Scientific Reproducibility

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11 papers in the last four weeks, up 175% on the four weeks before. 0.1% of all new papers.

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Oct 5, 2026cs.CL

Kurate: Scalable Scientific Quality Analysis

Scientific search systems can find papers that are relevant to a question, but they generally do not assess the quality of the evidence that those papers provide. We present Kurate, a system that uses large language models (LLMs) to assess the quality of published studies. Kurate uses both the paper and its related documents (e.g., the study's trial registration and protocol), and links each of its judgments to the passage of text on which that judgment is based. We applied Kurate to a corpus of 4,347 papers (3,913 of which report randomized trials) and scored each paper on 8 dimensions of study design and reporting: specifically, statistical power, causal identification, preregistration, selective reporting, measurement validity, analysis prespecification, reporting transparency, and conflict of interest and funding. Across the corpus, we found that papers most often exhibited issues with statistical power, selective reporting, and analysis prespecification, although average quality differed between clinical areas. When compared against expert annotations of 60 held-out clinical-trial documents, the information Kurate extracted matched the expert label in 221/242 protocol scorepoints and 294/370 results-publication scorepoints, with AC1 0.94 and 0.81, respectively. Using a well-reputed, high quality clinical trial as a worked example, we show how a single paper's overall grade breaks down into separate judgments, with each linked to specific evidence from the trial's registration, protocol, and published report. Together, these results show that large-scale quality assessment of this kind is feasible, and that it can be used to address meta-scientific research questions.

Matthew J. Vowels, Jamie Cummins

Kivira Health, U.S.A. · University of Bern, Bern, Switzerland

Scientific Reproducibility

Sep 30, 2026cs.SE

Code That Works, Environments That Don't: Measuring Environment Reproducibility in AI-Generated Software

Code generation has emerged as a central capability of large language models, with coding agents now able to produce functionally correct software projects from natural language prompts. However, functional correctness alone does not capture a critical dimension of generation quality: environment specification, defined as the accurate identification of the dependencies required to execute generated code, is equally critical. We develop an agent protocol for environment specification and introduce a three-layer framework comprising declared, runtime-installed, and necessary-and-sufficient dependencies to systematically assess coding agents for environment specification. Using this protocol, we evaluate the extent to which coding agents systematically misspecify software environment dependencies and how this misspecification varies across three agents, four languages, and fifty programming tasks. Our results show that current coding agents exhibit systematic generalization failures along this dimension, producing dependency specifications that are inconsistent, redundant, or incomplete in ways that functional tests do not detect. Across agents, dependency set agreement is as low as 7% for identical tasks, and newer agents show no meaningful improvement, suggesting the failure is not resolved by scale or recency. The largest divergence occurs between the declared and runtime dependency layers, implicating environment priors learned from the models' training distributions as the primary driver. Our findings establish environment specification as a distinct, measurable axis of code generation quality that current benchmarks do not capture, and motivate training objectives and evaluation protocols that jointly optimize for functional correctness and environmental portability.

Bhanu Prakash Vangala, Tanu Malik

Department of Electrical Engineering and Computer Science, University of Missouri–Columbia, Missouri, USA

Coding Agents Code Generation Code Generation Evaluation Scientific Reproducibility

Sep 29, 2026cs.AI

Can an AI Agent Rediscover a Blaschke-Curve Invariant?

We study generalized Blaschke curves as a controlled environment for AI-assisted mathematical rediscovery. For one fixed degree-four Blaschke product, an agent receives numerical coordinates of the six pair-lines determined by each of 80 boundary configurations. The target theorem is withheld from the task instructions. The saved research log reports rejected geometric hypotheses and a homogeneous cubic fitted to polygon sides. Its frozen coefficients predict 480 lines from 80 unseen parameter values, with a recorded RMS scale-free residual of

8.88\times10^{-17}

. Discovery-set diagonals provide an out-of-fit consistency check, not a fully held-out test. A separate one-configuration run reports insufficient evidence for invariance. A post-review deterministic degree-search baseline also recovers the cubic, so the experiment does not establish an advantage over polynomial fitting. We present this single-instance case study as a protocol for separating conjecture, numerical validation, and proof, with explicit limitations concerning agent metadata, prior knowledge, and reproducibility.

Yunus E. Zeytuncu

University of Michigan-Dearborn

AI Agents for Scientific Discovery AI Agent Evaluation Autonomous Scientific Discovery Scientific Reproducibility

Sep 28, 2026cs.SE

Research-Native by Construction: Minimal Nodes, Re-verifiable Workflows, and Compounding Memory for Long-Horizon Scientific Agents

We describe AfS (Agent for Science), a platform built for long-horizon scientific work, where a project runs for tens of hours across dozens of agent runs with a human present only occasionally. Most agents for science are general coding agents with a skills folder attached, and they inherit that lineage's failure mode: under pressure to finish, they fabricate, skip, or smooth over. Our design rests on one claim: most of the credibility of machine-made research can be moved from asking the model to behave to making the non-compliant state unrepresentable. We encode research discipline as mechanically enforced laws (commitment before measurement; unforgeable freezing; reports are not facts; evidence persists but verdicts do not; negative results are first-class; mechanical questions to the framework and semantic judgment to the model), organized around three time horizons: a minimal set of research nodes within a run, an inquiry contract with frozen closure conditions and a hash-chained artifact ledger within a project, and a two-tier knowledge base with promotion by rewriting across projects. This is a system description written under one rule: each mechanism appears in exactly one place, with the invariant it enforces, the failure it prevents, the way it is realized, and the cost it imposes. It covers the node contract, the write-path gates, the two-tier memory, and the runtime substrate. Three traces walk real failure attempts through the mechanisms that catch them, and two closed campaigns are included as worked illustrations rather than as an evaluation. We report no benchmark: a process-integrity suite that would support quantitative comparison is under construction, and what we can measure today is only the operating cost of the machinery.

