AI-Assisted Scientific Research

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14 papers in the last four weeks, up 133% on the four weeks before. 0.1% of all new papers.

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Latest papers 162

Apr 24, 2026cs.CY

Smaller, Younger, and More Impactful: How AI-Assisted Writing Transforms Research Teams

The era of Big Science has long been defined by increasingly large and specialized research teams pushing the frontiers of knowledge. However, recent advances in artificial intelligence (AI), particularly large language models (LLMs), are beginning to reshape academic writing and scientific research, potentially disrupting the longstanding trend toward ever-larger teams and transforming other dimensions of research team structure. Drawing on 147,074 full-text publications from the PLoS family and the Nature portfolio since 2020, we examined whether and how AI-assisted writing influences team structure and team outcomes in science. Using multiple methods, including ordinary least square, quantile regression, Poisson regression, logistic regression and propensity score matching, we found that research teams using AI-assisted writing tend to be younger and smaller. Importantly, this shift toward more compact, junior-leaning teams does not come at the expense of scientific impact. On the contrary, we observed a higher probability of research teams that employed AI-assisted writing producing highly impactful publications. These results highlight the significant role of AI-assisted writing in reshaping not only how research is produced, but also how research teams are formed and assembled. Our findings call for policy improvements in research evaluation, funding, and training to address this emerging trend.

Haoyang Wang, Mingze Zhang, Yi Bu +2

School of Information, University of Texas at Austin, Austin, TX 78701, USA · National Science Library, Chinese Academy of Sciences, Beijing 100190, China · Department of Information Resources Management, School of Economics and Management, University of Chinese Academy of Sciences, Beijing 100190, China +4

AI-Assisted Scientific Research

Apr 24, 2026cs.CL

SLIDERS: Systematic Reviews via Automated Evidence Synthesis and Reconciliation

Systematic reviews -- which requires comprehensive evidence collection and synthesis from large document corpora in response to targeted research questions -- are foundational in finance, social sciences, and other technical fields. Manual construction of evidence tables is labor-intensive, and recent LLM-based assistants relying on embedding or keyword based search often fail to meet the coverage standards of systematic reviews. We introduce SLIDERS, a novel LLM-based methodology for systematic reviews, by automatically assembling evidence tables tailored to research questions. In addition to extracting structured data from documents, SLIDERS can extract full-text excerpts that serve as direct evidence or as provenance for structured data. Core to SLIDERS is an automated evidence reconciliation agent that writes code to analyze and reconcile extracted evidence, bringing together information fragmented across documents, resolving inconsistencies across excerpts, and synthesizing overlapping findings into a coherent evidence table. In addition, SLIDERS allows users to ask follow-up questions in natural language to further explore the assembled evidence. We evaluate SLIDERS on three systematic-review-style tasks over large document collections. SLIDERS outperforms the best-performing baseline across benchmarks, remains near 90% accuracy across 6M-11M-token corpora. On two new follow-up analysis benchmarks SLIDERS can answer 77.9% and 58.3% followup questions accurately

Harshit Joshi, Priyank Shethia, Jadelynn Dao +1

Computer Science Department, Stanford University

AI-Assisted Scientific Research Document Information Extraction Evidence Retrieval

Apr 23, 2026cs.AI

Sound Agentic Science Requires Adversarial Experiments

LLM-based agents are rapidly being adopted for scientific data analysis, automating tasks once limited by human time and expertise. This capability is often framed as an acceleration of discovery, but it also accelerates a familiar failure mode, the rapid production of plausible, endlessly revisable analyses that are easy to generate, effectively turning hypothesis space into candidate claims supported by selectively chosen analyses, optimized for publishable positives. Unlike software, scientific knowledge is not validated by the iterative accumulation of code and post hoc statistical support. A fluent explanation or a significant result on a single dataset is not verification. Because the missing evidence is a negative space, experiments and analyses that would have falsified the claim were never run or never published. We therefore propose that non-experimental claims produced with agentic assistance be evaluated under a falsification-first standard: agents should not be used primarily to craft the most compelling narrative, but to actively search for the ways in which the claim can fail.

