Reproducibility

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

The generation of high-fidelity synthetic Electronic Health Records (EHR) is crucial for advancing medical research while preserving patient privacy. However, head-to-head comparison of existing generative models is hindered by disjointed codebases, incompatible data loaders, conflicting library dependencies, and inconsistent evaluation protocols. To address these gaps, we introduce a lightweight, end-to-end benchmarking framework for reproducible synthetic EHR evaluation, organized as a unified pipeline spanning data ingestion, standardized model training, and architecture-agnostic evaluation. Our current implementation targets the generation of longitudinal ICD diagnosis codes -- the most commonly studied modality in this literature -- and is built on the community-maintained PyHealth library. We reimplement and unify strong baselines (MedGAN, CorGAN, PromptEHR, HALO) under full ICD-9 vocabulary granularity, and add a lightweight GPT-2 baseline from the general-purpose sequence-modeling literature. We contribute a rigorous, architecture-agnostic privacy-utility evaluation suite that applies identically to GAN- and transformer-based generators, and report bootstrapped confidence intervals across all metrics. We further analyze the poor long-tailed performance of existing models and discuss the extensibility of our framework beyond diagnosis codes. By lowering the engineering barrier to running, extending, and evaluating under a single pipeline, we introduce a starting point for community-driven reproducibility and benchmarking synthetic EHR models.

In recent years, list replicability has emerged as a framework for formalizing reproducibility in learning theory. A central question is how the required list size relates to the accuracy parameter and natural complexity measures of the hypothesis class. To achieve sharp bounds on list replicability, we prove a novel topological sphere covering theorem, derived from the Borsuk-Ulam theorem. Specifically, if the $d$-sphere is covered by open sets, each of which lies in an open hemisphere, then $d+1$ of these sets must have a common intersection. Using this result, we obtain a sharp bound on the relationship between list size and accuracy for VC classes. We also show that for large-margin half-spaces, provided the margin is not too large, the optimal list size equals the ambient dimension. However, when the margin is taken to be very large, we devise a replicable algorithm achieving the minimal list size of $\lceil d/2 \rceil + 1$.

Large language models (LLMs) have shown strong potential for automated software vulnerability detection, particularly in retrieval-augmented generation (RAG) settings. However, for approaches relying on proprietary models and APIs, reproducibility and replicability remain largely unexplored, raising the question of whether reported results generalize or depend primarily on specific model choices. In this work, we present a reproducibility study of Vul-RAG, a RAG-based framework for source code vulnerability detection that enhances LLMs with high-level vulnerability knowledge. We first replicate the results in a fully local and open-weights setting using the reported open-weight baseline models. We then extend the evaluation to a diverse set of recent open-weight LLMs, including code-specialized, general-purpose, and reasoning models of varying parameter sizes. The results confirm that the findings of Vul-RAG are reproducible under local deployment, but with minor deviations. Across all evaluated models, we observe a performance plateau at approximately 0.30 pairwise accuracy (code pairs for which both the vulnerable and the patched function are correctly classified). Notably, this plateau persists even for more recent and advanced models, indicating that improvements in model capacity alone do not substantially enhance performance. Finally, we discuss practical implications and trade-offs between detection effectiveness, model capabilities, and model scale. Implementation and evaluation artifacts are publicly available at https://github.com/hs-esslingen-it-security/revisiting-Vul-RAG.

We study two reproducible failure modes of deep multi-agent reinforcement learning in continuous-time pricing markets: (i) tacit cartel formation between competing DDPG agents, and (ii) actor--critic instability at high event rates. We instantiate both inside a single CT-MARL benchmark (Poisson-clocked price updates, observation latency $δ$, interior-optimum logit demand), show that synchronous DDPG agents reliably trigger Failure Mode 1 with collusion index $Δ= 0.69 \pm 0.11$, and quantify a partial microstructure fix: asynchrony alone cuts collusion by 48% and adding latency drives it to a minimum of $Δ= 0.28$. The fix has clearly documented costs: it is partial ($Δ$ remains supra-Bertrand), it is non-monotone in $δ$, and it does not survive Failure Mode 2, which emerges as DDPG critic divergence at $λ= 5$ and corrupts the phase-diagram cell at $(λ{=}5, δ{=}1)$. We accompany the scalar collusion index with trajectory-level trace diagnostics that expose the within-episode signalling collapse and the post-shock non-recovery.

Copyleft, as implemented in licenses such as the GNU General Public License, was a legal hack that used copyright to guarantee user freedom by tying the availability of source code to every act of distribution. Its normative force rested on an implicit technical premise: that source code and object code stand in a well-defined, humanly auditable, and reproducible relationship. Large language models and, prospectively, Artificial General Intelligence (AGI) systems systematically violate this premise. The artifacts jointly required to reconstruct a model -- code, data, weights, hyperparameters, toolchain, and hardware configuration -- are each subject to independent legal, technical, and economic constraints that no current open-source framework fully resolves. Sufficiently capable AI systems can also rewrite licensed source into functionally equivalent derivatives stripped of their original obligations, a form of laundering against which copyleft has no effective defense. This paper argues that a functional analogue of copyleft for AGI must be grounded not in share-alike clauses over code, but in reproducible builds: a practice guaranteeing bit-exact reconstructability from declared inputs. We review the logic of copyleft, critically examine Maffulli's Second Liberation thesis according to which AI fulfills Stallman's dream, and show that the argument collapses unless AGI systems are themselves reproducible. Drawing on the Open Source AI Definition (OSAID), the Model Openness Framework (MOF), OpenMDW, and deterministic-inference research, we define seven requirements for AGI-oriented reproducible builds. We further argue that the Model Context Protocol (MCP) and analogous AI-to-AI coupling mechanisms constitute a new dynamic linking layer for which copyleft-style licensing is ill-suited, and that Masnick's "protocols, not platforms" framework offers a more promising governance template.

