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.

Jul 13Week of Sep 28

Latest papers 162

Oct 7, 2026cs.CY

When Scientific Cognition Is No Longer Scarce

AI could change which parts of science impede progress. Consider a world in which machine systems are better, faster, and cheaper than people at most scientific work that can be done through a computer. Our question is what would limit science in that world. Literature synthesis, hypothesis generation, software development, simulation, and analysis could become abundant, while experiments, observations, well-supported conclusions, and accountable institutional au- thority remain scarce. Science would then be constrained by a different set of resources. In this paper, we call this change the scarcity inversion and consider four parts of it: selection, physical access, validation, and organizational choice. This change is arriving first in mathematics and coding/software/algorithm design, where the whole scientific loop can run inside computation. For national laboratories, the change could be striking. Their distinctive role is to turn abundant machine reasoning into trustworthy results by combining controlled experiments, protected data, expert judgment, and accountable authority. The practical question is how facilities, verification, provenance, resource allocation, and scientific governance should change when reasoning is plentiful and trustworthy evidence is scarce.

Nathan DeBardeleben

Los Alamos National Laboratory

AI-Assisted Scientific Research AI Governance

Oct 7, 2026cond-mat.other

Progress and Prospect of AI in ARPES Workflow

Artificial intelligence (AI) is becoming an increasingly useful tool across the experimental sciences, including angle-resolved photoemission spectroscopy (ARPES), which routinely produces large, multidimensional datasets of electronic structure. Recent advances in AI and machine learning (ML) have opened new opportunities across the entire ARPES workflow, from automated sample preparation and real-time data acquisition to post-experiment data analysis and comparison with theoretical calculations. Despite this progress, a comprehensive review of ML applications, their capabilities, and reliability across the different stages of ARPES workflow is still lacking. In this review, we first introduce ML methods that are most relevant to experimentalists working in condensed matter physics and materials science. We then follow the ARPES workflow, reviewing existing ML applications at each step and discussing their advantages, limitations and potential for future development. We also examine the current ARPES data landscape, where several open databases are available but remain relatively small and fragmented compared with large, shared datasets such as ImageNet. Given these limitations, we suggest that the community focus on sharing pretrained models that can be further trained, adapted to specific tasks, and redistributed, while working toward a larger and standardized open ARPES dataset repository. Finally, we discuss our perspectives on the future of AI within the ARPES workflow using a six-level framework of laboratory automation, highlighting the opportunities and challenges in moving toward a fully autonomous, self-driving ARPES laboratory.

Sandy Adhitia Ekahana, Aalok Tiwari, Pratik Saud +4

Department of Physics, Carnegie Mellon University, Pittsburgh, 15213, PA, USA. · MAESTRO, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

AI-Assisted Scientific Research Scientific Workflow Automation Laboratory Automation

Oct 7, 2026cs.AR

When Algorithmic Exploration Becomes Cheap: A Case Study of Agentic Research in EDA

As EDA researchers, we conducted eight deliberate trials of agentic algorithm exploration, selecting several topics outside our areas of depth. One faculty member and seven students participated, including students without publication experience. With limited intervention in the algorithms, agents developed mathematical constructions, analyzed existing tools, and implemented improvements; some efforts fell short of their practical goals. We also used AI to collect, classify, and analyze 8,420 papers from four EDA conferences and two journals over 2022-2026. Among 2,380 primary-core papers, we classified 97.7% from titles and abstracts as computationally closed, including work on new formulations. Together, these observations suggest that much of EDA offers an executable environment for increasingly accessible algorithm research. We see an opportunity for tool developers to investigate ideas they previously lacked time to pursue. We also ask how EDA should validate and reward research when results become easier to produce than to examine, and what papers and venue labels will continue to tell us about a contribution.

Keren Zhu, Yu Deng, Xiaoyu Hao +6

College of Integrated Circuits and Micro-Nano Electronics Fudan University, Shanghai, China

AI-Assisted Scientific Research Autonomous Research Agents Electronic Design Automation Automated Algorithm Discovery

Oct 6, 2026cs.LG

Neural Petri flows for chemical reactions

Petri nets have been used to describe chemical processes such as reactions.They map well to chemistry: Places are the bonds between atoms and the free valence of each atom, a token is a unit of bond order, a transition forms or breaks a bond, the conserved quantities are the valence budgets of the atoms, and the enabling rule is the valence rule. These semantics are not guaranteed by learned models of reactions or neural networks that are built on Petri nets that use the net as a scaffold for message passing. Here, we ask what architecture remains a Petri net for every value of its weights. We find the answer in the theory, where all semantics of a net share the firing form

m^\prime=m+Cσ

, locality, as enabling reads only the inputs of a transition, and the enabling rule, and we prove that conservation forces the firing form and that non-negativity forces the enabling rule on local rate laws. This leaves free the rate law, which is the propensity of each transition to fire. We introduce Neural Petri Flow, which learns this rate law, or a readout for classification, and hard-wires the rest as parameter-free layers. On what we denote a valence net, atom mapping, reaction classification, and forward prediction become three tasks on one firing vector. Without training, the minimum firing vector maps 88.8% of the curated Golden set against 85.6% for RXNMapper, and 88.7 against 77.9% of the enzymatic reactions of EnzymeMap. On USPTO-480K, NPF trained on these firing vectors predicts 87.7% of the products and 67.4% when trained on a 1% subset of the training reactions. EC numbers of ECREACT are predicted at the third level for 90.2% of reactions, 5.6 points ahead of the best published method. With electrons as tokens, the same token game predicts 90.5% of the elementary steps of FlowER first, ahead of the published baseline, and every top-1 prediction is a valid molecule without a filter.

