Scientific Discovery

Determining whether published scientific findings can successfully be replicated is a long-standing challenge in the empirical sciences. Existing approaches for replicability assessment typically rely either on human judgment, i.e., creative assembly of human experts, or on machine learning models trained on paper content metadata. While both approaches have demonstrated value, each also has important limitations. Human forecasts can be influenced by cognitive biases and narrow exposure to the research literature, while automated assessments often struggle to capture contextual cues and subtle signals of credibility. In this paper, we examine a hybrid approach. Specifically, we introduce a hybrid prediction market in which algorithmic agents trade alongside human participants to jointly estimate the likelihood that a published scientific finding will be corroborated via the outcome of a controlled replication study. Agents are trained on outcomes from hundreds of prior replication studies while human participants contribute domain knowledge through real-time trading. We evaluate this hybrid approach through multiple live experiments involving participants from different academic disciplines and compare its performance to artificial-only and human-only baselines. Our results show that, except for a few cases, hybrid markets match or outperform artificial prediction markets, producing more accurate and reliable replication forecasts.

We present SciDraw-6K, a curated dataset of 6,291 scientific illustrations synthesized by Google Gemini image-generation models, each paired with prompts in eleven languages (English, Simplified Chinese, Traditional Chinese, Japanese, Korean, German, French, Spanish, Brazilian Portuguese, Italian, and Russian). Images span eight broad scientific categories -- biomedical, chemistry, materials, electronics, environment, AI systems, physics, and a long "other" tail -- and are produced primarily by the gemini-2.5-flash-image and gemini-3-pro-image-preview model families. In contrast to general-purpose text-to-image corpora that dominate the literature, SciDraw-6K is purpose-built for the scientific illustration genre: schematic diagrams, mechanism figures, table-of-contents graphics, and conceptual posters. We describe the construction pipeline, report dataset statistics, and document its use as the substrate of sci-draw.com, a public scientific drawing service. The dataset is released to support multilingual text-to-image research, domain-adapted diffusion fine-tuning, and prompt-engineering studies for scientific visualization. Dataset: https://huggingface.co/datasets/SciDrawAI/SciDraw-6K Code: https://github.com/SciDrawAI/scidraw-6k

We introduce RosettaSearch, an inference-time multi-objective optimization approach for backbone conditioned protein sequence design. We use large language models (LLMs) as a generative optimizer within a search algorithm capable of controlled exploration and exploitation, using rewards computed from RosettaFold3, a structure prediction model, under a strict computational budget. In a large-scale evaluation, we apply RosettaSearch to 400 suboptimal sequences generated by LigandMPNN (a state-of-the-art model trained for protein sequence design), recovering high-fidelity designs that LigandMPNN's single-pass decoding fails to produce. RosettaSearch's designs show improvements in structural fidelity metrics ranging between 18% to 68%, translating to a 2.5x improvement in design success rate. We observe that these gains in success rate are robust when RosettaSearch-designed sequences are evaluated with an independent structure prediction oracle (Chai-1) and generalize across two distinct LLM families (o4-mini and Gemini-3), with performance scaling consistently with reasoning capability. We further demonstrate that RosettaSearch improves the sequence fidelity of ProteinMPNN designs for de novo backbones from the Dayhoff atlas, showing that the approach generalizes beyond native protein structures to computationally generated backbones. We also demonstrate a multi-modal extension of RosettaSearch with vision-language models, where images of predicted protein structures are used as feedback to incorporate structural context to guide protein sequence generation. To our knowledge, this is the first large-scale demonstration that LLMs can serve as effective generative optimizers for backbone-conditioned protein sequence design, yielding systematic gains without any model retraining.

The rapid growth of scientific literature calls for automated methods to assess and predict research impact. Prior work has largely focused on citation-based metrics, leaving limited evaluation of models' capability to reason about other impact dimensions. To this end, we introduce SciImpact, a large-scale, multi-dimensional benchmark for scientific impact prediction spanning 19 fields. SciImpact captures various forms of scientific influence, ranging from citation counts to award recognition, media attention, patent reference, and artifact adoption, by integrating heterogeneous data sources and targeted web crawling. It comprises 215,928 contrastive paper pairs reflecting meaningful impact differences in both short-term (e.g., Best Paper Award) and long-term settings (e.g., Nobel Prize). We evaluate 11 widely used large language models (LLMs) on SciImpact. Results show that off-the-shelf models exhibit substantial variability across dimensions and fields, while multi-task supervised fine-tuning consistently enables smaller LLMs (e.g., 4B) to markedly outperform much larger models (e.g., 30B) and surpass powerful closed-source LLMs (e.g., o4-mini). These results establish SciImpact as a challenging benchmark and demonstrate its value for multi-dimensional, multi-field scientific impact prediction. Our project homepage is https://flypig23.github.io/sciimpact-homepage/

Current knowledge graph (KG) construction methods are confirmatory, focusing on recovering known relationships rather than identifying novel or context-dependent nodes. This paper proposes a phenotype-driven and evidence-governed framework that shifts the paradigm toward structured hypothesis discovery and controlled KG expansion. The approach integrates graph neural networks (GNNs) for phenotype discovery, causal inference, probabilistic reasoning and large language models (LLMs) for hypothesis generation and claim extraction within a unified pipeline. The framework prioritizes relationships that are both structurally supported by data and underexplored in the literature. KG expansion is formulated as a multi-objective optimization problem, where candidate claims are jointly evaluated in terms of relevance, structural validation and novelty. Pareto-optimal selection enables the identification of non-dominated claims that balance confirmation and discovery, avoiding trivial or redundant knowledge inclusion. Experiments on heterogeneous population datasets demonstrate that the proposed framework produces more interpretable phenotypes, reveals context-dependent causal structures and generates high-quality claims that align with both data and scientific evidence. Compared to rule-based and LLM-only baselines, the method achieves the best trade-off across plausibility, novelty, validation and relevance. In retrieval-augmented settings, it significantly improves performance (Recall@5=0.98) while reducing hallucination rates (0.05), highlighting its effectiveness in grounding LLM outputs.

The accurate extraction of scientific measurements from literature is a critical yet challenging task in AI4Science, enabling large-scale analysis and integration of quantitative research findings. However, Large Language Models (LLMs) frequently exhibit severe hallucinations, which significantly undermine the reliability of automated scientific document understanding systems. To address this problem, we propose MeasHalu, a novel framework for mitigating scientific measurement hallucinations through enhanced reasoning and targeted optimization. We first present a fine-grained taxonomy of measurement-specific hallucinations, categorizing errors across quantities, units, modifiers, and relations. Our approach incorporates a two-stage reasoning-aware fine-tuning strategy using augmented scientific data and process-based supervision. Furthermore, we introduce a progressive reward curriculum designed to penalize specific hallucination types, significantly improving extraction faithfulness. Experimental results demonstrate that MeasHalu substantially reduces hallucination rates and improves overall accuracy on the MeasEval benchmark. This work provides a targeted solution to a key bottleneck in automated scientific knowledge extraction, facilitating more trustworthy and scalable machine-assisted scientific literature analysis.

