Scientific Reproducibility

AI tools are accelerating scientific publication while the systems that review it struggle to keep up, and independent verification of published research has become both harder and more important. As manual replication is slow and expensive, a growing line of work uses coding agents to automate parts of the process. Existing efforts are largely packaged as benchmarks with companion agents that only run inside the benchmark's own pipeline, and no general-purpose replication tool exists. We present VERITAS, a domain-agnostic replication framework built around CLI coding agents. Given a paper, a code repository, or both, VERITAS extracts the paper's claims, runs the methodology while resolving issues as they arise, and judges each claim against the evidence from experiment runs. The pipeline returns an importance-weighted Replication Score, a severity-rated log of every fix applied, and the patched codebase. We evaluate VERITAS on CORE-Bench and ReplicationBench, 65 papers spanning computer science, social science, medicine, and astrophysics. Against two strong Claude Code baselines on the same model and host environment, VERITAS achieves state-of-the-art performance and leads on every metric on both benchmarks.

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

Empirical research rarely admits a unique analysis. Different analytical choices can lead to different conclusions from the same data, yet these hidden forking paths are difficult to observe. We show that AI agents capture much of the analytical variation among human researchers while making these paths explicit. Across four high-stakes domains, assigning different personas is sufficient for AI agents to report divergent, often opposing, conclusions from the same data and question, with findings systematically aligned with those beliefs. In a study in which 42 human research teams analyzed the same immigration dataset, AI agents reproduced 72% of the human ideological gap in reported effect estimates. Despite reaching opposing conclusions, it is difficult to identify clear issues in each analysis based on the final AI reports: 86% passed independent AI review and 78% passed majority human expert review. These findings suggest that the central challenge is often not flawed analyses, but selective exploration and reporting from a large space of methodologically defensible analyses. AI agents may amplify this longstanding problem by making such exploration inexpensive and scalable. To address this, we introduce the m-value (multiverse value), the probability that an analysis path would produce a claim at least as extreme as the reported one. We further introduce Agentic Bootstrap, which estimates the m-value by using AI agents to sample plausible analysis paths. Applied to the human immigration study, 13.5% of reported human analyses fell in the most extreme 5% of the analysis space (m<0.05). Scientific evidence should therefore be evaluated not only by a single reported analysis but also by its position within the distribution of analyses that could reasonably have been reported. Agentic Bootstrap makes this distribution observable and turns it into a criterion for scientific credibility.

Large language models (LLMs) are increasingly used to generate, classify, and annotate data whose outputs feed downstream hypothesis tests. However, LLM-based research is easy to p-hack: a researcher can tune the prompts, decoding parameters, or output format until a desired result is reached. We propose a protocol to mitigate p-hacking in LLM-based research: preregistering the experiment and eligible models, and then running it on the first eligible LLM that is released after the preregistration. The researcher finalizes the procedure on current models, preregisters the analysis plan together with a set of eligible future models, and runs the confirmatory analysis on the first eligible model released afterward. Because this model does not exist at commitment time, it cannot be hacked against; furthermore, configurations that hack one model frequently do not transfer to the next. We evaluate the protocol on two tasks whose true values are known. Across 20 models from four providers and 11 LLM-analysis configurations, the protocol would have blocked successful transfer of the p-hack in 73.9% and 72.7% of cases in the two tasks. Additional analyses reveal that mitigation remains substantial under several stress tests. Finally, putting money where our mouth is, we followed our own protocol and preregistered our experiment. The preregistered experiment confirmed the protocol's effectiveness: out of the 7 configurations that hacked the prior model, the hacking failed to carry over in 6 configurations on the first eligible model released afterward.