Dionizije Fa, Marko Culjak

Entropic

AI-Assisted Scientific Research LLM Agent Evaluation LLM Agent Reliability Scientific Claim Verification

Apr 23, 2026cs.AI

Rethinking Publication: A Certification Framework for AI-Enabled Research

AI research pipelines can now generate academic work that may satisfy existing peer review standards for quality, novelty, and methodological rigor. However, the publication system was built around the assumption that research is produced by human authors. It therefore lacks a clear way to evaluate work when the knowledge claim may be valid but the producer is partly or fully automated. This paper proposes a two-layer certification framework for AI-generated research. The first layer evaluates whether the knowledge claim is sound. The second layer evaluates the level of human contribution. This separation allows journals and conferences to assess pipeline-generated work more consistently without creating new institutions. The framework uses normative analysis, conceptual design, and dry-run validation against representative submission cases. It classifies human contribution into three categories: Category A, where the work is reachable by an automated pipeline; Category B, where human direction is required at identifiable stages; and Category C, where the work goes beyond current pipeline capability, especially at the problem-formulation stage. The paper also proposes dedicated benchmark slots for fully disclosed automated research. These slots would provide a transparent publication path and help reviewers calibrate judgments over time. The key argument is that publication has historically certified two things at once: that the knowledge is valid and that a human produced it. AI research pipelines separate these two claims. By decoupling knowledge certification from authorship attribution, the proposed framework responds to a structural change already underway. It can be implemented within existing editorial systems, works even when attribution is uncertain, and recognizes human frontier contribution based on epistemic value rather than human origin alone.

Yang Lu, Rabimba Karanjai, Lei Xu +1

AI-Assisted Scientific Research Scholarly Peer Review Authorship Attribution AI Governance

Apr 22, 2026cs.AI

pAI/MSc: ML Theory Research with Humans on the Loop

We present pAI/MSc, an open-source, customizable, modular multi-agent system for academic research workflows. Our goal is not autonomous scientific ideation, nor fully automated research. It is narrower and more practical: to reduce by orders of magnitude the human steering required to turn a specified hypothesis into a literature-grounded, mathematically established, experimentally supported, submission-oriented manuscript draft. pAI/MSc is built with a current emphasis on machine learning theory and adjacent quantitative fields.

Mahmoud Abdelmoneum, Pierfrancesco Beneventano, Tomaso Poggio

1Massachusetts Institute of Technology · 2Perseus Labs

Multi-Agent LLM Systems AI-Assisted Scientific Research Human-in-the-Loop AI

Apr 22, 2026cs.AI

MedSkillAudit: A Domain-Specific Audit Framework for Medical Research Agent Skills

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

Yingyong Hou, Xinyuan Lao, Huimei Wang +10

Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China · 1AIPOCH PTE. LTD., Singapore

Healthcare AI-Assisted Scientific Research AI Agent Evaluation

Apr 22, 2026cs.AI

Mol-Debate: Multi-Agent Debate Improves Structural Reasoning in Molecular Design

Text-guided molecular design is a key capability for AI-driven drug discovery, yet it remains challenging to map sequential natural-language instructions with non-linear molecular structures under strict chemical constraints. Most existing approaches, including RAG, CoT prompting, and fine-tuning or RL, emphasize a small set of ad-hoc reasoning perspectives implemented in a largely one-shot generation pipeline. In contrast, real-world drug discovery relies on dynamic, multi-perspective critique and iterative refinement to reconcile semantic intent with structural feasibility. Motivated by this, we propose Mol-Debate, a generation paradigm that enables such dynamic reasoning through an iterative generate-debate-refine loop. We further characterize key challenges in this paradigm and address them through perspective-oriented orchestration, including developer-debater conflict, global-local structural reasoning, and static-dynamic integration. Experiments demonstrate that Mol-Debate achieves state-of-the-art performance against strong general and chemical baselines, reaching 59.82% exact match on ChEBI-20 and 50.52% weighted success rate on S

^2

-Bench. Our code is available at https://github.com/wyuzh/Mol-Debate.

Wengyu Zhang, Xiao-Yong Wei, Qing Li

♠The Hong Kong Polytechnic University · ♡Sichuan University

AI-Assisted Scientific Research Multi-Agent Debate Molecular Generation Drug Discovery

Apr 21, 2026cond-mat.mtrl-sci

Predicting Scale-Up of Metal-Organic Framework Syntheses with Large Language Models

Scalable synthesis remains the gate between MOF discovery and industrial deployment, as scale-up know-how is fragmented across disparate reports. We introduce ScaleMOF, a literature-mined dataset and a positive-unlabeled learning strategy that fine-tunes large language models. Achieving 93.5% accuracy, this proof-of-concept serves as a literature-grounded ranking tool prioritizing plausible scale-up candidates.