Jose Eduardo Escrig Molina, Daniel Probst

Bioinformatics Group Bioprocess Engineering Group Wageningen Unversity Wageningen, the Netherlands

AI-Assisted Scientific Research

Oct 5, 2026cs.LG

Learning Scientific Exploration from Human Research Decision Trajectories

A key challenge in building AI systems for scientific research is enabling

\textit{scientific exploration}

: the systematic process of investigating unknown phenomena or ideas to gain new knowledge through sequences of research decisions and actions. Yet this process is largely missing from existing scientific corpora; for example, research papers primarily record final outcomes rather than the trajectories that produced them. In this work, we introduce

\textbf{ResearchTrails}

, a dataset of

\textbf{human research trajectories constructed from Git repositories}

, where

\textbf{commit histories}

serve as proxies for research exploration. We develop an automated and scalable pipeline that extracts structured research trajectories from repository commits, capturing successive changes to methods, experiments, and ablations. We characterize the resulting dataset and show that these trajectories contain meaningful signals about intermediate research decisions beyond what final papers reveal. We further demonstrate utilities of ResearchTrails in multiple use cases, including retrieving human research experience as external skills at test time and training models on research trajectories to improve generalization to new research decisions. Our results suggest a path toward AI systems that learn not only from the products of science, but from the evolving process of discovery itself.

Xuchen Gong, Shane Gu, Haokun Liu +3

University of Chicago

AI-Assisted Scientific Research

Oct 5, 2026cs.AI

FREA: A Multi-Source Expert Benchmark for Reaction Feasibility Verification

As generative models and AI agents propose chemical reactions at a scale beyond expert review, feasibility verifiers decide which proposals enter synthesis planning. But do their decisions agree with chemists across different kinds of candidates? We introduce FREA, a benchmark of 751 reactions labeled by expert chemists under an explicit feasibility criterion, drawn from retrosynthesis model proposals, zero-yield experimental records, edits by large language models (LLMs), and five negative candidate generation methods. Our evaluation finds that no verifier leads across all sources: LLMs given only the criterion are competitive with dedicated verifiers, while forward models perform best on retrosynthesis proposals but reject most feasible edits of recorded reactions at the evaluated operating points. Looking beyond aggregate scores, both forward models perform below chance when separating infeasible alternative disconnections from feasible generated candidates. To study whether negative supervision addresses these weaknesses, we also release a corpus of over 14 million recorded reactions and generated negative candidates. In matched training comparisons, adding a mixture of generated negatives to forward training raises mean AUROC across sources, but these gains do not extend to retrosynthesis proposals. Varying the generation method further shows that the largest gain on generated candidates coincides with worse proposal screening. These findings motivate evaluating verifiers against experts across sources and designing negatives for transfer to model proposals.

Botao Yu, Bo Zhou, Daniel Adu-Ampratwum +7

Department of Computer Science and Engineering, The Ohio State University · Department of Pharmaceutical Sciences, University of Illinois Chicago · College of Pharmacy, The Ohio State University +3

LLM Evaluation AI-Assisted Scientific Research

Sep 29, 2026astro-ph.IM

Gestalt: a meta-foundation model for astronomy

The Platonic Representation Hypothesis predicts that sufficiently scaled foundation models converge on a shared representation of the world. As each non-converged model gives a noisy view of a common structure when passed the same input, we ask whether we can combine models into a representation that outperforms its individual components. We test this on galaxies: we embed images via a basket of 22 frozen foundation models from eight families, whiten each view, and take a randomised SVD of the embedding concatenation. The resulting 1024-dimensional embedding outperforms every basket member on 19/21 of our tested metrics for physical property and galaxy morphology estimation for HSC, JWST, and DESI Legacy Survey imagery. We find that performance rises with basket size and basket architectural diversity, and that the meta-foundation model's performance transfers across astronomical surveys. We conclude that a useful astronomical foundation model can be assembled from existing generalist models with no training required beyond a single unsupervised projection. By leveraging the community's already-spent work, we save a lot of compute: a fresh pre-train of a comparable single-domain model would cost

\mathcal{O}(10^{4}

--

10^{5})

A100 GPU hours (emitting several tonnes of CO

_2

eq.), whereas assembling Gestalt requires minutes on a single machine.

Michael J. Smith, Shashwat Sourav

AstroAI · Center for Astrophysics | Harvard & Smithsonian · UniverseTBD +1

Ensemble Learning AI-Assisted Scientific Research

Sep 27, 2026cs.AI

RINI: Seeing the Prior Is Not Enough

A research proposal can describe an established mechanism correctly while claiming to introduce it. We study whether providing the earlier paper corrects such contribution claims. Three controlled experiments compare proposals generated with a contribution-bearing prior and a same-topic control. Providing the prior yields no clear aggregate reduction in unsupported novelty. Human analysis of 175 interpretable exposed proposals finds that 137 recognize the prior's relevance, but 61 correctly attribute the established contribution. Of 71 proposed remaining distinctions, 37 are covered by the same prior. We introduce Research Idea Novelty Inspection (RINI), which audits contribution claims against evidence, checks the remaining distinction, and applies local revisions. Five human annotators evaluate 1,080 original-revision pairs across three methods. On the same 240 originals judged to require correction, successful repair is 11.7% for Self-Revision, 39.1% for Retrieve-and-Revise, and 72.2% for RINI, with research tasks weighted equally. The improvement over same-evidence direct revision is 33.0 percentage points. The revised proposals retain their research questions and technical methods. These results motivate explicit contribution attribution when using literature to generate and revise research proposals.