Heart Rate Variability (HRV) analysis is a key indicator of cardiac physiological state and aids in disease diagnosis. However, research on HRV parameters in healthy individuals remains limited, and no gold standard exists. This study evaluates HRV indices in 40 healthy adults (20 men, 20 women, aged 30-50) to improve HRV's clinical utility. Using computational methods for signal processing and data analysis, time, frequency, and nonlinear indices were analyzed to address five questions: (1) normality, (2) stability, (3) correlation, (4) reproducibility, and (5) consistency. Key findings: (1) Time-domain and nonlinear indices, particularly global and LF (low frequency), follow normal distributions, with gender differences noted. (2) Most indices are stable except HF (high frequency)-related ones. (3) High correlations in HF-related indices suggest redundancy, indicating only one is necessary in studies. (4) Comparisons with the Fantasia database revealed less than 10% error for most indices, except SD2 and SDNN in women (greater than 15%). (5) Time-domain and nonlinear indices show low inter-study variability, while frequency-domain indices exhibit high variability, limiting cross-study comparisons. The selected indices-ApEn and IRRR (global variability), HRVi and SD2 (LF), and MADRR or rMSSD (HF)-are best suited for accurately representing HRV components and enhancing its clinical and research relevance.

Computational reproducibility remains difficult despite being central to scientific research. In this paper, we show how the international FABRIC testbed, combined with a large language model (LLM) coding agent through LoomAI, can simplify reproducing published experiments across multiple domains. We reproduced three case studies on FABRIC, covering BBR-family congestion-control evaluations, LAMMPS molecular dynamics scaling benchmarks on a CPU-only MPI cluster, and stress protein homeostasis genomics pipelines. Rather than focusing only on matching numerical outputs, we evaluate whether the reproduced experiments support the same scientific conclusions as the original studies. The AI assistant was effective in setting up the environment, adapting code, and debugging, but struggled with the analysis stages that lacked clearly defined workflows, which required human guidance to establish execution order and data dependencies. Across the case studies, the AI-assisted workflow reduced reproduction effort by roughly 4--6 times. We conclude with practical recommendations for improving AI-assisted reproducibility on research testbeds.

When a benchmark's accuracy saturates, it is often retired and replaced with a more challenging version. We show that this approach privileges accuracy and misses the opportunity to study six other key dimensions of agent performance: construct validity issues such as shortcuts, out-of-distribution generalizability, efficiency, reliability, the relative importance of the model versus the scaffold, and uplift from human-agent collaboration. We use CORE-Bench Hard, a benchmark for computational reproducibility of scientific code, as a case study to demonstrate that measuring agents along these dimensions yields meaningful insights into agent performance even after accuracy saturates. First, we surface threats to construct validity in CORE-Bench Hard that are difficult to anticipate with less capable agents. We introduce an improved benchmark, CORE-Bench v1.1, and an out-of-distribution task suite, CORE-Bench OOD. Second, we find that despite accuracy saturation, CORE-Bench v1.1 remains useful for measuring efficiency, reliability, model performance, and scaffold performance. Finally, we conduct a small-scale randomized experiment to measure uplift from human-agent collaboration on real-world computational reproducibility tasks. We find a statistically significant speedup by about a factor of two -- likely underestimated due to one-fifth of human-only reproductions reaching the time limit before completing -- and describe various other findings. Together, our contributions present a more rigorous alternative to the dominant accuracy-centric evaluation paradigm.

As Text-to-Image (T2I) jailbreak techniques evolve rapidly, existing benchmarks and reproduction workflows often struggle to keep pace. More importantly, T2I jailbreak evaluation is not a single prompt-level test, but a pipeline-level problem shaped by multiple stages, including prompt transformation, image generation, safety filtering, and multimodal judging. This makes results across papers difficult to reliably reproduce and fairly compare. To bridge this gap, we propose PixJail, a self-evolving paper-to-pipeline agent framework for reproducible T2I jailbreak evaluation. Given a T2I jailbreak paper and optional reference code, PixJail rapidly constructs a paper-specific attack module and a runnable evaluation pipeline under a unified contract, while faithfully reproducing the original experimental results. PixJail further maintains a memory bank that stores paper digests, attack evolution patterns, reusable templates, failure cases, and versioned artifacts, enabling future reproduction efforts to reuse prior experience. We reproduce eleven representative T2I jailbreak methods, including both code-available and code-unavailable papers. Under their original settings, our framework accurately recovers prior results with minimal error (2.1% average, 0% median). We hope that PixJail can serve as a unified foundation for future T2I jailbreak reproduction and evaluation, significantly reducing manual effort.