Peter Walther, Hongrui Sheng, Xinxin Liu +7

Department of Chemistry, Washington University, St. Louis, MO 63130, USA. · Department of Chemistry, Fudan University, Shanghai 200438, China. · Department of Computer and Information Science, University of Pennsylvania, PA 19104, USA. +2

AI-Assisted Scientific Research Materials Science Positive-Unlabeled Learning

Apr 21, 2026cs.AI

On Accelerating Grounded Code Development for Research

A major challenge for niche scientific and technical domains in leveraging coding agents is the lack of access to up-to-date, domain- specific knowledge. Foundational models often demonstrate limited reasoning capabilities in specialized fields and cannot inherently incorporate knowledge that evolves through ongoing research and experimentation. Materials scientists exploring novel compounds, communication engineers designing and evaluating new protocols, and bioengineering researchers conducting iterative experiments all face this limitation. These experts typically lack the resources to fine-tune large models or continuously embed new findings, creating a barrier to adopting AI-driven coding agents. To address this, we introduce a framework that gives coding agents instanta- neous access to research repositories and technical documentation, enabling real-time, context-aware operation. Our open-source im- plementation allows users to upload documents via doc-search.dev and includes zed-fork, which enforces domain-specific rules and workflows. Together, these tools accelerate the integration of coding agents into specialized scientific and technical workflows

Santosh Ganji

Coding Agents Code Generation AI-Assisted Scientific Research Scientific Code Generation

Apr 20, 2026q-bio.BM

ConforNets: Latents-Based Conformational Control in OpenFold3

Models from the AlphaFold (AF) family reliably predict one dominant conformation for most well-ordered proteins but struggle to capture biologically relevant alternate states. Several efforts have focused on eliciting greater conformational variability through ad hoc inference-time perturbations of AF models or their inputs. Despite their progress, these approaches remain inefficient and fail to consistently recover major conformational modes. Here, we investigate both the optimal location and manner-of-operation for perturbing latent representations in the AF3 architecture. We distill our findings in ConforNets: channel-wise affine transforms of the pre-Pairformer pair latents. Unlike previous methods, ConforNets globally modulate AF3 representations, making them reusable across proteins. On unsupervised generation of alternate states, ConforNets achieve state-of-the-art success rates on all existing multi-state benchmarks. On the novel supervised task of conformational transfer, ConforNets trained on one source protein can induce a conserved conformational change across a protein family. Collectively, these results introduce a mechanism for conformational control in AF3-based models.

Minji Lee, Colin Kalicki, Minkyu Jeon +3

Department of Computer Science, Columbia University, NY, USA · Department of Systems Biology, Columbia University, NY, USA · Department of Computer Science, Princeton University, Princeton, NJ, USA

Representation Learning Protein Structure Prediction Crystal Structure Prediction AI-Assisted Scientific Research

Apr 19, 2026cs.CV

Intervention-Aware Multiscale Representation Learning from Imaging Phenomics and Perturbation Transcriptomics

Microscopy-based phenotypic profiling is scalable for drug discovery but lacks the mechanistic depth of transcriptomics, which remains costly and scarce. Existing multimodal approaches either use images to support other modalities or naively align representations by sample identity, ignoring cell-type and dose variations in weakly paired data-limiting generalization to unseen interventions. In this paper, we introduce an intervention-aware distillation framework that leverages perturbational transcriptomics to guide image representation learning. A transcriptome-conditioned teacher integrates gene expression and intervention metadata to produce soft distributions over a chemistry-aware codebook organized by drug similarity. The teacher employs a fine-tuned single-cell foundation model to encode cell-type context and disentangle dose effects. An image-only student learns to predict these distributions from microscopy alone, distilling mechanistic knowledge while operating independently at test time. This design emphasizes intervention semantics rather than identity alignment and explicitly handles dose and cell-type mismatches. We provide theoretical guarantees showing that transcriptomic guidance tightens the risk bound for image-based prediction. On Cell Painting and RxRx datasets paired with L1000, our method significantly improves one-shot transfer to unseen interventions and drug-target gene discovery compared to self-supervised and alignment baselines.