Hongyi Du, Tianyi Zhang, Heng Wang +7

University of Illinois Urbana-Champaign · Harvey Mudd College · National University of Singapore +2

Novelty Search AI-Assisted Scientific Research Evidence-Grounded Generation Scientific Claim Verification

Sep 23, 2026cs.LG

LabFactory: Building and Evaluating Executable AI Labs

Scientific tasks specify a desired capability, but realizing it often requires building a computational system tailored to the task---acquiring data, designing representations, training models, implementing tools, and deciding how they are used at inference. We present LabFactory, a framework in which an AI builder turns a scientific brief into an executable AI lab: a task-specific solver that integrates models, knowledge resources, tools, and a controller behind a fixed interface. The builder develops and packages the lab in a metered workspace; a separate host then executes the delivered artifact on held-out inputs, with reference labels kept outside the solver's input interface, and scores its outputs under the task's protocol. This makes the delivered system, rather than the builder's account of its progress, the object of evaluation. We document 28 selected constructions across seven scientific task categories---from molecular and genomic prediction to physiological signals, clinical decision support, and biomedical text---whose delivered labs exceeded their configured reference values on all 33 subtests under host-side execution. Ten contain predictive models fitted during construction; the others assemble retrieval systems, executable analysis environments, and tool-driven workflows around a fixed platform LLM. Together they show that an AI agent can carry a scientific brief all the way to a working lab that can still be invoked, inspected, and checked after construction ends.

Jinge Wu, Hongjian Zhou, Mingde Zeng +6

University of Oxford

AI-Assisted Scientific Research AI Agent Evaluation Scientific Workflow Automation Autonomous Research Agents

Sep 22, 2026cs.AI

ChatT2: An Adaptive Framework for Developing a Large Language Model-Based Agent for Natural Product Domain Research

Scientific investigations into microbial natural products (NPs) present significant challenges for novices, largely due to the complexity of microbial systems, biochemical diversity, technical skill requirements, and the demands of bioinformatics and data analysis processes. To address these issues, we introduce ChatT2, a large language model (LLM)-based agent that is specifically tailored to the unique characteristics of bacterial type II polyketides. These polyketides form a structurally distinct and therapeutically important NP family. ChatT2 was developed within an autonomous multiagent framework composed of a mentor, an executor, and an evaluator, each with defined responsibilities. The mentor acts as an intermediary between ChatT2 and the user, utilizing chain-of-thought prompting to refine the intent of the user. Under the guidance of the mentor, the executor synthesizes multimodal information via retrieval-augmented generation techniques and seamlessly integrates bioinformatics and cheminformatics tools. The evaluator ultimately assesses the output of the executor to ensure the richness and accuracy of the retrieved information. Our research highlights how ChatT2, designed with this multiagent framework, addresses the challenges faced by general LLMs in terms of understanding limited, specialized corpora and complex biological information and provides both experts and novices with a valuable tool for exploring various NPs of interest. The ChatT2 webserver can be accessed at https://chatt2.site/#/chat.

Yihan Wang, Qiandi Gao, Yihui Zhuang +4

Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong, 519087, China.

Multi-Agent LLM Systems AI-Assisted Scientific Research Agentic RAG

Sep 21, 2026cs.CL

Jev for Scientific Decisions: Evaluating Semantic Choices and Their Consequences

Scientific workflows often require choosing among known relations before a deterministic calculation can proceed. Whether observations share a culture, treatment or reference standard can change the scientific meaning of the resulting count or comparison. We evaluate Jev as a semantic decision component using a harness that follows its documented guidance and assigns arithmetic to code. The study compares twelve model configurations on twenty source-grounded Choices across ten scientific cases, each repeated five times. We measure semantic selections, downstream outputs and final claim labels separately. Jev matched five other configurations at complete semantic correctness and achieved the lowest observed median latency among successful responses. Across three comparison models, seven wrong selections on one culture-history question changed downstream counts while preserving the correct final label. These results identify a useful role for Jev in prepared scientific decision tasks and show why evaluating that role requires checking the relations and quantities that a workflow will reuse.

Boyuan Deng, Shuyi Fan, Hongyang Zhang +1

Johns Hopkins University · Columbia University · The Hong Kong Polytechnic University +1

AI-Assisted Scientific Research LLM Decision-Making Scientific Reasoning in Language Models

Sep 16, 2026cs.AI

Time-Aligned Evolving Concept Graphs for Scientific Relation Forecasting

Forecasting scientific relations can guide discovery by identifying promising connections before they emerge. Existing approaches often model concept semantics and graph structure separately or summarize semantics over coarse historical snapshots, leaving semantic representations potentially misaligned with rapidly evolving graph evidence. We propose a time-aligned evolving concept graph framework that jointly models semantic and structural evolution. Its core idea is to treat dated papers as shared update events, reconstructing semantic and structural states from the same publication history through each prediction time. Pair-level fusion combines these states to forecast first co-occurrence, relation formation, and conditional relation type. Holding architecture and training fixed, refreshing context alongside graph updates improves mean relation AUPRC by 16.6% over frozen context. On a graph built from 187,848 papers with 270,687 concepts and 7.45 million co-occurrence links, the complete framework improves mean relation AUROC from 0.9290 for the strongest evaluated baseline to 0.9722, with mean population-weighted AUPRC 0.005778.