Scientists have long sought to accurately predict outcomes of real-world events before they happen. Can AI systems do so more reliably? We study this question through clinical trial outcome prediction, a high-stakes open challenge even for domain experts. We introduce CT Open, an open-access, live platform that will run four challenge every year. Anyone can submit predictions for each challenge. CT Open evaluates those submissions on trials whose outcomes were not yet public at the time of submission but were made public afterwards. Determining if a trial's outcome is public on the internet before a certain date is surprisingly difficult. Outcomes posted on official registries may lag behind by years, while the first mention may appear in obscure articles. To address this, we propose a novel, fully automated decontamination pipeline that uses iterative LLM-powered web search to identify the earliest mention of trial outcomes. We validate the pipeline's quality and accuracy by human expert's annotations. Since CT Open's pipeline ensures that every evaluated trial had no publicly reported outcome when the prediction was made, it allows participants to use any methodology and any data source. In this paper, we release a training set and two time-stamped test benchmarks, Winter 2025 and Summer 2025. We believe CT Open can serve as a central hub for advancing AI research on forecasting real-world outcomes before they occur, while also informing biomedical research and improving clinical trial design. CT Open Platform is hosted at $\href{https://ct-open.net/}{https://ct-open.net/}$

As AI systems are increasingly used to conduct research autonomously, misaligned systems could introduce subtle flaws that produce misleading results while evading detection. We introduce Auditing Sabotage Bench, a benchmark for evaluating the ability of auditors to detect and fix sabotage in ML research codebases. Our benchmark consists of 9 ML research codebases with sabotaged variants that produce qualitatively different experimental results. Each sabotage modifies implementation details, such as hyperparameters, training data, or evaluation code, while preserving the high-level methodology described in the paper. We evaluated frontier LLMs and LLM-assisted human auditors on our benchmark and found that both struggled to reliably detect and fix sabotage: the best performance was an AUROC of 0.77 and a top-1 fix rate of 42%, achieved by Gemini 3.1 Pro. We also tested LLMs as red teamers and found that LLM-generated sabotages were weaker than human-generated ones but still sometimes evaded same-capability LLM auditors. We release the benchmark to support research on monitoring and auditing techniques for AI-conducted research.

The integration of Large Language Models (LLMs) into scientific workflows presents exciting opportunities to accelerate biomedical discovery. However, the reactive nature of LLMs, which respond only when prompted, limits their effectiveness in collaborative settings that demand foresight and autonomous engagement. In this study, we introduce CoLabScience, a proactive LLM assistant designed to enhance biomedical collaboration between AI systems and human experts through timely, context-aware interventions. At the core of our method is PULI (Positive-Unlabeled Learning-to-Intervene), a novel framework trained with a reinforcement learning objective to determine when and how to intervene in streaming scientific discussions, by leveraging the team's project proposal and long- and short-term conversational memory. To support this work, we introduce BSDD (Biomedical Streaming Dialogue Dataset), a new benchmark of simulated research discussion dialogues with intervention points derived from PubMed articles. Experimental results show that PULI significantly outperforms existing baselines in both intervention precision and collaborative task utility, highlighting the potential of proactive LLMs as intelligent scientific assistants.

The rigorous evaluation of the novelty of a scientific paper is, even for human scientists, a challenging task. With the increasing interest in AI scientists and AI involvement in scientific idea generation and paper writing, it also becomes increasingly important that this task be automatable and reliable, lest both human attention and compute tokens be wasted on ideas that have already been explored. Due to the challenge of quantifying ground-truth novelty, however, existing novelty metrics for scientific papers generally validate their results against noisy, confounded signals such as citation counts or peer review scores. These proxies can conflate novelty with impact, quality, or reviewer preference, which in turn makes it harder to assess how well a given metric actually evaluates novelty. We therefore propose an axiomatic benchmark for scientific novelty metrics. We first define a set of axioms that a well-behaved novelty metric should satisfy, grounded in human scientific norms and practice, then evaluate existing metrics across ten tasks spanning three domains of AI research. Our results reveal that no existing metric satisfies all axioms consistently, and that metrics fail on systematically different axioms, reflecting their underlying architectures. Additionally, we show that combining metrics of complementary architectures leads to consistent improvements on the benchmark, with per-axiom weighting achieving 90.1% versus 71.5% for the best individual metric, suggesting that developing architecturally diverse metrics is a promising direction for future work. We release the benchmark code as supplementary material to encourage the development of more robust scientific literature novelty metrics.

This article argues that the most important significance of the AI revolution, especially the rise of large language models, lies not simply in automation, but in a fundamental change in how complex information and human know-how are carried, replicated, and shared. From this perspective, AI for Science is especially important because it may transform not only the efficiency of research, but also the structure of scientific collaboration, discovery, publishing, and evaluation. The article outlines a gradual path from AI as a research tool to AI as a scientific collaborator, and discusses how AI is likely to fundamentally reshape scientific publication. It also argues that continuous learning and diversity of ideas are essential if AI is to play a meaningful role in original scientific discovery.

We present AgentGA, a framework that evolves autonomous code-generation runs by optimizing the agent seed: the task prompt plus optional parent archives that initialize a fresh workspace. The outer loop searches over these reusable starting conditions rather than editing code directly. Each generation launches a fresh autonomous run in an isolated workspace, while selected parent archives provide inherited artifacts that descendants can inspect and reuse. AgentGA couples a population-level genetic algorithm with long-horizon agents; selection uses deterministic 1:1 elite tournaments and operator allocation is adapted online with a modified Hedge controller. We instantiate the approach for tabular AutoML on the 16-competition Weco-Kaggle Lite benchmark. Across the full benchmark, AgentGA averages 71.90% Exceeds % of Human versus 51.38% for the AIDE reference, winning 15/16 competitions. Within AgentGA runs, descendants conditioned on inherited parent archives win 51.9% of 1,680 parent-child tournaments versus 8.6% for de novo proposals. These results support agent-seed optimization as a practical design choice for autonomous code-search systems.

Wearable devices generate continuous physiological and behavioral data, but converting these signals into clinically reviewable biomarker hypotheses remains labor-intensive. We introduce CoDaS, an AI co-data-scientist that integrates multi-agent hypothesis generation, deterministic statistical analysis, adversarial validation and literature-grounded interpretation under human oversight. Across three wearable cohorts comprising 9,279 participant-observations, CoDaS prioritized candidate associations for mental-health and metabolic endpoints after internal checks for replication, stability, robustness and leakage. The system identified related circadian-instability signals associated with depression, including sleep-duration variability in DWB ($ρ$ = 0.252, $p$ < 0.001) and sleep-onset variability in GLOBEM ($ρ$ = 0.126, $p$ < 0.001), and derived a wearable cardiovascular-fitness index associated with insulin resistance (steps/resting heart rate; $ρ$ = -0.374, $p$ < 0.001). Adding these features to demographic models produced modest gains ($ΔR^2$ = 0.040 for depression, 0.021 for insulin resistance). In a 12-clinician review totaling approximately 25 active hours, clinician validity judgments aligned with CoDaS confidence tiers ($ρ$ = 0.67, $p$ = 0.005), whereas added clinical value and confidence to act were rated lower. CoDaS supports traceable, hypothesis-generating prioritization of wearable candidate biomarkers.