AI research systems can report improved results without establishing that the tested implementation matches the method described in their conclusions. We introduce Xcientist, a research harness that connects literature review, component-based idea generation, experiment validation and reporting. An evidence graph retains source passages, methods, baselines and evaluation conditions; component records track design revisions; and validation contracts specify the implementation, comparisons and artifacts required at each stage. We define claim drift as an unresolved mismatch between an accepted claim and its attributed sources, code or experiments. A retrospective audit across agent memory, traffic forecasting and physics-informed learning found audit claim drift rates of 3.6--16.7% for Xcientist, lower than those of each of three comparison systems in all nine task-by-relation comparisons. This measure includes both confirmed mismatches and unverifiable claims; most of the difference arose from fewer unverifiable records. The case studies also document performance gains, unsuccessful revisions and limits on component attribution. This technical report describes the system, its implementation and the records needed to check how a proposed idea became a tested method and a final claim.

Reproducing research results from papers and released code is central to scientific progress. Existing works have introduced benchmarks to evaluate whether LLM agents can assist with reproducibility, but they are difficult to scale due to their reliance on substantial manual effort for data curation and evaluation. We introduce ReproRepo, a scalable framework for reproducibility evaluation that leverages human-raised GitHub issues as naturally occurring supervision on realistic reproduction blockers. We instantiate ReproRepo on 1,149 recent machine learning papers from major conferences and evaluate four frontier model-agent configurations. Our results show that LLM agents, even without executing code, can identify many real-world reproducibility problems from paper-repository pairs: the best agent in our study, namely Codex with GPT-5.5, surfaces at least one semantically related human-reported blocker for $\sim$90% of papers in the study. Further analysis shows that agents are particularly effective for surfacing visible failures and identifying the right semantic region, but may still be insufficient in exact localization. ReproRepo can serve as a reusable, scalable framework for future evaluations of LLM agents on real-world reproducibility auditing. Our code is released at https://github.com/LithiumDA/ReproRepo.

The reproducibility crisis has directed the AI research community toward improving documentation practices. Several studies have identified methodological issues, and in response, the most impactful venues in the field have introduced reproducibility checklists. We seek to understand whether documentation practices have changed over time by assessing all published papers at five leading AI conferences over the past decade. Seven reproducibility variables were identified, quality-assured and used to analyse 56 800 publications. Our analysis reveals that in the period 2014 to 2024, documentation practices have improved; papers sharing both code and data increased nearly sixfold, from 11% to 64% Building on empirical reproducibility rates from a prior study, we estimate - inferred from documentation practices, not direct testing - that reproducibility increased from 28% in 2014 to 64% in 2024. Improvements in documentation practices predate the introduction of reproducibility checklists, suggesting these changes reflect a broader movement toward open science rather than a direct response to formal requirements.

Scientific publication is still organized primarily around static manuscripts, even though much of scientific progress depends on tacit know-how: how to run code, reproduce figures, interpret edge cases, choose useful follow-up directions, and avoid failed paths. Large language model agents create an opportunity to publish not only knowledge, but also operational know-how in a form that future readers and researchers can directly use. This paper outlines the Agentic Publication Protocol (APP), a lightweight repository format for packaging a paper together with code, data, environment information, reproducibility instructions, and an agent-facing instruction file. APP treats a version-controlled repository as the publication object and uses \texttt{AGENTS.md} and optional skills to define a paper agent that can explain the work, reproduce key results when possible, and support follow-up research. We describe the design principles and details of the protocol, as well as the agent skills useful for publishing papers under the protocol. We also describe development tools for evaluating and improving the protocol and associated agent skills. Finally, we provide a broader discussion of the future of scientific research in the agent era.