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.

Speech foundation models and Speech LLMs have advanced speech understanding, yet deployment-oriented model selection is hindered by non-comparable evaluations caused by mismatched post-processing, and by training results that are hard to reproduce across data scales and pipelines. We present SURE, a unified experimentation framework that standardizes prediction formats, normalization, and scoring. SURE evaluates strong systems across paradigms, from conventional pipelines to Speech LLMs, on representative tasks under realistic acoustic and linguistic stressors. Beyond evaluation, SURE introduces an agent-assisted training conversion flow that maps paper and code into versioned, runnable training pipelines under a unified protocol on matched open-data subsets. Overall, SURE improves comparability and reproducibility for deployment-oriented evaluation.

LLMs are increasingly deployed to simulate social interactions, yet many of the existing simulators remain ad hoc and monolithic. This lack of architectural standardization prevents reproducible research and complicates downstream evaluation. We advance a rigorous science of LLM-based multi-agent simulation by modularizing core components into Environments, Agents, Simulation engines, and Evaluation metrics (EASE). We demonstrate the utility of EASE configuration by wrapping it in an experimental study schema for orchestrating workflows centered around answering explicit research questions in generated scenarios. We contribute SiliSocS, an open-source, research-ready Silicon Society Sandbox implementing a study-structured EASE configuration to enable highly configurable and reproducible LLM-based social simulations. Using SiliSocS and EASE, we present three case studies, showcasing the system's comprehensive assessment of existing questions, ability to dive deeper into complex questions, and elaboration of existing studies, respectively. Together, these case studies highlight the limitations of current modeling approaches and isolate the impacts of design choices on key results.

AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchmark for evaluating autonomous scientific research across 40 tasks from 10 scientific domains. Each task is grounded in a real published paper, provides related literature and raw data, and hides the target paper during evaluation. Expert-curated multimodal rubrics decompose the target scientific artifacts into weighted criteria, enabling evaluation of target-paper-level re-discovery while leaving room for new discovery. We evaluate seven autonomous research (auto-research) agents under a unified protocol and seventeen native LLMs through the lightweight ResearchHarness. Current systems remain far from reliable re-discovery: the strongest autonomous agent, Claude Code, averages 21.5, and the strongest ResearchHarness LLM, Claude-Opus-4.7, averages 20.7, with an LLM frontier mean of only 26.5. Error analysis shows that failures concentrate in experimental protocol mismatch, evidence mismatch, and missing scientific core. ResearchClawBench provides a reproducible evaluation frontier for measuring progress toward autonomous scientific research.

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.

Reproducibility is fundamental to the scientific method, yet remains a critical challenge in machine learning. Contributing factors include underspecified execution details and brittle software environments. Human-centric remedies, such as checklists and manual verification, help but require intensive effort and fail to scale. To address this, we introduce Croissant Tasks: a declarative, machine-actionable metadata format that abstracts low-level implementation details into high-level specifications. This format enables conceptual reproducibility: verifying claims via independent, agent-generated implementations rather than brittle source code replication. We contribute: (1) the Croissant Tasks specification, formally decoupling task problem from solution; (2) an automated LLM pipeline that retrofits existing benchmarks into this format; and (3) empirical validation showing autonomous agents can ingest these specifications to generate functional, accurate reproduction pipelines from scratch. We envision this format as a new foundation for automated and conceptual reproducibility in machine learning.

Industrial Prognostics and Health Management (PHM) provides a representative case study for a broader challenge in applied machine learning: translating published papers into executable, benchmark-ready implementations. Reproducing under-specified methods in PHM is particularly difficult due to restricted access to industrial datasets, incomplete reporting of preprocessing and evaluation protocols, and implicit design choices (e.g., windowing, target construction, data splits) that critically affect performance. Existing paper-to-code systems generate implementations for individual papers, but these artifacts are often not directly comparable due to inconsistencies in assumptions and evaluation settings. We introduce \emph{agentic, framework-based PHM paper reproduction}, where an agent translates a paper into a shared PHM benchmark framework via a \emph{slot-binding interface}. This interface maps equations and protocol descriptions into structured components (task definitions, dataset adapters, windowing, targets, models, and evaluators), while explicitly recording unresolved assumptions. The resulting implementations are validated against standardized task contracts and evaluation hooks, enabling consistent and comparable benchmarking. We evaluate this approach on 16 PHM papers, comparing framework-enhanced, skill-based and prompt-based agentic reproduction against a recent framework-free paper-reproduction agent. We assess reproduction success, model-based code evaluation, framework binding of paper assumptions, and cross-paper benchmark comparability under standardized protocols. Our results show that coupling agentic generation with a shared framework transforms paper reproduction from isolated code synthesis into executable, assumption-aware, and systematically comparable benchmark implementations.

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.

Background: Large language models are typically evaluated as models, benchmarks, or short conversational episodes. Less is known about what happens when an agent is embedded persistently in a real academic research environment with durable memory, local files, external tools, scheduled routines, delegated roles, and explicit safety protocols. Methods: A structured self-observed implementation case study was conducted from January 31 to May 25, 2026. The unit of analysis was the persistent human-agent environment: researcher, agent runtime, memory layer, tools, repositories, scheduled jobs, specialized agent roles, and governance rules. Outcomes were organized using PARE-M (Persistent Agentic Research Environment Measurement), a measurement framework covering architecture, utilization, artifact production, resource use, reproducibility, and governance. Results: Recoverable main-agent telemetry contained 75,671 de-duplicated records across 96 active days, with 8,059 user-role and 23,710 assistant-role messages. The workspace included 502 memory-related files, 17 configured agent directories, and 57 skill files. Active system time was 579.7 hours (30-minute capped-gap estimate). Memory-derived records identified 482 output-proxy events and 889 failure, verification, correction, or protocol-proxy events. A strict May 2026 trajectory subset captured 627 model-completed events and 73.95 million recorded tokens, of which 82.9% were cache reads. Conclusions: The workflow was cache-dominant, suggesting that persistent agentic environments may shift the economic unit from cost per token to cost per completed artifact. Future evaluations should use artifact-level denominators, reproducible parsing rules, correction taxonomies, and independent coding of governance events.