Fred Sun, Jingze Wang, Minkun Xu +1

Center for Brain-Inspired Computing Research, Department of Precision Instrument, Tsinghua University, Beijing, China · Guangdong Institute of Intelligence Science and Technology, Zhuhai, China

AI-Assisted Scientific Research Temporal Link Prediction Dynamic Graph Learning

Sep 15, 2026cs.CY

AI and Human Approaches to Mathematical Problem Solving

AI systems have begun to report solutions, disproofs, and substantive advances on long-standing mathematical problems, raising questions about whether they approach research in the same way as mathematicians. This study compares public AI research accounts with the human literature on 11 such problems. The human corpus contains 58 papers that directly addressed the same mathematical targets later reported by AI sources as resolved, disproved, or substantially advanced; 31 within-problem comparisons were constructed from these materials. Six validated text-based measures capture problem resolution, method articulation, uncertainty and boundary specification, successor-question generation, generality, and cross-disciplinary integration. AI accounts place greater emphasis on resolving the focal problem and connecting ideas across fields. Human papers devote significantly more attention to explaining methods, specifying assumptions and limitations, and identifying questions for subsequent research. No precise difference is detected in generality. The estimated directions remain unchanged when each mathematical problem is removed in turn. The findings reveal two distinct research profiles: AI accounts concentrate on closing and recombining problems, whereas mathematical papers more extensively document the procedures, limits, and research opportunities through which results become cumulative knowledge. Evaluating research AI therefore requires attention to the organization of inquiry, not only whether a target is solved.

Yang Ding

University of Edinburgh Business School, Edinburgh EH8 9JS, UK. · Centre for Technomoral Futures, Edinburgh Futures Institute, University of Edinburgh, Edinburgh EH3 9EF, UK. · Manchester Institute of Innovation Research, Alliance Manchester Business School, University of Manchester, Manchester M13 9PL, UK.

AI-Assisted Scientific Research Mathematical Reasoning

Sep 15, 2026cs.AI

ScienceBuddy: Recursive-in-Recursive Self-Improvement for Interactive Scientific Agents

We introduce and release ScienceBuddy, an interactive scientific research workspace that brings continually improving scientific agents into researchers' everyday workflows. ScienceBuddy supports researchers in carrying out scientific tasks while transforming their requests, feedback, and execution evidence into tasks and evaluation rubrics for continual learning. At its core is recursive-in-recursive self-improvement, a paradigm that couples harness evolution with model reinforcement learning: the inner recursion improves the harness with the model fixed, while the outer recursion trains the model under the improved harness. Harness evolution shapes training experience, and model learning creates new opportunities for harness adaptation. We present case studies of researcher interaction, harness refinement, and model learning, with the benchmark cases spanning four scientific task families. By releasing ScienceBuddy as a research product, we make this paradigm available to the scientific community and take a step toward discovery intelligence: scientific AI that advances through sustained collaboration with researchers and evolves alongside the research it supports. Website: http://science-buddy.io

Shuhan Xue, Jianyuan Zhong, Ziyuan Nan +10

Continual Learning for LLM Agents AI-Assisted Scientific Research LLM Agent Self-Improvement Recursive Self-Improvement RL for LLM Agents Autonomous Research Agents

Sep 15, 2026cs.CL

PaperDoctor: Evidence-Grounded and Actionable Feedback for Scientific Papers in Progress

Autoresearch agents are reshaping the research ecosystem, but they can also let flawed claims enter the literature at scale. Human advisors catch such issues in drafts through careful, traceable feedback, yet advisor-style assessment requires extensive manual effort and does not scale. To shift automated paper assessment from a judge to a diagnostician, we introduce PaperDoctor, an agent framework for pre-submission feedback with three key innovations. First, a holistic hierarchical framework evaluates writing, layout, references, code, theory, prior work, and experiments through three layers: L1 surface screening, L2 typed verifiers that route each claim to the appropriate evidence, and L3 reproducers that rerun experiments by priority. Second, each finding contains an observation, a pointer to specific evidence such as a sentence, equation, or code line, and a revision suggestion, making critiques auditable and actionable. Third, PaperDoctor selectively rebuilds and reruns experiments based on claim importance and compute budget, surfacing reproducibility gaps and quantitative limitations that are invisible from the manuscript alone. We evaluate PaperDoctor on 30 in-progress papers, yielding 70.6% agreement and all positive holistic scores, and on 40 manuscripts across machine learning, natural science, and social science, covering human- and AI-authored papers with code. Overall, PaperDoctor produces more auditable feedback than human and other agentic reviewers, pairs critiques with concrete suggestions by design, and complements dimensions often overlooked by human reviewers. We also develop an interactive interface that lets authors browse findings grounded in their paper. PaperDoctor reframes automated paper assessment as diagnosis rather than verdict, taking a concrete step toward AI advisors for more rigorous AI-assisted scientific discovery.

