Daily Papers

Scientific workflow management systems (WMS) support scalable and reproducible execution of complex pipelines, but workflow design, implementation, and debugging remain largely manual and require significant expertise. Recent approaches using large language models (LLMs) show promise for workflow generation from natural language, but often rely on direct code synthesis, which limits transparency, reproducibility, and integration with workflow systems. We present an AI-assisted approach to scientific workflow management that combines specification-driven workflow generation, automated debugging, and distributed execution. The method introduces a structured specification phase that separates workflow intent, design, and implementation, allowing validation prior to code generation. We also develop an LLM-based debugging agent that diagnoses and resolves failures across multiple system layers. To support distributed execution and user interaction, we integrate Pegasus, a widely used WMS, with a Model Context Protocol (MCP) layer, providing a unified interface for workflow submission, monitoring, and control. We evaluate the approach using a federated learning workflow for medical imaging, chosen for its parallel, iterative, and dependency-intensive structure. The system generated and executed large-scale workflows with thousands of jobs, reduced debugging effort, and allowed non-expert users to construct workflows with expert-level design patterns. These results indicate that end-to-end AI-assisted workflow generation and execution is feasible, and point toward AI-driven platforms for managing the scientific workflow lifecycle.

Scientific agents increasingly analyze data, execute code, and produce research artifacts, yet most benchmarks emphasize final answers, isolated programs, or a single domain. We introduce FrontierChallenge, a cross-domain benchmark comprising 300 end-to-end scientific workflows. In this paper, we release and evaluate 97 of these tasks, spanning quantum chemistry, molecular dynamics, materials characterization, analytical chemistry, life science, and electrochemistry/environment. Each task provides fixed inputs and specifies a bundle of required scientific deliverables. We evaluate twelve frontier models with three agent scaffolds. Pass Rate measures the fraction of tasks satisfying the full-completion criterion, while Avg. Score captures partial progress. Each of the best-performing configurations completed only 20 of the 97 released tasks, yielding a Pass Rate of 20.6%. Partial progress translated especially poorly into complete delivery in analytical chemistry and electrochemistry/environment: Avg. Scores reached 87.6 and 94.9, but the highest Pass Rates were only 4% and 0%. Among non-passing Claude Code trajectories, 75.5% still ended with language claiming completion. These findings show that neither high partial scores nor confident claims of completion reliably indicate that a scientific task has been fully delivered, highlighting the need to evaluate end-to-end workflow execution and the completeness of scientific deliverables together.

Scientific innovation relies on detailed workflows, which include critical steps such as analyzing literature, generating ideas, validating these ideas, interpreting results, and inspiring follow-up research. However, scientific publications that document these workflows are extensive and unstructured. This makes it difficult for both human researchers and AI systems to effectively navigate and explore the space of scientific innovation. To address this issue, we introduce MASSW, a comprehensive text dataset on Multi-Aspect Summarization of Scientific Workflows. MASSW includes more than 152,000 peer-reviewed publications from 17 leading computer science conferences spanning the past 50 years. Using Large Language Models (LLMs), we automatically extract five core aspects from these publications -- context, key idea, method, outcome, and projected impact -- which correspond to five key steps in the research workflow. These structured summaries facilitate a variety of downstream tasks and analyses. The quality of the LLM-extracted summaries is validated by comparing them with human annotations. We demonstrate the utility of MASSW through multiple novel machine-learning tasks that can be benchmarked using this new dataset, which make various types of predictions and recommendations along the scientific workflow. MASSW holds significant potential for researchers to create and benchmark new AI methods for optimizing scientific workflows and fostering scientific innovation in the field. Our dataset is openly available at https://github.com/xingjian-zhang/massw.

Large Action Models (LAMs) extend large language models by enabling autonomous decision-making and tool execution, making them promising for automating scientific workflows. However, scientific workflows impose strict requirements on reproducibility, auditability, and deterministic execution, which are not satisfied by generic LLM-based agents. Unconstrained action generation can lead to silent state changes, non-deterministic executions, and irreproducible experimental results, limiting the applicability of LAMs in scientific settings. In this paper, we propose R-LAM, a reproducibility-constrained framework for applying Large Action Models to scientific workflow automation. R-LAM introduces structured action schemas, deterministic execution policies, and explicit provenance tracking to ensure that every action and intermediate artifact is auditable and replayable. The framework supports failure-aware execution loops and controlled workflow forking, enabling iterative experimentation without compromising reproducibility. We implement R-LAM as a lightweight Python framework and release it as an open-source PyPI package to facilitate reproducible research. An experimental evaluation of representative scientific workflows demonstrates that R-LAM improves reproducibility success rates and execution reliability compared to unconstrained LLM-based agents, while retaining adaptive control over workflow execution.

Large Language Models (LLMs) have extended their impact beyond Natural Language Processing, substantially fostering the development of interdisciplinary research. Recently, various LLM-based agents have been developed to assist scientific discovery progress across multiple aspects and domains. Among these, computer-using agents, capable of interacting with operating systems as humans do, are paving the way to automated scientific problem-solving and addressing routines in researchers' workflows. Recognizing the transformative potential of these agents, we introduce ScienceBoard, which encompasses two complementary contributions: (i) a realistic, multi-domain environment featuring dynamic and visually rich scientific workflows with integrated professional software, where agents can autonomously interact via different interfaces to accelerate complex research tasks and experiments; and (ii) a challenging benchmark of 169 high-quality, rigorously validated real-world tasks curated by humans, spanning scientific-discovery workflows in domains such as biochemistry, astronomy, and geoinformatics. Extensive evaluations of agents with state-of-the-art backbones (e.g., GPT-4o, Claude 3.7, UI-TARS) show that, despite some promising results, they still fall short of reliably assisting scientists in complex workflows, achieving only a 15% overall success rate. In-depth analysis further provides valuable insights for addressing current agent limitations and more effective design principles, paving the way to build more capable agents for scientific discovery. Our code, environment, and benchmark are at https://qiushisun.github.io/ScienceBoard-Home/.

Existing prompt-optimization techniques rely on local signals to update behavior, often neglecting broader and recurring patterns across tasks, leading to poor generalization; they further rely on full-prompt rewrites or unstructured merges, resulting in knowledge loss. These limitations are magnified in research-coding workflows, which involve heterogeneous repositories, underspecified environments, and weak feedback, where reproducing results from public codebases is an established evaluation regime. We introduce Reflective Evolving Research Engineer (REVERE), a framework that continuously learns from Global Training Context, recognizes recurring failure modes in cross-repository execution trajectories, distills them into reusable heuristics, and performs targeted edits across three configurable fields: the system prompt, a task-prompt template, and a cumulative cheatsheet. REVERE, via this reflective optimization framework, improves performance over prior state-of-the-art expert-crafted instructions on research coding tasks by 4.50% on SUPER, 3.51% on ResearchCodeBench, and 4.89% on ScienceAgentBench across their respective metrics. These results demonstrate that agents equipped with mechanisms for continual learning and global memory consolidation can meaningfully evolve their capabilities over time.

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding real-time researcher guidance. This paper introduces Deep Research, a multi-agent system enabling interactive scientific investigation with turnaround times measured in minutes. The architecture comprises specialized agents for planning, data analysis, literature search, and novelty detection, unified through a persistent world state that maintains context across iterative research cycles. Two operational modes support different workflows: semi-autonomous mode with selective human checkpoints, and fully autonomous mode for extended investigations. Evaluation on the BixBench computational biology benchmark demonstrated state-of-the-art performance, achieving 48.8% accuracy on open response and 64.4% on multiple-choice evaluation, exceeding existing baselines by 14 to 26 percentage points. Analysis of architectural constraints, including open access literature limitations and challenges inherent to automated novelty assessment, informs practical deployment considerations for AI-assisted scientific workflows.

The emerging paradigm of AI co-scientists focuses on tasks characterized by repeatable verification, where agents explore search spaces in 'guess and check' loops. This paradigm does not extend to problems where repeated evaluation is impossible and ground truth is established by the consensus synthesis of theory and existing evidence. We evaluate a Gemini-based AI environment designed to support collaborative scientific assessment, integrated into a standard scientific workflow. In collaboration with a diverse group of 13 scientists working in the field of climate science, we tested the system on a complex topic: the stability of the Atlantic Meridional Overturning Circulation (AMOC). Our results show that AI can accelerate the scientific workflow. The group produced a comprehensive synthesis of 79 papers through 104 revision cycles in just over 46 person-hours. AI contribution was significant: most AI-generated content was retained in the report. AI also helped maintain logical consistency and presentation quality. However, expert additions were crucial to ensure its acceptability: less than half of the report was produced by AI. Furthermore, substantial oversight was required to expand and elevate the content to rigorous scientific standards.

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.

Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to seamlessly integrate and orchestrate multiple tools for complex scientific workflows. Here, we present SciToolAgent, an LLM-powered agent that automates hundreds of scientific tools across biology, chemistry, and materials science. At its core, SciToolAgent leverages a scientific tool knowledge graph that enables intelligent tool selection and execution through graph-based retrieval-augmented generation. The agent also incorporates a comprehensive safety-checking module to ensure responsible and ethical tool usage. Extensive evaluations on a curated benchmark demonstrate that SciToolAgent significantly outperforms existing approaches. Case studies in protein engineering, chemical reactivity prediction, chemical synthesis, and metal-organic framework screening further demonstrate SciToolAgent's capability to automate complex scientific workflows, making advanced research tools accessible to both experts and non-experts.

Scientific research is being reshaped by AI systems that move beyond isolated assistance toward longer-horizon workflows spanning literature grounding, hypothesis generation, experimentation, validation, reporting, and revision. This shift marks a transition from task-level AI for science to workflow-level research automation. Yet current systems remain fragmented, differing in autonomy, domain scope, execution environment, validation mechanism, and human oversight, while still struggling with evidence preservation, reproducibility, weak-direction rejection, provenance tracking, cross-domain robustness, and accountable scientific closure. This survey examines these developments through AutoResearch, defined as the developmental spectrum of AI-powered scientific workflow automation. Within it, Vibe Research denotes the human-steered region of prompt-based assistance and human-verified execution, whereas emerging AI-led systems coordinate larger portions of the discovery loop without achieving robust autonomy. We analyze how research systems redistribute control, evidence, execution, validation, and accountability across workflows and organize the field around five workflow conditions: literature and research grounding; hypothesis formation and planning; experimentation and tool use; feedback, validation, and review; and reporting and knowledge communication. We further synthesize AI scientist systems, mixed-initiative co-research frameworks, benchmarks, domain deployments, and open-source infrastructures. Finally, we propose five evaluation dimensions--novelty, validity, impact, reliability, and provenance--and show that AutoResearch autonomy is domain-conditioned, being more credible in structured, executable, and rapidly verifiable settings but limited in embodied, delayed, heterogeneous, ethical, or institutionally accountable contexts.

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

The rapid advancement of large language models (LLMs) and multimodal foundation models has sparked growing interest in their potential for scientific research. However, scientific intelligence encompasses a broad spectrum of abilities ranging from understanding fundamental knowledge to conducting creative discovery, and existing benchmarks remain fragmented. Most focus on narrow tasks and fail to reflect the hierarchical and multi-disciplinary nature of real scientific inquiry. We introduce HiSciBench, a hierarchical benchmark designed to evaluate foundation models across five levels that mirror the complete scientific workflow: Scientific Literacy (L1), Literature Parsing (L2), Literature-based Question Answering (L3), Literature Review Generation (L4), and Scientific Discovery (L5). HiSciBench contains 8,735 carefully curated instances spanning six major scientific disciplines, including mathematics, physics, chemistry, biology, geography, and astronomy, and supports multimodal inputs including text, equations, figures, and tables, as well as cross-lingual evaluation. Unlike prior benchmarks that assess isolated abilities, HiSciBench provides an integrated, dependency-aware framework that enables detailed diagnosis of model capabilities across different stages of scientific reasoning. Comprehensive evaluations of leading models, including GPT-5, DeepSeek-R1, and several multimodal systems, reveal substantial performance gaps: while models achieve up to 69\% accuracy on basic literacy tasks, performance declines sharply to 25\% on discovery-level challenges. HiSciBench establishes a new standard for evaluating scientific Intelligence and offers actionable insights for developing models that are not only more capable but also more reliable. The benchmark will be publicly released to facilitate future research.