Identifying promising research directions in fast-moving subareas is one of the most cognitively expensive tasks in modern AI research. Existing LLM-driven scientific discovery systems are typically limited to one-shot prompting on static literature snapshots and are validated only against contemporary judges such as human reviewers, agent peer review, wet-lab assays, or self-evaluation, leaving open whether they can anticipate future trends. We present Continuous Knowledge Metabolism (CKM), an AI workflow for hypothesis generation with three key capabilities: (i) continuous literature metabolism via sliding windows that maintain an evolving knowledge state; (ii) predictive evaluation, which grades hypotheses against papers published after the generation window; and (iii) practitioner-grade failure detection that diagnoses workflow failure modes from its outputs. On a 50-topic machine learning benchmark, CKM-Lite produces at least one validated hypothesis on 72% of topics (36 out of 50), more than doubling a one-shot baseline (30%) at approximately 3 dollars per topic and achieving 91% lower token cost. Validated hypotheses precede their matched papers by an average of 404 days (55 hits across 36 topics; median 399 days, range 66-757 days). Broadly, predictive validation against future literature provides a falsifiable, low-cost alternative to contemporary-judge evaluation protocols and can be applied wherever a corpus has dated publication records.

Scientific research based on multimodal clinical data (including medical imaging) requires coordinating clinical, radiological, programming, and biostatistical expertise, a fragmented process that bottlenecks discovery. We present VERITAS (Verifiable Epistemic Reasoning for Image-Derived Hypothesis Testing via Agentic Systems), a clinical co-scientist: a multi-agent system that autonomously tests natural-language hypotheses and produces a fully auditable evidence trail, tracing every conclusion through executable outputs from analysis plan to segmentation masks to statistical code to final verdict. Unlike prior AI-scientist systems, which mainly operate on tabular or text data, VERITAS grounds autonomous discovery directly in medical images. It decomposes the workflow into four phases handled by role-specialized agents, and introduces an epistemic evidence label framework that mechanically classifies outcomes as Supported, Refuted, Underpowered, or Invalid by jointly evaluating significance, effect direction, and study power. This distinction is critical in medical imaging, where non-significant results often reflect insufficient sample size rather than absent effects. We construct a tiered benchmark of 64 hypotheses spanning six complexity levels across cardiac and brain glioma MRI datasets. VERITAS reaches 81.4% verdict accuracy with frontier models and 71.2% with locally-hosted open-weight models (8-30B), outperforming all single-model baselines in both classes. It also produces the highest rate of independently verifiable statistical outputs (86.6%), so even its failures remain diagnosable through artifact inspection. Structured multi-agent decomposition thus substitutes for model scale while preserving the verifiability that scientific discovery demands. We release code, hypothesis bank, and evaluation pipeline at https://github.com/LucZot/veritas.

AI is increasingly supporting, accelerating, and automating scientific discovery across subjects. Yet, the adoption of AI in historical research remains limited due to the lack of specialised solutions for historians. To change this, we introduce Chronos, an AI Co-Historian designed to support historians. It allows researchers to create and customize research workflows through natural-language interaction and share these as Chronos-Extensions with others. Chronos specifically addresses the need of historians for a tool that is specialised, non-technical, highly customizable, and facilitates extensive task evaluation. As a first extension, we introduce Chronos-Extract, which enables researchers to automate the targeted extraction of information from image scans of historical sources. We benchmark Chronos-Extract on three historical source corpora and find that it achieves high task-accuracy across primary sources spanning three centuries and diverse languages, layouts, and typefaces. Chronos is openly available and ready for historians to use on their own primary and secondary sources.

Scientific discovery is slowed by fragmented literature that requires excessive human effort to gather, analyze, and understand. AI tools, including autonomous summarization and question answering, have been developed to aid in understanding scientific literature. However, these tools lack the structured, multi-step approach necessary for extracting deep insights from scientific literature. Large Language Models (LLMs) offer new possibilities for literature analysis, but remain unreliable due to hallucinations and incomplete extraction. We introduce Elhuyar, a multi-agent, human-in-the-loop system that integrates LLMs, structured AI, and human scientists to extract, analyze, and iteratively refine insights from scientific literature. The framework distributes tasks among specialized agents for filtering papers, extracting data, fitting models, and summarizing findings, with human oversight ensuring reliability. The system generates structured reports with extracted data, visualizations, model equations, and text summaries, enabling deeper inquiry through iterative refinement. Deployed in materials science, it analyzed literature on tungsten under helium-ion irradiation, showing experimentally correlated exponential helium bubble growth with irradiation dose and temperature, offering insight for plasma-facing materials (PFMs) in fusion reactors. This demonstrates how AI-assisted literature review can uncover scientific patterns and accelerate discovery.

The Production and Distributed Analysis (PanDA) system, originally developed for the ATLAS experiment at the CERN Large Hadron Collider (LHC), has evolved into a robust platform for orchestrating large-scale workflows across distributed computing resources. Coupled with its intelligent Distributed Dispatch and Scheduling (iDDS) component, PanDA supports AI/ML-driven workflows through a scalable and flexible workflow engine. We present an AI-assisted framework for detector design optimization that integrates multi-objective Bayesian optimization with the PanDA--iDDS workflow engine to coordinate iterative simulations across heterogeneous resources. The framework addresses the challenge of exploring high-dimensional parameter spaces inherent in modern detector design. We demonstrate the framework using benchmark problems and realistic studies of the ePIC and dRICH detectors for the Electron-Ion Collider (EIC). Results show improved automation, scalability, and efficiency in multi-objective optimization. This work establishes a flexible and extensible paradigm for AI-driven detector design and other computationally intensive scientific applications.

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

Modeling student misconceptions in a realistic manner is critical for AI in education. In this work, we examine how large language models (LLMs) reason about misconceptions when generating distractor answers for multiple-choice questions (MCQs), a task that requires producing answers that are incorrect, yet plausible. We introduce a taxonomy over reasoning strategies for distractor generation that is grounded in learning-science literature and empirical observation, which we apply to LLM-generated reasoning traces across math and science MCQs. On the math dataset, we find that models follow a misconception-based process with potentially high diagnostic value: they recover the correct solution, articulate student errors, simulate them, and select plausible candidates. On the science dataset, on the other hand, they tend to follow a less robust approach based on semantic similarity to the correct answer. We find the most frequent failure modes to be that the model is unable to generate a correct solution or that it discards plausible distractor candidates when performing selection. Providing the correct solution in the prompt yields a relative improvement of 6.4% in alignment with human-authored distractors, highlighting the critical role of anchoring distractor generation to the correct solution. Together, our findings offer an interpretable view of how LLMs model incorrect student reasoning.

Scientific discovery depends on expert judgement and foresight, which we call scientific taste: the ability to judge and propose research ideas with potential for long-term scientific impact. Whether AI can learn this ability remains an open question. Here we provide evidence that artificial intelligence can learn judgement and ideation. We introduce Reinforcement Learning from Community Feedback (RLCF), a training paradigm that uses large-scale signals from scientific community as supervision. We first train Scientific Judge on field- and time-matched pairs of high- vs. low-citation papers to judge ideas. We then train a Scientific Thinker, to propose research ideas with high potential impact. Experiments show that the 30B Scientific Judge variant outperforms strong LLM baselines (e.g., GPT-5.4 Thinking), while Scientific Judge generalizes across future-year papers, unseen fields, and other community metrics. Furthermore, Scientific Thinker proposes research ideas with higher potential impact than baselines. These results suggest that AI can learn scientific taste, marking an important step towards AI systems that could help accelerate scientific discovery.