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.

Multimodal Large Language Models (MLLMs) achieve versatility by reformulating diverse tasks into a unified instruction-following framework via instruction tuning. However, real-world deployment requires continuous adaptation to emerging tasks, motivating Multimodal Continual Instruction Tuning (MCIT). Despite its growing importance, current MCIT research is hindered by severe engineering bottlenecks. Existing methods are typically implemented by directly modifying the base MLLM codebase, which imposes substantial implementation overhead and yields method-specific architectures that severely limit code reuse and fair comparison. To address this, we introduce Prism, a plug-in reproducible codebase specifically designed for scalable MCIT research. It separates algorithmic development from the backbone implementation via a lightweight plugin registration mechanism, enabling new strategies to be integrated as independent plugins without modifying the underlying MLLM codebase, thereby eliminating structural fragmentation and accelerating method development. Prism natively supports widely used large-scale training pipeline, thereby enabling reproducible and scalable MCIT experimentation. Code is available at https://github.com/LAMDA-CL/Prism.

AI answer engines generate answers from retrieved pages but cite only a few sources. This makes visibility depend not just on ranking, but on being cited. We study competitive Generative Engine Optimization (GEO): when two retrieved candidates compete, what makes one more likely to be cited first? We build a controlled two-document retrieval-augmented generation (RAG) testbed that injects exactly two candidate sources into the model context and measures which source is referenced by the first citation marker in the output. Across six LLMs we execute 252,000 trials, repeated paired comparisons under one factorial program over 18 content factors. In each trial the two sources differ in exactly one factor; we use brand anonymization and counterbalanced source order to separate content effects from position bias. Mixed-effects models show that topical relevance and list position are the biggest drivers of being cited first. Including explicit price information and a recent timestamp also helps consistently. Completeness and trust cues add smaller gains, while formatting-only edits have little impact. We release a reproducible evaluation protocol and a prioritized GEO checklist for practitioners, and we exercised it in an early internal pilot at Sprinklr, where teams reported positive qualitative feedback on workflow usability.

Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biological foundation models, specifically nucleotide foundation models (NFMs), the field lacks a unified standard for viral genomics to facilitate community development and enforce biosecurity constraints. To address this, we introduce ViroBench, the first comprehensive and large-scale benchmark specifically designed for NFMs in viral settings. ViroBench evaluates models across two critical dimensions: biological understanding and latent biosecurity risk, covering 18 diverse scenarios within 4 task types. Extensive evaluation of 66 NFMs across diverse architectures yields three critical conclusions. Firstly, NFMs exhibit a performance degradation in biological understanding under phylogenetic and temporal shifts, indicating weak extrapolation capabilities. Secondly, generation tasks reveal a decoupling between statistical likelihood and biological functional validity, posing latent biosecurity risks. Thirdly, controlled ablation studies reveal that taxonomic diversity in pretraining data outweighs parameter scale. Specifically, a lightweight baseline trained on diverse data achieves a 67.5% performance gain over its original model. Overall, ViroBench provides interpretable, diagnostic evaluations and a reproducible measurement framework for future research on viral nucleotide foundation models. The datasets and code are publicly available at https://github.com/QIANJINYDX/ViroBench.

Recent advances in imitation learning and vision-language models highlight the need for high-fidelity tactile perception, with 6-DoF tactile object pose estimation providing a crucial foundation for precise robotic manipulation. We introduce InvariantCloud, a 6-DoF pose estimation framework that leverages the global invariance of surface marker constellations on vision-based tactile sensors. In contrast to recent approaches, our one-shot globally invariant point cloud registration suppresses cumulative drift and overcomes long-standing limitations in accurately estimating yaw (Z-axis) rotation. Experimental verifications show that InvariantCloud achieves superior yaw tracking accuracy and re-localization repeatability compared to existing benchmarks, demonstrating its precision and robustness in long-sequence manipulation tasks.

Soft pneumatic actuators are widely used in soft robotics because they can produce large motions while remaining compliant enough to interact safely with objects, environments, and the human body. However, their performance is not solely determined by pressure. Instead, the response depends on the way the actuator is built, including the shape of its chambers, the placement of reinforcements, the use of folds, material stiffness, and the constraints that guide its deformation. As the literature has expanded, it has become more difficult to determine which mechanism is most suitable for a given application and which reported results can be compared across studies. This review examines soft pneumatic actuators according to the design strategies used to generate four motion classes: linear, bending, twisting, and omnidirectional actuation. For each class, it analyzes the structural features that define the deformation path, including braid angle, fold geometry, fiber orientation, chamber arrangement, structural asymmetry, and internal constraint layers. It then discusses how the design choice affect motion output, force generation, air demand, repeatability, durability, fabrication difficulty, and robotic integration. The review further identifies key conditions that must be considered when selecting or comparing actuators, including pressure, loading condition, actuator size, pneumatic supply, and hysteresis This approach helps explain why actuators with similar motion outputs may differ substantially in design requirements, pneumatic demand, and practical suitability. It also highlights the design priorities needed for compact, efficient, repeatable, and deployable soft pneumatic systems in wearable, biomedical, and mobile robotic applications.