Jiayuan Chen, Ruoqi Liu, Zishan Gu +1

The Ohio State University

Cross-Modal Knowledge Distillation Cross-Modal Representation Learning AI-Assisted Scientific Research Drug Discovery

Apr 19, 2026cs.CL

Bidirectional Small-Granularity Search between Code and Text

We introduce the novel task of bidirectional small-granularity search between code and text, where the queries are small snippets of text or code and the results are also small fragments of the opposite modality, i.e., code or text. This task establishes direct links between text in scientific publications and corresponding code segments, in support of better and faster understanding of scientific methods. We introduce a large dataset for the proposed task that includes a training partition with textual descriptions of code generated automatically using GPT-4, and three testing partitions, one in-domain and two out-of-domain (OOD) that contain manually-annotated data as well as material from other domains. We also propose a modular approach to address this task. Our approach shares an encoder across four different subtasks that learn start/end of answer spans in both directions. We show that our method achieves good results in-domain, and encouraging results OOD. This suggests that addressing this task with automatically-generated data is possible, but there is exciting future work to be done.

Marco A. Valenzuela-Escárcega, Enrique Noriega-Atala, Gus Hahn-Powell +2

Lex Machina · The University of Arizona, Tucson, AZ, USA

AI-Assisted Scientific Research Cross-Modal Retrieval Information Retrieval

Apr 18, 2026cs.CL

Bolzano: Case Studies in LLM-Assisted Mathematical Research

We report new results on eight problems in mathematics and theoretical computer science, produced with the assistance of Bolzano, an open-source multi-agent LLM system. Bolzano orchestrates rounds of interaction between parallel prover agents and a verifier agent while maintaining a persistent knowledge base that is carried across rounds. Classified using the significance-autonomy taxonomy of Feng et al., six of the eight results reach the level of publishable research, and five of the eight were produced essentially autonomously by Bolzano. Our results provide evidence that LLMs can contribute meaningfully to mathematical research, complementing recent reports by Bubeck et al., Woodruff et al., and others.

Martin Balko, Jan Grebík, Pavel Hubáček +5

Department of Applied Mathematics, Charles University · Computer Science Institute, Charles University · Institute of Mathematics, Czech Academy of Sciences +1

AI-Assisted Scientific Research Autonomous Research Agents

Apr 17, 2026cs.LG

An Interpretable Framework Applying Protein Words to Predict Protein-Small Molecule Complementary Pairing Rules

Despite the high accuracy of 'black box' deep learning models, drug discovery still relies on protein-ligand interaction principles and heuristics. To improve interpretability of protein-small molecule binding predictions, we developed the PWRules framework, which applies binding affinity data to identify privileged small molecule fragments and subsequently defines complementary pairing rules between these fragments and protein words (semantic sequence units) through an interpretability module. The resulting word-fragment rules are then ranked by the PWScore function to prioritize active compounds. Evaluations on benchmark datasets show that PWScore achieves competitive performance comparable to the physics-based model (Glide) and the deep learning model (PSICHIC) and shows broad applicability for protein targets outside the training dataset, e.g., SARS-CoV-2 main protease. Notably, PWScore captures complementary interaction information, yielding superior enrichment performance when integrated with these established methods. Structural analysis of protein-ligand complexes indicates that learned word-fragment rules are significantly enriched near ligand-binding pockets, despite training without explicit structural guidance. By extracting and applying complementary pairing rules, PWRules provides an interpretable framework for drug discovery.

Jingke Chen, Jingrui Zhong, Tazneen Hossain Tani +3

MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China

Protein-Ligand Binding Affinity Prediction Interpretable ML AI-Assisted Scientific Research Molecular Representation Learning Drug Discovery

Apr 16, 2026cs.CL

"Excuse me, may I say something..." CoLabScience, A Proactive AI Assistant for Biomedical Discovery and LLM-Expert Collaborations

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.