Di Wang, Yu Liu, Bing Cui +5

IdeaHorizon Team

Runtime Enforcement for AI Agents Scientific Reproducibility Long-Horizon LLM Agents Memory-Augmented Agents Autonomous Research Agents

Sep 28, 2026cs.CL

Papers Without Code: Availability of GitHub Repositories Linked in *CL Publications

Source code and data published at computational linguistics (*CL) venues are increasingly being shared via GitHub. While this generally is a favourable development for the accessibility and potential reusability of research artifacts in natural language processing (NLP), the long-term availability of such repositories has not been evaluated. In this squib, we discuss the availability of repositories linked in papers published in the Computational Linguistics (CL) journal as well as at ACL and its co-located events over the past ten years. Contrary to our expectations, we find that GitHub repositories linked in more recent ACL publications are unavailable at similar rates as in older publications, in parts due to an increase in empty and placeholder repositories. Similar trends hold for other *CL venues, but not for platforms other than GitHub.

Selina Meyer, Michael Roth

University of Technology Nuremberg

Scientific Reproducibility

Sep 22, 2026cs.AI

Reproducible AI Requires Reproducible Randomness

Pseudorandom number generators (PRNGs) constitute indispensable computational tools across multiple scientific domains, including Monte Carlo simulations, stochastic computing, and artificial intelligence (AI). The reproducibility of such applications critically depends on the ability of PRNG implementations to generate identical sequences across software environments when initialized from the same internal state. These algorithms enable the simulation of stochastic processes while providing deterministic and repeatable behaviour, thereby facilitating reproducible experiments. Modern PRNG implementations may be initialized through either a seed or, more accurately, an initial state that exceeds the capacity of a conventional integer seed. However, reliance on a simple seed alone frequently proves insufficient to ensure consistent program execution traces across different implementations. A natural assumption is that transferring the complete internal state of a generator should guarantee identical outputs regardless of the software library used. This study examines the validity of this assumption by investigating whether complete initial states can ensure cross-library fidelity and portability of PRNG streams. We focus on two widely deployed generators, Mersenne Twister and Philox, and evaluate their implementations across four major Python ecosystems-Random, NumPy, PyTorch, and TensorFlow. We compare the sequences produced by these implementations against those generated by the original reference algorithms under identical initialization conditions. Our results demonstrate that reproducibility cannot be assumed from PRNG state transfer alone, even when implementations claim to follow the same underlying algorithm. While fidelity was successfully achieved for several implementations, significant discrepancies were observed in others. Most notably, the Philox implementation in PyTorch exhibits fundamental incompatibilities with the reference algorithm, preventing exact reproduction of generator outputs across environments. These findings challenge the common expectation that access to a full internal state of a PRNG is sufficient to ensure reproducibility across software stacks. They further highlight that implementation-specific design choices can introduce hidden barriers to experimental replication, particularly in AI workflows that rely on multiple frameworks. This work shows that implementation fidelity of a PRNG is a necessary condition for scientific reproducibility and makes two primary contributions. First, it identifies practical guidelines for achieving reliable PRNG usage and reproducibility within the Python scientific and AI ecosystem. Second, it evaluates the extent to which cross-library portability and fidelity can be recovered through user-level techniques, without requiring modifications to library source code.

Anthony Bertrand, Tom Schmitt, Engelbert Mephu Nguifo +1

UCA, LIMOS · Université Clermont Auvergne, Clermont Auvergne INP, CNRS, LIMOS, F-63000 Clermont–Ferrand, France · UCA +2

ML Reproducibility Scientific Reproducibility

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 14, 2026physics.optics

A Programmable Optics Cloud Laboratory

Laboratory automation can improve experimental throughput, accessibility, and reproducibility, but many robotic laboratory systems remain difficult to reconfigure. This challenge is especially pronounced in free-space optics, where experiments are built from heterogeneous components, require precise alignment, and are frequently rearranged as experimental goals change. In this work, we present the Programmable Infrastructure for Cloud Optics (PICO), a robotic cloud-laboratory architecture designed to make reconfigurable optical experiments easier to program, operate, and reproduce. PICO provides a common domain-specific abstraction and software layer through which experimental configurations and actions can be controlled across different user interfaces. This enables the same physical laboratory to support remote interactive use, scripted experiments, autonomous routines, and features such as version control. We implement PICO on a robotic free-space optics platform and demonstrate it through an experimental case study.