Multimodal Large Language Models (MLLMs) excel in general domains but struggle with complex, real-world science. We posit that polymer science, an interdisciplinary field spanning chemistry, physics, biology, and engineering, is an ideal high-stakes testbed due to its diverse multimodal data. Yet, existing benchmarks related to polymer science largely overlook real-world workflows, limiting their practical utility and failing to systematically evaluate MLLMs across the full, practice-grounded lifecycle of experimentation. We introduce PolyReal, a novel multimodal benchmark grounded in real-world scientific practices to evaluate MLLMs on the full lifecycle of polymer experimentation. It covers five critical capabilities: (1) foundational knowledge application; (2) lab safety analysis; (3) experiment mechanism reasoning; (4) raw data extraction; and (5) performance & application exploration. Our evaluation of leading MLLMs on PolyReal reveals a capability imbalance. While models perform well on knowledge-intensive reasoning (e.g., Experiment Mechanism Reasoning), they drop sharply on practice-based tasks (e.g., Lab Safety Analysis and Raw Data Extraction). This exposes a severe gap between abstract scientific knowledge and its practical, context-dependent application, showing that these real-world tasks remain challenging for MLLMs. Thus, PolyReal helps address this evaluation gap and provides a practical benchmark for assessing AI systems in real-world scientific workflows.

Advances in AI-assisted research have introduced powerful tools for literature retrieval, hypothesis generation, experimentation, and manuscript preparation. However, systems remain fragmented and lack human-centred workflows. To address these gaps, we introduce AIssistant, an agentic, open-source Human-AI collaborative framework designed to simplify the end-to-end creation of scientific workflows. Since our development is still in an early stage, we present here the first experiments with AIssistant for perspective and review research papers in machine learning. Our system integrates modular tools and agents for literature synthesis, section-wise experimentation, citation management, and automatic LaTeX paper text generation, while maintaining human oversight at every stage to ensure accuracy, coherence, and scholarly rigour. We conducted a comprehensive evaluation across three layers: (1) Independent Human Review, following NeurIPS double-blind standards; (2) Automated LLM Review, using GPT-5 as a scalable human review proxy; and (3) Program Chair Oversight, where the chair monitors the entire review process and makes final validation and acceptance decisions. The results demonstrate that AIssistant improves drafting efficiency and thematic consistency. Nonetheless, Human-AI collaboration remains essential for maintaining factual correctness, methodological soundness, and ethical compliance. Despite its effectiveness, we identify key limitations, including hallucinated citations, difficulty adapting to dynamic paper structures, and incomplete integration of multimodal content.

Leveraging Multi-modal Large Language Models (MLLMs) to accelerate frontier scientific research is promising, yet how to rigorously evaluate such systems remains unclear. Existing benchmarks mainly focus on single-document understanding, whereas real scientific workflows require integrating evidence from multiple papers, including their text, tables, and figures. As a result, multi-modal, multi-document scientific reasoning remains underexplored and lacks systematic evaluation. To address this gap, we introduce PaperScope, a multi-modal multi-document benchmark designed for agentic deep research. PaperScope presents three advantages: (1) Structured scientific grounding. It is built on a knowledge graph of over 2,000 AI papers spanning three years, providing a structured foundation for research-oriented queries. (2) Semantically dense evidence construction. It integrates semantically related key information nodes and employs optimized random-walk article selector to sample thematically coherent paper sets, thereby ensuring adequate semantic density and task complexity. (3) Multi-task evaluation of scientific reasoning. It contains over 2,000 QA pairs across reasoning, retrieval, summarization, and problem solving, enabling evaluation of multi-step scientific reasoning. Experimental results show that even advanced systems such as OpenAI Deep Research and Tongyi Deep Research achieve limited scores on PaperScope, highlighting the difficulty of long-context retrieval and deep multi-source reasoning. PaperScope thus provides a rigorous benchmark alongside a scalable pipeline for constructing large-scale multi-modal, multi-source deep research datasets.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Autonomous scientific research agents are increasingly applied to end-to-end scientific workflows, including literature review, data analysis, experimentation, and report generation. However, open-ended research tasks often do not clearly specify the analyses, methods, and success criteria required to complete the task. As a result, agents may miss important analyses, use inappropriate methods, or draw conclusions that are insufficiently supported by evidence. To address the problem, we present AutoSciRub, an evaluation-first framework that induces a task-specific executable rubric before research execution, and uses it to guide execution, criterion-level verification as well as iterative revision. AutoSciRub decomposes an underspecified instruction into atomic scientific goals, grounds them in relevant literature and task-visible data, and synthesizes specific, actionable, and verifiable criteria. The resulting rubric makes implicit experimental and evidential requirements explicit, providing guidance for experiments and analyses. During revision, rubric-guided verification identifies unmet criteria and enables targeted refinement of the research report and its supporting artifacts. On ResearchClawBench, AutoSciRub consistently improves all tested configurations, with an average gain of 2.08 points across three backbone LLMs under the fixed Codex harness and 2.95 points across three agent harnesses using a fixed DeepSeek-V4-Flash backbone. On a randomly sampled 20-task subset of AstaBench E2E Discovery, AutoSciRub further achieves an average improvement of 16.8 points across three agent harnesses, while maintaining or increasing the number of successfully completed tasks. These results demonstrate that evaluation-first guidance provides an effective and generalizable control mechanism for autonomous scientific research (Code: https://github.com/zjunlp/AutoSciRub).

Autonomous research systems increasingly make the scientific workflow executable: agents can propose ideas, run code, inspect results, and draft papers. But executable workflows do not by themselves produce research judgment. We analyze where current systems lose trial experience: weak evidence becomes prose, pilot signals become broad claims, memory remains textual, and recurring process failures do not change later behavior. We introduce Sibyl-AutoResearch, a self-evolving AutoResearch framework built around Scientific Trial-and-Error Harnesses. A harness lets agents run bounded trials, preserve positive and negative outcomes, and route lessons into later planning, validation, claim scope, scheduling, critique, writing, and harness repair. We formalize this through two auditable conversion units: trial-to-behavior conversion, which links trial signals to later research actions, and trial-to-harness-behavior conversion, which links recurring process failures to system updates. We implement the framework in SIBYL, a file-backed autonomous research system that exposes the state, roles, memory, gates, and artifact traces needed to inspect these conversion paths. A retrospective audit identifies eight high-confidence conversion events, with a median latency of one iteration and a maximum latency of three iterations. A recovered-failure registry further shows how five naturally occurring failure classes, including duplicate results, stale numbers, and unsupported statistics, were blocked, downgraded, or routed into later repair. These traces do not establish a comparative performance claim; they show that the proposed conversion units are recoverable from realistic autonomous-research workspaces. The SIBYL framework and system are available at https://github.com/Sibyl-Research-Team/AutoResearch-SibylSystem.

AI systems can increasingly automate scientific workflows, but the reasoning that links prior evidence, generated ideas, experiments and final claims often remains implicit inside model inference. Here we introduce Xcientist, a research harness that externalizes research synthesis and experimental validation into inspectable, contract-governed processes. Xcientist organizes literature evidence, idea states, implementation plans, ablation records and repair traces as persistent research artifacts, so that generated mechanisms can be grounded, executed, tested and revised without losing their evidential basis. We identify claim drift as a failure mode of automated research, where runnable artifacts no longer support the mechanism originally claimed. Across training-free memory systems, graph-structured traffic forecasting and multi-scale physics-informed neural networks, Xcientist preserves traceable trajectories from problem formulation to mechanism design, validation and bounded revision. These results suggest that AI scientists should be evaluated not only by their final artifacts, but by whether their synthesis and validation processes remain attributable, inspectable and scientifically accountable.

Agentic artificial intelligence systems promise to accelerate scientific workflows, but neuroimaging poses unique challenges: heterogeneous modalities (sMRI, fMRI, dMRI, EEG), long multi-stage pipelines, and persistent reproducibility risks. To address this gap, we present NeuroClaw, a domain-specialized multi-agent research assistant for executable and reproducible neuroimaging research. NeuroClaw operates directly on raw neuroimaging data across formats and modalities, grounding decisions in dataset semantics and BIDS metadata so users need not prepare curated inputs or bespoke model code. The platform combines harness engineering with end-to-end environment management, including pinned Python environments, Docker support, automated installers for common neuroimaging tools, and GPU configuration. In practice, this layer emphasizes checkpointing, post-execution verification, structured audit traces, and controlled runtime setup, making toolchains more transparent while improving reproducibility and auditability. A three-tier skill/agent hierarchy separates user-facing interaction, high-level orchestration, and low-level tool skills to decompose complex workflows into safe, reusable units. Alongside the NeuroClaw framework, we introduce NeuroBench, a system-level benchmark for executability, artifact validity, and reproducibility readiness. Across multiple multimodal LLMs, NeuroClaw-enabled runs yield consistent and substantial score improvements compared with direct agent invocation. Project homepage: https://cuhk-aim-group.github.io/NeuroClaw/index.html

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

Large language models (LLMs) are increasingly used across the scientific workflow, including to draft peer-review reports. However, many AI-generated reviews are superficial and insufficiently actionable, leaving authors without concrete, implementable guidance and motivating the gap this work addresses. We propose RbtAct, which targets actionable review feedback generation and places existing peer review rebuttal at the center of learning. Rebuttals show which reviewer comments led to concrete revisions or specific plans, and which were only defended. Building on this insight, we leverage rebuttal as implicit supervision to directly optimize a feedback generator for actionability. To support this objective, we propose a new task called perspective-conditioned segment-level review feedback generation, in which the model is required to produce a single focused comment based on the complete paper and a specified perspective such as experiments and writing. We also build a large dataset named RMR-75K that maps review segments to the rebuttal segments that address them, with perspective labels and impact categories that order author uptake. We then train the Llama-3.1-8B-Instruct model with supervised fine-tuning on review segments followed by preference optimization using rebuttal derived pairs. Experiments with human experts and LLM-as-a-judge show consistent gains in actionability and specificity over strong baselines while maintaining grounding and relevance.

Multimodal large language models are increasingly capable of complex reasoning, yet their performance often degrades when they must externalize a problem through a tool and then reason over the tool's output, specifically when they rely on visual aids. This gap is especially important because real engineering and scientific workflows often rely on visualization tools for analysis, validation, and decision-making. To study this discrepancy, we introduce VAMPS (Visual-Assisted Mathematical Problem Solving), a benchmark for graph-assisted mathematics. VAMPS contains 1,168 multimodal, bilingual multiple-choice question-answer pairs drawn from Iranian University Entrance Exam algebra and calculus problems and expanded with human-reviewed LLM-generated synthetic variants, all selected so that plotting provides a natural solution strategy by revealing intersections, extrema, asymptotes, etc. Designed for both benchmarking and diagnosis, VAMPS goes beyond prior multimodal benchmarks that primarily evaluate reasoning over fixed visual inputs by testing whether a model can benefit from constructing a useful graph and grounding its answer in the resulting visualization. Overall, we found that across a diverse set of models, direct analytical solving surprisingly outperforms tool-enabled visual solving, even on problems where plotting is a natural strategy.

Fitting quantitative models to data is a central step in scientific workflows, yet it remains one of the least automated. Recent agent-based systems leverage language and vision-language models (VLMs) to iteratively propose and refine statistical models, but these systems struggle on more challenging modeling tasks. To address these limitations, we introduce VESTA: Visual Exploration with Statistical Tool Agents, a framework that equips VLMs with a dynamically growing exploration toolkit to guide model refinement through data transformations, hypothesis-driven visualizations, and robust statistical tests. Unlike prior systems that rely on iterative critique alone, VESTA actively explores data before and during refinement by selecting or creating diagnostic tools, which accumulate in the model's context and can be reused later. We evaluate VESTA against established baselines in three toolkit configurations: no tools, static expert-written tools, and dynamic model-written tools. To support this evaluation, we introduce DAWN (Dataset for Automated Workflows and Numerical Modeling), a benchmark targeting distribution fitting and time series modeling with varying difficulty tiers, and culminating in real-world astronomy tasks including modeling initial mass functions and gravitational-wave chirp signals. We find that VESTA's dynamic tool creation outperforms prior agentic pipelines, with the largest gains on complex and domain-specific tasks. We further show that dynamically generated tools are substantially more sophisticated than those produced by existing visual tool-creation systems, covering more diagnostic categories per function and strongly preferring visual outputs that the VLM critic can reason over directly.

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers, hindering the applicability of LLM agents in domains which demand large numbers of highly specialised tools, like in life sciences and medicine. Motivated by the growing trend of scientific studies accompanied by public code repositories, we propose ToolMaker, a novel agentic framework that autonomously transforms papers with code into LLM-compatible tools. Given a short task description and a repository URL, ToolMaker autonomously installs required dependencies and generates code to perform the task, using a closed-loop self-correction mechanism to iteratively diagnose and rectify errors. To evaluate our approach, we introduce a benchmark comprising 15 diverse and complex computational tasks spanning both medical and non-medical domains with over 100 unit tests to objectively assess tool correctness and robustness. ToolMaker correctly implements 80% of the tasks, substantially outperforming current state-of-the-art software engineering agents. ToolMaker therefore is a step towards fully autonomous agent-based scientific workflows.