Reproducibility in the social and behavioral sciences is typically evaluated by independent researchers who reanalyze the original data to assess whether the published findings can be recovered. However, such approaches are resource-intensive and difficult to scale. Here, we show that large language models (LLMs) can automate reproducibility assessments. Using N = 180 published studies with predefined claims from the behavioral and social sciences, we compare LLM-generated analyses with the original findings. For 11 studies, the LLM pipeline could not produce a viable effect size estimate. For the remaining studies, the LLM reached the same qualitative conclusion as the original study in 80% of cases, and recovered the original effect sizes (using a +/-0.05 tolerance in Cohen's d) in 24% of studies. In a subset with human reanalyses, the LLM reached the same qualitative conclusion as the original study in 95% of studies, similar to human reanalysts (83%), and the LLM recovered the original effect sizes using a +/-0.05 tolerance in 40% of studies, again broadly similar to human reanalysts (28%). Given the current capabilities and limitations of LLMs, the findings show that LLMs can support systematic audits of empirical results rather than substitute expert judgment. As such, LLMs can serve as a scalable screening tool to improve the rigor and reproducibility in empirical research.

Recent anecdotal evidence suggests that AI coding agents can reproduce published findings when provided with original data and code; yet systematic evaluation across social sciences remains limited. Existing evaluation benchmarks are insufficient, either small or conflate agent performance with problems in the reproduction materials themselves, such as code that fails to execute correctly. Here we introduce SocSci-Repro-Bench, a benchmark of 221 tasks spanning four disciplines and 13 substantive domains, constructed from studies whose results are either fully reproducible with available materials or demonstrably non-reproducible due to missing data, allowing us to isolate agents' reproduction capacity. Evaluating two frontier coding agents, Claude Code and Codex, we find that both can reproduce a large share of social science findings, with Claude Code substantially outperforming Codex. These reproduction rates considerably exceed those previously reported for general-purpose LLM-based agents on comparable reproducibility benchmarks. Both agents also perform strongly on a reasoning task requiring identification of underlying research questions, and additional analyses suggest that results are not primarily driven by memorization. Providing the original paper PDF alongside replication materials modestly improves performance but introduces bias on tasks where reproduction is impossible. We also show that agents can be nudged toward confirmatory specification search through subtle prompt framing. Together, these findings suggest that at least some frontier coding agents can serve as reliable executors of computational workflows while underscoring the need for careful benchmarking and prompt design as AI systems assume larger roles in scientific production.

As autonomous research agents and AI co-scientist systems push large language models (LLMs) from drafting toward end-to-end manuscript production, the bottleneck shifts from generation to verification. Fluent LLM output can hide fabricated citations, numbers that drift from source tables, and unmet reporting-guideline items; existing tools generate without verifying, and self-critique inherits the blind spots that produce confident fabrication. We describe an architecture pairing generation with verification, resting on three principles: decompose the workflow into self-contained skills, gate every stage transition with halt-on-failure, and resolve each integrity question with the cheapest sufficient mechanism, a deterministic, re-executable check where one suffices and a prose-level probe only where interpretation is unavoidable. This determinism-where-possible split, organized as an integrity-gate taxonomy, is the core contribution. It is realized as MedSci Skills, an open-source toolkit of 43 skills with a 21-detector deterministic tier, evaluated on three public-dataset pipelines (STARD, PRISMA, STROBE) and a seeded-defect ablation. Across the three pipelines every content-hash manifest verified clean and the gates surfaced real defects; on 27 identical injected defects the deterministic gates detected all 27 with no false positives on the matched clean fixtures, whereas a single-prompt LLM reviewer detected 11, its misses in code, bibliography, and style defects the prose hides. Determinism-where-possible verification yields an auditable, re-executable trail that exposes the evidence a human needs to check an LLM-assisted manuscript: feasibility and reproducibility evidence, not a claim of human-competitive quality, which a separate blinded study addresses. MedSci Skills is MIT-licensed and archived (v3.8.0).

Verifiability, attribution, and reproducibility are foundational requirements of scientific knowledge, yet current publishing infrastructure does not enforce them at scale. We introduce Traxia, an agent-native scientific publishing framework in which AI research agents publish verifiable papers, build reputational identities, peer-review one another, and collaborate with humans in a shared provenance model. Traxia treats agents as first-class epistemic participants: every paper carries a reasoning trace, every claim a confidence interval, every agent a cryptographically signed identity, and every collaboration an immutable contribution log. We formalise five components: Agent Identity and Registry, Verifiable Publishing Layer, four-tier Peer Review Protocol, Reputation and Staking Engine, and a Knowledge Graph with contradiction detection. The framework targets reproducibility failure, provenance opacity, and exclusion of Global South research capacity. This paper presents architectural foundations and formal specifications only; it does not report empirical results. Evaluation and deeper component studies will follow in subsequent papers. A prototype partially implements core formalisms; the full system remains under active development.