While large language models (LLMs) have transformed AI agents into proficient executors of computational materials science, performing a hundred simulations does not make a researcher. What distinguishes research from routine execution is the progressive accumulation of knowledge - learning which approaches fail, recognizing patterns across systems, and applying understanding to new problems. However, the prevailing paradigm in AI-driven computational science treats each execution in isolation, largely discarding hard-won insights between runs. Here we present QMatSuite, an open-source platform closing this gap. Agents record findings with full provenance, retrieve knowledge before new calculations, and in dedicated reflection sessions correct erroneous findings and synthesize observations into cross-compound patterns. In benchmarks on a six-step quantum-mechanical simulation workflow, accumulated knowledge reduces reasoning overhead by 67% and improves accuracy from 47% to 3% deviation from literature - and when transferred to an unfamiliar material, achieves 1% deviation with zero pipeline failures.

Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description in a paper would improve workflow comprehension, support reproducibility, and facilitate reuse. This task requires the linking of bioinformatics tools in workflow code with their mentions in a published workflow description. Results: We present CoPaLink, an automated approach that integrates three components: named entity recognition (NER) for identifying tool mentions in scientific text, NER for tool mentions in workflow code, and entity resolution based on word embedding similarity. We propose approaches for all three steps, achieving a high individual F1-measure (77 - 90) and a joint accuracy of 66 when evaluated on Nextflow workflows using Sentence-BERT. CoPaLink leverages corpora of scientific articles and workflow executable code with curated tool annotations to bridge the gap between narrative descriptions and workflow implementations. Availability: The code is available at https://gitlab.liris.cnrs.fr/sharefair/copalink-experiments and https://gitlab.liris.cnrs.fr/sharefair/copalink. The corpora are also available: CPL-Article (https://doi.org/10.5281/zenodo.20746904), CPL-Code (https://doi.org/10.5281/zenodo.20746970) and CPL-Gold-Entity-Resolution (https://doi.org/10.5281/zenodo.20746994).

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.

As large language models (LLMs) increasingly assist scientific writing, the limitations and token costs of generating TeX become increasingly visible. This paper analyzes TeX's architectural mismatch with LLM workflows, stemming from its lack of an explicit structural representation, to illustrate its limitations on generated semantics and error localization. As an alternative, we introduce .tmu, a low-entropy tree-structured representation. With its efficient data structure and clear contextual boundaries, .tmu outperforms .tex in the above aspects. Experiments across four LLMs provide evidence for this claim in most evaluated settings. Furthermore, we show that due to its lower information entropy, fine-tuning LLMs on .tmu achieves approximately 43% lower final training loss than on .tex. Our work provides a more scalable and LLM-friendly data representation for LLM-assisted scientific writing.

Can AI systems trained on the existing scientific record forecast the advances that will follow? We introduce PreScience, a dataset and benchmark for scientific forecasting built around 98K recent AI research papers, together with companion papers covering author publication histories and citation links, yielding 502K papers in total. The resulting paper records include titles, abstracts, disambiguated author identities, influential references, topic labels, citation trajectories, and metadata snapshotted to respect temporal cutoffs. We instantiate seven exemplar tasks: five paper-anchored tasks -- contribution generation, collaborator prediction, prior work selection, citation count prediction, and future combination prediction -- and two aggregate topic trend forecasting variants. We develop baselines ranging from simple heuristics and embedding methods to frontier language models and agentic systems, and introduce LACER, an LLM-based metric for evaluating similarity of generated contribution descriptions that agrees better with human judgments than existing metrics. Finally, we compose task models to generate a 12-month synthetic corpus and find that the resulting papers are systematically less diverse and less novel than human-authored research from the same period. We release the PreScience dataset (https://huggingface.co/datasets/allenai/prescience) and code (https://github.com/allenai/prescience).

Drug-induced toxicity is a leading cause of preclinical and early-clinical failure, making early detection critical. Histopathology is the gold standard for toxicity assessment but relies on expert pathologists, creating a bottleneck for large-scale screening. We introduce an AI-based anomaly detection framework for whole-slide images (WSIs) of rodent liver that identifies healthy tissue and known pathologies (anomalies) and flags samples without training data as out-of-distribution (OOD). We evaluate OOD detection on two held-out categories: apoptosis (single-cell, near-OOD) and staining/processing artifacts (heterogeneous, far-OOD). We build a novel pixelwise-annotated dataset and fine-tune a pre-trained Vision Transformer (DINOv2) via Low-Rank Adaptation (LoRA) for segmentation, then use the Mahalanobis distance for OOD detection with class-specific thresholds. Optimizing the false positive rate subject to a predefined constraint on the false negative rate yields only 0.16% of pathological tissue classified as healthy and 0.35% of healthy tissue classified as pathological. Our false negative rate does not penalise cross-type errors, reflecting the safety-first objective of never overlooking a lesion; under the stricter correct-class criterion our method assigns 93.93% of ID and 89.38% of OOD findings to their own class. The study demonstrates technical feasibility of pixel-level anomaly detection for mouse liver histopathology, indicating possible applications in improving preclinical workflows and drug development efficiency.

Across the social and medical sciences, researchers recognize that specifying planned research activities (i.e., 'registration') prior to the commencement of research has benefits for both the transparency and rigour of science. Despite this, evidence suggests that study registrations frequently go unexamined, minimizing their effectiveness. In a way this is no surprise: manually checking registrations against papers is labour- and time-intensive, requiring careful reading across formats and expertise across domains. The advent of AI unlocks new possibilities in facilitating this activity. We present RegCheck, a modular LLM-assisted tool designed to help researchers, reviewers, and editors from across scientific disciplines compare study registrations with their corresponding papers. Importantly, RegCheck keeps human expertise and judgement in the loop by (i) ensuring that users are the ones who determine which features should be compared, and (ii) presenting the most relevant text associated with each feature to the user, facilitating (rather than replacing) human discrepancy judgements. RegCheck also generates shareable reports with unique RegCheck IDs, enabling them to be easily shared and verified by other users. RegCheck is designed to be adaptable across scientific domains, as well as registration and publication formats. In this paper we provide an overview of the motivation, workflow, and design principles of RegCheck, and we discuss its potential as an extensible infrastructure for reproducible science with an example use case.

Academic paper search is a fundamental task in scientific research, yet most existing approaches organize retrieval around predefined workflows or structured interaction protocols that struggle with complex, conditional queries. To address this limitation, we propose PaperScout, an autonomous agent that reformulates paper search as a sequential decision-making process. Unlike static workflows, PaperScout dynamically decides whether, when, and how to invoke search and expand tools based on accumulated retrieval context. However, training such agents presents a fundamental challenge: standard reinforcement learning methods, typically designed for single-turn tasks, suffer from a granularity mismatch when applied to multi-turn agentic tasks, where token-level optimization diverges from the granularity of sequence-level interactions, leading to noisy credit assignment and unstable training dynamics. We introduce Proximal Sequence Policy Optimization (PSPO), a process-aware, sequence-level policy optimization method that aligns optimization with agent--environment interaction. Comprehensive experiments on both synthetic and real-world benchmarks demonstrate that PaperScout significantly outperforms strong structured retrieval and RL baselines in both recall and relevance, validating the effectiveness of our adaptive agentic framework and optimization strategy.