Sachin Vaidya, Caio Silva, Seou Choi +2

Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · NSF Institute for Artificial Intelligence and Fundamental Interactions and the Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Laboratory Automation Scientific Reproducibility Scientific Workflow Automation

Sep 14, 2026cs.AI

OpenAI4S: Code as Action, Science as Sessions

AI co-scientists could accelerate computational research, but over a long-running study the workflow also has to stay inspectable, resumable and reproducible, which requires persistent computational state and provenance. Here we present OpenAI4S, an open-source scientific research agent built around the principle of \emph{Code as Action, Science as Sessions}. OpenAI4S combines a persistent computing runtime with research-session management: orchestration is handled through structured tool calls, while scientific actions are represented as complete code cells executed in persistent Python and R kernels. An append-only Action Ledger, per-cell execution records, versioned artifacts, environment records, and workspace checkpoints preserve how results were produced and support session recovery, branching, and extension. Configurable sandboxing, permission controls, and code and trajectory screening provide complementary safeguards. We evaluate OpenAI4S on 36 research scenarios spanning retrosynthesis, molecular dynamics, protein binder design, protein mutation, catalyst screening, and mineral spectroscopy, measuring scientific task accuracy, workflow completeness, and reproducibility of the resulting repositories. OpenAI4S achieves an overall score of 7.83, compared with 5.7--6.4 for a general-purpose coding harness evaluated with three frontier models, with the largest gains on long-horizon and computation-intensive workflows. These results suggest that integrating persistent execution with session-level provenance can improve the reliability of AI-assisted scientific workflows. Environment specification and full rerunnability remain weak for every evaluated system, ours included, so reproducibility is still an open problem for scientific agents. The system is available under the MIT license at github.com/PKU-YuanGroup/OpenAI4S.

Gongbo Zhang, Hao Li, Yu Wang +15

Peking University Shenzhen Graduate School, Shenzhen, 518055, China · Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China · Independent Researcher +1

Data Provenance Runtime Enforcement for AI Agents Scientific Reproducibility Scientific Workflow Automation Autonomous Research Agents

Sep 11, 2026cs.CL

Overview of the NLPCC 2026 Shared Task 11: Agent-Based Experiment Reproduction from Scientific Papers

Reproducibility is essential to scientific progress, yet the growing volume and complexity of scientific publications make exhaustive manual verification increasingly impractical. Although recent advances in large language model (LLM) agents enable automated experiment reproduction, existing evaluations largely focus on final repositories and are typically limited to machine learning (ML). We introduce AgentActionBench, a process-oriented benchmark for evaluating agent-based experiment reproduction across ML and AI4Science domains. Our framework uses an MCP-based Action Recorder to capture agents' behaviour throughout the reproduction process and evaluates the resulting traces with paper-specific rubrics. AgentActionBench contains 150 papers, including 120 ML papers and 30 AI4Science papers. A human-annotated subset covering 10% of the benchmark provides validation data, while model-assisted augmentation expands the full benchmark to more than 10,000 rubric items. Experimental results show that current systems remain limited, with execution as the primary bottleneck. Meanwhile, the strong Pearson and Spearman correlations between model-generated and human-annotated rubrics validate the reliability of our scalable rubric-generation approach.

Hanhua Hong, Yizhi Li, Luu Gia Huy +3

The University of Manchester · IQuest Research · Vietnam National University +2

AI Agent Evaluation Agent Evaluation AI Agent Benchmarks Scientific Reproducibility

Sep 9, 2026cs.CL

IdeaAMBIG: Benchmarking Implementation-Critical Gaps in Research-Idea Specifications

A research idea may be novel, coherent, and scientifically plausible, yet its proposed method may remain insufficiently specified for faithful implementation. We study the codification readiness of implementation-facing research-method specifications, defined by whether they provide sufficient methodological information for a competent implementer or coding agent to construct the intended method without unsupported assumptions. We construct evidence-grounded specifications and their supported resolutions from papers, codebases, issue threads, and reproduction artifacts. We introduce IdeaAMBIG, a benchmark of 660 evidence-grounded instances: 163 real-world gaps from reproducibility reports and GitHub issues, and 497 controlled synthetic gaps injected into codification-ready references. IdeaAMBIG evaluates three capabilities: codification-readiness assessment, defect localization, and clarification action generation. Defect localization receives only the specification, whereas clarification additionally receives the annotated defect. Across 13 LLMs, the best model achieves 9.6% Macro Defect Recovery Rate on real-world instances but 80.6% Macro Clarification Action Success Rate when given the defect. In an oracle study, supplying the gold resolution raises the downstream codification-ready rate from 14% to 98%. Across all evaluated models, defect localization is the main bottleneck, with stronger clarification given the defect.

Yiling Ma, Yilun Zhao, Sihong Wu +2

Yale University · TCS Research

Benchmark Design Clarification Question Generation Scientific Reproducibility Code Generation Benchmarks

Sep 7, 2026cs.AI

Model Retirement Creates Reproducibility Risk in Biomedical AI Publications

Background. Large language models (LLMs) are being adopted in biomedical research at a rapid and accelerating pace, yet commercial services that host many widely used models operate under deprecation schedules that can complicate scientific reproducibility. Methods. We searched PubMed for original research articles from 2022 through March 2026 that applied a specific LLM to a biomedical task. An extraction agent identified model names from 61,077 article abstracts with human reviewers validating a subset for extraction accuracy. Extracted model names were normalized to canonical model identifiers. Lifecycle data (release date, retirement date, status) were compiled for the 50 most frequently used models. Results. We identified 8,931 paper-model mentions spanning 5,242 unique publications after restricting the analysis to the 50 most frequently used models. Among these mentions, 77.7% cited a commercial closed-weight model. Overall, 42% involved a model that was already retired by the time of official publication or is scheduled to retire within two years of publication. The median interval from publication to model retirement was 538 days. Conclusion. Many biomedical publications using LLMs are on a trajectory toward computational non-reproducibility after publication. Model deprecation should be treated as a core reporting and preservation issue for biomedical research.