Yang Wu, Jinhong Yu, Jingwei Xiong +2

Worcester Polytechnic Institute, Worcester, MA, USA · University of California, Davis, CA, USA · Jiangsu University, Zhenjiang, Jiangsu, China

AI-Assisted Scientific Research LLM Agents Human-AI Collaboration RL for LLM Agents

Apr 16, 2026astro-ph.EP

ExoNet: Calibrated Multimodal Deep Learning for TESS Exoplanet Candidate Vetting using Phase-Folded Light Curves, Stellar Parameters, and Multi-Head Attention

The discovery of exoplanets at scale has become one of the defining data science challenges in modern astrophysics. NASA's Transiting Exoplanet Survey Satellite (TESS) had catalogued over 7,800 planet candidates by early 2026, yet confirmation stands at fewer than 720. This paper introduces ExoNet, a multimodal deep learning framework that jointly processes phase-folded global and local light curve views alongside stellar parameter features through a calibrated late-fusion architecture combining 1D Convolutional Neural Networks, 8-head Multi-Head Attention over temporal feature maps, and a residual fusion head with post-hoc Temperature Scaling calibration. Trained on 7,585 labeled Kepler Objects of Interest, ExoNet achieves Test AUC = 0.9549 and 86.3% accuracy. Applied to 4,720 verified unconfirmed TESS Planet Candidates with TOI-TIC cross-identification verified against the NASA Exoplanet Archive, the model yields 1,754 high-confidence signals, 52 habitable-zone candidates, and six Earth-sized habitable-zone targets below 1.6 Earth radii. TOI-5728.01 and TOI-6716.01 emerge as the most Earth-like unconfirmed candidates. Full ablation confirms each modality improves AUC. Code and catalog are openly released.

Md. Rashadul Islam

Dept. of Computer Science and Engineering Daffodil International University Dhaka, Bangladesh

Time Series Classification AI-Assisted Scientific Research Multimodal Fusion Multi-Head Attention

Apr 8, 2026cs.DL

TiAb Review Plugin: A Browser-Based Tool for AI-Assisted Study Selection in Systematic Reviews

Server-based screening tools impose subscription costs, while open-source alternatives require coding skills, and full-text screening has remained outside the scope of no-code open-source tools. We developed TiAb Review Plugin, an open-source Chrome browser extension that provides no-code, serverless artificial intelligence (AI)-assisted study selection covering both title and abstract (T&A) screening and full-text screening. It uses Google Sheets as a shared database and Google Drive as a PDF store, and users supply their own large language model (LLM) API key. For T&A screening, it offers manual review, LLM batch screening, and machine learning (ML) active learning. For full-text screening, it retrieves open-access PDFs from PubMed Central, Europe PMC, Unpaywall, OpenAlex, and publisher pages, supports blinded dual review with structured exclusion reasons and adjudication, optionally obtains an LLM judgment with page-anchored evidence, and computes PRISMA 2020 flow counts. We re-implemented the default ASReview algorithm (TF-IDF with Naive Bayes) in TypeScript and compared it with the Python original using 10-fold cross-validation on six datasets. For LLM T&A screening, we compared 16 parameter configurations on a benchmark dataset, validated the best (Gemini 3.0 Flash, low thinking budget, TopP 0.95) on five public datasets (1,038 to 5,628 records; 0.5% to 2.0% prevalence), and benchmarked nine further models from four developers. The TypeScript classifier produced top-100 rankings identical to ASReview on all six datasets. LLM T&A screening achieved recall of 94% to 100% with precision of 2% to 15%, and work saved over sampling at 95% recall (WSS@95) of 46.3% to 89.3%. No additional model exceeded the 96.1% recall of the reference configuration; the most recent models traded recall for precision. The classification accuracy of the full-text stage has not yet been evaluated.

Yuki Kataoka, Masahiro Banno, Michihito Kyo +8

Center for Postgraduate Clinical Training and Career Development, Nagoya University Hospital, 65, Tsurumai-cho, Showa-ku, Nagoya-city, Aichi, Japan · Center for Medical Education, Graduate School of Medicine, Nagoya University, 65, Tsurumai-cho, Showa-ku, Nagoya-city, Aichi, Japan · Scientific Research WorkS Peer Support Group (SRWS-PSG), Osaka, Japan +16

Evidence Selection AI-Assisted Scientific Research

Apr 4, 2026cs.AI

Chronos: The AI Co-Historian

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.