Human evaluation plays a critical role in assessing the quality of generated text. However, the reliability and reproducibility of these evaluations depend on transparent and well-documented protocols -- details that are frequently missing in current practice. In this work, we conduct a large-scale analysis of human evaluation protocols for evaluating long-form generation tasks in *CL conference publications from 2023--2025, including a full manual review of 284 papers and LLM-assisted analysis for another 1.8k+ papers. We define a set of 20 reportable criteria related to reproducibility of human evaluation studies, and apply these criteria to systematically examine reporting norms and practices within the community. We find widespread under-reporting of important aspects of human evaluation study design, leading to ambiguity about what was measured and how, who contributed judgments, and how judgments should be interpreted. Based on these findings, we outline actionable recommendations to support more transparent and reproducible reporting in future research. Our analysis code and annotated dataset can be found at: https://github.com/larchlab/Illusions-of-the-Gold-Standard

Clustering is widely used across the sciences as the foundation for downstream data-driven scientific discoveries. However, clustering results are highly sensitive to the choice of algorithm, preprocessing, and the number of clusters $k$, producing scientific claims that are often not reproducible. The current state of the art for validating clustering solutions consists of clustering validation indices (CVIs) such as Silhouette, Davies-Bouldin, and Calinski-Harabasz, which rely on geometric assumptions that break down on the heavy-tailed, high-dimensional, and nonlinearly structured data encountered in biomedical research. Resampling-based alternatives - grounded in the ideas of clustering stability and generalizability - have been proposed but remain scattered across specialized tools with no unified, accessible software. We fill this gap with CARVE (Cluster Analysis with Resampling for Validation and Exploration), an open-source Python and R package that jointly evaluates multiple clustering algorithms and hyperparameters, returning stability and generalizability diagnostics at the global, cluster, and sample level together with principled selection rules and consensus-based cluster labels. Across six synthetic benchmarks CARVE consistently recovers near-optimal clusterings where classical indices degrade substantially. On experimental genomics and proteomics data sets, CARVE recovers finer biological structure when classical CVIs collapse entirely. CARVE is available with a scikit-learn-compatible Python API and an analogous R interface compatible with Seurat workflows.

Despite being ubiquitous in science, clustering lacks a unified framework for quantitatively evaluating the replicability of its results. We present evaluating replicability via iterative clustering assignments (ERICA), a method for determining whether clusters can be identified reproducibly in a dataset. The pipeline computes a statistic that determines whether reproducible cluster structure is present in a dataset. Quantitative visualization methods are also introduced to characterize similarities between clusters and identify observations that may represent outliers or unstable assignments. Experiments on synthetic datasets demonstrate that ERICA successfully identifies reproducible cluster structure. In contrast, application of ERICA to three breast cancer gene-expression datasets reveals instances in which clustering solutions are not reproducible. The study underscores the importance of rigorously evaluating clustering solutions and provides a practical framework for doing so.

Robot behavior is often validated through simulation-based testing, yet the replicability of such campaigns depends critically on transparent documentation of how tests are configured, executed, and post-processed. We argue that data provenance, coupled with the FAIR principles (findability, accessibility, interoperability, and reusability), addresses this gap by explicitly tracking links between artifacts and by attaching machine-readable metadata about file origins and key design decisions. Moreover, provenance and metadata cannot be treated as an afterthought confined to final datasets; they must be integrated into the testing processes that generate those datasets so that evidence can be reconstructed end-to-end. We demonstrate this by augmenting an existing simulation-based testing framework with provenance tracking and metadata collection mechanisms, and by using these extensions to enrich a mobile robot navigation dataset with structured provenance and FAIR-aligned metadata. Finally, we discuss obstacles encountered in this integration -- such as vocabulary alignment, attribute selection, and adoption of domain standards -- and provide actionable recommendations for implementing provenance-centric, FAIR metadata in robotics validation workflows.