Nathan Wolfrath, Meghan Conroy, Thomas Kosten +7

Bud and Sue Selig Hub for Surgical Data Science, Department of Surgery, Medical College of Wisconsin · Division of Biostatistics, Data Science Institute, Medical College of Wisconsin · Department of Computer and Electrical Engineering, Marquette University +1

ML Reproducibility Scientific Reproducibility

Aug 19, 2026physics.chem-ph

Science Done on a Machine by a Machine: AI Agents in Computational Chemistry

We are witnessing an explosion of agentic systems for computational chemistry: from four in 2024 to seventeen in 2025 and over sixty now, surveyed here. What is delegated to these systems is shifting from single calculations to whole in silico experiments and even manuscript writing. The ultimate destination is a fully autonomous AI scientist, where the entirety of computational chemistry is performed on a machine by a machine, without human supervision. Our survey shows that these systems are turning into vetted chemistry skills on general-purpose coding agents, and that they must be evaluated not only on their final answers but also on whether their calculations actually support these answers. The role of the human computational chemist is shifting from performing calculations to directing and supervising them, and the field should invest in the judgement that makes the supervision reliable: we propose a reporting standard, an evaluation reproducing published studies, a controlled comparison with general-purpose coding agents, and how to teach.

Pavlo O. Dral, Hassan Nawaz, Arif Ullah

State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen, Fujian 361005, China · Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziadzka 5, 87-100 Toruń, Poland · Institute of Advanced Studies, Nicolaus Copernicus University in Toruń, ul. Wileńska 4, 87-100 Toruń, Poland +2

AI Agents for Scientific Discovery AI Agent Evaluation Scientific Reproducibility Autonomous Research Agents

Aug 13, 2026cs.LG

Training AI Scientists to Replicate Research

The replicability of papers is a cornerstone of scientific knowledge, ensuring the reliability of existing results and providing a base for further experiments. The act of replication typically illuminates details that were previously underspecified, and thus requires similar hypothesis-driven exploration to open-ended research. In this work, we develop Replica, a scalable task space for paper replication. To provide reward signal, we introduce an auto-generated rubric-based judge that has low noise and agrees with human assessment of replication quality. We post-train Faraday, a 27B-parameter "AI Scientist" agent that leverages coding agents as tools, surpassing the performance of Claude Opus 4.8 and GPT-5.5 on held-out replication tasks. Qualitative analysis of individual rollouts reveals that Faraday adopts a more scientifically-principled approach. We believe that our results provide a stepping stone towards AI agents capable of long-horizon scientific innovation without requiring complex harnesses.

Damon Falck, Samer Sabri, Anja Surina +8

1Inherent

AI Agents for Scientific Discovery AI Agent Benchmarks LLM Agent Training Scientific Reproducibility

Aug 11, 2026cs.AI

ChemWorld: Programmable Chemical Worlds for Controlled and Replayable Agent Experimentation

Autonomous chemistry increasingly depends on environments in which agents can repeatedly act, observe, and adapt.Physical laboratories provide essential real-material evidence but are costly to repeat and difficult to use for tightly matched interventions, whereas most digital environments keep the underlying experimental world largely fixed. We introduce ChemWorld, a programmable chemical environment in which reusable process and observation components are compiled into executable worlds. ChemWorld separates the public experimental contract available to an agent from evaluator-owned chemical and material laws. Researchers can therefore vary world composition and operating conditions, or change a single hidden law while holding the public task and interaction conditions fixed. Transactional execution records operations, failures, resource changes, and state transitions, allowing complete environment-action trajectories to be replayed exactly and audited. Full-census qualification covered the reference registry, 52 generated compositions, and module, interface, compilation, and invalid-action tests. Eight deterministic experimental cases demonstrated shared lifecycle semantics, failure recovery, and exact replay, while six parent-child world-fork pairs isolated the effects of single private-law interventions under matched public conditions. An independent agent also completed a full lifecycle in a non-reference world through the same public interface. Within the declared component and model domain, ChemWorld provides a controlled and replayable substrate for studying experimentation across systematically varied chemical worlds, complementary to physical-laboratory evidence and calibration.

Jiangjie Qiu, Yijun Li, Xiaonan Wang

Beijing Key Laboratory of Artificial Intelligence for Advanced Chemical Engineering Materials, State Key Laboratory of Chemical Engineering and Low-Carbon Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China

AI Agents for Scientific Discovery Scientific Reproducibility Autonomous Experimentation

Aug 11, 2026cs.AI

Nutrition Data Infrastructure for the AI Era: Operationalizing FAIR for Agent-Mediated Research

AI agents can accelerate nutrition research, but their analyses inherit the identity, semantic, and release ambiguities of the underlying data. We present Nutrition Data Service (NDS), source-preserving infrastructure that operationalizes FAIR for automated use: description resolution makes release-specific records findable; typed crosswalks connect independently released resources; machine-readable interfaces expose versioned sources and crosswalks, supporting replayable and auditable analyses. On food-description benchmarks, NDS outperforms the best published language-model result on NutriBench. External and blinded crosswalk evaluations show that its typed contract favors defensible links and rejects unsupported mappings. In a person-level glycemic-index analysis, pinned NDS inputs produce identical outputs across models and repeated runs, while open-web reconstruction remains unstable. Together, these results show that agent-mediated nutrition research requires a new infrastructure that makes data identity, search, and crosswalk policy explicit.