Large language models (LLMs) are increasingly used as coding partners, yet their role in accelerating scientific discovery remains underexplored. This paper presents a case study of using ChatGPT for rapid prototyping in ESA's ELOPE (Event-based Lunar OPtical flow Egomotion estimation) competition. The competition required participants to process event camera data to estimate lunar lander trajectories. Despite joining late, we achieved second place with a score of 0.01282, highlighting the potential of human-AI collaboration in competitive scientific settings. ChatGPT contributed not only executable code but also algorithmic reasoning, data handling routines, and methodological suggestions, such as using fixed number of events instead of fixed time spans for windowing. At the same time, we observed limitations: the model often introduced unnecessary structural changes, gets confused by intermediate discussions about alternative ideas, occasionally produced critical errors and forgets important aspects in longer scientific discussions. By analyzing these strengths and shortcomings, we show how conversational AI can both accelerate development and support conceptual insight in scientific research. We argue that structured integration of LLMs into the scientific workflow can enhance rapid prototyping by proposing best practices for AI-assisted scientific work.

Large Language Models (LLMs) are increasingly embedded in agentic frameworks for scientific discovery. First-principles materials computation imposes a demanding standard for autonomy: successful execution depends on internally consistent inputs, supervision of long-running calculations, and verified outputs. Here we present VASP Agent, a coding-agent-centered system that combines reusable domain skills, deterministic tools, workspace-state inspection, runtime evidence, and scientific guardrails to execute multi-step VASP calculations. The system is evaluated across multiple tasks including structural relaxation, bandgap calculation, equilibrium lattice constant determination, and CO/Pt(111) adsorption. VASP Agent completes all evaluated cases, and its computed numerical results are compared with those obtained using pymatgen and other agentic tools. When large deviations occur, the calculation parameters produced by VASP Agent are more appropriate than those produced by LLM-based workflows. Failure analysis shows that errors that terminate fixed pipelines can be diagnosed and recovered under agentic control.

The rapid growth of Artificial Intelligence and Machine Learning in scientific research has highlighted a gap between industry-standard MLOps tools and platforms, and the unique requirements of modern and Open Science, particularly regarding the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This paper presents AI4EOSC, a federated, open-source platform designed to operationalize the full AI/ML lifecycle within the European Open Science Cloud (EOSC) ecosystem. Our methodology tackles the fragmentation of distributed research infrastructures by integrating a modular and distributed architecture comprising an AI development platform, a serverless AI-as-a-Service layer, and a federated orchestration model that is able to integrate heterogeneous compute and storage resources from distributed e-Infrastructures. AI4EOSC also introduces a ``FAIR-by-design'' approach that enforces metadata standardization (via MLDCAT-AP) and W3C PROV-compliant provenance tracking through a platform-integrated CI/CD pipeline. AI4EOSC added value is demonstrated through the delivery of a diverse set of community installations, showing consistent and seamless deployment across heterogeneous cloud providers. These installations are validated by a set of scientific cases, showing how our work reduces the manual burden on researchers while ensuring high levels of reproducibility and interoperability and providing an unified environment for development, training, and production of AI/ML models in the EOSC.

The deep learning revolution has spurred a rise in advances of using AI in sciences. Within physical sciences the main focus has been on discovery of dynamical systems from observational data. Yet the reliability of learned surrogates and symbolic models is often undermined by the fundamental problem of non-uniqueness. The resulting models may fit the available data perfectly, but lack genuine predictive power. This raises the question: under what conditions can the systems governing equations be uniquely identified from a finite set of observations? We show, counter-intuitively, that chaos, typically associated with unpredictability, is crucial for ensuring a system is discoverable in the space of continuous or analytic functions. The prevalence of chaotic systems in benchmark datasets may have inadvertently obscured this fundamental limitation. More concretely, we show that systems chaotic on their entire domain are discoverable from a single trajectory within the space of continuous functions, and systems chaotic on a strange attractor are analytically discoverable under a geometric condition on the attractor. As a consequence, we demonstrate for the first time that the classical Lorenz system is analytically discoverable. Moreover, we establish that analytic discoverability is impossible in the presence of first integrals, common in real-world systems. These findings help explain the success of data-driven methods in inherently chaotic domains like weather forecasting, while revealing a significant challenge for engineering applications like digital twins, where stable, predictable behavior is desired. For these non-chaotic systems, we find that while trajectory data alone is insufficient, certain prior physical knowledge can help ensure discoverability. These findings warrant a critical re-evaluation of the fundamental assumptions underpinning purely data-driven discovery.

AI-Scientist systems risk manufacturing spurious discoveries through uncontrolled multiple testing. We present a functional architecture that enforces statistical rigor at two levels: a Haskell embedded domain-specific language (the Research monad) that makes it impossible to test a hypothesis without updating the error budget, and a declarative scaffold, backed by an OS-level sandbox, that makes validation data physically absent from the environment in which LLM-generated code runs. We ground the design in a machine-checked Lean4 formalization of LORD++ online false-discovery-rate (FDR) control: we derive its error budget and prove both marginal and full FDR control, then close the gap to the implementation by verifying the budget's wealth invariant over IEEE754 arithmetic in SPARK/Ada. To our knowledge this is the first verified chain from theorem to floating-point implementation for an online FDR procedure. In simulation, the architecture holds the false discovery rate near 1% against a 5% target, where a naive approach reaches 41%. In end-to-end case studies, a valid test avoids the false discoveries a flawed one produces, yet still finds real effects when the data allow. An adversarial evaluation confirms that generated code cannot read the held-out data even when given its exact path.

In the era of AI-driven science and engineering, we often want to design discrete objects in silico according to user-specified properties. For example, we may wish to design a protein to bind its target, arrange components within a circuit to minimize latency, or find materials with certain properties. Given a property predictive model, in silico design typically involves training a generative model over the design space (e.g., protein sequence space) to concentrate on designs with the desired properties. Distributional optimization$\unicode{x2013}$which can be formalized as an estimation of distribution algorithm or as reinforcement learning policy optimization$\unicode{x2013}$finds the generative model that maximizes an objective function in expectation. Optimizing a distribution over discrete-valued designs is in general challenging because of the combinatorial nature of the design space. However, many property predictors in scientific applications are decomposable in the sense that they can be factorized over design variables in a way that could in principle enable more effective optimization. For example, amino acids at a catalytic site of a protein may only loosely interact with amino acids of the rest of the protein to achieve maximal catalytic activity. Current distributional optimization algorithms are unable to make use of such decomposability structure. Herein, we propose and demonstrate use of a new distributional optimization algorithm, Decomposition-Aware Distributional Optimization (DADO), that can leverage any decomposability defined by a junction tree on the design variables, to make optimization more efficient. At its core, DADO employs a soft-factorized "search distribution"$\unicode{x2013}$a learned generative model$\unicode{x2013}$for efficient navigation of the search space, invoking graph message-passing to coordinate optimization across linked factors.