ESG and climate risk data remain fragmented across heterogeneous Scope 1, Scope 2, and Scope 3 reporting environments, while conventional validation pipelines lack provenance aware auditability, hidden drift detection, and reproducibility oriented governance. This paper proposes a deterministic climate risk intelligence framework integrating single source of truth orchestration, temporal anomaly detection, imbalance aware ensemble learning, and explainability oriented governance for auditable ESG validation. To support open reproducibility, we construct and release a synthetic ESG validation benchmark calibrated against publicly reported characteristics of the GHG Protocol, PCAF, and ISSB standards. The methodology incorporates temporal drift analysis, SMOTE based rare event optimization, ensemble learning, provenance aware orchestration, and TreeSHAP based interpretability for governance inspection and audit reconstruction. We evaluate the framework against statistical classifiers, anomaly detection methods, temporal forecasting baselines, and a threshold based system using classification metrics (recall, F1, ROC AUC), calibration metrics (ECE, Brier score), and a governance oriented audit trace completeness metric measuring the fraction of flagged anomalies for which a deterministic source to escalation provenance chain can be reconstructed. Results are reported as mean and standard deviation across stratified five fold cross validation with paired significance testing. The framework reframes ESG reporting toward deterministic climate risk governance infrastructure supporting reproducibility, explainability, and operational auditability.

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.

As Large Language Models (LLMs) transition from research environments to production deployments, evaluating their performance against strict Service Level Objectives (SLOs) has become critical. However, current evaluation methodologies suffer from severe measurement bias at scale. We demonstrate that widely used benchmarking utilities rely on single-process, asyncio-driven architectures that introduce fundamental client-side queuing bottlenecks under high concurrency. By modeling the benchmarking client as an $M/G/1$ queue, we mathematically demonstrate how the Python Global Interpreter Lock (GIL) artificially inflates Time to First Token (TTFT) and Time Per Output Token (TPOT) metrics as request rates scale. To resolve this systematic inaccuracy, we propose an unbiased, multi-process evaluation framework that effectively distributes client-side load, ensuring negligible queuing overhead. Furthermore, we formalize a composite metric, Normalized Time Per Output Token (NTPOT), to robustly amortize end-to-end latency, including prefill and scheduling delays across sequence lengths. Our empirical evaluation demonstrates that this methodology successfully isolates pure serving engine performance, enabling accurate, reproducible profiling of LLMs at production scales exceeding thousands of queries per second.

Small changes to how a buyer phrases a question -- "best CRM" vs "top CRM" vs "best CRM for a SaaS startup" -- produce substantially different brand recommendations from AI assistants. Across ~6,000 paraphrase runs and ~6,000 same-prompt rerun controls on OpenAI and Anthropic models, the recommendation-set similarity (Jaccard) between two paraphrases of the same underlying buying intent is 0.288 for cosmetic rewordings (clustered 95% CI [0.215, 0.361]) and 0.135 for constraint-adding rewordings ([0.098, 0.175], pooling region/language and specificity-ladder axes) -- both far below the 0.50-0.61 same-prompt rerun baseline. The prompt string, not the underlying buyer intent, is the dominant input to which brands surface. Increasing reasoning effort does not narrow the gap (bounded by +/-0.05). This is a direct challenge to an increasingly popular AEO/GEO practice. Tracking a brand's "AI visibility" by counting brand mentions over a fixed set of prompts produces a metric whose dominant source of variance is which paraphrase the tracker happens to issue, not the model's behavior toward the brand: the same buyer intent in two natural paraphrases produces recommendation sets that overlap 14-29% in Jaccard versus 50-61% for same-prompt reruns. Sampling more paraphrases per intent reduces the artifact in principle, and efficient multi-prompt evaluation methods exist in the academic literature, but the natural buyer-phrasing space is much larger than the benchmark-scale prompt sets those methods have been validated on, and far beyond what any commercial tracker issues per brand-intent combination. Prompt-by-prompt mention tracking is therefore structurally unstable as a unit of measurement; meaningful improvement likely requires a different unit rather than a larger prompt set.

In-network learning (INL) trains distributed neural modules by exchanging latent activations and backpropagated errors over a communication graph. This letter proposes Dijkstra-pruned INL (D-INL), which removes non-tree links by retaining a capacity-aware shortest-path tree rooted at the fusion node. To balance sparsity and predictive information, local routing (or aggregation) is modeled as a finite-rate stochastic gate with rate $R_g=I(Z; T)$. We derive a rate-distortion-generalization bound and validate the method on a reproducible distributed-classification experiment, where D-INL reduces training exchange by $70.4\%$ while preserving accuracy within the standard deviation of dense INL. Adding finite-rate regularization further reduces the estimated latent rate by $45.7\%$ relative to unregularized Dijkstra INL.

Katharevousa Greek remains poorly served by contemporary NLP pipelines despite its importance for legal, administrative, and parliamentary archives. We present a reproducible workflow for building and evaluating a Universal Dependencies-style parsing resource for Katharevousa parliamentary questions from Greece's early post-junta period. The pipeline links OCR-aware reconstruction, schema-constrained LLM-assisted annotation, automatic validation, deterministic CoNLL-U snapshotting, fixed-split evaluation, and model-family comparison. The frozen automatically validated reference set contains 1{,}697 sentences, split into 1{,}357 training sentences and 340 held-out test sentences. We compare off-the-shelf Greek and Ancient Greek parsers, a feature-based parser, mBERT, XLM-R, and custom Stanza training under the same scoring protocol. Off-the-shelf systems show substantial register mismatch: the strongest external baseline, spaCy Greek, reaches 0.4183 LAS. The best structural parser, an XLM-R model, reaches 0.8893 UPOS accuracy, 0.7250 dependency-relation F1, 0.6098 UAS, and 0.5162 LAS, an absolute LAS gain of 0.0980 over the best external baseline. The feature-based model remains competitive for UPOS and relation labeling, indicating that transparent lexical-context features still matter at this data scale. Beyond scores, the paper contributes an auditable methodology for turning difficult historical parliamentary OCR into reusable syntactic NLP infrastructure. The entire pipeline -- code, schema, frozen reference annotations, fixed train/test split, and per-model benchmark reports -- is released as an open-access companion to this paper.