Lin Liao, Peng Li

AI for Science Entity Resolution Data Provenance Scientific Reproducibility

Aug 4, 2026cs.SE

CURATE: Leveraging LLM Agents to Compose, Catalog, and Deploy Reproducible Workflows

Agentic code generation has the potential to accelerate the development of computational workflows while also reducing barriers to entry. However, a key gap remains: existing coding agents focus on code generation and do not address the entire workflow lifecycle, including deployment and sharing. As a result, users develop and stitch modules independently while managing deployment on their own. To address this gap, we propose CURATE (Composition, User-in-the-loop, Reuse, and Automated Task Execution), a novel human-in-the-loop multi-agent system that uses LLM agents to manage and develop composable workflows across their entire lifecycle. A key feature of the system is a catalog that allows for the storage and reuse of modules across workflows. Module catalogs provide a foundation that can be expanded to support FAIR principles by facilitating the sharing and reuse of curated modules and subgraphs. We demonstrate the feasibility of our system with an initial prototype and 6 experiments.

Nolan Cutler, Chia-Chen Kuo, Nanda Velugoti +2

School of EECS Oregon State University · School of CBEE Oregon State University

Multi-Agent LLM Systems Human-in-the-Loop AI Scientific Reproducibility Scientific Workflow Automation

Jul 30, 2026cs.MA

VISA: A Structured Description Protocol for Agent-Based Simulation Models Towards Machine Reproducibility

Agent-based models (ABMs) are difficult to reproduce: their behavior is spread across prose narratives, platform-specific code, and implicit assumptions, so that two readers routinely reconstruct different models from the same documentation. We present VISA, a structured, symbol-based description protocol that specifies a model in eight interconnected tables---four at the agent level (Agent, Variable, Sensing, Internal Function) and four at the model level (Associated Data, Input/Output, Schedule, Validation)---under the principle of minimality with completeness. VISA makes a model machine-parseable and unambiguous via two artifacts: nineteen executable consistency rules that turn model validity into a checkable property, and three reusable LLM-executable skills (authoring, checking, and code generation) that operationalize the full author--check--code--reproduce loop. We validate the protocol on three external, independently authored ABMs spanning three platforms: we reproduce two cross-language (NetLogo to Python) directly from their VISA specifications, and we capture a third, an industrial AnyLogic model, in eight tables (passing all nineteen rules) while honestly demarcating where reproduction is blocked by a proprietary movement library and unavailable data---itself a transparency contribution. VISA moves the reproduction barrier from the model, where it is invisible, to a named, localized dependency, where it is actionable.

Zhou He

University of Chinese Academy of Sciences, Beijing, China

Agent-Based Modeling Scientific Reproducibility

Jul 30, 2026cs.DL

SciSchema.org: A Multidisciplinary Collection of Schemas for Structured Scientific Process Descriptions

Scientific processes are often described in heterogeneous article discourse, with details needed for comparison, reproducibility, reuse, and automation dispersed across prose, tables, figures, protocols, and supplementary files. We present the first release of SciSchema.org, a multidisciplinary collection of 16 expert-annotated schemas spanning Biology & Biotechnology, Materials & Chemistry, Imaging & Measurement, Physics, and Psychology. Each schema defines reusable fields for describing process instances, including inputs, outputs, materials, instruments or software, parameters, conditions, procedural steps, measurements, and provenance-related information. The schemas were created through a human-in-the-loop schema-mining workflow in which large language models generated candidate structures from process specifications, scientific articles, and expert feedback, followed by domain-expert construction of final master schemas. The dataset contains final schemas in JSON Schema and SHACL formats, intermediate model-generated schemas, expert-feedback records, source-paper metadata, community-development materials, and analysis scripts. Technical validation assessed schema structure, development provenance, expert review, and syntactic conformance. The collection supports structured annotation, metadata enrichment, scientific knowledge graphs, information extraction, semantic publishing, and cross-study comparison.

Jennifer D'Souza, Sameer Sadruddin, Anisa Rula +23

TIB Leibniz Information Centre for Science and Technology, Hannover, Germany · University of Brescia, Brescia, Italy · University of Alicante, Alicante, Spain +15

Knowledge Representation Structured Output Generation Scientific Reproducibility

Jul 30, 2026cs.AI

Evaluating Agentic Bioinformatics through Function, Evidence, and Validation

Large language model agents increasingly plan, execute, and interpret biological analyses, yet fluent responses, successful tool calls, and benchmark performance alone do not establish scientific credibility. Existing reviews primarily organize biological agents by application, architecture, and agentic capability, but do not jointly operationalize the accountability of agent-generated workflows. We address this gap by treating the inspectable workflow trajectory, rather than architecture or final output alone, as the primary unit of analysis. We introduce the Function--Evidence--Validation (FEV) framework, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation. Using FEV, we map 109 agentic or agent-adjacent systems and 28 benchmark or evaluation resources, representing 128 unique publications across genomics, single-cell and spatial omics, protein science, drug discovery, computational pathology, and general bioinformatics automation. Across domains, planning and tool-mediated execution have advanced more rapidly than replayability, provenance, robust scientific assessment, external validation, and prospective empirical testing. We therefore argue that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone. FEV provides a practical basis for comparing systems and designing transparent, auditable, and scientifically accountable bioinformatics workflows.