In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible, rerunning and verifying experiments is usually hard due to a lack of standards. Therefore, reusing existing scientific data processing code from state-of-the-art research is hard as well. This is why we introduce CLAIMED, which has a proven track record in scientific research for addressing the repeatability and reusability issues in modern data-driven science. CLAIMED is a framework to build reusable operators and scalable scientific workflows by supporting the scientist to draw from previous work by re-composing workflows from existing libraries of coarse-grained scientific operators. Although various implementations exist, CLAIMED is programming language, scientific library, and execution environment agnostic.

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

Agentic frameworks powered by Large Language Models (LLMs) can be useful tools in scientific workflows by enabling human-AI co-creation. A key challenge is recommending the next steps during workflow creation without relying solely on LLMs, which risk hallucination and require fine-tuning with scarce proprietary data. We propose an episodic memory architecture that stores and retrieves past workflows to guide agents in suggesting plausible next tasks. By matching current workflows with historical sequences, agents can recommend steps based on prior patterns.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

Machine learning-based surrogate models have emerged as a powerful tool to accelerate simulation-driven scientific workflows. However, their widespread adoption is hindered by the lack of large-scale, diverse, and standardized datasets tailored to physics-based simulations. While existing initiatives provide valuable contributions, many are limited in scope-focusing on specific physics domains, relying on fragmented tooling, or adhering to overly simplistic datamodels that restrict generalization. To address these limitations, we introduce PLAID (Physics-Learning AI Datamodel), a flexible and extensible framework for representing and sharing datasets of physics simulations. PLAID defines a unified standard for describing simulation data and is accompanied by a library for creating, reading, and manipulating complex datasets across a wide range of physical use cases (gitlab.com/drti/plaid). We release six carefully crafted datasets under the PLAID standard, covering structural mechanics and computational fluid dynamics, and provide baseline benchmarks using representative learning methods. Benchmarking tools are made available on Hugging Face, enabling direct participation by the community and contribution to ongoing evaluation efforts (huggingface.co/PLAIDcompetitions).

Large language models are increasingly deployed as autonomous coding agents and have achieved remarkably strong performance on software engineering benchmarks. However, it is unclear whether such success transfers to computational scientific workflows, where tasks require not only strong coding ability, but also the ability to navigate complex, domain-specific procedures and to interpret results in the context of scientific claims. To address this question, we present AutoMat, a benchmark for evaluating LLM-based agents' ability to reproduce claims from computational materials science. AutoMat poses three interrelated challenges: recovering underspecified computational procedures, navigating specialized toolchains, and determining whether the resulting evidence supports a claim. By working closely with subject matter experts, we curate a set of claims from real materials science papers to test whether coding agents can recover and execute the end-to-end workflow needed to support (or undermine) such claims. We then evaluate multiple representative coding agent settings across several foundation models. Our results show that current LLM-based agents obtain low overall success rates on AutoMat, with the best-performing setting achieving a success rate of only 54.1%. Error analysis further reveals that agents perform worst when workflows must be reconstructed from paper text alone and that they fail primarily due to incomplete procedures, methodological deviations, and execution fragility. Taken together, these findings position AutoMat as both a benchmark for computational scientific reproducibility and a tool for diagnosing the current limitations of agentic systems in AI-for-science settings.

The chemical reaction recommendation is to select proper reaction condition parameters for chemical reactions, which is pivotal to accelerating chemical science. With the rapid development of large language models (LLMs), there is growing interest in leveraging their reasoning and planning capabilities for reaction condition recommendation. Despite their success, existing methods rarely explain the rationale behind the recommended reaction conditions, limiting their utility in high-stakes scientific workflows. In this work, we propose ChemMAS, a multi-agent system that reframes condition prediction as an evidence-based reasoning task. ChemMAS decomposes the task into mechanistic grounding, multi-channel recall, constraint-aware agentic debate, and rationale aggregation. Each decision is backed by interpretable justifications grounded in chemical knowledge and retrieved precedents. Experiments show that ChemMAS achieves 20-35% gains over domain-specific baselines and outperforms general-purpose LLMs by 10-15% in Top-1 accuracy, while offering falsifiable, human-trustable rationales, which establishes a new paradigm for explainable AI in scientific discovery.

With the rapid development of Large Language Models (LLMs), AI agents have demonstrated increasing proficiency in scientific tasks, ranging from hypothesis generation and experimental design to manuscript writing. Such agent systems are commonly referred to as "AI Scientists." However, existing AI Scientists predominantly formulate scientific discovery as a standalone search or optimization problem, overlooking the fact that scientific research is inherently a social and collaborative endeavor. Real-world science relies on a complex scientific infrastructure composed of collaborative mechanisms, contribution attribution, peer review, and structured scientific knowledge networks. Due to the lack of modeling for these critical dimensions, current systems struggle to establish a genuine research ecosystem or interact deeply with the human scientific community. To bridge this gap, we introduce OmniScientist, a framework that explicitly encodes the underlying mechanisms of human research into the AI scientific workflow. OmniScientist not only achieves end-to-end automation across data foundation, literature review, research ideation, experiment automation, scientific writing, and peer review, but also provides comprehensive infrastructural support by simulating the human scientific system, comprising: (1) a structured knowledge system built upon citation networks and conceptual correlations; (2) a collaborative research protocol (OSP), which enables seamless multi-agent collaboration and human researcher participation; and (3) an open evaluation platform (ScienceArena) based on blind pairwise user voting and Elo rankings. This infrastructure empowers agents to not only comprehend and leverage human knowledge systems but also to collaborate and co-evolve, fostering a sustainable and scalable innovation ecosystem.

We report a case study of four end-to-end attempts to autonomously generate ML research papers using a pipeline of six LLM agents mapped to stages of the scientific workflow. Of these four, three attempts failed during implementation or evaluation. One completed the pipeline and was accepted to Agents4Science 2025, an experimental inaugural venue that required AI systems as first authors, passing both human and multi-AI review. From these attempts, we document six recurring failure modes: bias toward training data defaults, implementation drift under execution pressure, memory and context degradation across long-horizon tasks, overexcitement that declares success despite obvious failures, insufficient domain intelligence, and weak scientific taste in experimental design. We conclude by discussing four design principles for more robust AI-scientist systems, implications for autonomous scientific discovery, and we release all prompts, artifacts, and outputs at https://github.com/Lossfunk/ai-scientist-artefacts-v1

LLM-based reasoning models have enabled the development of agentic systems that act as co-scientists, assisting in multi-step scientific analysis. However, evaluating these systems is challenging, as it requires realistic, end-to-end research scenarios that integrate data analysis, interpretation, and the generation of new insights from the experimental data. To address this limitation, we introduce HeurekaBench, a framework to create benchmarks with exploratory, open-ended research questions for experimental datasets. Each such question is grounded in a scientific study and its corresponding code repository, and is created using a semi-automated pipeline that leverages multiple LLMs to extract insights and generate candidate workflows, which are then verified against reported findings. We instantiate the framework in single-cell biology to obtain sc-HeurekaBench benchmark and use it to compare state-of-the-art single-cell agents. We further showcase the benefits of our benchmark for quantitatively analyzing current design choices in agentic systems. We find that the addition of a critic module can improve ill-formed responses for open-source LLM-based agents by up to 22% and close the gap with their closed-source counterparts. Overall, HeurekaBench sets a path toward rigorous, end-to-end evaluation of scientific agents, grounding benchmark construction in real scientific workflows.

In professional life sciences workflows, scientists routinely interpret visual artifacts (gel blots, microscopy images, plasmid maps, flow cytometry plots, molecular structures, ...) to inform research decisions. We introduce VIALS, a visual question-answering benchmark with 161 such interpretation tasks, spanning the types of artifacts examined throughout experimental workflows in the biotech industry (rather than polished figures from publications and textbooks). While frontier vision-language models can now fluently describe natural images, we find that they are unable to accurately interpret these scientific images, reflecting limitations in domain knowledge and domain-specific visual reasoning capabilities. In contrast, scientists with relevant domain expertise find these visual interpretation tasks straightforward. AI that cannot similarly interpret such images will have limited utility in professional life sciences workflows, where such artifacts are central to how scientists reason, communicate, and make decisions.

Impact craters are a cornerstone of planetary surface analysis. However, while most deep learning pipelines treat craters solely as a detection problem, critical scientific workflows such as catalog deduplication, cross-observation matching, and morphological analog discovery are inherently retrieval tasks. To address this, we formulate crater analysis as an instance-level image retrieval problem and introduce CraterBench-R, a curated benchmark featuring about 25,000 crater identities with multi-scale gallery views and manually verified queries spanning diverse scales and contexts. Our baseline evaluations across various architectures reveal that self-supervised Vision Transformers (ViTs), particularly those with in-domain pretraining, dominate the task, outperforming generic models with significantly more parameters. Furthermore, we demonstrate that retaining multiple ViT patch tokens for late-interaction matching dramatically improves accuracy over standard single-vector pooling. However, storing all tokens per image is operationally inefficient at a planetary scale. To close this efficiency gap, we propose instance-token aggregation, a scalable, training-free method that selects K seed tokens, assigns the remaining tokens to these seeds via cosine similarity, and aggregates each cluster into a single representative token. This approach yields substantial gains: at K=16, aggregation improves mAP by 17.9 points over raw token selection, and at K=64, it matches the accuracy of using all 196 tokens with significantly less storage. Finally, we demonstrate that a practical two-stage pipeline, with single-vector shortlisting followed by instance-token reranking, recovers 89-94% of the full late-interaction accuracy while searching only a small candidate set. The benchmark is publicly available at hf.co/datasets/jfang/CraterBench-R.

Foundation models for weather science are pre-trained on vast amounts of structured numerical data and outperform traditional weather forecasting systems. However, these models lack language-based reasoning capabilities, limiting their utility in interactive scientific workflows. Large language models (LLMs) excel at understanding and generating text but cannot reason about high-dimensional meteorological datasets. We bridge this gap by building the first agentic framework for weather science. Our framework includes a Python code-based environment for agents (ZephyrusWorld) to interact with weather data, featuring tools including a WeatherBench 2 dataset indexer, geolocator for geocoding from natural language, weather forecasting, climate simulation capabilities, and a climatology module for querying precomputed climatological statistics (e.g., means, extremes, and quantiles) across multiple timescales. We design Zephyrus, a multi-turn LLM-based weather agent that iteratively analyzes weather datasets, observes results, and refines its approach through conversational feedback loops. We accompany the agent with a new benchmark, ZephyrusBench, with a scalable data generation pipeline that constructs diverse question-answer pairs across weather-related tasks, from basic lookups to advanced forecasting, extreme event detection, and counterfactual reasoning. Experiments on this benchmark demonstrate the strong performance of Zephyrus agents over text-only baselines, outperforming them by up to 44 percentage points in correctness. However, the hard tasks are still difficult even with frontier LLMs, highlighting the challenging nature of our benchmark and suggesting room for future development. Our codebase and benchmark are available at https://github.com/Rose-STL-Lab/Zephyrus.

Climate data science faces persistent barriers stemming from the fragmented nature of data sources, heterogeneous formats, and the steep technical expertise required to identify, acquire, and process datasets. These challenges limit participation, slow discovery, and reduce the reproducibility of scientific workflows. In this paper, we present a proof of concept for addressing these barriers through the integration of a curated knowledge graph (KG) with AI agents designed for cloud-native scientific workflows. The KG provides a unifying layer that organizes datasets, tools, and workflows, while AI agents -- powered by generative AI services -- enable natural language interaction, automated data access, and streamlined analysis. Together, these components drastically lower the technical threshold for engaging in climate data science, enabling non-specialist users to identify and analyze relevant datasets. By leveraging existing cloud-ready API data portals, we demonstrate that "a knowledge graph is all you need" to unlock scalable and agentic workflows for scientific inquiry. The open-source design of our system further supports community contributions, ensuring that the KG and associated tools can evolve as a shared commons. Our results illustrate a pathway toward democratizing access to climate data and establishing a reproducible, extensible framework for human--AI collaboration in scientific research.

Large language models (LLMs) integrated with autonomous agents hold significant potential for advancing scientific discovery through automated reasoning and task execution. However, applying LLM agents to drug discovery is still constrained by challenges such as large-scale multimodal data processing, limited task automation, and poor support for domain-specific tools. To overcome these limitations, we introduce DrugPilot, a LLM-based agent system with a parameterized reasoning architecture designed for end-to-end scientific workflows in drug discovery. DrugPilot enables multi-stage research processes by integrating structured tool use with a novel parameterized memory pool. The memory pool converts heterogeneous data from both public sources and user-defined inputs into standardized representations. This design supports efficient multi-turn dialogue, reduces information loss during data exchange, and enhances complex scientific decision-making. To support training and benchmarking, we construct a drug instruction dataset covering eight core drug discovery tasks. Under the Berkeley function-calling benchmark, DrugPilot significantly outperforms state-of-the-art agents such as ReAct and LoT, achieving task completion rates of 98.0%, 93.5%, and 64.0% for simple, multi-tool, and multi-turn scenarios, respectively. These results highlight DrugPilot's potential as a versatile agent framework for computational science domains requiring automated, interactive, and data-integrated reasoning.