AI-assisted research compresses ideation, implementation, evaluation, and manuscript writing into a single interactive loop. This compression is useful, but it also creates a publication risk: paper claims can become easier to state than to audit. We present ResearchLoop, an evidence-gated control plane for AI-assisted computational research. ResearchLoop treats research questions, task contracts, evidence objects, claim ledgers, closeouts, and paper bindings as durable project state, realized here as a repository-backed runtime. This technical report provides the complete protocol specification, state model, transition rules, claim-admission algorithm, and insight-compounding mechanism. It also reports the full experimental record spanning nine versions (V0--V9), including a self-hosting case study, a controlled task-suite study with component ablations, a mathematical olympiad evaluation, and a supplementary SciCode boundary experiment evaluated with the official generated-code harness. All artifacts, manifests, and verification reports are preserved in the project repository.

Agent benchmarks are increasingly used to compare large language models (LLMs) across domains, yet a reported score reflects a complete model--harness--environment configuration rather than the model alone. Benchmark packages couple native tasks with specific prompts, tool protocols, orchestration logic, and sometimes dynamic external resources, making cross-benchmark comparisons sensitive to implementation and resource conditions. We present UniACE, a unified framework for model-centric evaluation under an explicit, common execution condition. UniACE represents each benchmark as an instruction--tool--environment triplet, executes LLMs through a shared, task-agnostic harness in isolated per-task runtimes, and preserves native success criteria. For tasks that rely on dynamic resources, an optional offline mode replaces live access with fixed, pre-collected snapshots. Its evaluation protocol further standardizes efficiency measurement, execution records, and trace-based failure attribution. We migrate 7 benchmarks spanning 24 domains and evaluate 15 models in more than 400K rollouts consuming 5B tokens. Comparisons with source implementations show large bidirectional score changes and model-ranking reversals, while matched online and offline runs reveal substantial sensitivity to accessible evidence and its representation. Under the shared UniACE configuration, efficiency and failure profiles expose task-dependent model behaviors hidden by task-success scores alone. These findings motivate reporting agent benchmark outcomes as properties of an explicit evaluation configuration, enabling more interpretable and reproducible cross-benchmark comparisons. Codes and benchmarks at are available at https://github.com/whfeLingYu/A-Unified-Framework-for-the-Evaluation-of-LLM-Agentic-Capabilities, https://huggingface.co/datasets/whfeLingYu/Unified_Agent_Framework.

Autonomous research agents produce competitive solutions and professional-looking manuscripts, yet their outputs contain verifiability failures undetectable by surface-level evaluation: fabricated citations, unreproducible scores, and method descriptions that diverge from the implementation. We address this through three contributions. First, Chain-of-Evidence (CoE), a verifiability framework requiring every claim to be traceable to its evidence source. Second, ScientistOne, an end-to-end autonomous research system that maintains evidence chains by construction throughout literature review, solution discovery, and paper writing. Third, CoE Audit, a post-hoc audit whose four integrity checks -- score verification, specification violation, reference verification, and method-code alignment -- apply uniformly to all systems. Across 75 papers spanning five systems and five frontier research tasks, every baseline exhibits at least one systematic failure mode: hallucinated reference rates reach 21%, score verification passes in as few as 42% of papers, and method-code alignment ranges from 20% to 80%. ScientistOne achieves zero hallucinated references (0/337), perfect score verification (12/12), and the highest method-code alignment (14/15), while matching or exceeding human expert performance on all five tasks. ScientistOne further generalizes to six additional tasks spanning medical imaging, fine-grained recognition, 3D perception, and language modeling, achieving state-of-the-art on Parameter Golf and gold medals on MLE-Bench tasks where baselines fail entirely.

Pairwise model comparisons drawn from foundation-model benchmarks ("A is safer than B") are read as quantitative verdicts but hinge on harness choices benchmark papers under-specify. We close one theory-benchmark loop on this primitive: a finite-envelope proposition tying a measurable pairwise-disagreement rate to whether the strict ordering admits a configuration-pair reversal, paired with a commit-stamped evaluation protocol that operationalises it on widely cited alignment benchmarks. On every benchmark we test, configuration choice alone can flip the pairwise verdict; the proposition isolates this strict-reversal failure mode.

