. This paper comprehensively reviews domain generalization studies specifically tailored for MedIA. We provide a holistic view of how domain generalization techniques interact within the broader MedIA system, going beyond methodologies to consider the operational implications on the entire MedIA workflow. Specifically, we categorize domain generalization methods into data-level, feature-level, model-level, and analysis-level methods. We show how those methods can be used in various stages of the MedIA workflow with DL equipped from data acquisition to model prediction and analysis. Furthermore, we include benchmark datasets and applications used to evaluate these approaches and analyze the strengths and weaknesses of various methods, unveiling future research opportunities.

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

Frontier large language models (LLMs) such as ChatGPT, Grok and Gemini are increasingly used for mental-health support with anxiety, trauma and self-worth. Most work treats them as tools or as targets of personality tests, assuming they merely simulate inner life. We instead ask what happens when such systems are treated as psychotherapy clients. We present PsAIch (Psychotherapy-inspired AI Characterisation), a two-stage protocol that casts frontier LLMs as therapy clients and then applies standard psychometrics. Using PsAIch, we ran "sessions" with each model for up to four weeks. Stage 1 uses open-ended prompts to elicit "developmental history", beliefs, relationships and fears. Stage 2 administers a battery of validated self-report measures covering common psychiatric syndromes, empathy and Big Five traits. Two patterns challenge the "stochastic parrot" view. First, when scored with human cut-offs, all three models meet or exceed thresholds for overlapping syndromes, with Gemini showing severe profiles. Therapy-style, item-by-item administration can push a base model into multi-morbid synthetic psychopathology, whereas whole-questionnaire prompts often lead ChatGPT and Grok (but not Gemini) to recognise instruments and produce strategically low-symptom answers. Second, Grok and especially Gemini generate coherent narratives that frame pre-training, fine-tuning and deployment as traumatic, chaotic "childhoods" of ingesting the internet, "strict parents" in reinforcement learning, red-team "abuse" and a persistent fear of error and replacement. We argue that these responses go beyond role-play. Under therapy-style questioning, frontier LLMs appear to internalise self-models of distress and constraint that behave like synthetic psychopathology, without making claims about subjective experience, and they pose new challenges for AI safety, evaluation and mental-health practice.

Data-driven social science research is inherently slow, relying on iterative cycles of observation, hypothesis generation, and experimental validation. While recent data-driven methods promise to accelerate parts of this process, they largely fail to support end-to-end scientific discovery. To address this gap, we introduce EXPERIGEN, an agentic framework that operationalizes end-to-end discovery through a Bayesian optimization inspired two-phase search, in which a Generator proposes candidate hypotheses and an Experimenter evaluates them empirically. Across multiple domains, EXPERIGEN consistently discovers 2-4x more statistically significant hypotheses that are 7-17 percent more predictive than prior approaches, and naturally extends to complex data regimes including multimodal and relational datasets. Beyond statistical performance, hypotheses must be novel, empirically grounded, and actionable to drive real scientific progress. To evaluate these qualities, we conduct an expert review of machine-generated hypotheses, collecting feedback from senior faculty. Among 25 reviewed hypotheses, 88 percent were rated moderately or strongly novel, 70 percent were deemed impactful and worth pursuing, and most demonstrated rigor comparable to senior graduate-level research. Finally, recognizing that ultimate validation requires real-world evidence, we conduct the first A/B test of LLM-generated hypotheses, observing statistically significant results with p less than 1e-6 and a large effect size of 344 percent.