Multi-agent systems (MAS) utilizing multiple Large Language Model agents with Retrieval Augmented Generation and that can execute code locally may become beneficial in cosmological data analysis. Here, we illustrate a first small step towards AI-assisted analyses and a glimpse of the potential of MAS to automate and optimize scientific workflows in Cosmology. The system architecture of our example package, that builds upon the autogen/ag2 framework, can be applied to MAS in any area of quantitative scientific research. The particular task we apply our methods to is the cosmological parameter analysis of the Atacama Cosmology Telescope lensing power spectrum likelihood using Monte Carlo Markov Chains. Our work-in-progress code is open source and available at https://github.com/CMBAgents/cmbagent.

Deep research agents are Large Language Model (LLM)-based systems designed for autonomous, multi-step scientific reasoning, and they hold immense potential for accelerating research in the physical sciences. However, comprehensive and in-depth evaluations of their capabilities within this domain remain lacking. To address this gap, we introduce PhySciBench, a benchmark highly relevant to physical science research, comprising 200 expert-curated questions, balanced between physics and chemistry, across six task categories that reflect real-world scientific workflows. Evaluations of state-of-the-art models and agent systems on PhySciBench reveal limited performance; even the strongest baseline, Gemini Deep Research, achieves an accuracy of only 33.5%. Analysis of failure cases identifies three recurrent deficiencies: fragility in extended reasoning chains, limited knowledge transfer across steps, and a lack of physics-grounded self-verification. Motivated by these findings, we develop DelveAgent, a modular multi-agent framework equipped with an adaptive planning loop, dual-granularity memory, and a hierarchical physics-grounded reflection mechanism. Across four scientific benchmarks, DelveAgent improves accuracy by up to 7.5 percentage points while reducing inference costs to approximately one-third of the strongest baseline. These results establish the significance of PhySciBench as a critical benchmark for evaluating AI systems in the physical sciences and demonstrate that architectural specialization can effectively enhance the reliability of autonomous scientific research.

The Materials Genome Initiative catalyzed the proliferation of centralized platforms--SaaS, PaaS, and IaaS--that aggregate computational and experimental resources for accelerated materials discovery. In parallel, breakthroughs in large language models (LLMs) and autonomous agents have created powerful new reasoning capabilities for scientific research. Yet a critical "last mile" problem remains: while we possess world-class models and vast repositories of materials data, we lack the organizational infrastructure to compose these capabilities securely across institutional boundaries. The development of structural and functional materials for harsh service environments--high-temperature alloys, radiation resistant steels, corrosion-resistant coatings--remains characterized by long-term iteration, mechanistic complexity, and high domain expertise--demands that exceed both monolithic agent systems and traditional centralized platforms. To address this gap we propose OpenAaaS, an open-source hierarchical and distributed Agent-as-a-Service framework that enables organized multi-agent collaboration for intelligent materials design. OpenAaaS is built on a single foundational principle: code flows, data stays still. A Master Agent plans and decomposes complex research tasks without requiring direct access to subordinate agents' managed data and computational resources. Sub-agents, deployed as near-data execution nodes, retain full sovereignty over local datasets, proprietary algorithms, and specialized hardware. This architecture guarantees that raw data never leaves its domain of origin while enabling cross-scale, cross-domain secure integration of previously isolated materials intelligence silos. We validate the framework through two representative case studies: (i) AlphaAgent, an evidence-grounded materials literature analysis executor that achieves 4.66/5.0 on deep analytical questions against single-pass RAG baselines; and (ii) an ultra-large-scale hexa-high-entropy alloy descriptor database service that demonstrates secure near-data execution and domain-specific scientific workflows under strict data-sovereignty constraints. OpenAaaS establishes a principled pathway toward "organized research" via agent collectives, offering a scalable foundation for next-generation materials intelligent design platforms. All source code is available at https://github.com/Wolido/OpenAaaS.

Scientific discovery workflows usually contain and rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Such informative lab notes preserve evolving scientific reasoning and author uncertainty, rather than polished final results exhibited in publications, providing a valuable opportunity for AI to engage in scientific exploration at a more comprehensive and deeper level. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because lab notes often intermingle validated observations, tentative judgments, and possible experimental next steps within the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across seven conditions and three wet-lab sessions, Notes2Skills is the only configuration that neither mistakes uncertain notes for firm instructions nor discards firm ones. We show that certainty preservation is the missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

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.

We define Agency as the emergent capacity of AI systems to function as autonomous agents actively discovering problems, formulating hypotheses, and executing solutions through self-directed engagement with environments and tools. This fundamental capability marks the dawn of the Age of AI Agency, driven by a critical industry shift: the urgent need for AI systems that don't just think, but work. While current AI excels at reasoning and generating responses, industries demand autonomous agents that can execute tasks, operate tools, and drive real-world outcomes. As agentic intelligence becomes the defining characteristic separating cognitive systems from productive workers, efficiently cultivating machine autonomy becomes paramount. Current approaches assume that more data yields better agency, following traditional scaling laws from language modeling. We fundamentally challenge this paradigm. LIMI (Less Is More for Intelligent Agency) demonstrates that agency follows radically different development principles. Through strategic focus on collaborative software development and scientific research workflows, we show that sophisticated agentic intelligence can emerge from minimal but strategically curated demonstrations of autonomous behavior. Using only 78 carefully designed training samples, LIMI achieves 73.5% on comprehensive agency benchmarks, dramatically outperforming state-of-the-art models: Kimi-K2-Instruct (24.1%), DeepSeek-V3.1 (11.9%), Qwen3-235B-A22B-Instruct (27.5%), and GLM-4.5 (45.1%). Most strikingly, LIMI demonstrates 53.7% improvement over models trained on 10,000 samples-achieving superior agentic intelligence with 128 times fewer samples. Our findings establish the Agency Efficiency Principle: machine autonomy emerges not from data abundance but from strategic curation of high-quality agentic demonstrations.

Despite the growing adoption of large language models (LLMs) in scientific research workflows, automated support for academic rebuttal, a crucial step in academic communication and peer review, remains largely underexplored. Existing approaches typically rely on off-the-shelf LLMs or simple pipelines, which struggle with long-context understanding and often fail to produce targeted and persuasive responses. In this paper, we propose DRPG, an agentic framework for automatic academic rebuttal generation that operates through four steps: Decompose reviews into atomic concerns, Retrieve relevant evidence from the paper, Plan rebuttal strategies, and Generate responses accordingly. Notably, the Planner in DRPG reaches over 98% accuracy in identifying the most feasible rebuttal direction. Experiments on data from top-tier conferences demonstrate that DRPG significantly outperforms existing rebuttal pipelines and achieves performance beyond the average human level using only an 8B model. Our analysis further demonstrates the effectiveness of the planner design and its value in providing multi-perspective and explainable suggestions. We also showed that DRPG works well in a more complex multi-round setting. These results highlight the effectiveness of DRPG and its potential to provide high-quality rebuttal content and support the scaling of academic discussions. Codes for this work are available at https://github.com/ulab-uiuc/DRPG-RebuttalAgent.

There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular structures with spectral information, is the core step in understanding the experimental results and to close the loop. However, current approaches usually divide the task into either database-dependent retrieval and database-independent generation and neglect the inherent complementarity between them. In this study, we proposed Vib2Mol, a general deep learning model designed to flexibly handle diverse spectrum-to-structure tasks according to the available prior knowledge by bridging the retrieval and generation. It achieves state-of-the-art performance, even for the most demanding Raman spectra, over previous models in predicting reaction products and sequencing peptides as well as analyzing experimental spectra and integrating multi-modal spectral data. Vib2Mol enables vibrational spectroscopy a real-time guide for autonomous scientific discovery workflows.

Large language models (LLMs) have enabled agent-based systems that aim to automate scientific research workflows. Most existing approaches focus on fully autonomous discovery, where AI systems generate research ideas, conduct analyses, and produce manuscripts with minimal human involvement. However, empirical research in economics and the social sciences poses additional constraints: research questions must be grounded in available datasets, identification strategies require careful design, and human judgment remains essential for evaluating economic significance. We introduce HLER (Human-in-the-Loop Economic Research), a multi-agent architecture that supports empirical research automation while preserving critical human oversight. The system orchestrates specialized agents for data auditing, data profiling, hypothesis generation, econometric analysis, manuscript drafting, and automated review. A key design principle is dataset-aware hypothesis generation, where candidate research questions are constrained by dataset structure, variable availability, and distributional diagnostics, reducing infeasible or hallucinated hypotheses. HLER further implements a two-loop architecture: a question quality loop that screens and selects feasible hypotheses, and a research revision loop where automated review triggers re-analysis and manuscript revision. Human decision gates are embedded at key stages, allowing researchers to guide the automated pipeline. Experiments on three empirical datasets show that dataset-aware hypothesis generation produces feasible research questions in 87% of cases (versus 41% under unconstrained generation), while complete empirical manuscripts can be produced at an average API cost of 0.8-1.5 per run. These results suggest that Human-AI collaborative pipelines may provide a practical path toward scalable empirical research.

Diffusion and flow models have become the dominant paradigm for generative modeling on Riemannian manifolds, with successful applications in protein backbone generation and DNA sequence design. However, these methods require tens to hundreds of neural network evaluations at inference time, which can become a computational bottleneck in large-scale scientific sampling workflows. We introduce Riemannian MeanFlow~(RMF), a framework for learning flow maps directly on manifolds, enabling high-quality generations with as few as one forward pass. We derive three equivalent characterizations of the manifold average velocity (Eulerian, Lagrangian, and semigroup identities), and analyze parameterizations and stabilization techniques to improve training on high-dimensional manifolds. In promoter DNA design and protein backbone generation settings, RMF achieves comparable sample quality to prior methods while requiring up to 10times fewer function evaluations. Finally, we show that few-step flow maps enable efficient reward-guided design through reward look-ahead, where terminal states can be predicted from intermediate steps at minimal additional cost.

Scientific literature search often requires more than retrieving papers from a single query: users' intents are underspecified, preference-dependent, and evolve through interaction. Existing search agents typically rely on fixed pipelines or implicit language-only reasoning, making their search strategies difficult to control, inspect, and refine. We introduce PaperPilot, a multi-turn literature search agent that frames scientific search as workflow induction. Given an anchor paper and a user query, PaperPilot constructs an executable DAG of paper-search operators, including keyword search, citation expansion, filtering, scoring, reranking, and evidence extraction. User feedback is then used to refine both the query and the workflow itself. We train PaperPilot with supervised workflow imitation and preference optimization over controlled workflow corruptions. Experiments show that PaperPilot-9B improves over the base Qwen3.5-9B toolset agent under multi-turn interaction, increasing Hit@5 from 58.0 to 77.0, MRR from 47.5 to 59.4, and nDCG@10 from 26.8 to 32.5, while reducing workflow execution errors from 9.5% to 0%. These results show that explicit, editable search workflows provide an effective and controllable interface for aligning literature search agents with complex scientific intent.

Extracting structured information from unstructured text is crucial for modeling real-world processes, but traditional schema mining relies on semi-structured data, limiting scalability. This paper introduces schema-miner, a novel tool that combines large language models with human feedback to automate and refine schema extraction. Through an iterative workflow, it organizes properties from text, incorporates expert input, and integrates domain-specific ontologies for semantic depth. Applied to materials science--specifically atomic layer deposition--schema-miner demonstrates that expert-guided LLMs generate semantically rich schemas suitable for diverse real-world applications.

Recent advances in agentic visualization have enabled the translation of natural language into executable scientific visualization (SciVis) workflows. While general-purpose coding agents show strong capabilities, they often lack the tool-specific expertise required for SciVis tasks. In this work, we present SciVisAgentSkills, a collection of reusable agent skills that augment coding agents for scientific data analysis and visualization by encoding environment assumptions, tool usage patterns, and domain heuristics across scientific tools such as ParaView, napari, VMD, and TTK. We evaluate these skills on Codex and Claude Code using SciVisAgentBench, a benchmark of 108 expert-designed multi-step tasks. Results show that agent skills improve mean task scores across the evaluated suites, with token-efficiency benefits that depend on the agent harness and tool setting. These findings highlight the importance of structured procedural knowledge for enabling reliable, long-horizon SciVis workflows, while also showing that skills should be studied alongside the execution harness that loads and applies them. The skills are available at https://github.com/KuangshiAi/SciVisAgentSkills.