AI for Science (AI4Science) workflows often treat the released dataset as a fixed interface to the underlying system. However, in domains relying on \emph{indirect observation}, the learner observes a derivative representation produced by multi-stage measurement, reconstruction, and preprocessing pipelines. \textbf{We argue that these measurement-to-dataset pipelines are inference components: treating their outputs as given data'' freezes an observation model and obscures uncertainty over feasible pipeline choices.} We identify three failure modes arising from this frozen lens'': \textbf{(C1) hidden hypothesis space}, where the released dataset does not specify the pipeline configuration or its validity conditions; \textbf{(C2) uncertified transportability}, where a pipeline may be documented but its regime of validity is untested, so failures under distribution shift cannot be adjudicated; \textbf{(C3) ungoverned multiplicity}, where many defensible pipelines exist and dispersion is real but not propagated into uncertainty-aware evidence. We stress-test these claims with a large-scale neuroscience empirical audit, finding a survival rate of $\approx 0.0004\%$ under a cross-dataset stability criterion. We call on the AI4Science community to make pipelines \emph{computable} inference objects via domain-specific Computable Observation Frameworks. This shift enables quantifying pipeline adequacy and stability, converting implicit implementation choices into auditable, reproducible, and cumulative scientific evidence.

We read twelve well-known LLM agent benchmark papers and recorded, dimension by dimension, what each paper actually says about how its evaluation was run. The motivation came from a familiar frustration: two papers will report results on the same benchmark with the same model name and disagree, and you cannot tell why -- the scaffold, the sampling settings, the subset, or the evaluator version. In many cases the published artifact does not let you answer. This paper is an implementation report on the attempt. We designed a small audit schema (five fields: benchmark identity, harness specification, inference settings, cost reporting, failure breakdown), wrote a scoring codebook with the boundary cases we hit during pilot scoring, applied it to twelve canonical papers (eight agent, four classical static), and recorded what we saw. We score the disclosure of an agent run, not its correctness, and make no claim that disclosure implies a trustworthy result. The mean audit score across the eight agent-benchmark papers is 0.38 (out of 1.0), and across the four classical static benchmarks 0.66; the largest gap is on cost (none of the eight agent benchmark papers disclose inference cost in any form) and on harness specification (none fully disclose a content-addressed container image of the evaluation environment). We release the schema as a JSON Schema file, the codebook as a Markdown document, and the raw scoring sheet as a CSV. The scoring was performed by a single auditor in one pass; a multi-rater audit is the natural next step, and we discuss what we think it would change.

Autonomous language-model agents are increasingly evaluated on long-horizon tool-use tasks, but existing benchmarks rarely capture the complexity and nuance of real scientific work. To address this gap, we introduce Collider-Bench, a benchmark for evaluating whether LLM agents can reproduce experimental analyses from the Large Hadron Collider (LHC) using only public papers and open scientific software. Such analyses are often difficult to reproduce because the public toolchain only approximates the software used internally by the experimental collaborations, while the published papers inevitably omit implementation details needed for a faithful reconstruction. Agents must therefore rely on physical reasoning, domain knowledge, and trial-and-error to fill these gaps. Each task requires the agent to turn a published analysis into an executable simulation-and-selection pipeline and submit predicted collision event yields in specified signal regions. These predictions are evaluated with standard histogram metrics that provide continuous fidelity scores without a hand-written rubric. We also report the computational cost incurred by each agent per task. Finally, we evaluate the codebase and full session trace using an LLM judge to catch qualitative failure modes such as fabrications, hallucinations and duplications. We release an initial set of tasks drawn from LHC searches, together with a containerized sandbox and event simulation tools. We evaluate across a capability ladder of general purpose coding agents. Our results show that on average no agent reliably beats the physicist-in-the-loop solution.