Autonomous research systems increasingly make the scientific workflow executable: agents can propose ideas, run code, inspect results, and draft papers. But executable workflows do not by themselves produce research judgment. We analyze where current systems lose trial experience: weak evidence becomes prose, pilot signals become broad claims, memory remains textual, and recurring process failures do not change later behavior. We introduce Sibyl-AutoResearch, a self-evolving AutoResearch framework built around Scientific Trial-and-Error Harnesses. A harness lets agents run bounded trials, preserve positive and negative outcomes, and route lessons into later planning, validation, claim scope, scheduling, critique, writing, and harness repair. We formalize this through two auditable conversion units: trial-to-behavior conversion, which links trial signals to later research actions, and trial-to-harness-behavior conversion, which links recurring process failures to system updates. We implement the framework in SIBYL, a file-backed autonomous research system that exposes the state, roles, memory, gates, and artifact traces needed to inspect these conversion paths. A retrospective audit identifies eight high-confidence conversion events, with a median latency of one iteration and a maximum latency of three iterations. A recovered-failure registry further shows how five naturally occurring failure classes, including duplicate results, stale numbers, and unsupported statistics, were blocked, downgraded, or routed into later repair. These traces do not establish a comparative performance claim; they show that the proposed conversion units are recoverable from realistic autonomous-research workspaces. The SIBYL framework and system are available at https://github.com/Sibyl-Research-Team/AutoResearch-SibylSystem.

The growing sophistication of GAN-based image manipulation presents significant challenges for digital forensics. This study compares the performance of four pretrained CNN architectures including VGG16, ResNet50, EfficientNetB0, and XceptionNet for fake image detection using a unified preprocessing and training pipeline. A dataset of real and manipulated images was processed through resizing, normalization, and augmentation to address class imbalance and improve generalization. Models were evaluated using Accuracy, Precision, Recall, F1-score, and ROC-AUC. VGG16 achieved the highest accuracy at 91%, with XceptionNet, ResNet50, and EfficientNetB0 each reaching 90%. EfficientNetB0 showed stronger sensitivity to fake images but reduced reliability on real samples, reflecting imbalance-driven bias. Limitations include dataset imbalance, overfitting, and limited interpretability, which affect cross-domain robustness. The study provides a reproducible baseline and underscores the need for balanced datasets, advanced augmentation, and fairness-aware training to develop reliable fake image detection systems.

Vision-Language-Action (VLA) models have shown strong promise for general-purpose robotic manipulation, but their real-world evaluation remains limited by a lack of accessible, reproducible, and consistent benchmarks. Simulation benchmarks fail to capture real-world complexity, while existing real-world benchmarks often require expensive hardware, centralized evaluation, or are limited in task diversity. We introduce VLA-REPLICA, a low-cost, easily reproducible real-world benchmark for evaluating VLA models. Built from off-the-shelf components, our system can be quickly assembled and replicated across laboratories, providing a consistent environment for policy evaluation anywhere in the world. VLA-REPLICA includes a diverse suite of manipulation tasks and a small-scale demonstration dataset for target-domain adaptation, with real-world evaluation protocols for both in-distribution and out-of-distribution settings. Experiments with imitation learning and state-of-the-art VLA models reveal model strengths and limitations, while consistent results across independently constructed setups demonstrate the reproducibility of our benchmark.

AI-assisted theorem proving can now generate substantial Lean developments for olympiad-level mathematics, but the evidential status of such developments depends on which declarations are actually verified. This paper reports a Lean 4 formalization case study of an Aristotle API proof attempt for the Grasshopper problem, originally posed as IMO 2009 Problem 6. The generated artifact states a generalized Lean version of the theorem, contains four verified helper lemmas for local components of a maximality and adjacent-swap exchange strategy, and leaves the main theorem grasshopper closed directly by one unresolved sorry. The verified components establish that the final partial sum equals the total sum, that an adjacent transposition can affect only the relevant intermediate partial sum, that the changed partial sum has the expected form, and that maximality at a position admitting an adjacent successor swap forces a corresponding forbidden-set membership fact. The Aristotle output summary identifies the intended remaining mathematical step as the global counting step needed to show that these membership facts produce at least n distinct forbidden values, contradicting the cardinality assumption |M| < n; the Lean source itself does not reduce the main theorem to a separately encoded counting lemma. This case study gives an inspectable example of a central limitation in AI-assisted formalization, namely that local proof search can succeed while the global combinatorial bookkeeping required for a theorem remains unresolved. The paper contributes a reproducible Lean artifact and a precise analysis of its verified and unverified proof content.

Autonomous research systems capable of generating complete scientific manuscripts have advanced rapidly, yet robust and realistic evaluation frameworks have failed to keep pace. To bridge this gap, we introduce MLReplicate, an end-to-end benchmark evaluating autonomous research systems on machine learning reproducibility. The benchmark was constructed from ICML 2025 outstanding papers reformulated into standardized input specifications and evaluated across 6 state-of-the-art research systems: AI SCIENTIST-V1, AI SCIENTIST-V2, AGENT LABORATORY, CYCLERESEARCHER, AI RESEARCHER, and TINY SCIENTIST, yielding 45 generated manuscripts, with 3 failed experiments. Outputs are assessed using a dual-protocol approach that combines automated conference-style review and structured expert human evaluation, while tracking computational cost, runtime, and the amount of required human intervention. The automated conference-style review accepted 10 out of 37 valid submissions. An additional 8 submissions were desk-rejected before review for failing to meet the minimum page threshold. In contrast to automated reviews, human reviewers consistently identified methodological flaws, hallucinated experimental results, and reproducibility failures across all systems, and 59% of accepted automated reviews contained fabricated or unsupported claims. We further find that neither token budget nor computational cost predicts output quality: the cheapest system outperforms the most resource-intensive system in human evaluation, despite a 38-fold difference in input tokens. We thus demonstrate that autonomous research workflow design matters more than the scale of compute. MLReplicate exposes a substantial gap between current autonomous research systems and genuine scientific rigor, and establishes a practical, extensible evaluation framework for systematic progress toward trustworthy AI-driven scientific discovery.