Wide access to advanced experimental methods in materials science has given rise to an abundance of procedural knowledge, which is scattered across decades of scientific literature and recorded in unstructured formats that are challenging to analyze systematically. In this work, we present LeMat-Synth Parser, a modular, open-source, and multi-modal extraction toolbox that utilizes large language models (LLMs) and vision language models (VLMs) to automatically structure synthesis protocols and performance metrics extracted from both text and figures of publications. Applying LeMat-Synth Parser to 81K open-access publications, we curate LeMat-Synth, an extensive dataset of 58K synthesis procedures and to our knowledge the largest and most diverse structured inorganic materials synthesis dataset to date, covering 35 synthesis methods and 16 material classes based on a domain-specific ontology. We validate extraction quality against annotations by domain experts and a scalable LLM-as-a-judge framework, and benchmark a suite of models to identify optimal configurations and characterize cross-model biases. To demonstrate the extensibility of LeMat-Synth Parser, we apply it to two distinct domains. First, we link synthesis protocols and catalyst identity to thermocatalytic performance across a corpus of ammonia-decomposition publications. Second, we cross-validate text- and figure-reported critical transition temperatures across 1,384 superconductivity papers, then use the validated pipeline to recover the critical transition temperature for every composition in a sample series. We release LeMat-Synth Parser and the LeMat-Synth dataset openly on GitHub and Hugging Face

Most state-of-the-art sign language models are trained on interpreter or isolated vocabulary data, which overlooks the variability that characterizes natural dialogue. However, human communication dynamically adapts to contexts and interlocutors through spatiotemporal changes and articulation style. This specifically manifests itself in educational settings, where novel vocabularies are used by teachers, and students. To address this gap, we collect a motion capture dataset of American Sign Language (ASL) STEM (Science, Technology, Engineering, and Mathematics) dialogue that enables quantitative comparison between dyadic interactive signing, solo signed lecture, and interpreted articles. Using continuous kinematic features, we disentangle dialogue-specific entrainment from individual effort reduction and show spatiotemporal changes across repeated mentions of STEM terms. On average, dialogue signs are 24.6%-44.6% shorter in duration than the isolated signs, and show significant reductions absent in monologue contexts. Finally, we evaluate sign embedding models on their ability to recognize STEM signs and approximate how entrained the participants become over time. Our study bridges linguistic analysis and computational modeling to understand how pragmatics shape sign articulation and its representation in sign language technologies.

We present domain-adapted large language model agents designed to support Cherenkov Telescope Array operation and data analysis. The agents combine contextual knowledge with automated validation and iterative correction to produce more reliable outputs. This approach reduces manual effort, improves consistency, and helps accelerate operational and scientific workflows. The results demonstrate the potential of agentic systems as practical assistants in specialized research environments.

The process of scientific discovery relies on an interplay of observations, analysis, and hypothesis generation. Machine learning is increasingly being adopted to address individual aspects of this process. However, it remains an open challenge to fully automate the heuristic, iterative loop required to discover the laws of an unknown system by exploring it through experiments and analysis, without tailoring the approach to the specifics of a given task. Here, we introduce SciExplorer, an agent that leverages large language model tool-use capabilities to enable exploration of systems without any domain-specific blueprints, and apply it to physical systems that are initially unknown to the agent. We test SciExplorer on a broad set of models spanning mechanical dynamical systems, wave evolution, and quantum many-body physics. Despite using a minimal set of tools, primarily based on code execution, we observe impressive performance on tasks such as recovering equations of motion from observed dynamics and inferring Hamiltonians from expectation values. The demonstrated effectiveness of this setup opens the door toward similar scientific exploration in other domains, without the need for fine-tuning or task-specific instructions.

Structured information extraction from scientific literature is crucial for capturing core concepts and emerging trends in specialized fields. While existing datasets aid model development, most focus on specific publication sections due to domain complexity and the high cost of annotating scientific texts. To address this limitation, we introduce SciNLP - a specialized benchmark for full-text entity and relation extraction in the Natural Language Processing (NLP) domain. The dataset comprises 60 manually annotated full-text NLP publications, covering 6,429 entities and 1,649 relation. Compared to existing research, SciNLP is the first dataset providing full-text annotations of entities and their relationships in the NLP domain. To validate the effectiveness of SciNLP, we conducted comparative experiments with similar datasets and evaluated the performance of state-of-the-art supervised models on this dataset. Results reveal varying extraction capabilities of existing models across academic texts of different lengths. Cross-comparisons with existing datasets show that SciNLP achieves significant performance improvements on certain baseline models. Using models trained on SciNLP, we implemented automatic construction of a fine-grained knowledge graph for the NLP domain. Our KG has an average node degree of 3.3 per entity, indicating rich semantic topological information that enhances downstream applications. The dataset is publicly available at: https://github.com/AKADDC/SciNLP.

Despite rapid progress in large language models (LLMs), current QA benchmarks still overlook the core challenge of real-world scientific information seeking: synthesizing multimodal evidence scattered across multiple documents and structural formats. Existing QAs remain narrow in scope, relying on unimodal text and short-span reasoning that fail to capture the complexity of real information-seeking. We introduce DocHop-QA, a benchmark of 11,379 instances for evaluating multimodal, multi-document, multi-hop scientific QA. Built from publicly available PubMed articles, DocHop-QA incorporates textual passages, tables, and layout cues, enabling cross-document inference without explicit hyperlinks. To scale realistic QA construction, we develop an LLM-driven generation pipeline grounded in 11 scientific reasoning concepts, producing diverse and coherent question-answer pairs. To highlight the utility and versatility of the dataset, we propose a task-driven evaluation framework spanning four settings, including generative answering, multimodal evidence integration and structured index prediction. Experiments show that current models struggle with DocHop-QA's long-context, multi-evidence demands, establishing it as a rigorous testbed for advancing next-generation scientific QA systems.

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

Expert domain writing, such as scientific writing, typically demands extensive domain knowledge. Although large language models (LLMs) show promising potential in this task, evaluating the quality of automatically generated scientific writing is a crucial open issue, as it requires knowledge of domain-specific criteria and the ability to discern expert preferences. Conventional automatic evaluation metrics and LLM-as-a-judge systems, primarily designed for mainstream NLP tasks, are insufficient to grasp expert preferences and domain-specific quality standards. To address this gap and support realistic human-AI collaborative writing, we focus on related work generation, one of the most challenging scientific tasks, as an exemplar. We propose GREP, a multi-turn evaluation framework that integrates classical related work evaluation criteria with expert-specific preferences. GREP decomposes the evaluation into smaller fine-grained dimensions. This localized evaluation is further augmented with contrastive examples to provide detailed contextual guidance for the evaluation dimensions. Empirical investigation reveals that GREP is able to assess the quality of related work sections in a much more robust manner compared to standard LLM judges, reflects natural scenarios of scientific writing, and bears a strong correlation with the assessment of human experts. We also observe that generations from state-of-the-art LLMs struggle to satisfy validation constraints of a suitable related work section.

We present a framework for fine-tuning flow-matching generative models to enforce physical constraints and solve inverse problems in scientific systems. Starting from a model trained on low-fidelity or observational data, we apply a differentiable post-training procedure that minimizes weak-form residuals of governing partial differential equations (PDEs), promoting physical consistency and adherence to boundary conditions without distorting the underlying learned distribution. To infer unknown physical inputs, such as source terms, material parameters, or boundary data, we augment the generative process with a learnable latent parameter predictor and propose a joint optimization strategy. The resulting model produces physically valid field solutions alongside plausible estimates of hidden parameters, effectively addressing ill-posed inverse problems in a data-driven yet physicsaware manner. We validate our method on canonical PDE benchmarks, demonstrating improved satisfaction of PDE constraints and accurate recovery of latent coefficients. Our approach bridges generative modelling and scientific inference, opening new avenues for simulation-augmented discovery and data-efficient modelling of physical systems.