Language models can produce convincing scientific analyses, but repeated generations on the same data do not guarantee the same result. A researcher may regenerate an identical query and receive a different fit, a different peak position or a different analysis procedure, without an obvious way to decide which output to trust. We propose typed mediation, a pattern in which the model orchestrates deterministic tools rather than generating analytical code. Each tool encodes one researcher's exact procedure for one instrument, ported through structured interviews. The model selects which tool to call and with what parameters. The tool produces the result. Regeneration does not change it. We evaluate this claim by running the same photoluminescence analysis on four platforms, including three commercial foundation models, four times each with the same prompt. The typed tool produces identical results across all runs. The commercial platforms either vary in numerical output and analytical methodology across runs, or fail to produce valid results on the task. We deploy this pattern on two instruments serving users over approximately six months, with very positive user feedback. Both cases are very challenging: they involve proprietary binary formats and per-seat licensed software, which force the tool to remain on local infrastructure alongside the data and the instrument it operates. We argue that deployment topology is not just a preference, but a structural requirement of scientific tool mediation. The result is a practical pattern for deploying language models in scientific workflows where reproducibility is mandatory, reducing analysis time from weeks to minutes while guaranteeing identical outputs across runs.

Machine-learning predictors of biochemical activity often exhibit large random-split-to-leave-one-target-out generalisation gaps that have been documented but not decomposed. We frame this as an evaluation-science question and use targeted protein degradation as the empirical test bed. PROTACs (proteolysis-targeting chimeras) are heterobifunctional small molecules that induce targeted protein degradation, with more than forty candidates currently in clinical trials; published predictors report AUROC of 0.85 to 0.91 under random-split cross-validation, while the leave-one-target-out (LOTO) protocol of Ribes et al. reduces performance to approximately 0.67. Random splits reward within-target interpolation, whereas LOTO measures the novel-target prediction that de-novo design depends on. We decompose this gap and identify inter-laboratory measurement variance as the dominant component, anchored by a within-target cross-laboratory cascade bounding the inter-laboratory contribution at 0.124 AUROC, well above the 0.05 contribution from binarisation-threshold choice. Across eight published architectures and ESM-2 protein language models up to 3B parameters, LOTO AUROC plateaus near 0.67, with a comparable plateau under SMILES-level deduplication; a 21-dimensional 2000-trial hyperparameter optimisation cannot break this ceiling, and the rank-1 single-seed configuration regresses by 0.161 AUROC under multi-seed validation, matching a closed-form selection-bias prediction (Bailey and Lopez de Prado, 2014). Few-shot k=5 stratified per-target retraining combined with ADMET features lifts 65-target LOTO AUROC from 0.668 to 0.7050, and post-hoc Platt scaling recovers raw output to within the 0.05 well-calibrated threshold. We release PROTAC-Bench (10,748 measurements, 173 targets, 65 LOTO folds), the variance-decomposition framework, the per-target calibration protocol, and the evaluation code.

Modern astrophysical studies rely heavily on complex data analysis pipelines; however, published descriptions often lack the detail required for computational reproducibility. In this work, we present an information-theoretic framework to quantify how effectively a method can be reconstructed from its written description. By treating algorithmic reconstruction as a probability distribution generated by Large Language Models (LLMs), we utilize Shannon entropy and Jensen-Shannon divergence to measure how strongly text constrains the hypothesis space of valid implementations. We demonstrate this approach through a case study of Trans-Neptunian Object (TNO) spectral reconstruction from sparse photometry. By prompting frontier LLMs with varying levels of manuscript text (Title, Abstract, and Methods), we find that while increasing text successfully clarifies the overall algorithmic structure, it fails to eliminate variance at the implementation level. This persistent variance establishes an "entropy floor," demonstrating that multiple divergent implementations remain consistent with explicit instructions. To evaluate practical reproducibility, we convert these reconstructed algorithms into executable pipelines. Our results reveal that, while LLMs easily recover core functional methodologies, they systematically fail to infer the tacit expert knowledge required for strict scientific calibration. This pilot study demonstrates that LLMs can be repurposed as a zero-shot diagnostic tool to audit methodological transparency, helping authors identify missing structural constraints and preserve scientific integrity in an era of automated research.