Kevin Qinghong Lin, Siyuan Hu, Pan Lu +14

University of Oxford · 3National University of Singapore · 2Stanford University +3

AI-Assisted Scientific Research Scientific Reproducibility Automated Peer Review Scientific Claim Verification

Sep 15, 2026cs.AI

AquiLLM: Evaluating Faithfulness in Open-Weight RAG-LLM Systems for Scientific Research

Scientific research increasingly relies on large, heterogeneous data sources, motivating interest in retrieval-augmented generation (RAG) systems that provide natural language access to scientific knowledge and research workflows. Researchers are exploring the viability of these systems as natural language interfaces for document search and for generating analysis code and pipeline components. At the same time, concerns about data privacy and control over research infrastructure have motivated interest in open-weight models and open-source deployments hosted within research institutions. In astronomy, this development follows a long history of computational infrastructure development, from archival databases and Structured Query Language (SQL)-based systems to large language model (LLM)-assisted research tools. This paper presents a domain-expert evaluation of faithfulness for AquiLLM, an open-weight, offline RAG-LLM platform designed to support scientific research groups in the use and preservation of tacit and formal knowledge. We define faithfulness as the extent to which generated responses remain grounded in retrieved scientific context without unsupported claims or omissions. We report results from an astronomy case study evaluating AquiLLM across retrieval and scientific analysis tasks. AquiLLM performs most reliably on explicit retrieval-oriented questions grounded in the RAG collection, while faithfulness degrades for queries requiring synthesis or ambiguity resolution. These results highlight both the promise and limitations of open-weight RAG-LLM systems for scientific research and demonstrate the importance of domain-expert evaluation beyond standard benchmark leaderboards.

Bernie Boscoe, Srinath Saikrishnan, Vikram Seenivasan +6

Dept. of Computer Science, Southern Oregon University, USA · Dept. of Computer Science, University of California, Los Angeles, USA · Dept. of Physics & Astronomy, University of California, Los Angeles, USA +1

AI-Assisted Scientific Research Open-Weight Language Models RAG Evaluation

Sep 14, 2026cs.AI

The AI-Enabled Scientific Frontier

As artificial intelligence's capabilities improve, it is increasingly viewed as a general scientific method. But how true are these claims? Does AI outperform all techniques, or only some, and how is this changing? To assess the claims, we assemble a corpus of 2,507 head-to-head comparisons between AI and other scientific analysis techniques across 27 scientific disciplines from papers published between 2000 and early 2025. We find a profound dichotomy. Relative to traditional statistics, AI often outperforms, but at a significantly higher computational cost. But there are also nearly a quarter of cases where AI is both more expensive and performs worse than traditional statistical techniques and this fraction has been stable for a decade. Relative to scientific computing, AI often underperforms, but at lower computational cost. This has begun to change: since 2020, AI's performance against scientific computing has notably strengthened and it now outperforms on more than half of comparisons. These patterns suggest that AI is therefore not a universal replacement for existing methods, but rather a valuable -- and improving -- part of a new AI-enabled scientific frontier.

Gabriel Manso, Emma Fu, Neil Thompson

1MIT CSAIL, MIT FutureTech

AI for Science AI-Assisted Scientific Research

Sep 14, 2026cs.SE

PRISMA-LLM: An Empirical Reporting Framework for AI-Assisted Systematic Reviews

Large language models (LLMs) and AI-enabled software increasingly participate in systematic-review decisions, yet the information needed to audit these workflows is reported inconsistently. We analyze SciLitBench, a corpus of 888 review-automation papers with 14,726 annotations, to characterize changes in methods, review-stage use, evaluation and reported limitations. Automation has shifted toward LLM- and software-facing workflows, including stages that can alter the evidence base. Since 2023, 38.0% of software/product papers reported no evaluation, compared with 9.3% of LLM papers. Reporting coverage increased with LLM workflow complexity, yet 52% of positive-only LLM evaluations still reported an unmet reliability or performance requirement. From these patterns, we introduce PRISMA-LLM, an empirically grounded framework separating implementation disclosure from consequence-sensitive evaluation and limitation reporting.

Miguel Zabaleta, Baihan Lin

Department of AI and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA · Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA · Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA

LLM Auditing AI-Assisted Scientific Research LLM Reliability Automated Evaluation

Sep 12, 2026cs.CY

(Whose defaults?) Is artificial intelligence reorienting archaeological methods?

Generative AI and the practice of "vibe coding" are changing how archaeologists carry out computational research, but their effects on the discipline's range of methods is still understudied. In this paper, we evaluate whether large language models (LLMs) are narrowing the variety of methods archaeologists use. We first analysed approximately 119,000 archaeology abstracts from Scopus, covering publications from 2010 to 2025. Using a locally run LLM, we identified the computational methods reported in each abstract and organised them into 25 broad categories (L2) and 241 finer clusters (L3). A Bayesian Dirichlet-multinomial model of method composition within sub-disciplines found a small but credible shift in method use after 2023. However, this shift was smaller than the variation already present across the full study period. No individual technique showed a significant change, and overall methodological diversity increased rather than declined. We then ran a controlled experiment to see whether LLMs recommend a narrower set of methods than archaeologists have used in practice. Two different open-weight models were asked to suggest methods for 28 archaeological research problems, with prompts providing three levels of methodological guidance: novice, intermediate, and expert. Recommendation diversity was much lower than in the published literature, particularly without methodological guidance. The models also tended to favour methods that were widely used before 2023, and their recommendations more closely resembled the post-2023 literature. Taken together, these results are consistent with LLMs pushing methodological choice towards convergence, although our study cannot establish a causal effect. They raise a broader question: how can archaeology retain methodological diversity as LLMs become more involved in research?