Synthetic persona datasets cite alignment with official demographics as a basis for trust, yet downstream users consume them as joint structures across age, sex, region, occupation, education, name, and institutional status. Marginal alignment does not imply that these joints are preserved. We propose the Independence-Assumption Footprint (IAF), an audit primitive that operates on the attribute combinations a dataset card itself documents as treated independently. For each such combination, IAF compares the synthetic joint against an external official or institutional reference, using direct joint tables where available and rule-implied checks otherwise. Applied to NVIDIA Nemotron-Personas-Korea (one million Korean synthetic personas), IAF finds that NPK aligns with KOSIS marginals while three joints fail. The major-by-occupation distribution against the KEIS graduate universe carries a large conditional mismatch. The age profile of military service is institutionally inconsistent. Female representation in male-dominated occupations is substantially over-flattened toward parity, with the strict screening verdict mapping-dependent and age-robust under direct standardisation. A transferability demonstration across six further NPK locales finds locale-dependent rather than universal diagnostics, with reference-taxonomy cardinality confounding cross-locale flag counts. For synthetic personas used as silicon samples, marginal claims must therefore be paired with disclosure-anchored joint audits before reuse. The released audit artefacts (reference manifests, occupational crosswalks, derived metrics, reproducibility scripts) instantiate this protocol on the NPK family and are released for retargeting at other synthetic persona resources.

LLM agents routinely serve as first (and sometimes only) readers of academic papers, skimming for sub-claims, extracting reproducibility steps, and generalizing scope. Standard prose papers produce recurring failures in this role: sub-claims that cannot be cited at sub-paper granularity, scope overextension beyond what the paper tests, and figure commands buried in codebases rather than the paper itself. We propose paper.json, a companion JSON file that travels with the PDF and addresses each failure with a lightweight convention: stable claim IDs (C1), an explicit does-not-claim list (C2), exact per-figure shell commands (C3), and stable definition IDs (C5). A fifth convention (C4) holds that minimum viable compliance, hand-written JSON alongside the PDF, is achievable in under an hour for a finished paper without touching the human-readable output. C1, C2, C3, and C5 are open invitations: an agent that reads a compliant paper and acts on it produces evidence for or against them. This paper is itself compliant: uv run validator.py paper.json --against paper.typ passes. Repo: https://github.com/arquicanedo/paper-json

We investigate growth dynamics in deterministic equational discovery substrates. Across three toy domains (arithmetic, boolean, higher-order list; n=592 trajectories), short-range substrate sizes fit a power-law N(t) proportional to t^b. Within each substrate b is architecture-sensitive (cross-validated R^2 approximately 0.82); the regression does not transfer across substrates (arith+bool to list yields R^2 approximately -0.84). A heuristic mean-field closure model predicts a saturating power-law dN/dt = K N^k exp(-mu N) of which the pure power-law is the short-range approximation. Three robustness checks: bootstrap intervals on (k, mu) are tight in 4/5 toy trajectories and degenerate in 1/5; out-of-sample forecasting on toy data (fit first 100 epochs, predict next 400) is won by pure power-law 5/5, indicating the toy trajectories do not reach saturation; on two real-world growth proxies the result splits. New Mathlib/*.lean file additions per month (mathlib4, 60 months, 9701 files) support the saturating form on OOS forecasting by approximately 7x over pure power-law; Coq mathcomp monthly commits (129 months, 3083 commits) favour pure power-law on both tests with mu collapsing to zero. The dynamics are substrate-conditional at two levels: within-substrate architecture-to-b regressions do not transfer, and the preferred functional family for N(t) itself (pure vs. saturating power-law) differs by substrate. We propose "saturating power-law growth with substrate-conditional (k, mu), observable when the substrate has reached its saturation regime" as a working framing.

Interactive agent benchmarks face a tension between scalable construction and realistic workflow evaluation. Hand-authored tasks are expensive to extend and revise, while static prompt evaluation misses failures that only appear when agents operate over persistent state. Existing interactive benchmarks have advanced agent evaluation significantly, but most initialize tasks from clean state and do not systematically test how agents handle pre-existing partial, stale, or conflicting artifacts. We present \textbf{ClawForge}, a generator-backed benchmark framework for executable command-line workflows under state conflict. The framework compiles scenario templates, grounded slots, initialized state, reference trajectories, and validators into reproducible task specifications, and evaluates agents step by step over persistent workflow surfaces using normalized end state and observable side effects rather than exact trajectory matching. We instantiate this framework as the ClawForge-Bench (17 scenarios, 6 ability categories). Results across seven frontier models show that the best model reaches only 45.3% strict accuracy, wrong-state replacement remains below 17% for all models, and the widest model separation (17% to 90%) is driven by whether agents inspect existing state before acting. Partial-credit and step-efficiency analyses further reveal that many failures are near-miss closures rather than early breakdowns, and that models exhibit qualitatively different failure styles under state conflict.