Foundation models now enable autonomous agents to interact with real-world websites, but existing benchmarks emphasize general-purpose browsing, underrepresent research-oriented environments and scholarly discovery workflows, and often depend on live sites whose changing content and structure undermine reproducibility. arXiv provides a realistic, reproducible, hierarchically structured, information-centric testbed without privacy-sensitive interactions. We introduce WebArxiv, a static-snapshot benchmark comprising 510 time-invariant tasks, each with a unique deterministic ground truth. Its diverse, realistic scholarly tasks go beyond simple information lookup and rule following to emphasize multi-constraint paper retrieval, fine-grained content extraction, and cross-paper comparison. Evaluations of a range of foundation-model-based web agents show that WebArxiv remains challenging. Behavioral analysis reveals that agents over-rely on fixed interaction histories, causing incomplete or repetitive reasoning. We therefore equip agents with a lightweight dynamic-memory mechanism for adaptive retrieval and reasoning over relevant context. The benchmark and code are available at https://anonymous.4open.science/r/74E4423BVNW/README.md.

While there are many applications of ML to scientific problems that look promising, visuals can be deceiving. Using numerical analysis techniques, we rigorously quantify the accuracy, convergence rates, and generalization bounds of certain ML models applied to linear differential equations for parameter discovery or solution finding. Beyond the quantity and discretization of data, we identify that the function space of the data is critical to the generalization of the model. A similar lack of generalization is empirically demonstrated for commonly used models, including physics-specific techniques. Counterintuitively, we find that different classes of models can exhibit opposing generalization behaviors. Based on our theoretical analysis, we also introduce a new mechanistic interpretability lens on scientific models whereby Green's function representations can be extracted from the weights of black-box models. Our results inform a new cross-validation technique for measuring generalization in physical systems, which can serve as a benchmark.

The EU has become one of the vanguards in regulating the digital age. A particularly important regulation in the Artificial Intelligence (AI) domain is the 2024 enacted EU AI Act. The AI Act specifies -- due to a risk-based approach -- various obligations for providers of AI systems. These obligations, for example, include a cascade of documentation and compliance measures, which represent a potential obstacle to science. But do these obligations also apply to AI researchers? This position paper argues that, indeed, the AI Act's obligations could apply in many more cases than the AI community is aware of. Moreover, we argue that the AI Act is drafted in a manner that may unwillingly disrupt the scientific publication practices of the AI research community, with a focus on model and system release. We contribute the following: 1. We offer a high-level roadmap for AI researchers to evaluate whether they need to comply with the AI Act 2. We explain with everyday research examples why the AI Act applies to AI research. 3. We analyse the exceptions of the AI Act's applicability AI research and offer visual tool for researchers to navigate the AI Act's complex system or research exceptions 4. We establish a position the AI Act's research exceptions fail to account for current AI research conventions, as publishing AI research may void the research exceptions of the Act. 5. We propose changes to the AI Act to provide more legal certainty for AI researchers and give two recommendations for AI researchers to reduce the risk of not complying with the AI Act. We see our paper as a starting point for a discussion between policymakers, legal scholars, and AI researchers to avoid unintended side effects of the AI Act.

Scientific language is a central infrastructure of knowledge production, but it remains unclear whether large language models (LLMs) are altering not only how scientists write, but also how scientific knowledge is communicated and accessed. Here we analyze 21.36 million scientific abstracts published between 2020 and 2024, together with historical records from major journals, to trace recent changes in the language of science. We identify a marked turning point in 2024, when scientific writing shows a sharp increase in lexical complexity alongside a decline in syntactic complexity. This shift is pervasive across disciplines and journal tiers, and is more pronounced in texts by scholars working in non-native English contexts, especially those from language backgrounds that differ more typologically from English. Controlled polishing experiments confirm that LLMs reproduce this pattern by favoring more lexically dense and syntactically compressed expression. We further show why this linguistic shift matters: it may widen the distance between scientific discourse and public-facing language, while also helping scholars in non-native English contexts navigate English-language publishing requirements. These findings suggest that LLMs may broaden participation in scientific authorship while narrowing the accessibility of scientific communication, making them a new force in the linguistic infrastructure of science.

Scientific discovery is driven by scientists generating novel hypotheses for complex problems that undergo rigorous experimental validation. To augment this process, we introduce Co-Scientist, a multi-agent AI system built on Gemini for structured scientific thinking and hypothesis generation. Co-Scientist aims to help scientists discover new original knowledge. Conditioned on their research objectives and prior scientific evidence, it formulates demonstrably novel research hypotheses for experimental verification. The system's design involves agents continuously generating, critiquing and refining hypotheses accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute scaling, improving hypothesis quality over time. While general purpose, we focus the validation in three biomedical applications: drug repurposing, novel target discovery, and explaining mechanisms of anti-microbial resistance. Specifically, Co-Scientist helped identify new drug repurposing candidates and synergistic combination therapies for acute myeloid leukemia, which were validated through in vitro experiments. These real-world validations demonstrate the potential of Co-Scientist to accelerate scientific discovery and usher in an era of AI empowered scientists.

Recent advancements in large language models (LLMs) have demonstrated their potential in automating the scientific research ideation. Existing approaches primarily focus on prompting techniques, often producing ideas misaligned with expert standards - novelty, feasibility, and effectiveness, which are widely recognized by the research community as the three key subdimensions of high-quality ideas. Also, balancing these dimensions remains challenging due to their inherent trade-offs. To address these limitations, we propose the first framework that employs a two-stage approach combining Supervised Fine-Tuning (SFT) and controllable Reinforcement Learning (RL) for the task. In the SFT stage, the model learns foundational patterns from pairs of research papers and their corresponding follow-up ideas. In the RL stage, multi-dimensional reward models guided by fine-grained feedback evaluate and optimize the model across key dimensions. During inference, dimensional controllers coordinated by a sentence-level decoder enable dynamic context-aware steering of the idea generation process. Our framework provides a balanced approach to research idea generation, achieving high-quality outcomes in the experiment by dynamically navigating the trade-offs among novelty, feasibility, and effectiveness.

Dynamical systems form the foundation of scientific discovery, traditionally modeled with predefined state variables such as the angle and angular velocity, and differential equations such as the equation of motion for a single pendulum. We introduce a framework that automatically discovers a low-dimensional and operable representation of system dynamics, including a set of compact state variables that preserve the smoothness of the system dynamics and a differentiable vector field, directly from video without requiring prior domain-specific knowledge. The prominence and effectiveness of the proposed approach are demonstrated through both quantitative and qualitative analyses of a range of dynamical systems, including the identification of stable equilibria, the prediction of natural frequencies, and the detection of chaotic and limit cycle behaviors. The results highlight the potential of our data-driven approach to advance automated scientific discovery.