The integration of Large Language Models (LLMs) and Multimodal LLMs (MLLMs) into scientific peer-review workflows introduces novel and significant risks for adversarial manipulation, especially given the multimodal nature of scientific papers where figures, not just text, convey core evidence. This creates a significant gap: current robustness studies on AI peer-review are overwhelmingly text-only. Moreover, the problem is distinct from standard jailbreaking, as a peer-review attack seeks to induce a domain-specific, targeted failure (e.g., "inflate this score") rather than a general safety policy violation, for which no practical defenses exist. To address this, we introduce PaperGuard, the first comprehensive benchmark designed to systematically evaluate and defend AI-generated peer-review against these domain-specific, cross-modal attacks. Our framework is built on three pillars: (1) a new multimodal peer-review dataset spanning multiple scientific domains; (2) a unified suite of attacks, including black-box prompt injections and white-box perturbations, specifically designed to target both text (GCG) and figures (PGD); and (3) a practical defense, motivated by the long-context challenge of academic papers, that uses chunk-based embedding search to efficiently localize and mitigate harmful instructions. Our extensive experiments, conducted across state-of-the-art models, confirm that AI reviewers are pervasively vulnerable. PaperGuard establishes the foundational benchmark, protocols, and actionable defense necessary to pioneer trustworthy, attack-resilient AI-assisted scholarly reviewing.

The growing volume of academic papers has made it increasingly difficult for researchers to efficiently extract key information. While large language models (LLMs) based agents are capable of automating question answering (QA) workflows for scientific papers, there still lacks a comprehensive and realistic benchmark to evaluate their capabilities. Moreover, training an interactive agent for this specific task is hindered by the shortage of high-quality interaction trajectories. In this work, we propose AirQA, a human-annotated comprehensive paper QA dataset in the field of artificial intelligence (AI), with 13,948 papers and 1,246 questions, that encompasses multi-task, multi-modal and instance-level evaluation. Furthermore, we propose ExTrActor, an automated framework for instruction data synthesis. With three LLM-based agents, ExTrActor can perform example generation and trajectory collection without human intervention. Evaluations of multiple open-source and proprietary models show that most models underperform on AirQA, demonstrating the quality of our dataset. Extensive experiments confirm that ExTrActor consistently improves the multi-turn tool-use capability of small models, enabling them to achieve performance comparable to larger ones.

Large language models (LLMs) show the promise in supporting scientific research implementation, yet their ability to generate correct and executable code remains limited. Existing works largely adopt one-shot settings, ignoring the iterative and feedback-driven nature of realistic workflows of scientific research development. To address this gap, we present RECODE-H, a benchmark of 102 tasks from research papers and repositories that evaluates LLM agents through multi-turn interactions with LLM-simulated human feedback. It includes structured instructions,unit tests, and a five-level feedback hierarchy to reflect realistic researcher-agent collaboration. We further present ReCodeAgent, a framework that integrates feedback into iterative code generation. Experiments with leading LLMs, including GPT-5, Claude-Sonnet-4, DeepSeek-V3.1, and Gemini 2.5, show substantial performance gains with richer feedback, while also highlighting ongoing challenges in the generation of complex research code. RECODE-H establishes a foundation for developing adaptive, feedback-driven LLM agents in scientific research implementation

As large language models and harness frameworks continue to advance, agents operating in terminals are increasingly capable of performing a broader range of general computer-use tasks beyond coding. However, existing benchmarks do not adequately evaluate general-purpose terminal computer-use agents (TUAs): general computer-use benchmarks primarily target graphical user interfaces (GUIs), whereas terminal-based benchmarks largely emphasize technical and programming-centric workflows historically native to the shell. We introduce TUA-Bench, a general-purpose benchmark for terminal-use agents. TUA-Bench includes 120 real-world tasks across five task families, covering routine digital activities-including document editing, email management, and live-web information seeking-as well as scientific and engineering workflows co-designed with PhD-level domain experts that require specialized software. This breadth distinguishes TUA-Bench from prior shell-focused or domain-specific benchmarks. Each task is manually designed, runs in a real terminal with a deterministic setup script, and is evaluated by an execution-based scoring protocol. We find that the strongest frontier agent, Claude Code with Claude Opus 4.8 max reasoning effort, achieves 65.8% overall performance, with substantial gaps across both tracks. By providing a broad and realistic evaluation of terminal-use capabilities, TUA-Bench aims to accelerate the transition from narrow, task-specific assistants to general-purpose agents capable of operating reliably across diverse digital environments.

The rapid development of large language models (LLMs) has renewed interest in agent-based modeling (ABM). However, current LLM-based ABM research faces several key challenges: modeling evolving agent-environment interactions, enabling flexible counterfactual reasoning, and automating simulation workflows for scientific research. In this paper, we propose Eco3S, a socio-economic system simulation framework for economic research and policy analysis that addresses these challenges through three key mechanisms: (1) Co-evolving Environment Design, a bidirectional feedback loop where agents and the environment co-evolve, producing realistic emergent behaviors; (2) Structural Causal Simulation, a structural causal model (SCM)-inspired counterfactual mechanism that allows flexible interventions for diverse causal inference tasks; (3) Simulation-Analysis-Refinement Paradigm, a self-corrective mechanism that iteratively refines experimental designs based on prior simulation results. Experiments on diverse economic scenarios confirm Eco3S's effectiveness in replicating multiple established economic studies (canal decay, origins of governance, and information propagation) and phenomena across domains. Additional results further demonstrate its scalability and generalizability, highlighting the framework's potential for rigorous economic research and policy-making.

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

In recent times, transformer networks have achieved state-of-the-art performance in a wide range of natural language processing tasks. Here we present a workflow based on the fine-tuning of BERT models for different downstream tasks, which results in the automated extraction of structured information from unstructured natural language in scientific literature. Contrary to existing methods for the automated extraction of structured compound-property relations from similar sources, our workflow does not rely on the definition of intricate grammar rules. Hence, it can be adapted to a new task without requiring extensive implementation efforts and knowledge. We test our data-extraction workflow by automatically generating a database for Curie temperatures and one for band gaps. These are then compared with manually-curated datasets and with those obtained with a state-of-the-art rule-based method. Furthermore, in order to showcase the practical utility of the automatically extracted data in a material-design workflow, we employ them to construct machine-learning models to predict Curie temperatures and band gaps. In general we find that, although more noisy, automatically extracted datasets can grow fast in volume and that such volume partially compensates for the inaccuracy in downstream tasks.

Generating engaging, accurate short-form videos from scientific papers is challenging due to content complexity and the gap between expert authors and readers. Existing end-to-end methods often suffer from factual inaccuracies and visual artifacts, limiting their utility for scientific dissemination. To address these issues, we propose SciTalk, a novel multi-LLM agentic framework, grounding videos in various sources, such as text, figures, visual styles, and avatars. Inspired by content creators' workflows, SciTalk uses specialized agents for content summarization, visual scene planning, and text and layout editing, and incorporates an iterative feedback mechanism where video agents simulate user roles to give feedback on generated videos from previous iterations and refine generation prompts. Experimental evaluations show that SciTalk outperforms simple prompting methods in generating scientifically accurate and engaging content over the refined loop of video generation. Although preliminary results are still not yet matching human creators' quality, our framework provides valuable insights into the challenges and benefits of feedback-driven video generation. Our code, data, and generated videos will be publicly available.

Scientific machine learning papers typically make computational claims, e.g., that the relative mean square error is less than 5% or that the 95% predictive credible interval covers the test data. A coding agent can be prompted to replicate those claims from paper materials alone, but the prompt does not by itself reliably preserve progress or check whether generated evidence supports the paper's claims. We introduce Paper-replication, a workflow that makes each selected paper claim a target with recorded evidence, and implement it as a coding-agent skill. The workflow makes the agent record those targets, reconstruct the paper's method, run computational experiments, link generated outputs to provenance and comparisons with the paper's claims, record where matched evidence appears in the replication report, and pass validation checks before completion. We evaluate Paper-replication on twelve independent runs across four scientific machine learning papers. All twelve workspaces pass the completion gate, and all 158 recorded targets are matched with report coverage. Even in this completed workspace state, repeated runs differ in how papers are divided into targets, in numerical fidelity to the source papers, in elapsed replication time, in the number of intermediate executions replaced before final evidence is accepted, and in the rules used to accept evidence. Paper-replication makes completion depend on workspace evidence and validation checks rather than on the agent's final message.

Scientific research follows multi-turn, multi-step workflows that require proactively searching the literature, consulting figures and tables, and integrating evidence across papers to align experimental settings and support reproducible conclusions. This joint capability is not systematically assessed in existing benchmarks, which largely under-evaluate proactive search, multi-evidence integration and sustained evidence use over time. In this work, we introduce EpiBench, an episodic multi-turn multimodal benchmark that instantiates short research workflows. Given a research task, agents must navigate across papers over multiple turns, align evidence from figures and tables, and use the accumulated evidence in the memory to answer objective questions that require cross paper comparisons and multi-figure integration. EpiBench introduces a process-level evaluation framework for fine-grained testing and diagnosis of research agents. Our experiments show that even the leading model achieves an accuracy of only 29.23% on the hard split, indicating substantial room for improvement in multi-turn, multi-evidence research workflows, providing an evaluation platform for verifiable and reproducible research agents.

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.

Editing the figures in a research paper is a routine and time-consuming part of everyday research practice: authors relabel components, rearrange panels, and restyle visuals as they revise their manuscripts. Automating this editing workflow under a natural-language instruction, however, is challenging, because a scientific figure is a dense infographic in which heterogeneous visual elements such as schematics, plots, photos, captions, and arrows are composed under a tight visual grammar to advance a specific argument. To address this, we present SciDiagramEdit, a benchmark and skill-evolution framework that learns from natural paper revisions and operates on the figure's editable vector source, where users can inspect and co-edit individual primitives alongside the agent. Our benchmark mines before/after figure pairs from arXiv version histories, each grounded in the authors' own revision intent. To accommodate the diversity of editing instructions, we adopt agentic learning via skill evolution: an agentic proposer continually refines the agent's skill specification from execution traces over multiple epochs. The resulting skill progressively lifts edit accuracy on a held-out validation set, providing evidence that natural paper revisions are an effective training signal for instruction-driven figure editing.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.

Critical peer review of scientific manuscripts presents a significant challenge for Large Language Models (LLMs), partly due to data limitations and the complexity of expert reasoning. This report introduces Persistent Workflow Prompting (PWP), a potentially broadly applicable prompt engineering methodology designed to bridge this gap using standard LLM chat interfaces (zero-code, no APIs). We present a proof-of-concept PWP prompt for the critical analysis of experimental chemistry manuscripts, featuring a hierarchical, modular architecture (structured via Markdown) that defines detailed analysis workflows. We develop this PWP prompt through iterative application of meta-prompting techniques and meta-reasoning aimed at systematically codifying expert review workflows, including tacit knowledge. Submitted once at the start of a session, this PWP prompt equips the LLM with persistent workflows triggered by subsequent queries, guiding modern reasoning LLMs through systematic, multimodal evaluations. Demonstrations show the PWP-guided LLM identifying major methodological flaws in a test case while mitigating LLM input bias and performing complex tasks, including distinguishing claims from evidence, integrating text/photo/figure analysis to infer parameters, executing quantitative feasibility checks, comparing estimates against claims, and assessing a priori plausibility. To ensure transparency and facilitate replication, we provide full prompts, detailed demonstration analyses, and logs of interactive chats as supplementary resources. Beyond the specific application, this work offers insights into the meta-development process itself, highlighting the potential of PWP, informed by detailed workflow formalization, to enable sophisticated analysis using readily available LLMs for complex scientific tasks.

We propose a semi-automatic staging area for efficiently building an accurate database of experimental physical properties of superconductors from literature, called SuperCon2, to enrich the existing manually-built superconductor database SuperCon. Here we report our curation interface (SuperCon2 Interface) and a workflow managing the state transitions of each examined record, to validate the dataset of superconductors from PDF documents collected using Grobid-superconductors in a previous work. This curation workflow allows both automatic and manual operations, the former contains ``anomaly detection'' that scans new data identifying outliers, and a ``training data collector'' mechanism that collects training data examples based on manual corrections. Such training data collection policy is effective in improving the machine-learning models with a reduced number of examples. For manual operations, the interface (SuperCon2 interface) is developed to increase efficiency during manual correction by providing a smart interface and an enhanced PDF document viewer. We show that our interface significantly improves the curation quality by boosting precision and recall as compared with the traditional ``manual correction''. Our semi-automatic approach would provide a solution for achieving a reliable database with text-data mining of scientific documents.

Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical scientific use-cases more fragmented and less clear in pathways to impact. This paper introduces an ontology for scientific benchmarking developed through a unified, community-driven effort that extends the MLCommons ecosystem to cover physics, chemistry, materials science, biology, climate science, and more. Building on prior initiatives such as XAI-BENCH, FastML Science Benchmarks, PDEBench, and the SciMLBench framework, our effort consolidates a large set of disparate benchmarks and frameworks into a single taxonomy of scientific, application, and system-level benchmarks. New benchmarks can be added through an open submission workflow coordinated by the MLCommons Science Working Group and evaluated against a six-category rating rubric that promotes and identifies high-quality benchmarks, enabling stakeholders to select benchmarks that meet their specific needs. The architecture is extensible, supporting future scientific and AI/ML motifs, and we discuss methods for identifying emerging computing patterns for unique scientific workloads. The MLCommons Science Benchmarks Ontology provides a standardized, scalable foundation for reproducible, cross-domain benchmarking in scientific machine learning. A companion webpage for this work has also been developed as the effort evolves: https://mlcommons-science.github.io/benchmark/

As large language models (LLMs) advance, the ultimate vision for their role in science is emerging: we could build an AI collaborator to effectively assist human beings throughout the entire scientific research process. We refer to this envisioned system as ResearchGPT. Given that scientific research progresses through multiple interdependent phases, achieving this vision requires rigorous benchmarks that evaluate the end-to-end workflow rather than isolated sub-tasks. To this end, we contribute CS-54k, a high-quality corpus of scientific Q&A pairs in computer science, built from 14k CC-licensed papers. It is constructed through a scalable, paper-grounded pipeline that combines retrieval-augmented generation (RAG) with multi-stage quality control to ensure factual grounding. From this unified corpus, we derive two complementary subsets: CS-4k, a carefully curated benchmark for evaluating AI's ability to assist scientific research, and CS-50k, a large-scale training dataset. Extensive experiments demonstrate that CS-4k stratifies state-of-the-art LLMs into distinct capability tiers. Open models trained on CS-50k with supervised training and reinforcement learning demonstrate substantial improvements. Even 7B-scale models, when properly trained, outperform many larger proprietary systems, such as GPT-4.1, GPT-4o, and Gemini 2.5 Pro. This indicates that making AI models better research assistants relies more on domain-aligned training with high-quality data than on pretraining scale or general benchmark performance. We release CS-4k and CS-50k in the hope of fostering AI systems as reliable collaborators in CS research.

While synthetic data has proven effective for improving scientific reasoning in the text domain, multimodal reasoning remains constrained by the difficulty of synthesizing scientifically rigorous images. Existing Text-to-Image (T2I) models often produce outputs that are visually plausible yet scientifically incorrect, resulting in a persistent visual-logic divergence that limits their value for downstream reasoning. Motivated by recent advances in next-generation T2I models, we conduct a systematic study of scientific image synthesis across generation paradigms, evaluation, and downstream use. We analyze both direct pixel-based generation and programmatic synthesis, and propose ImgCoder, a logic-driven framework that follows an explicit "understand - plan - code" workflow to improve structural precision. To rigorously assess scientific correctness, we introduce SciGenBench, which evaluates generated images based on information utility and logical validity. Our evaluation reveals systematic failure modes in pixel-based models and highlights a fundamental expressiveness-precision trade-off. Finally, we show that fine-tuning Large Multimodal Models (LMMs) on rigorously verified synthetic scientific images yields consistent reasoning gains, with potential scaling trends analogous to the text domain, validating high-fidelity scientific synthesis as a viable path to unlocking massive multimodal reasoning capabilities.

Recent efforts have aimed to automate scientific diagram generation from paper content (Lin et al., 2026; Zhu et al., 2026a). However, fully satisfying an author's visual and communicative preferences in a single turn is challenging: in our formative user study (N = 14), all participants requested further revisions after viewing an initial draft, and 86% of them rated the refined diagrams as more satisfactory. Despite the clear demand, the multi-turn workflow remains largely underexplored. To bridge this gap, we present MTPaperBananaBench, a benchmark for multi-turn diagram generation containing 292 images annotated with 3,518 user requirements. To reduce expensive human studies and enable scalable benchmarking, we construct a user simulator that, at each turn, identifies unsatisfied requirements and converts k of them into natural language feedback. Evaluating both requirement satisfaction and overall diagram quality reveals two key failure modes shared across baseline multiturn systems: (1) quality drift, where diagram quality progressively declines over turns, and (2) forgetting, where previously implemented features are lost in subsequent turns. To address these issues, we introduce PaperBanana-Interact, a multi-agent system that refines diagrams via an internal critique-and-refine loop. PaperBanana-Interact consistently improves rather than degrades diagram quality across turns, outperforming baselines by 11.9-18.6 points in quality score and reducing forgetting by 3.7-6.2 points.

Existing benchmarks for scientific data analysis evaluate LLMs primarily on code execution or workflow completion, overlooking that scientific analysis serves to support distinct types of scientific claims: hypothesis exploration, statistical inference, mechanistic explanation, each with different assumptions and validity criteria. We introduce SDABench, a benchmark that reorganizes evaluation around six capabilities (descriptive, exploratory, inferential, predictive, causal, and mechanistic) across five domains (Biology, Chemistry, Environment, Geography, Physics). SDABench comprises 527 real-data instances (SDA-Real) and 6000 synthetic instances (SDA-Synth), each in both multiple-choice and open-ended formats, constructed through an automated pipeline. Evaluating 15 representative LLMs, we find that models handle descriptive analysis well but degrade sharply on tasks requiring assumption selection, latent-process modeling, or mechanistic reasoning. SDABench further provides a five-stage error analysis framework that locates where LLMs fail: more advanced models more reliably identify the relevant scope and variables, but still struggle to select appropriate analytical procedures, model variable relationships, and draw valid conclusions.

AI technologies are moving rapidly from research to production. With the popularity of Foundation Models (FMs) that generate text, images, and video, AI-based systems are increasing their complexity. Compared to traditional AI-based software, systems employing FMs, or GenAI-based systems, are more difficult to design due to their scale and versatility. This makes it necessary to document best practices, known as design patterns in software engineering, that can be used across GenAI applications. Our first contribution is to formalize two techniques, Task Decomposition and Retrieval-Augmented Generation (RAG), as design patterns for GenAI-based systems. We discuss their trade-offs in terms of software quality attributes and comment on alternative approaches. We recommend to AI practitioners to consider these techniques not only from a scientific perspective but also from the standpoint of desired engineering properties such as flexibility, maintainability, safety, and security. As a second contribution, we describe our industry experience applying Task Decomposition and RAG to build a complex real-world GenAI application for enterprise users: Workflow Generation. The task of generating workflows entails generating a specific plan using data from the system environment, taking as input a user requirement. As these two patterns affect the entire AI development cycle, we explain how they impacted the dataset creation, model training, model evaluation, and deployment phases.

The exponential growth of academic publications poses challenges for the research process, such as literature review and procedural planning. Large Language Models (LLMs) have emerged as powerful AI tools, especially when combined with additional tools and resources. Recent LLM-powered frameworks offer promising solutions for handling complex domain-specific tasks, yet their domain-specific implementation limits broader applicability. This highlights the need for LLM-integrated systems that can assist in cross-disciplinary tasks, such as streamlining the research process across science and engineering disciplines. To address this need, we introduce Artificial Research Innovator Assistant (ARIA), a four-agent, multi-LLM framework. By emulating a team of expert assistants, ARIA systematically replicates the human research workflow to autonomously search, retrieve, and filter hundreds of papers, subsequently synthesizing relevant literature into actionable research procedures. In a case study on dropwise condensation enhancement, ARIA demonstrates its capability to streamline research tasks within an hour, maintaining user oversight during execution and ultimately liberating researchers from time-intensive tasks.

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

Scientific illustrations are essential for depicting conceptual designs, methodologies, and experimental workflows in research, playing a pivotal role in communicating complex academic insights. However, creating high-quality scientific illustrations remains a labor-intensive task for human scientists. While recent generative image models have advanced prompt-based editing, the synthesis of fully editable figures remains a fundamental challenge. Valid editability involves structured transformations of graphical elements, scales, attributes, and text, rather than simple pixel-level changes. Existing models generate raster outputs that do not support manual correction or layout adjustment, limiting their utility in scientific publishing, where editable vector figures are typically required for submission. To address this challenge, we introduce LiveFigure, an agentic framework driven by VLM agents that imitates the multi-step drawing workflow of human researchers. It first plans figure blueprints by drawing inspiration from high-quality references in previous works, then generates executable scripts that produce figures via the PowerPoint interface based on skills and experience, and finally refines the outputs with targeted visual diagnostics, producing fully vectorized, editable figures that meet publication standards. Extensive experiments demonstrate that LiveFigure generates inherently editable figures, achieving 80% publication-readiness in only 17 manual edits, far surpassing the 24% rate of the strongest baseline, NanoBanana. Human preference studies further validate this advantage, with LiveFigure securing a 60% win rate against NanoBanana. Our code is available at https://github.com/tsinghua-fib-lab/LiveFigure.git.

Modern scientific research relies on large-scale data, complex workflows, and specialized tools, which existing LLMs and tool-based agents struggle to handle due to limitations in long-horizon planning, robust goal maintenance, and continual learning from execution. To address these issues, in this work, we propose S1-NexusAgent, a self-evolving agent framework designed for multidisciplinary scientific research. S1-NexusAgent adopts a hierarchical Plan-and-CodeAct execution paradigm, decoupling global scientific planning from subtask-level tool execution through a dual-loop architecture, thereby enabling stable modeling of complex research workflows. The system natively supports the Model Context Protocol (MCP), integrates up to thousands of cross-disciplinary scientific tools, and achieves efficient orchestration of heterogeneous research tools via intention-aware dynamic tool retrieval and hot-plug mechanisms. To address long-context and large-scale data challenges in scientific settings, S1-NexusAgent introduces object-reference-based sparse context management, which enables sub-task context isolation and intermediate result compression. Building on this, a Critic Agent automatically evaluates complete execution trajectories and distills high-quality research paths into reusable Scientific Skills, forming a closed loop for continuous self-evolution, which is valuable for sustainable and long-horizon scientific research. Experiments on authoritative scientific benchmarks involving long-horizon planning and complex specialized tool orchestration, including biomini-eval (biology), ChemBench (chemistry), and MatSciBench (material science), demonstrate that S1-NexusAgent achieves state-of-the-art performance, validating its effectiveness and generalization capability in complex scientific tasks.

The history of science is punctuated by serendipitous discoveries, where unexpected observations, rather than targeted hypotheses, opened new fields of inquiry. While modern autonomous laboratories excel at accelerating hypothesis testing, their optimization for efficiency risks overlooking these crucial, unplanned findings. To address this gap, we introduce SciLink, an open-source, multi-agent artificial intelligence framework designed to operationalize serendipity in materials research by creating a direct, automated link between experimental observation, novelty assessment, and theoretical simulations. The framework employs a hybrid AI strategy where specialized machine learning models perform quantitative analysis of experimental data, while large language models handle higher-level reasoning. These agents autonomously convert raw data from materials characterization techniques into falsifiable scientific claims, which are then quantitatively scored for novelty against the published literature. We demonstrate the framework's versatility across diverse research scenarios, showcasing its application to atomic-resolution and hyperspectral data, its capacity to integrate real-time human expert guidance, and its ability to close the research loop by proposing targeted follow-up experiments. By systematically analyzing all observations and contextualizing them, SciLink provides a practical framework for AI-driven materials research that not only enhances efficiency but also actively cultivates an environment ripe for serendipitous discoveries, thereby bridging the gap between automated experimentation and open-ended scientific exploration.

Understanding the current capabilities and risks of AI Scientist systems is essential for ensuring trustworthy and sustainable AI-driven scientific progress while preserving the integrity of the academic ecosystem. To this end, we develop Jr. AI Scientist, a state-of-the-art autonomous AI scientist system that mimics the core research workflow of a novice student researcher: Given the baseline paper from the human mentor, it analyzes its limitations, formulates novel hypotheses for improvement, validates them through rigorous experimentation, and writes a paper with the results. Unlike previous approaches that assume full automation or operate on small-scale code, Jr. AI Scientist follows a well-defined research workflow and leverages modern coding agents to handle complex, multi-file implementations, leading to scientifically valuable contributions. For evaluation, we conducted automated assessments using AI Reviewers, author-led evaluations, and submissions to Agents4Science, a venue dedicated to AI-driven scientific contributions. The findings demonstrate that Jr. AI Scientist generates papers receiving higher review scores than existing fully automated systems. Nevertheless, we identify important limitations from both the author evaluation and the Agents4Science reviews, indicating the potential risks of directly applying current AI Scientist systems and key challenges for future research. Finally, we comprehensively report various risks identified during development. We hope these insights will deepen understanding of current progress and risks in AI Scientist development.