Lorenz Hufe, Niclas Griesshaber, Gavin Greif +2

Fraunhofer HHI · University of Oxford

Historical Document Analysis AI-Assisted Scientific Research Document Information Extraction Human-AI Collaboration Historical Document Processing

Apr 1, 2026cs.AI

A Multi-Agent Human-LLM Collaborative Framework for Closed-Loop Scientific Literature Summarization

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.

Maxwell J. Jacobson, Daniel Xie, Jackson Shen +6

Department of Computer Science, Purdue University, IN, USA · School of Materials Science and Engineering, Purdue University, IN, USA

Multi-Agent LLM Systems AI-Assisted Scientific Research Text Summarization Human-in-the-Loop AI LLM Information Extraction

Mar 31, 2026cond-mat.dis-nn

Sampling at intermediate temperatures is optimal for training large language models in protein structure prediction

Using a statistical mechanics framework, we investigate the parameter space of transformer models trained on protein sequence data. We sample the loss landscape at varying temperatures using Langevin dynamics to characterize the low-loss manifold, and to understand the mechanisms underlying transformers' superior performance in protein structure prediction. We find that, at variance with networks not based on the attention mechanism, the lack of a first--order--like transition in the loss of the transformer produces a range of intermediate temperatures with good learning properties; this is true both for synthetic and natural protein sequences. We also show that the parameters of most layers are highly conserved at these temperatures if the dimension of the embedding is optimal, and we provide an operative way to find this dimension. Additionally, we show that the attention matrix is more predictive of the contact maps of the protein at higher temperatures and for higher dimensions of the embedding than those optimal for learning. Finally, we showed that the models sampled at intermediate temperatures can predict the free-energy variation upon mutation, better than models obtained through standard optimization techniques.

L. Ghiringhelli, A. Zambon, G. Tiana

Department of Physics, via Celoria 16, 20133 Milano, Italy · Department of Physics and INFN, via Celoria 16, 20133 Milano, Italy

Protein Structure Prediction AI-Assisted Scientific Research Protein Language Models Transformer Attention LLM Training

Mar 23, 2026cs.CL

EviSearch: Trustworthy Extraction and Synthesis of Clinical Trial Evidence with Agents that Improve with Use

Structured extraction of evidence from clinical trial publications underpins systematic reviews and clinical guidelines, yet large language models are adopted for it only hesitantly: their outputs are difficult to verify, their use commonly requires transmitting documents to proprietary services, and they do not improve from the corrections their users make. We present EviSearch, a multi-agent system that addresses these three obstacles. Three tool-augmented agents with complementary access to a publication extract every column of an evidence table, and a value is admitted only after an attribution verifier has read it on its cited page, so that every value carries a page-level attribution. Disagreement between independent agents directs human review to the cells most likely to be wrong, and reviewer feedback refines the schema definitions and a curation knowledge base without updating model parameters. The agentic system runs entirely offline on open-weight models. On a clinician-annotated benchmark of randomized-trial publications, EviSearch attributes 100.0% of its values, reaches 91.70% accuracy autonomously, and reaches 95.22% after review of 15.6% of cells, exceeding random review of the strongest single agent at equal effort by 1.75 points.

Naman Ahuja, Abhijit Chakraborty, Muhammad Ali Khan +4

Arizona State University · Mayo Clinic

AI-Assisted Scientific Research Human-in-the-Loop AI Clinical Information Extraction Multi-Agent Systems

Mar 23, 2026cs.DL

Research Novelty in Information Systems Journals After ChatGPT: Differences Across Institutional Language Contexts

Large language models are increasingly used in scholarly work, yet it remains unclear whether their productivity gains are accompanied by changes in research novelty. We examine how relative abstract-level semantic novelty in Information Systems journals changed after ChatGPT became widely available and whether this change differed across institutional language contexts. We analyze 13,847 articles published from 2020 to 2025 in 44 A* and A Information Systems journals. Using SPECTER2 representations of titles and abstracts, we measure each article's semantic distance from its nearest recent predecessors and estimate a comparative pre/post model. Articles whose first authors were affiliated with institutions in non-English-dominant countries show a 0.176 standard deviation larger post-2022 decline in relative semantic novelty than articles from English-dominant affiliations, equivalent to about 7 percentile points. The pattern is similar across several alternative specifications, although the balanced-author estimate is less precise. We interpret this finding through a tension in generative AI-supported knowledge work. GenAI can widen access to prior knowledge and support new combinations, but it can also make established frames easier to reproduce. Because individual LLM use is not observed, the result identifies a heterogeneous post-2022 shift rather than an effect of LLM adoption. The study extends research on LLMs and scholarly productivity by shifting attention from publication counts to the semantic positioning of published articles and by showing that post-2022 change differs across institutional contexts.