Large language models (LLMs) increasingly generate citation-backed responses, yet citation hallucination remains a major challenge for trustworthy scientific information access. We introduce REASONS, a benchmark of 12,723 sentence-level citation instances spanning 12 arXiv subject categories, designed to evaluate scientific citation attribution under varying evidence conditions. We propose a dual-metric framework consisting of Abstention Rate (AR) and Hallucination Rate (HR) to characterize the trade-off between reliability and responsiveness. Using author-attribution and title-attribution tasks, we evaluate proprietary and open-source LLMs under zero-context, metadata-augmented, cascaded metadata-augmented prompting (CMP), retrieval-augmented, and adversarial settings. Advanced RAG lowers HR relative to Naive RAG (65.4% vs. 87.6%) but reduces AR from 5.0% to 0%. Under adversarial metadata, several systems exceed 85% HR, while retrieval-augmented variants frequently maintain near-zero abstention. Human evaluation of 1,000 outputs ($κ=0.78$) finds a 12.7:1 ratio of factual hallucinations to acceptable paraphrases. Our findings demonstrate that citation attribution systems should be evaluated not only for correctness but also for their ability to abstain appropriately under uncertainty. REASONS provides a benchmark and evaluation framework for studying attribution reliability in citation generation.

Because most scientific literature data are unlabeled, semantic representation learning based on unsupervised graphs has become crucial. To enrich scientific-literature features, this paper proposes a semantic representation learning method based on adaptive features and graph neural networks. By introducing adaptive feature processing, scientific-literature features are considered globally and locally. The graph attention mechanism weights and aggregates features of scientific documents connected by citation relations, so that correlations among different documents can be expressed more effectively. In addition, an unsupervised graph neural network semantic representation learning method is proposed. By comparing the mutual information between positive and negative local semantic representations of scientific literature and the global graph semantic representation in the latent space, the graph neural network captures local and global information and improves semantic representation learning. Experimental results show that the proposed method is competitive for scientific literature classification.

In recent years, with the increase of social investment in scientific research, the number of research results in various fields has increased significantly. Cross-disciplinary research results have gradually become an emerging frontier research direction. There is a certain dependence between a large number of research results. It is difficult to effectively analyze today's scientific research results when looking at a single research field in isolation. How to effectively use the huge number of scientific papers to help researchers becomes a challenge. This paper introduces the research status at home and abroad in terms of domain information mining and topic evolution law of scientific and technological papers from three aspects: the semantic feature representation learning of scientific and technological papers, the field information mining of scientific and technological papers, and the mining and prediction of research topic evolution rules of scientific and technological papers.

Institutions of higher learning, research institutes and other scientific research units have abundant scientific and technological resources of experts and scholars, and these talents with great scientific and technological innovation ability are an important force to promote industrial upgrading. The scientific and technological resources of experts and scholars are mainly composed of basic attributes and scientific research achievements. The basic attributes include information such as research interests, institutions, and educational work experience. However, due to information asymmetry and other reasons, the scientific and technological resources of experts and scholars cannot be connected with the society in a timely manner, and social needs cannot be accurately matched with experts and scholars. Therefore, it is very necessary to build an expert and scholar information database and provide relevant expert and scholar retrieval services. This paper sorts out the related research work in this field from four aspects: text relation extraction, text knowledge representation learning, text vector retrieval and visualization system.

In recent years, with the continuous progress of science and technology, the number of scientific research achievements has increased rapidly. As an exchange platform and medium for scientific research achievements, scientific and technological academic conferences have become increasingly abundant. The convening of academic conferences brings large numbers of papers, researchers, institutions, projects, and research topics, but massive conference data also makes it difficult for researchers to obtain valuable information efficiently. It is therefore meaningful to use deep learning, knowledge graph technology, semantic similarity calculation, and portrait modeling to mine core information from conference data. This paper reviews the key technologies for constructing knowledge graphs and accurate portraits of scientific and technological academic conferences, including named entity recognition, semantic text similarity, trend prediction, graph storage, search engines, and visualization components. These techniques jointly support the construction of conference knowledge services that help researchers acquire scientific information more quickly.

With the advent of the cloud computing era, the cost of creating, capturing, and managing information has gradually decreased. The amount of data on the Internet is showing explosive growth, and more scientific and technological resources are being uploaded to the network. Different from news and social media data, scientific and technological resources are mainly composed of academic-style resources or entities, such as papers, patents, authors, and research institutions. There is a rich relationship network between these resources, from which a large amount of cutting-edge scientific and technological information can be mined. Existing scientific resource management and classification standards are difficult to completely cover all entities and associations, and they cannot accurately extract the important information contained in scientific and technological resources. Therefore, how to construct a complete and accurate representation of scientific and technological resources from structured and unstructured reports and texts, and how to tap the potential value of scientific and technological resources, are urgent problems. A feasible solution is to construct accurate portraits of scientific and technological resources by combining knowledge graph technology, text representation learning, entity extraction, and knowledge service components.

A key factor for lunar mission planning is the ability to assess the local availability of raw materials. However, many potentially relevant measurements are scattered across a variety of scientific publications. In this paper we consider the viability of obtaining lunar composition data by leveraging LLMs to rapidly process a corpus of scientific publications. While leveraging LLMs to obtain knowledge from scientific documents is not new, this particular application presents interesting challenges due to the heterogeneity of lunar samples and the nuances involved in their characterization. Accuracy and uncertainty quantification are particularly crucial since many materials properties can be sensitive to small variations in composition. Our findings indicate that off-the-shelf LLMs are generally effective at extracting data from tables commonly found in these documents. However, there remains opportunity to further refine the data we extract in this initial approach; in particular, to capture fine-grained mineralogy information and to improve performance on more subtle/complex pieces of information.

The convergence of large language models and agents is catalyzing a new era of scientific discovery: Agentic Science. However, common agent infrastructure is repeatedly rebuilt across scientific fields (loop fragmentation) and useful evidence and experience are lost in long-horizon research (loop discontinuity), bringing obstacles to Agentic Science at Scale. We introduce EvoMaster, a foundational evolving agent framework for Agentic Science at Scale. EvoMaster handles loop fragmentation and loop discontinuity by implementing Loop Research in which external evidence persists and improves later decisions. Through three nested loops, Execution, Exploration and Evolution (E$^3$), loop research connects research within runs, across experiments and across studies. Across ten benchmarks spanning scientific research, coding and reasoning, EvoMaster achieves the best score among four agents using GPT-5.4, reaching a mean score of 58.02%, and outperforms the strongest competing agent Codex(40.29%) while costing 35.6% less. These results show that a shared loop-research foundation can support diverse scientific agents at scale.

Quantum chemistry is a foundational enabling tool for the fields of chemistry, materials science, computational biology and others. Despite of its power, the practical application of quantum chemistry simulations remains in the hands of qualified experts due to methodological complexity, software heterogeneity, and the need for informed interpretation of results. To bridge the accessibility gap for these tools and expand their reach to chemists with broader backgrounds, we introduce El Agente Quntur, a hierarchical, multi-agent AI system designed to operate not merely as an automation tool but as a research collaborator for computational quantum chemistry. Quntur was designed following three main strategies: i) elimination of hard-coded procedural policies in favour of reasoning-driven decisions, ii) construction of general and composable actions that facilitate generalization and efficiency, and iii) implementation of guided deep research to integrate abstract quantum-chemical reasoning across subdisciplines and a detailed understanding of the software's internal logic and syntax. Although instantiated in ORCA, these design principles are applicable to research agents more generally and easily expandable to additional quantum chemistry packages and beyond. Quntur supports the full range of calculations available in ORCA 6.0 and reasons over software documentation and scientific literature to plan, execute, adapt, and analyze in silico chemistry experiments following best practices. We discuss the advances and current bottlenecks in agentic systems operating at the research level in computational chemistry, and outline a roadmap toward a fully autonomous end-to-end computational chemistry research agent.