The rapid advancements of AI agents have ignited the long-held ambition of leveraging them to accelerate scientific discovery. Achieving this goal requires a deep understanding of the frontiers of human knowledge. As such, Humanity's Last Exam (HLE) provides an exceptionally challenging touchstone for evaluating scientific AI agents. In this work, we aim to construct the foundational architecture for general-purpose agents and validate the capabilities through leading performance on HLE. To achieve this, we introduce X-Master, a tool-augmented reasoning agent designed to emulate human researchers by interacting flexibly with external tools during its reasoning process. This agent, guided by the conceptualization of code as an interaction language, can flexibly leverage built-in Python libraries and our customized tools to augment the reasoning. We further scale its capabilities through X-Masters, a scattered-and-stacked agentic workflow that systematically enhances breadth and depth of reasoning. Our open-source solution, X-Masters, sets a new state-of-the-art record on HLE with a score of 32.1%, surpassing OpenAI's and Google's Deep Research (26.6% and 26.9%) and becoming the first to exceed the 30% threshold. This work allows us to gain a deeper understanding of complex task-solving and accumulates valuable experience that can inform future advancements, guiding subsequent model training.

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.

The integration of Large Language Models (LLMs) into the scientific ecosystem raises fundamental questions about the creativity and originality of AI-generated research. Recent work has identified ``smart plagiarism'' as a concern in single-step prompting approaches, where models reproduce existing ideas with terminological shifts. This paper investigates whether agentic workflows -- multi-step systems employing iterative reasoning, evolutionary search, and recursive decomposition -- can generate more novel and feasible research plans. We benchmark five reasoning architectures: Reflection-based iterative refinement, Sakana AI v2 evolutionary algorithms, Google Co-Scientist multi-agent framework, GPT Deep Research (GPT-5.1) recursive decomposition, and Gemini~3 Pro multimodal long-context pipeline. Using evaluations from thirty proposals each on novelty, feasibility, and impact, we find that decomposition-based and long-context workflows achieve mean novelty of 4.17/5, while reflection-based approaches score significantly lower (2.33/5). Results reveal varied performance across research domains, with high-performing workflows maintaining feasibility without sacrificing creativity. These findings support the view that carefully designed multi-stage agentic workflows can advance AI-assisted research ideation.

We present MOFA, an open-source generative AI (GenAI) plus simulation workflow for high-throughput generation of metal-organic frameworks (MOFs) on large-scale high-performance computing (HPC) systems. MOFA addresses key challenges in integrating GPU-accelerated computing for GPU-intensive GenAI tasks, including distributed training and inference, alongside CPU- and GPU-optimized tasks for screening and filtering AI-generated MOFs using molecular dynamics, density functional theory, and Monte Carlo simulations. These heterogeneous tasks are unified within an online learning framework that optimizes the utilization of available CPU and GPU resources across HPC systems. Performance metrics from a 450-node (14,400 AMD Zen 3 CPUs + 1800 NVIDIA A100 GPUs) supercomputer run demonstrate that MOFA achieves high-throughput generation of novel MOF structures, with CO_2 adsorption capacities ranking among the top 10 in the hypothetical MOF (hMOF) dataset. Furthermore, the production of high-quality MOFs exhibits a linear relationship with the number of nodes utilized. The modular architecture of MOFA will facilitate its integration into other scientific applications that dynamically combine GenAI with large-scale simulations.

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

Autonomous scientific discovery with large language model (LLM)-based agents has recently made substantial progress, demonstrating the ability to automate end-to-end research workflows. However, existing systems largely rely on runtime-centric execution paradigms, repeatedly reading, summarizing, and reasoning over large volumes of scientific literature online. This on-the-spot computation strategy incurs high computational cost, suffers from context window limitations, and often leads to brittle reasoning and hallucination. We propose Idea2Story, a pre-computation-driven framework for autonomous scientific discovery that shifts literature understanding from online reasoning to offline knowledge construction. Idea2Story continuously collects peer-reviewed papers together with their review feedback, extracts core methodological units, composes reusable research patterns, and organizes them into a structured methodological knowledge graph. At runtime, underspecified user research intents are aligned to established research paradigms, enabling efficient retrieval and reuse of high-quality research patterns instead of open-ended generation and trial-and-error. By grounding research planning and execution in a pre-built knowledge graph, Idea2Story alleviates the context window bottleneck of LLMs and substantially reduces repeated runtime reasoning over literature. We conduct qualitative analyses and preliminary empirical studies demonstrating that Idea2Story can generate coherent, methodologically grounded, and novel research patterns, and can produce several high-quality research demonstrations in an end-to-end setting. These results suggest that offline knowledge construction provides a practical and scalable foundation for reliable autonomous scientific discovery.

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

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.

Large Language Model (LLM)-based multi-agent systems (MAS) demonstrate remarkable potential for scientific discovery. Existing approaches, however, often automate scientific discovery using predefined workflows that lack rationality constraints. This often leads to aimless hypothesizing and a failure to consistently link hypotheses with evidence, thereby hindering systematic uncertainty reduction. Overcoming these limitations fundamentally requires systematic uncertainty reduction. We introduce PiFlow, an information-theoretical framework, treating automated scientific discovery as a structured uncertainty reduction problem guided by principles (e.g., scientific laws). In evaluations across three distinct scientific domains -- discovering nanomaterial structures, bio-molecules, and superconductor candidates with targeted properties -- our method significantly improves discovery efficiency, reflected by a 73.55\% increase in the Area Under the Curve (AUC) of property values versus exploration steps, and enhances solution quality by 94.06\% compared to a vanilla agent system. Overall, PiFlow serves as a Plug-and-Play method, establishing a novel paradigm shift in highly efficient automated scientific discovery, paving the way for more robust and accelerated AI-driven research. Code is publicly available at our https://github.com/amair-lab/PiFlow{GitHub}.

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.

Large Language Models (LLMs) and other foundation models are increasingly used as the core of AI agents. In agentic workflows, these agents plan tasks, interact with humans and peers, and influence scientific outcomes across federated and heterogeneous environments. However, agents can hallucinate or reason incorrectly, propagating errors when one agent's output becomes another's input. Thus, assuring that agents' actions are transparent, traceable, reproducible, and reliable is critical to assess hallucination risks and mitigate their workflow impacts. While provenance techniques have long supported these principles, existing methods fail to capture and relate agent-centric metadata such as prompts, responses, and decisions with the broader workflow context and downstream outcomes. In this paper, we introduce PROV-AGENT, a provenance model that extends W3C PROV and leverages the Model Context Protocol (MCP) and data observability to integrate agent interactions into end-to-end workflow provenance. Our contributions include: (1) a provenance model tailored for agentic workflows, (2) a near real-time, open-source system for capturing agentic provenance, and (3) a cross-facility evaluation spanning edge, cloud, and HPC environments, demonstrating support for critical provenance queries and agent reliability analysis.

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.

Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing routines, adapting them for new use cases, sharing and scaling them across collaborators, and stabilizing them with reproducible execution environments. We present Album, an open-source framework for packaging and sharing scientific routines as executable artifacts through two minimal primitives: (i) the solution, a Python-native executable entry point that combines machine-readable metadata, arguments, environment specifications, and lifecycle hooks; and (ii) the catalog, a decentralized, git-native distribution mechanism with indexed search and optional web rendering for discovery, provenance, and governance. Album uses a two-context execution model in which a host controller evaluates manifests and prepares per-solution environments, while lifecycle hooks execute inside isolated solution environments. This design supports reproducible execution, post-environment setup, and the composition of routines with incompatible dependencies. Album can be used in conjunction with LLM agents: solutions can be drafted and revised with LLM assistance, and a MCP interface exposes cataloged solutions as callable tools for tool-grounded discovery and orchestration. We evaluate Album through four realworld imaging deployments spanning interactive visualization of electron microscopy data, integration of multiple segmentation methods, the orchestration of cryo-electron tomography competition workflows, and mineral quantification pipelines. Overall, Album complements package managers, workflow systems, and container runtimes by making scientific routines executable, shareable artifacts. Documentation and examples are available at https://album.solutions.

Identifying transition states (TSs) on potential energy surfaces is a central computational bottleneck in mechanistic studies of catalytic materials. A TS search is not a single calculation but a long-horizon, multi-step workflow of atomistic simulations with delayed, asynchronous feedback and heterogeneous failure modes that require a joint multimodal analysis of scalar convergence diagnostics and atomic geometries along the reaction path. To address this challenge, we propose TSAgent, an agentic workflow that automates TS search directly at the density functional theory (DFT) level of quantum chemical accuracy. TSAgent operates through a persistent plan-execute-analyze-replan loop, continuously adapting its strategy based on convergence diagnostics and geometric feedback without human intervention. We evaluate TSAgent on a diverse 100-example subset of the OC20NEB heterogeneous catalysis benchmark, where it successfully locates TSs with 83% accuracy. In a direct comparison against expert DFT practitioners on 10 held-out examples, TSAgent achieves a 70% success rate compared to a human-expert average of 73 +/- 12%. Finally, TSAgent independently reproduces Bronsted-Evans-Polanyi scaling relationships for NH3 dissociation on metal and single-atom alloy surfaces from a published heterogeneous catalysis study, demonstrating that its utility extends beyond curated benchmarks to real scientific investigations.

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

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

Existing benchmarks for evaluating foundation models mainly focus on single-document, text-only tasks. However, they often fail to fully capture the complexity of research workflows, which typically involve interpreting non-textual data and gathering information across multiple documents. To address this gap, we introduce M3SciQA, a multi-modal, multi-document scientific question answering benchmark designed for a more comprehensive evaluation of foundation models. M3SciQA consists of 1,452 expert-annotated questions spanning 70 natural language processing paper clusters, where each cluster represents a primary paper along with all its cited documents, mirroring the workflow of comprehending a single paper by requiring multi-modal and multi-document data. With M3SciQA, we conduct a comprehensive evaluation of 18 foundation models. Our results indicate that current foundation models still significantly underperform compared to human experts in multi-modal information retrieval and in reasoning across multiple scientific documents. Additionally, we explore the implications of these findings for the future advancement of applying foundation models in multi-modal scientific literature analysis.

Traditional scientific discovery relies on an iterative hypothesise-experiment-refine cycle that has driven progress for centuries, but its intuitive, ad-hoc implementation often wastes resources, yields inefficient designs, and misses critical insights. This tutorial presents Bayesian Optimisation (BO), a principled probability-driven framework that formalises and automates this core scientific cycle. BO uses surrogate models (e.g., Gaussian processes) to model empirical observations as evolving hypotheses, and acquisition functions to guide experiment selection, balancing exploitation of known knowledge and exploration of uncharted domains to eliminate guesswork and manual trial-and-error. We first frame scientific discovery as an optimisation problem, then unpack BO's core components, end-to-end workflows, and real-world efficacy via case studies in catalysis, materials science, organic synthesis, and molecule discovery. We also cover critical technical extensions for scientific applications, including batched experimentation, heteroscedasticity, contextual optimisation, and human-in-the-loop integration. Tailored for a broad audience, this tutorial bridges AI advances in BO with practical natural science applications, offering tiered content to empower cross-disciplinary researchers to design more efficient experiments and accelerate principled scientific discovery.

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/.

Scientific discovery increasingly depends on high-throughput characterization, yet automation is hindered by proprietary GUIs and the limited generalizability of existing API-based systems. We present Owl-AuraID, a software-hardware collaborative embodied agent system that adopts a GUI-native paradigm to operate instruments through the same interfaces as human experts. Its skill-centric framework integrates Type-1 (GUI operation) and Type-2 (data analysis) skills into end-to-end workflows, connecting physical sample handling with scientific interpretation. Owl-AuraID demonstrates broad coverage across ten categories of precision instruments and diverse workflows, including multimodal spectral analysis, microscopic imaging, and crystallographic analysis, supporting modalities such as FTIR, NMR, AFM, and TGA. Overall, Owl-AuraID provides a practical, extensible foundation for autonomous laboratories and illustrates a path toward evolving laboratory intelligence through reusable operational and analytical skills. The code are available at https://github.com/OpenOwlab/AuraID.

The rapid evolution of large language models (LLMs) is transforming artificial intelligence into autonomous research partners, yet a critical gap persists in complex scientific domains such as combustion modeling. Here, practical AI assistance requires the seamless integration of domain literature knowledge with robust execution capabilities for expertise-intensive tools such as computational fluid dynamics (CFD) codes. To bridge this gap, we introduce FlamePilot, an LLM agent designed to empower combustion modeling research through automated and self-corrective CFD workflows. FlamePilot differentiates itself through an architecture that leverages atomic tools to ensure the robust setup and execution of complex simulations in both OpenFOAM and extended frameworks such as DeepFlame. The system is also capable of learning from scientific articles, extracting key information to guide the simulation from initial setup to optimized results. Validation on a public benchmark shows FlamePilot achieved a perfect 1.0 executability score and a 0.438 success rate, surpassing the prior best reported agent scores of 0.625 and 0.250, respectively. Furthermore, a detailed case study on Moderate or Intense Low-oxygen Dilution (MILD) combustion simulation demonstrates its efficacy as a collaborative research copilot, where FlamePilot autonomously translated a research paper into a configured simulation, conducted the simulation, post-processed the results, proposed evidence-based refinements, and managed a multi-step parameter study to convergence under minimal human intervention. By adopting a transparent and interpretable paradigm, FlamePilot establishes a foundational framework for AI-empowered combustion modeling, fostering a collaborative partnership where the agent manages workflow orchestration, freeing the researcher for high-level analysis.