Phuc Pham, Truong-Son Hy

Department of Computer Science, The University of Alabama at Birmingham, USA

AI Agents for Scientific Discovery Data Provenance LLM Agent Evaluation Scientific Reproducibility Scientific Workflow Automation

Jul 28, 2026cs.DL

F(AI)2R: Who Did What, and Who Checked? Verifiable AI Provenance as an Executable Skill

F(AI)2R is FAIR research with AI in the loop, twice: an AI-assisted authoring pass and a machine-readable audit pass over every artefact. AI systems now draft, refactor, and verify research artefacts, yet their contributions are rarely recorded in a form a later human or machine can audit. Building on the original F(AI)2R experiment, we generalize its provenance model beyond scholarly writing into aiprov, a PROV-O extension covering any AI-in-the-loop artefact, and we package the method as an executable skill that an AI agent operates itself: setup asks the human operator for their ORCID ID, resolves their identity from the public registry, and scaffolds continuous integration that gates every push on graph conformance and publishes the current build of this very paper. The paper is its own case study. Every activity, claim, and source in its production is recorded in the repository's provenance graph under two invariants: no parentless claim, and verification rungs that only humans may grant.

Florian Krebs

Deutsches Zentrum für Luft- und Raumfahrt (DLR)

Data Provenance AI Agent Governance Scientific Reproducibility Human Oversight of AI

Jul 28, 2026cs.CV

Forensic Reproducibility Audit of a Radiology Vision-Language Model Benchmark: From Intended Protocol to Released Artifact

Medical-imaging AI benchmarks combine datasets, DICOM rendering, prompts, provider APIs, automated labels, statistical code, manuscripts, and repository releases. Agreement across these artifacts is usually assumed rather than tested. We performed a retrospective forensic reproducibility audit of a preserved chest-radiograph vision-language model (VLM) pilot; no model was called again and no image or report was newly annotated. We traced prompt bindings, DICOM metadata, output completeness, label extraction, matched analyses, and release propagation. Of 300 planned model-prompt calls, 297 yielded nonempty reports. Sixty Claude calls labeled A/B were executed with the same C prompt. The 30 studies represented 28 patients. Four MONOCHROME1 images were rendered without required polarity inversion, dataset split membership was not retained, and the unvalidated extractor truncated five reports to 4000 characters. Reconstructing one common cohort of 369 complete case-finding blocks changed Cochran's Q from 154.73 to 182.29. Of 45 McNemar comparisons, 27 had unadjusted p < 0.05 and 20 remained below 0.05 after Holm adjustment. These values describe only the archived automated-label matrix; they do not recover the intended prompt comparison or establish clinical performance. We withdraw the original performance, ranking, prompt-effect, and clinical claims and specify machine-verifiable controls for cohort, DICOM rendering, prompt and model identity, call status, annotation provenance, keyed analysis, and derived artifacts.

Mateusz Kozłowski

Independent Researcher, Kraków, Poland

VLM Evaluation Radiology VLMs Scientific Reproducibility Medical Image Benchmarks

Jul 27, 2026cs.AI

Plato-Bio: verification-first biological novelty screening with temporal rediscovery and structural benchmarks

Large language model research agents can connect literature retrieval, analysis code, and manuscript preparation, but coherent output does not establish scientific validity. We developed Plato-Bio, a biology-routed extension of the open Plato/Denario architecture that couples explicit workflow states with provenance records, citation checks, claim-to-evidence links, scoped file writes, and publication gates. A source audit identified and repaired three defects that could distort evaluation: loss of task domain in the default factory, omission of declared method signals from scoring, and evidence sidecars that lacked the drafted-claim denominator. On the current clean revision, the full Python suite completed with 931 passes, six skips, and no failures or errors; targeted biology, genomics, evidence/citation, and adversarial-safety suites likewise completed without failure. We evaluated two narrow use cases. In a frozen historical rediscovery task, independent pre-1986 literature bridges ranked the later-studied relation between fish oil and Raynaud phenomenon first; TF-IDF ranked it second and corpus frequency third. This single curated task measures retrospective ranking, not prospective discovery. In a separate comparison of AlphaFold models with experimental structures for 15 human proteins, 11 targets had high-confidence-core C-alpha RMSD below 1 Angstrom (median 0.501 Angstrom). Four targets exceeded 2 Angstrom, and confidence masking reduced the SUMO1 discrepancy from 16.61 to 2.58 Angstrom over 74 residues. The workflow emitted 27 traceable discrepancy regions, all retained as unvalidated hypotheses. Plato-Bio therefore provides reproducible software contracts and auditable screening baselines; broader claims of agent efficacy or biological novelty require preregistered evaluation, independent review, and prospective validation.