Large Language Models (LLMs) trained on web-scale corpora inherently absorb toxic patterns from their training data. This leads to toxic degeneration where even innocuous prompts can trigger harmful outputs. This phenomenon poses significant risks for real-world deployments. Thus, necessitating effective mitigation strategies that should maintain model utility while ensuring safety. In this comprehensive replication study, we evaluate the efficacy of DExperts (Decoding-time Experts), which is an inference-time mitigation technique that steers generation without requiring model retraining. We structured our research into three systematic phases: (1) establishing baseline toxicity measurements using RealToxicityPrompts on standard GPT-2 models; then (2) implementing and evaluating DExperts to mitigate explicit toxicity; and finally (3) stress-testing the method against implicit hate speech using the adversarial ToxiGen dataset. Our empirical results confirm that while DExperts achieves near-perfect safety rates (100%) on explicit toxicity benchmarks, it exhibits brittleness against adversarial, implicit hate speech, with safety rates dropping to 98.5%. Furthermore, we quantify a critical trade-off. The method introduces a 10x latency penalty (from 0.2s to 2.0s per generation), posing challenges for real-time deployment scenarios. This study contributes to the growing body of work on AI safety by highlighting the robustness gap between explicit and implicit toxicity mitigation. We emphasize the need for more sophisticated approaches that generalize across diverse hate-speech patterns without incurring prohibitive computational costs.

As generative AI models such as large language models (LLMs) become more pervasive, ensuring the safety, robustness, and overall trustworthiness of these systems is paramount. However, AI is currently facing a reproducibility crisis driven by unreliable evaluations and unrepeatable experimental results. While human raters are often used to assess models for utility and safety, they introduce divergent biases and subjective opinions into their annotations. Overcoming this variance is exceptionally challenging because very little data exists to study how experimental repeatability actually improves as the annotator pool grows. Standard evaluation practices typically rely on a small number of annotations per item (often 3 to 5) and lack the persistent rater identifiers necessary to model individual variance across items. In this work, we introduce a multi-level bootstrapping approach to realistically model annotator behavior. Leveraging datasets with a large number of ratings and persistent rater identifiers, we analyze the tradeoffs between the number of items ($N$) and the number of responses per item ($K$) required to achieve statistical significance.

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.

Neuroscience data are highly fragmented across labs, formats, and experimental paradigms, and reuse often requires substantial manual effort. A persistent roadblock to data reuse and integration is the need to decipher bespoke and diverse data formatting choices. Common data formats have been proposed in response, but the field continues to struggle with a fundamental tension: formats flexible enough to accommodate diverse experiments are rarely descriptive enough to be self-explanatory, and sufficiently descriptive formats demand detailed documentation and curation effort that few labs can sustain. Agentic AI is a natural candidate to solve this problem: LLMs read code and text faster and with sustained attention to the low-level details humans tend to skim over. To measure how well agentic AI performs on this task, we selected eight recent papers studying large-scale mouse neural population recordings that shared both data and code, spanning diverse recording modalities, behavioral paradigms, and dataset formats (e.g., NWB, specialized APIs, and general-purpose Python or MATLAB files). We provided agents with the data, code, and paper, and prompted them to load, understand, and reformat the data for a common downstream task: training a decoder from neural activity to task or behavioral variables. General-purpose coding agents commonly used by scientists performed well on each sub-task, but rarely strung together a fully error-free end-to-end solution. We characterize the types of mistakes agents made and the dataset properties that elicited them, and propose data-sharing best practices for the agentic-AI era. We further find that agents-as-judges are unreliable at catching errors, especially without ground-truth references, so interactive, human-in-the-loop coding remains necessary.

Background: Many different approaches to controlled text generation (CTG) have been proposed over recent years, but it is difficult to get a clear picture of which approach performs best, because different datasets and evaluation methods are used in each case to assess the control achieved. Objectives: Our aim in the work reported in this paper is to develop an approach to evaluation that enables us to comparatively evaluate different CTG systems in a manner that is both informative and fair to the individual systems. Methods: We use a level-playing-field (LPF) approach to comparative evaluation where we (i) generate and process all system outputs in a standardised way, and (ii) apply a shared set of evaluation methods and datasets, selected based on those currently in use, in order to ensure fair evaluation. Results: When re-evaluated in this way, performance results for a representative set of current CTG systems differ substantially from originally reported results, in most cases for the worse. This highlights the importance of a shared standardised way of assessing controlled generation. Conclusions: The discrepancies revealed by LPF evaluation demonstrate the urgent need for standardised, reproducible evaluation practices in CTG. Our results suggest that without such practices, published performance claims may substantially misrepresent true system capabilities.

Reproducibility problems that have long affected machine learning and reinforcement learning are now surfacing in agent research: papers compare systems by reported scores while leaving the rollout records behind those scores difficult to inspect. For agentic tasks, this matters because the same behaviour can receive different reported scores when evaluations select different parts of a rollout or apply different reporting rules. In a structured audit of 50 popular training and evaluation repositories, we find that none report how many runs failed, errored, or were skipped alongside headline scores. We also document 37 cases where reporting rules can change task-success rates, cost/token accounting, or timing measurements for fixed evidence, sometimes dramatically. We treat rollout records, not reported scores, as the unit of reproducibility for agent research. We introduce rollout cards: publication bundles that preserve the rollout record and declare the views, reporting rules, and drops manifests behind reported scores. We validate rollout cards in two settings. First, four partial public releases in tool safety, multi-agent systems, theorem proving, and search let us compute analyses their original reports did not include. Second, re-grading preserved benchmark outputs across short-answer, code-generation, and tool-use tasks shows that changing only the reporting rule can change reported scores by 20.9 absolute percentage points and, in some cases, invert rankings of frontier models. We release a reference implementation integrated into Ergon, an open-source reinforcement learning gym, and publicly publish Ergon-produced rollout-card exports for benchmarks spanning tool use, software engineering, web interaction, multi-agent coordination, safety, and search to support future research.