Lorenzo Cardarelli, Roberto Ragno

Seminar für Ur- und Frühgeschichte Georg-August-Universität Göttingen Göttingen, Germany · McDonald Institute for Archaeological Research University of Cambridge Cambridge, UK

AI-Assisted Scientific Research Large Language Model-Based Recommendation

Sep 7, 2026cs.AI

The Emerging AI Paper-Review Arms Race: Adversarial Co-Evolution in Scholarly Publishing

Generative and agentic AI are reshaping both the production and evaluation of scientific research. These developments are often studied separately, as questions of how AI can produce research and how AI can review it. We argue that this separation misses an increasingly important feature of scholarly publishing: changes on one side alter the incentives, constraints, and behavior of the other. We synthesize 230 scholarly publications and institutional records using a taxonomy of six connected dynamics: production scaling, evaluation automation, evaluation manipulation, defense mechanisms and policy responses, evasion and side effects, and long-horizon ecosystem feedback. The literature shows an emerging progression in which cheaper and faster research production increases pressure on evaluation, AI-mediated evaluation becomes more scalable and repeatable, participants can exploit evaluator regularities, and institutions respond with technical safeguards and policy controls. These responses can in turn induce evasion, redistribute errors and workload, and shape the scholarly records reused by future research and evaluation systems. Evidence is strongest for production and evaluation at scale, reproducible manipulation, and institutional response, while post-policy adaptation and artifact-level long-horizon feedback remain less directly observed. This systems view shifts attention from isolated AI capabilities toward how scholarly actors and AI systems adapt to one another over time.

Chenguang Wang, Ming Li, Adebayo Braimah +6

Virginia Tech · University of Maryland · Stony Brook University +1

AI-Assisted Scientific Research Scholarly Peer Review AI Governance Automated Peer Review

Sep 2, 2026cs.LG

ProbeMatchDTI: Probe-Driven Multi-Scale Biochemical Pattern Matching for Drug-Target Interaction Prediction

Drug-target interaction (DTI) prediction is an important task in AI-driven drug discovery. Although recent biochemical representation learning methods have improved DTI prediction, their passive feature aggregation tends to favor dominant molecular patterns while suppressing weak yet binding-relevant signals, such as functional groups and residue-context patterns, limiting the modeling of multi-scale biochemical correspondences. To address this issue, we propose ProbeMatchDTI, a pattern-probe-driven framework comprising IterProbe and BindingProbe. IterProbe explicitly retains contextual states across refinement depths and uses learnable probes to select them at each position before cross-entity matching, thereby preserving weak biochemical patterns and strengthening associations among functional groups, local motifs, and molecular scaffolds. BindingProbe then characterizes cross-entity drug-protein complementarity at local biochemical-unit and whole-pair levels, jointly modeling fine-grained interactions and multi-scale correspondences while preserving weaker binding-relevant associations. Extensive experiments demonstrate the superiority of ProbeMatchDTI, achieving 2.0% and 0.5% higher AUC-ROC on BindingDB and DrugBank, respectively. Feature-level pattern analyses further characterize its probe-driven behavior in cross-scale biochemical pattern matching. We further connect ProbeMatchDTI predictions with an evidence-guided downstream drug-discovery workflow, demonstrating their utility for candidate refinement and validation planning. Our code is available at https://github.com/developer-hq/ProbeMatchDTI

Quan Hao, Mengyue Fan, Zifan Dong +8

School of Computer Science and Engineering, University of New South Wales, Sydney, Australia

Drug Discovery AI-Assisted Scientific Research Hierarchical Representation Learning

Sep 1, 2026cs.DL

Citing Less Critically: LLMs Reshape the Rhetoric and Reach of Scientific Citation

Scientific citations carry rhetorical intent. Scholars may cite prior work positively (supporting), negatively (contrasting), or neutrally (mentioning). As large language models (LLMs) increasingly assist scientific writing, whether they reproduce citations with the same rhetorical intent as humans remains unclear. We introduce a masked-citation task to compare human and LLM-generated citation behavior. For each citation context, an LLM generates a replacement citation sentence, producing a counterfactual corpus directly comparable to human citation. We analyze what, whom, and how models cite, using an LLM-as-a-judge to classify citation intent and a 20-million-edge coauthorship network to measure social distance between cited authors. Across six popular LLMs and 1,746 top NLP conference papers (63k+ contexts, 132k+ citations), three patterns emerge: (1) Compared with human citation, LLMs cite significantly less critically; (2) LLMs over-cite popular and older papers, a tendency amplified for contrasting citations where human writing more often draws on recent, niche work; (3) Whereas humans often cite within their close social network, especially for supporting citations, LLMs tend to draw on more socially distant authors. Together, these differences are double-edged: LLM citation reaches beyond a scholar's close collaborators while being less critical and amplifying visibility bias, reshaping the rhetoric and reach of scientific citation.