Stefan G. Creadore

Praxa Labs, an independent open-source research initiative, United States

Data Provenance Scientific Reproducibility Scientific Workflow Automation

Jul 19, 2026cs.LG

A multiverse-consensus pipeline for reproducible feature selection in untargeted LC-MS metabolomics

Background: Untargeted LC-MS metabolomics requires a long chain of preprocessing decisions, each with several equally defensible options. Analysts typically commit to one pipeline and report the resulting feature shortlist. How strongly that shortlist depends on choices that were never varied stays invisible. Results: We adapt multiverse analysis to untargeted metabolomics feature selection. We present an auditable, configuration-driven pipeline that (i) applies a ten-stage quality-control filter cascade in which every feature's fate is logged, and (ii) runs the downstream analysis as a multiverse over four contrasting preprocessing philosophies, each combined with four feature-ranking methods under bootstrap stability selection and label-permutation testing. Only features recurring across paths enter a tiered consensus. On a demonstration dataset of five breast-cancer cell lines (30,370 detected features), the four single pipelines individually returned shortlists of 4-20 features whose pairwise agreement was as low as Jaccard = 0.05. The multiverse consensus retained 15 features (>=2/4 paths), of which one recurred across all four, although two paths (sharing normalization and drift-correction methods) dominate the consensus. A pipeline-wide label-permutation test found no false discoveries in 50 null permutations. Conclusions: Reporting only preprocessing-robust features, with a complete kept/dropped audit trail, converts hidden analytical degrees of freedom into an explicit, inspectable output. We discuss scope and limitations, including single-batch design and the need for independent validation.

Mohammed Saeed Al-Huraibi, Ihsan Yozgat, Ahmet Kaplan

1Istanbul Medipol University, Istanbul, Turkey · 2Istinye University, Istanbul, Turkey

Feature Selection Mass Spectrometry Scientific Reproducibility

Jul 14, 2026cs.CL

Can LLMs Write Reliable Rubrics? A Meta-Evaluation for Experiment Reproduction

Rubric-based evaluation is a promising approach for assessing open-ended outputs from LLM-based research agents, particularly in paper reproduction, where direct paper-to-repository comparison is prone to hallucination. However, constructing paper-specific rubrics requires substantial expert effort, limiting the scalability of benchmarks such as PaperBench. In this work, we present, to our knowledge, the first systematic meta-evaluation of LLM-generated rubrics for paper reproduction. We reformulate rubrics into a checklist-style format and evaluate four generation settings across two backbone models. We meta-evaluate generated rubrics intrinsically by semantic similarity and extrinsically by score alignment with ground-truth rubrics. Our results show that the augmented settings substantially improves downstream evaluation alignment, with the strongest setting approaching the human baseline, while intrinsic gains are more modest. Further analyses reveal that LLM-generated rubrics are often overly fine-grained, biased toward high scores, and less adaptive to paper domains, highlighting both the affordances and limitations.

Hanhua Hong, Yizhi Li, Jiaoyan Chen +4

The University of Manchester · IQuest Research · University of Information Technology, VNU +2

LLM Evaluation Rubric-Based Evaluation Rubric-Guided Generation Scientific Reproducibility

Jul 14, 2026cs.SE

XScientist: A Git-Like Research Protocol for Long-Running Autonomous Scientific Discovery

Autonomous research systems can generate plausible papers while losing the decisions, failed branches, and evidence needed to inspect or continue the work. We present XScientist, a local-first, git-like protocol that treats research state, rather than a manuscript, as the unit of continuation. Hypotheses, experiment attempts, observations, claims, reviews, and handoffs are represented as typed, content-addressed objects in an exploration graph. Immutable checkpoints, explicit negative outcomes, claim-evidence closure, replay boundaries, and authority-aware gates make each transition inspectable without treating a passing integrity check as scientific truth. The protocol exports a portable Agent-Native Research Artifact (ARA) that another agent or human can inspect, fork, verify, and extend. A reference implementation integrates planning, execution, review, repair, and supervised long-running operation while preserving provenance across these stages. We evaluate the protocol with controlled artifact-integrity workloads and matched external task pilots, keeping native task performance separate from evidence and audit claims. The result is an interoperability and accountability layer for long-running autonomous science, with explicit boundaries where human judgment and independent evaluation remain necessary.

Jixiang Luo

Data Provenance Autonomous Scientific Discovery Scientific Reproducibility Scientific Workflow Automation Autonomous Research Agents

Jul 13, 2026cs.DC

Toward Trustworthy Autonomous Science: A Two-Year Community Roadmap

One year ago, the AISLE roadmap argued that autonomous laboratories operated as isolated islands and proposed a grassroots network organized around five critical dimensions. The field has since moved faster than anticipated. Multi-agent systems have produced experimentally validated hypotheses, self-driving laboratories have grown more interoperable and orchestrated, reasoning-trained and domain foundation models have raised the capability ceiling, and the Genesis Mission has placed autonomous experimentation at the center of U.S. federal science strategy, with industry emerging as a primary actor. Progress has met a sobering counter-current, including a corrected flagship discovery result, benchmarks showing that agents which rival experts on closed-ended questions still complete only a fraction of open-ended research, and fabricated citations surfacing at leading venues. We read this as the defining tension of the field. Producing a candidate discovery is no longer the hard part, but verifying it is, and this asymmetry now limits autonomous science more than raw model capability. We update the roadmap around seven dimensions, revisiting the original five and elevating two former cross-cutting concerns, trust, verification, and reproducibility, and safety, security, and governance, to first-class status. We assess the original milestones (M1 through M14) as achieved, partially achieved, reframed, or open, add four new milestones (M15 through M18), and scope the path forward to a two-year horizon. The first year concentrates on interfaces, protocol adoption, and the scaffolding of verification, and the second targets federation, zero-trust coordination, and governance. Throughout, we position the grassroots network as the interoperability fabric that lets national programs, international initiatives, and commercial platforms connect rather than re-silo.