Ali Safari, Sahar Babaei

Department of Information Technology and Decision Sciences, University of North Texas, Denton, Texas, USA · Texas Tech University, Lubbock, Texas, USA

AI-Assisted Scientific Research

Mar 13, 2026cs.LG

RetroReasoner: A Reasoning LLM for Strategic Retrosynthesis Prediction

Retrosynthesis prediction aims to identify reactants that can synthesize a given product molecule. Although molecular large language models (LLMs) have recently shown promising results, most existing methods either generate reactants directly or provide only generic product-level analysis, without explicitly reasoning about bond-disconnection strategies that justify specific reactant choices. This paper proposes RetroReasoner, a retrosynthetic reasoning model that captures chemists' strategic disconnection-based thinking. RetroReasoner is trained with supervised fine-tuning and reinforcement learning. For supervised fine-tuning, SyntheticRetro generates structured disconnection rationales paired with reactant predictions. For reinforcement learning, a round-trip reward evaluates predicted reactants by passing them through a forward synthesis model and rewarding predictions that reconstruct the original product. RetroReasoner can also be applied to multi-step retrosynthetic planning by incorporating it into a parallelized Monte Carlo tree search framework, reducing search time while increasing the number and diversity of valid synthetic pathways. Experimental results show that RetroReasoner outperforms prior baselines, including not only molecular LLMs but also retrosynthesis-specific expert models, and generates a broader range of feasible reactant proposals, especially for challenging reaction instances. The code is available at https://github.com/KU-AGI/RetroReasoner.

Hanbum Ko, Chanhui Lee, Ye Rin Kim +4

Department of Artificial Intelligence, Korea University · Materials Intelligence Lab, LG AI Research · Department of Statistics, Korea University

AI-Assisted Scientific Research Language Modeling LLM Reasoning

Mar 3, 2026cs.CL

.tmu: A Low-Entropy Tree-Structured Representation for LLM-Assisted Scientific Writing

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.

Tianyou Liu, Ziqiang Li, Xurui Liu +2

Southern University of Science and Technology · Alibaba · Tsinghua University +2

AI-Assisted Scientific Research LLM Training

Feb 27, 2026q-bio.BM

Inference-time optimization for experiment-grounded protein ensemble generation

Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data. Recent experiment-guided generators attempt to address this by steering the reverse diffusion process. However, these methods are limited by fixed sampling horizons and sensitivity to initialization, often yielding thermodynamically implausible results. We introduce a general inference-time optimization framework to solve these challenges. First, we optimize over latent representations to maximize ensemble log-likelihood, rather than perturbing structures post hoc. This approach eliminates dependence on diffusion length, removes initialization bias, and easily incorporates external constraints. Second, we present novel sampling schemes for drawing Boltzmann-weighted ensembles. By combining structural priors from AlphaFold3 with force-field-based priors, we sample from their product distribution while balancing experimental likelihoods. Our results show that this framework consistently outperforms state-of-the-art guidance, improving diversity, physical energy, and agreement with data in X-ray crystallography and NMR, often fitting the experimental data better than deposited PDB structures. Finally, inference-time optimization experiments maximizing ipTM scores reveal that perturbing AlphaFold3 embeddings can artificially inflate model confidence. This exposes a vulnerability in current design metrics, whose mitigation could offer a pathway to reduce false discovery rates in binder engineering.