Yixuan Liu, Lin Chen, Zhuoqi Liu +2

1Network Science Institute, Northeastern University · Department of Physics, Northeastern University · Department of Electrical and Computer Engineering, Northeastern University +1

AI-Assisted Scientific Research

Aug 31, 2026cond-mat.stat-mech

A Human-AI Theorem Connecting Spontaneous and Field-Induced Mechanisms of Collective Behavior in One Dimension

Can an artificial intelligence (AI) generate a scientific hypothesis outside a human collaborator's active hypothesis space (AHS), and can human-AI research be organized to make such breakthroughs more likely? We document such a case while proving a theorem that connects two basic organizing mechanisms of statistical physics: collective behavior arising in zero field from competing interactions and that induced or controlled by an external field. A zero-field

O(n)

-vector open chain with arbitrary inhomogeneous nearest- and next-nearest-neighbor interaction functions

U_i(S_i\cdot{S}_{i+1})

and

V_i(S_i\cdot{S}_{i+2})

is microscopically, via a temperature-independent mapping at the Hamiltonian level, equivalent to a simpler

O(n)

open chain with nearest-neighbor interaction

V_i(\boldsymbolσ_i\cdot\boldsymbolσ_{i+1})

and axial single-spin potential

U_i(σ_i^z)

for every integer

n\ge1

and every system size

L\ge1

. The homogeneous linear specialization maps the foundational frustrated

J_1

-

J_2

model onto the canonical

J

-

h

field model---with

n=1,2,3

being the Ising, XY, and Heisenberg classical spin models, respectively; the theorem resolved a longstanding challenge for

n=3

published in 1990. Its proof was done with an AI-synthesized recursive Householder moving frame and understood via a human-recognized hidden reciprocity. An analogous theorem holds when the continuous

O(n)

spins are replaced by the

q

-state Potts spins, implying a closed-form exact solution of the

J_1

-

J_2

standard Potts open chain for every

q\ge2

and every

L\ge1

. The emergence of these theorems from a human-AI co-development framework suggests that sustained AI involvement throughout a systematic research program may incubate autonomous scientific breakthroughs and make aspects of the discovery process experimentally testable.

Weiguo Yin

Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, New York 11973, USA

AI-Assisted Scientific Research Scientific Hypothesis Generation Human-AI Co-Creation

Aug 27, 2026cs.CL

RATIO: A Benchmark for Retrieval Across Typed Ideation Operations in Scientific Literature

Retrieved scientific literature can serve as inspiration for both human and AI scientists. Inspiration can take different forms: prior work may directly suggest how to address a problem, or surface directions at different levels of abstraction - zooming out to a more general view or zooming in to a concrete realization. We introduce RATIO (Retrieval Across Typed Ideation Operations), a large-scale benchmark in which relevance is defined by three operations which we name ideation moves: Address retrieves potential approaches for stated problems, Broaden retrieves more general formulations, and Specify retrieves concrete instantiations. RATIO is constructed from millions of full-text scientific papers across CS literature via a general recipe that extends discourse-marker distant supervision - previously used only for classification - to corpus-scale retrieval, combined with extensive LLM and human vetting. Experiments show that operation-specific fine-tuning substantially boosts retrievers but leaves much room for further improvements. RATIO provides a scalable training and evaluation framework for retrieval components that support literature-grounded ideation, opening up new research avenues on scientific inspiration retrieval.

Maayan Sharon, Tom Hope

The Hebrew University of Jerusalem · The Allen Institute for AI (AI2)

AI-Assisted Scientific Research IR Evaluation

Aug 11, 2026cs.AI

Long-Horizon AI Research for Grothendieck Constant: A Case Study in Human-AI Mathematical Collaboration

AI agents are increasingly used in mathematics research, but it is often unclear how to use them effectively. Towards this, we present an extensive case study of how AI was used to improve bounds on the Grothendieck constant

K_G

, which captures the hardness between combinatorial problems and their continuous relaxations. Specifically, while the precise value of

K_G

is not known, we recently tightened the best known bounds to

\frac{6π}{11} \;\le\; K_G \;\le\; \fracπ{2\log(1+\sqrt2)} - 10^{-4}.

Crucially, these improvements were achieved using an AI research system that could arrive at insights deemed novel by domain experts. We give a detailed discussion of our experience using AI for mathematics research, particularly touching upon its strengths and weaknesses, as well as our experience with creating ideal conditions for AI to arrive at breakthrough insights.

Alan Li, Rahul Saha, Anton Xue +4

Deep Research Agents AI-Assisted Scientific Research Human-AI Collaboration LLM Mathematical Reasoning

Aug 10, 2026cs.AI

Causal Behavioral Evaluation of AI Agents at Scale via Automated Behavioral Science

As AI agents are increasingly deployed in complex and new environments, knowing the conditions that influence their behavior becomes an indispensable step for their reliable and safe deployment. Yet causal behavioral evaluation of AI agents remains manual and labor-intensive. We introduce Abs2Sim and AEROBAT, a system of methods that support causal behavioral evaluation of AI agents via automated behavioral science. Given a user-specified target behavior, the methods automatically execute a full pipeline of behavioral science research---generating hypotheses about the behavior, designing and executing controlled experiments, making behavioral assessments, analyzing the results, and writing reports. For 12 target behaviors, the methods generated and tested 73 hypotheses: designing 1,160 controlled experiments and executing 22,954 simulation rounds in total. Moderate-to-strong statistical evidence emerged for 30 hypotheses, revealing potential modulators of AI behavior. In sum, our results demonstrate that automated behavioral science can extend the reach of behavioral evaluation of AI agents.