Rafael Ferreira da Silva, Milad Abolhasani, Peter Beaucage +25

Oak Ridge National Laboratory

Autonomous Scientific Discovery AI Agent Governance Scientific Reproducibility Autonomous Experimentation

Jul 12, 2026cs.LG

Evaluating Reliability in Machine Learning Models for Early Chronic Kidney Disease Prediction: A Systematic Review of Data Leakage and Predictor Stability

The early detection of Chronic Kidney Disease using machine learning has attracted significant interest in healthcare-related computer science. Despite rapid advancements in this field, many reported studies remain inconsistent and potentially misleading. A significant drawback is the lack of organized evaluation regarding methodological concerns. Key issues include data leakage, limited access to temporal patient records and inconsistency in reported clinical indicators. This research offers a systematic literature review of existing CKD prediction studies using interpretable machine learning techniques, where nineteen relevant studies were selected via systematic searches across major academic databases. To assess methodological reliability, this study introduces a structured taxonomy of information leakage and a quantitative leakage scoring framework to systematically evaluate reliability across CKD prediction studies. The analysis reveals a strong relationship between leakage and inflated performance. Here, High leakage-studies report an average accuracy of 95.48%, compared to 80.2% for leakage-free studies, reflecting an increase of approximately 15.28%. Furthermore, a cross-study feature stability analysis shows that only a small subset of predictors is consistently reproducible, with over 80% lacking reliability. Overall, the findings suggest that many reported performance improvements stem from methodological limitations rather than true predictive capability.

Mashrul Hossain, Nafesa Kibria, Fahim Shahriar

East West University, Dhaka, Bangladesh

Data Leakage Clinical Prediction Scientific Reproducibility Clinical Risk Prediction

Jul 9, 2026cs.CV

Metrics or Mirage? An Audit of Evaluation Inconsistencies in Colonoscopy Polyp Segmentation Benchmarks

Progress in colonoscopy polyp segmentation is routinely reported through leaderboard comparisons on a small set of public benchmarks. We argue that this apparent progress is difficult to verify: a systematic audit of \textbf{27 papers} published between 2015 and 2026 reveals three structural problems in how the community evaluates models. \textbf{First}, 25 of 27 papers \textit{omit the Hausdorff distance}. Hausdorff distance is a boundary-accuracy metric with direct clinical relevance for detecting flat or small polyps, and is a standard in radiotherapy segmentation. \textbf{Second}, at least five \textit{incompatible train/test split protocols} co-exist across papers reporting results on the same two datasets (Kvasir-SEG and CVC-ClinicDB), making published Dice scores non-comparable even when they appear in the same leaderboard column. \textbf{Third}, 26 of 27 papers make \textit{performance claims without any statistical significance test}. Strikingly, four papers published \emph{after} the Metrics Reloaded framework~\cite{metricsreloaded2024} (Maier-Hein et al., \textit{Nature Methods} 2024) perpetuate these same problems, suggesting that general-purpose metric guidance has not yet reached the colonoscopy sub-community. To show these problems are not merely cosmetic, we re-evaluate five representative models under three controlled protocols with a single uniform scorer, and find that the reported metric conceals large boundary and recall failures, that the ``best'' model changes with the metric, and that near-tied rankings reverse across random splits. We propose a five-point \textbf{Polyp Segmentation Reporting Checklist}~(PSRC) as a lightweight, domain-adapted corrective.

Aisha Urooj, Zain Ul Abdien, Neelu Madan

Lunit, South Korea · RPTU Kaiserslautern, Germany · Aalborg University & Pioneer Center, Denmark

Polyp Segmentation Medical Image Segmentation Scientific Reproducibility Medical Image Benchmarks

Jul 7, 2026cs.HC

Plainbook: Data Science, in Plain Language

Jupyter Notebooks have become widely adopted in data science, as they allow the sharing of reproducible computational analysis. They are, however, accessible only to people who understand computer code. To reach the broader audience of scientists interested in data analysis and computation, but unfamiliar with code, we introduce Plainbook, notebooks centered on natural language rather than code. Plainbook is based on two principles: promote the natural language descriptions, and verify the values. In plainbook, the natural language descriptions are preserved, rather than the resulting code; the code is generated automatically from the cell descriptions. As natural language is read top to bottom, Plainbook adopts a linear execution semantics, in which cells are guaranteed to be executed in the order in which they appear; there is no "hidden state" or out-of-order execution as in Jupyter. To allow users who may not understand code to verify the correctness of the computation, we have built into Plainbook verification mechanisms centered on values and value inspection. These include mechanisms that focus on individual cells, akin to unit tests, as well as global mechanisms. Both the linear execution semantics, and the verification mechanisms, are underpinned by a snapshot kernel that caches execution states and makes execution and verification efficient.

Luca de Alfaro, Mathis Aubert, Ranjit Jhala +2

University of California · Santa Cruz, California, USA · San Diego, California, USA +2

Scientific Code Generation Scientific Reproducibility