Advaith Maddipatla, Anar Rzayev, Marco Pegoraro +5

Institute of Science and Technology, Austria · University of Zurich, Switzerland · Tel Hai – University of Kiryat Shmona in the Galilee, Israel +4

Diffusion Model Guidance Inference-Time Optimization AI-Assisted Scientific Research

Feb 5, 2026cs.LG

Two Stages of Folding: Convergent Mechanisms in AI Protein Folding Trunks

How do protein structure prediction models fold proteins? We investigate this question through causal interventions on the folding trunks of ESMFold, OpenFold, and Boltz-1. Across all three models, we find a shared two-stage computational structure. In the first stage, early blocks initialize pairwise biochemical signals: features like charge propagate from sequence into pairwise representations through architecture-specific pathways. In the second stage, late blocks develop pairwise spatial features: distance and contact information accumulate in the pairwise representation. We verify these mechanisms causally by showing that steering charge and distance features induces predictable structural changes. Furthermore, these representations are functionally interchangeable: pairwise states can be linearly aligned and substituted across models. Together, these results suggest that folding trunks with different architectures, inputs, and training procedures converge on a shared representational organization for mapping sequence chemistry into spatial geometry.

Kevin Lu, Jannik Brinkmann, Stefan Huber +4

1Northeastern University · 2TU Clausthal · 3Harvard University +2

Protein Structure Prediction AI-Assisted Scientific Research Mechanistic Interpretability Representation Alignment

Jan 21, 2026cs.DL

The Rise of Large Language Models and the Direction and Impact of US Federal Research Funding

Federal research funding shapes the direction, diversity, and impact of the US scientific enterprise. Large language models (LLMs) are rapidly diffusing into scientific practice, holding substantial promise while raising widespread concerns. Despite growing attention to AI use in scientific writing and evaluation, little is known about how the rise of LLMs is reshaping the public funding landscape. Here, we examine LLM involvement at key stages of the federal funding pipeline by combining two complementary data sources: confidential National Science Foundation (NSF) and National Institutes of Health (NIH) proposal submissions from two large US R1 universities, including funded, unfunded, and pending proposals, and the full population of publicly released NSF and NIH awards. We find that LLM use rises sharply beginning in 2023 and exhibits a bimodal distribution, indicating a clear split between minimal and substantive use. Across both private submissions and public awards, higher LLM involvement is consistently associated with lower semantic distinctiveness, positioning projects closer to recently funded work within the same agency. The consequences of this shift are agency-dependent. LLM use is positively associated with proposal success and higher early-stage publication output at NIH, whereas no comparable associations are observed at NSF. Notably, the productivity gains at NIH are concentrated in non-hit papers rather than the most highly cited work. Together, these findings provide large-scale evidence that the rise of LLMs is reshaping how scientific ideas are positioned, selected, and translated into publicly funded research, with implications for portfolio governance, research diversity, and the long-run impact of science.

Yifan Qian, Zhe Wen, Alexander C. Furnas +3

Center for Science of Science and Innovation, Northwestern University, Evanston, IL, USA · Ryan Institute on Complexity, Northwestern University, Evanston, IL, USA · Northwestern Innovation Institute, Northwestern University, Evanston, IL, USA +2

AI-Assisted Scientific Research

Jan 8, 2026cs.AI

Conversational AI for Rapid Scientific Prototyping: A Case Study on ESA's ELOPE Competition

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.

Nils Einecke

Honda Research Institute Europe GmbH, Offenbach, Germany

AI-Assisted Scientific Research Human-AI Collaboration LLM Code Generation

Dec 18, 2025cs.DC

AI4EOSC: a Federated Cloud Platform for Artificial Intelligence in Scientific Research

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.

Ignacio Heredia, Álvaro López García, Fernando Aguilar Gómez +28

Instituto de Física de Cantabria (IFCA), CSIC-UC, Avda. los Castros s/n, Santander, 39006, Cantabria, Spain · Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC - Universitat Politècnica de València (UPV), Camino de Vera s/n, Valencia, 46022, Valencia, Spain · Karlsruher Institut für Technologie, Kaiserstraße 12, Karlsruhe, 76131, Germany +7

AI-Assisted Scientific Research Scientific Workflow Automation

Nov 4, 2025cs.LG

Leveraging Discrete Function Decomposability for Scientific Design

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

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which can be formalized as an estimation of distribution algorithm or as reinforcement learning policy optimization

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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"

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a learned generative model

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for efficient navigation of the search space, invoking graph message-passing to coordinate optimization across linked factors.

James C. Bowden, Sergey Levine, Jennifer Listgarten

Department of Electrical Engineering and Computer Sciences, UC Berkeley. · Center for Computational Biology, UC Berkeley. · UC Berkeley–UCSF Graduate Program in Bioengineering, UC San Francisco.

AI-Assisted Scientific Research Combinatorial Optimization