Soo Yong Lee, Jongha Lee, Jaewan Chun +8

KAIST, Kim Jaechul Graduate School of AI · Yale, Department of Psychiatry · University of Haifa, School of Public Health +3

AI-Assisted Scientific Research AI Agent Evaluation Autonomous Experimentation

Aug 9, 2026cs.AI

AquiLLM: An Architecture for Supporting Tacit Knowledge Capture in Research Groups

Recent advances in retrieval-augmented generation (RAG) and large language models (LLMs) enable researchers to integrate AI into scientific workflows. However, using proprietary commercial AI systems raises concerns about transparency, reproducibility and privacy, which are essential for scientific practices. To this end, AquiLLM was developed as an open-source modular RAG-LLM framework using open-weight models, designed to support research groups in capturing tacit knowledge. In this work, we present a series of architectural improvements and feature enhancements to AquiLLM, including local embedding and reranking, multimodal capabilities, OpenAI-compatible inference interfaces, user interface improvements, semantic and episodic memory capabilities, and skills support. These enhancements were informed by discussions with domain experts, including astrophysicists and environmental researchers, and represent a step toward AI systems more closely aligned with scientific research practices.

Jack Stark, Srinath Saikrishnan, Vikram Seenivasan +3

University of California, Los Angeles, Los Angeles, California, USA · Southern Oregon University, Ashland, Oregon, USA

Memory-Augmented Language Models Knowledge Augmentation for Language Models AI-Assisted Scientific Research

Aug 7, 2026cs.AI

QuantumMind: Constraint-Grounded Agentic Reasoning for Speedup Analysis in Quantum Computing

Identifying a meaningful quantum speedup requires more than matching a classical problem to a familiar quantum primitive: the claim must preserve the task, respect access and output models, expose required promises, and remain within a defensible complexity scope. We present QuantumMind, an auditable agentic workflow for generating and conservatively screening quantum-acceleration hypotheses. A fixed sequence of typed, role-specialized actions formalizes the public task, analyzes structure and classical bottlenecks, matches a source-linked registry of quantum primitives and barriers, and constructs a scoped candidate scheme. A deterministic ten-check validator assigns the authoritative verdict; completed states are compiled into a Quantum Acceleration Evidence Graph and passed through a downward-only research screen that cannot strengthen the decision. We evaluate QuantumMind against seven task-adapted prompting and agentic controls on 582 identical open-discovery tasks. Under the frozen Open-Discovery Score (ODS), QuantumMind obtains 53.1 mean ODS, exceeding the strongest baseline by 17.3 points (48.2% relative), and wins 355 of 582 paired tasks against that baseline. It passes the graph audit on 99.8% of tasks, compared with 43.6% for the strongest baseline, and ranks first in all seven task families. The results indicate that typed state transitions and deterministic evidence control contribute beyond fluent generation alone.

Yijing Zuo, Zhe Fu, Zihan Nie +2

University of Illinois at Urbana-Champaign · Rensselaer Polytechnic Institute · Ohio State University

Automated Algorithm Discovery AI-Assisted Scientific Research Agentic Workflows Agentic Reasoning

Aug 7, 2026cs.AI

Authoring and Management of Transparent Research Integrity Assessments of Randomised Clinical Trial Publications Using LLM-assisted Tools and Provenance Knowledge Graphs

Systematic reviews of Randomised Controlled Trials (RCTs) are routinely used as evidence for clinical care guidelines. Such evidence has to meet high research integrity standards to prevent low quality or false research outputs influencing the clinical care. However, assessing research integrity of published RCTs is a complex process requiring manual effort, and potentially resulting in diverse opinions of the human assessors. This paper describes INSPECT-AI, an LLM-based interactive tool that assists human reviewers with research integrity assessments of published RCTs based on the community approved INSPECT-SR framework, and the Research Integrity Provenance and Evidence ontology (RIPE-O) for documenting the provenance of the assessment process. In addition, we present the Research Integrity Provenance and Evidence knowledge graph (RIPE-KG), an initial set of 140 expert research integrity assessments of 95 RCT publications generated by INSPECT-AI and described using RIPE-O.

Milan Markovic, Goutham Indukuri, Somayajulu Sripada +7

Interdisciplinary Institute, University of Aberdeen, UK · Department of Computing Science, University of Aberdeen, UK · Department of Epidemiology and Biostatistics, Indiana University, USA +3

Data Provenance AI-Assisted Scientific Research

Aug 6, 2026cs.AI

Research Assistant: AstraZeneca's Agentic System for R&D

We describe Research Assistant, an internal LLM-based system developed at AstraZeneca to help scientists and clinicians explore biomedical questions across a broad range of data sources. The system provides a chat-style interface that brings together evidence from scientific literature, knowledge graphs, chemistry, clinical trials, safety resources, expression data, and internal experimental systems. It supports both a fast mode for direct question answering and a multi-step mode for more complex research tasks. Responses are grounded in retrieved evidence and linked back to the original sources, allowing users to review and further explore the underlying data. In this technical note, we outline the system architecture, the main design choices behind the product, and lessons learned from deploying it at scale to support day-to-day R&D workflows across AstraZeneca.

Piotr Grabowski, Mohamed Alameen, Jorge Bretones +16

AstraZeneca, RDIT, Biological Insights Knowledge Graph

AI-Assisted Scientific Research Biomedical QA Agentic RAG