Scientific laboratories increasingly rely on AI systems to reason about experiments, but the physical act of doing science remains largely outside their reach. AI can help read literature, generate hypotheses, and plan protocols, yet the execution of those protocols at the bench still requires a human operator. Vision-Language-Action (VLA) models provide one possible interface between written protocols and robot execution, but existing policies are trained mostly on household and tabletop demonstrations and rarely encounter the instruments, transparent liquids, or fixed protocol workflows found in scientific laboratories. Closing this gap requires both laboratory-specific supervision and a unified learning framework that can accommodate the diverse robot embodiments used to execute experimental protocols. We therefore identify data and embodiment as central bottlenecks alongside model design. To address the data side, we build RoboGenesis, a simulation-based workflow and data engine that composes configured laboratory workflows from atomic skills, validates and filters rollouts, and exports structured demonstrations across supported robot profiles. On the policy side, we present LabVLA, trained with a two-stage recipe: FAST action token pretraining first makes the Qwen3-VL-4B-Instruct backbone action aware before any continuous control is learned, and flow matching posttraining then attaches a DiT action expert under knowledge insulation. On the LabUtopia benchmark, LabVLA achieves the highest average success rate among all evaluated baselines under both in-distribution and out-of-distribution settings.

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol documents, sensor streams, and existing biomedical ontologies. We present a repeatable structured expert elicitation methodology and federated Semantic Knowledge Graph (SKG) architecture for capturing and querying this knowledge, demonstrated through deployment at the Biochemical and Cellular Pharmacology Department of Genentech. Knowledge is elicited via the Protocol Intelligence Co-pilot, a purpose-built AI interview agent that applies structured elicitation lenses to surface tacit procedural knowledge with expert-assigned confidence scores, producing graph representations across three tiers: program-level decision milestones, assay protocol knowledge, and physical execution infrastructure. Separately constructed subgraphs, exemplified by immunoassay (ELISA), quantitative mass spectrometry (LC-MS/PRM), and laboratory automation, are aligned through a shared upper ontology and queried as a single federated graph. Evaluation demonstrates seven query types structurally unavailable from any individual data source, including a cross-subgraph traversal that identifies automation-masked silent failures -- conditions where execution logs report success while scientific validity is compromised. Critically, the MASKED_BY graph relationship encodes a class of laboratory risk invisible to current informatics platforms -- the structural gap that prevents existing systems from reasoning about scientific validity. This architecture provides the semantic world model that AI laboratory agents currently lack: a queryable representation of where workflows fail silently, where human judgment is irreplaceable, and which execution assets mask rather than detect failure.

We present a multi-agent system for automation of scientific research tasks, cmbagent (https://github.com/CMBAgents/cmbagent). The system is formed by about 30 Large Language Model (LLM) agents and implements a Planning & Control strategy to orchestrate the agentic workflow, with no human-in-the-loop at any point. Each agent specializes in a different task (performing retrieval on scientific papers and codebases, writing code, interpreting results, critiquing the output of other agents) and the system is able to execute code locally. We successfully apply cmbagent to carry out a PhD level cosmology task (the measurement of cosmological parameters using supernova data) and evaluate its performance on two benchmark sets, finding superior performance over state-of-the-art LLMs. The source code is available on GitHub, demonstration videos are also available, and the system is deployed on HuggingFace and will be available on the cloud.

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.

Scientific problem-solving involves synthesizing information while applying expert knowledge. We introduce CURIE, a scientific long-Context Understanding,Reasoning and Information Extraction benchmark to measure the potential of Large Language Models (LLMs) in scientific problem-solving and assisting scientists in realistic workflows. This benchmark introduces ten challenging tasks with a total of 580 problems and solution pairs curated by experts in six disciplines - materials science, condensed matter physics, quantum computing, geospatial analysis, biodiversity, and proteins - covering both experimental and theoretical work-flows in science. We evaluate a range of closed and open LLMs on tasks in CURIE which requires domain expertise, comprehension of long in-context information,and multi-step reasoning. While Gemini Flash 2.0 and Claude-3 show consistent high comprehension across domains, the popular GPT-4o and command-R+ fail dramatically on protein sequencing tasks. With the best performance at 32% there is much room for improvement for all models. We hope that insights gained from CURIE can guide the future development of LLMs in sciences. Evaluation code and data are in https://github.com/google/curie

Scientific discovery is driven by the iterative process of background research, hypothesis generation, experimentation, and data analysis. Despite recent advancements in applying artificial intelligence to scientific discovery, no system has yet automated all of these stages in a single workflow. Here, we introduce Robin, the first multi-agent system capable of fully automating the key intellectual steps of the scientific process. By integrating literature search agents with data analysis agents, Robin can generate hypotheses, propose experiments, interpret experimental results, and generate updated hypotheses, achieving a semi-autonomous approach to scientific discovery. By applying this system, we were able to identify a novel treatment for dry age-related macular degeneration (dAMD), the major cause of blindness in the developed world. Robin proposed enhancing retinal pigment epithelium phagocytosis as a therapeutic strategy, and identified and validated a promising therapeutic candidate, ripasudil. Ripasudil is a clinically-used rho kinase (ROCK) inhibitor that has never previously been proposed for treating dAMD. To elucidate the mechanism of ripasudil-induced upregulation of phagocytosis, Robin then proposed and analyzed a follow-up RNA-seq experiment, which revealed upregulation of ABCA1, a critical lipid efflux pump and possible novel target. All hypotheses, experimental plans, data analyses, and data figures in the main text of this report were produced by Robin. As the first AI system to autonomously discover and validate a novel therapeutic candidate within an iterative lab-in-the-loop framework, Robin establishes a new paradigm for AI-driven scientific discovery.

Computational Fluid Dynamics (CFD) is an essential simulation tool in various engineering disciplines, but it often requires substantial domain expertise and manual configuration, creating barriers to entry. We present Foam-Agent, a multi-agent framework that automates complex OpenFOAM-based CFD simulation workflows from natural language inputs. Our innovation includes (1) a hierarchical multi-index retrieval system with specialized indices for different simulation aspects, (2) a dependency-aware file generation system that provides consistency management across configuration files, and (3) an iterative error correction mechanism that diagnoses and resolves simulation failures without human intervention. Through comprehensive evaluation on the dataset of 110 simulation tasks, Foam-Agent achieves an 83.6% success rate with Claude 3.5 Sonnet, significantly outperforming existing frameworks (55.5% for MetaOpenFOAM and 37.3% for OpenFOAM-GPT). Ablation studies demonstrate the critical contribution of each system component, with the specialized error correction mechanism providing a 36.4% performance improvement. Foam-Agent substantially lowers the CFD expertise threshold while maintaining modeling accuracy, demonstrating the potential of specialized multi-agent systems to democratize access to complex scientific simulation tools. The code is public at https://github.com/csml-rpi/Foam-Agent

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion (VISION) by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an X-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instrument and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex -- a synthetic extension to the cognition of scientists -- may radically transform scientific practice and discovery.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or web environments, molecular LLM agents must perceive, reason about, and act upon chemical objects across symbolic strings, molecular graphs, 3D conformations, spectra, simulations, and wet-lab measurements. Their capabilities depend on chemically faithful molecular perception, an LLM-centered agent framework, domain-specific tool grounding, and computational or experimental feedback, in addition to planning and tool use. This work develops a conceptual framework for molecular LLM agents from two complementary perspectives. First, we introduce an architectural view of molecular-agent design, covering molecular representation and perception, the agent framework, domain-specific toolboxes, and learning and optimization. Second, we propose a scientific autonomy ladder inspired by staged autonomy in engineering systems, categorizing agents into four levels: L1 assistive or fixed workflows, L2 adaptive computational agents, L3 feedback-aware physical experiment agents, and L4 scientific-agenda agents. Together, these two perspectives establish a comprehensive framework for comparing existing molecular LLM agents, identifying missing capabilities and deployment risks, and guiding the design, evaluation, and deployment of future agents in molecular discovery workflows.

Early-stage molecular design is an iterative process, not just a task of generating molecules. Researchers turn broad goals into design strategies, refine candidates, assess many properties, and gather evidence before synthesis and tests. AI methods can generate molecules, optimize several goals, predict properties, dock compounds, and account for synthesis. Yet these functions are spread across specialized tools. Experts must still coordinate each step, judge interim results, and integrate evidence. The central challenge is thus to turn research intent into adaptive, traceable runs grounded in scientific tools. We cast this challenge as intent-to-evidence molecular design workflow execution and present CAi Copilot, an expert-oriented agent with three linked layers. The Research Interface Layer turns intent into an executable plan. The Agent Reasoning Layer uses interim results to guide each run. The Execution Substrate supplies molecular tools, metrics, reusable utilities, and backend services. Across 45 tasks, CAi achieves the strongest overall performance, with an outcome score of 84.59, exceeding the next-best result by 18.07 points. Additional benchmarks test how CAi coordinates generation, screening, and multi-criteria evaluation, while exposing limits in long-horizon execution. These results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence.

Multi-agent large language model frameworks are promising for complex multi step reasoning, yet existing systems remain weak for scientific and knowledge intensive domains due to static prompts and agent roles, rigid workflows, and homogeneous model reliance, leading to poor domain adaptation, limited reasoning flexibility, and high latency on heterogeneous or long-horizon scientific tasks. They also struggle to revise earlier decisions when intermediate reasoning diverges, reducing reliability in structured and calculation heavy settings. To address these limitations, we propose a scientific domain oriented interactive two tier multi model orchestration framework. A dedicated orchestration model analyzes each task, dynamically constructs a domain aware reasoning pipeline, and instantiates specialized expert agents with tailored prompts, while an execution model performs each step under generated role and instruction specifications. The orchestrator iteratively updates the pipeline based on intermediate feedback, enabling dynamic replanning, role reallocation, and prompt refinement across multi turn interactions, strengthening robustness and specialization for scientific reasoning through structured heterogeneous model collaboration. The framework is model agnostic and supports heterogeneous LLM integration with different capacities or costs, enabling flexible performance efficiency trade offs in practical scientific deployments. Experiments show consistent improvements over existing multi agent systems and strong baselines across diverse reasoning and scientific style benchmarks.

The complexity of modern bioinformatics analysis has created a critical gap between data generation and developing scientific insights. While large language models (LLMs) have shown promise in scientific reasoning, they remain fundamentally limited when dealing with real-world analytical workflows that demand iterative computation, tool integration and rigorous validation. We introduce K-Dense Analyst, a hierarchical multi-agent system that achieves autonomous bioinformatics analysis through a dual-loop architecture. K-Dense Analyst, part of the broader K-Dense platform, couples planning with validated execution using specialized agents to decompose complex objectives into executable, verifiable tasks within secure computational environments. On BixBench, a comprehensive benchmark for open-ended biological analysis, K-Dense Analyst achieves 29.2% accuracy, surpassing the best-performing language model (GPT-5) by 6.3 percentage points, representing nearly 27% improvement over what is widely considered the most powerful LLM available. Remarkably, K-Dense Analyst achieves this performance using Gemini 2.5 Pro, which attains only 18.3% accuracy when used directly, demonstrating that our architectural innovations unlock capabilities far beyond the underlying model's baseline performance. Our insights demonstrate that autonomous scientific reasoning requires more than enhanced language models, it demands purpose-built systems that can bridge the gap between high-level scientific objectives and low-level computational execution. These results represent a significant advance toward fully autonomous computational biologists capable of accelerating discovery across the life sciences.

It is desirable to coarsely classify short scientific texts, such as grant or publication abstracts, for strategic insight or research portfolio management. These texts efficiently transmit dense information to experts possessing a rich body of knowledge to aid interpretation. Yet this task is remarkably difficult to automate because of brevity and the absence of context. To address this gap, we have developed a novel approach to generate and appropriately assign coarse domain-specific labels. We show that a Large Language Model (LLM) can provide metadata essential to the task, in a process akin to the augmentation of supplemental knowledge representing human intuition, and propose a workflow. As a pilot study, we use a corpus of award abstracts from the National Aeronautics and Space Administration (NASA). We develop new assessment tools in concert with established performance metrics.

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.