LLM inference and serving systems have become security-critical infrastructure; however, many of their most concerning failures arise from the serving layer rather than from model behavior alone. Modern inference engines combine KV cache, batching, prefix sharing, speculative decoding, adapters, and multi-tenant scheduling, creating shared-state behavior that only emerges under realistic concurrent workloads and is missed by standard model, safety, and API tests. We present GRIEF, a greybox fuzzer for LLM inference engines that treats timed multi-request traces as first-class inputs, uses lightweight oracles to detect crashes, hangs, performance pathologies, and silent output corruption, and applies controlled replay with log-probability checks to confirm reproducible serving-layer failures. Across early campaigns on vLLM and SGLang, GRIEF discovers 15 vulnerabilities, 10 confirmed by engine developers, including 2 CVEs, spanning KV-cache isolation failures, cross-request performance interference, and crash or liveness bugs. These results show that concurrency, caching, and state reuse can induce silent cross-request contamination, noisy-neighbor denial of service, and delayed crashes without malformed inputs or explicit server errors, making concurrent serving behavior a first-class security and reliability boundary for LLM infrastructure.

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.

Deploying machine learning in regulated financial environments -- credit risk, fraud detection, and anti-money laundering -- exposes critical vulnerabilities in algorithmic reproducibility. While early financial ML addressed statistical challenges such as backtest overfitting, deep neural networks and Generative AI have introduced mechanical nondeterminism rooted in hardware and architecture. This survey provides a systems perspective on reproducibility failures across three modalities now dominant in financial AI: tabular models (post-hoc explanation variance), graph networks (stochastic sampling and temporal asynchrony), and LLM-based agentic workflows (batch-dependent divergence and trajectory drift). We supplement the literature analysis with first-party experiments on public financial datasets -- quantifying explanation rank instability in credit scoring, prediction flip rates in GNN-based fraud detection, and tensor-parallel-induced output divergence in LLM entity extraction. We propose a layered evaluation framework linking modality-specific metrics (RBO, D_cos, TDI, PSD) to audit readiness, and empirically validate the complementarity of logit-level and semantic-level determinism measures.

Transparent and standardized reporting is essential for reproducible scientific research, yet adherence to reporting guidelines remains inconsistent because of the manual effort required to select and complete checklists. We present CheckSupport, an open-source, locally deployable system that uses large language models to automate the recommendation of reporting checklists and the evidence-grounded completion of checklists for scientific manuscripts. CheckSupport employs a staged prompting strategy that decomposes reporting workflows into constrained inference tasks, prioritizing faithful extraction over generative text synthesis. All inference is performed locally using instruction-tuned models, preserving data privacy and enabling reproducible, auditable workflows. Evaluated on a corpus of peer-reviewed manuscripts, CheckSupport achieved 90% overall accuracy for checklist recommendations and 88% overall accuracy for item-level completion while operating on CPU-only hardware. On average, the wall-clock time per manuscript was 12.5 seconds, including the checklist recommendation and full checklist completion. These results demonstrate that large language models, when applied as structured inference components, can reduce reporting burden and support more transparent and reproducible scientific reporting across disciplines.

Execution-based evaluation of LLM-generated code implicitly treats successful execution as a proxy for correctness. In scientific simulation, this proxy is insufficient: a generated input file can run, mesh, and converge while encoding governing equations that differ from the user's intent. We call this mismatch between intended physics and generated code the comprehension-generation gap. We instantiate this in MOOSE, where Kernel and BC objects map compositionally to weak-form residual terms, enabling deterministic reconstruction of the encoded PDE and comparison against an intended contract. We formalize this comparison as the Intent Fidelity Score (IFS), a structural metric covering governing terms, BCs, ICs, coefficients, and time scheme. Building on IFS, we develop a PDE-grounded refinement loop that uses deterministic violation reports to correct generated code iteratively. We evaluate on MooseBench, a 220-case multiphysics benchmark with PDE-level ground truth released with this work. On this benchmark, our method consistently improves mean IFS over direct generation, with gains concentrated on hard cases. On the subset where direct generation falls below IFS 0.7, refinement adds +0.22 to +0.41 absolute IFS. In the deployment audit, execution-only repair improves execution success while leaving 39-40% of all 220 cases runnable but still solving the wrong physics across the three main deployment-audit models, exposing executability and intent fidelity as separable failure modes. Static proof-of-concept experiments on four PDE-oriented DSLs (UFL/FEniCS, FreeFEM, FiPy, and Devito) suggest that the reconstruction-and-comparison pattern extends beyond MOOSE. These findings reinforce that executable simulation code should be verified against the mathematical structure it is intended to encode, not accepted on execution alone.

Ancient and endangered languages pose a unique challenge for NLP: their datasets are inherently scarce, difficult to expand, and built from formulaic corpora -- making data-quality issues especially consequential yet rarely audited. Motivated by the need to understand what current NMT can realistically achieve for such languages, we investigate hieroglyphic-to-German translation, where a recent study reported 61.5 BLEU using fine-tuned M2M-100. Our reproduction yields only 37.0 BLEU with the released model. Investigating this gap, we find 2% of test targets appear identically in training (16/50; 50% under 8-gram overlap at 70% threshold). This contamination inflates scores dramatically: contaminated samples achieve up to 83.8 BLEU / 0.924 COMET-22 versus 30.9--39.2 BLEU / 0.622--0.676 COMET-22 on clean samples across five model configurations spanning two architectures. Document-level decontamination reduces contaminated BLEU by only 4.6 points because 8/16 targets persist via other source documents -- target-level deduplication is required. We release a decontaminated 34-sample test set and establish corrected baselines (30.9--39.2 BLEU), providing a realistic assessment of NMT capability for this endangered writing system.

Large Language Models (LLMs) are increasingly used in analytical workflows, but their suitability as exploratory data analysis (EDA) agents in business settings remains uncertain. In practice, a deployable EDA agent must provide not only useful average performance but also sufficient repeatability to support trust in its outputs. We evaluate this requirement in a controlled, business-relevant benchmark built on an agent-based supply chain simulation. The task is to identify supplier-product combinations responsible for low quality and downstream sales loss by reasoning from indirect operational traces rather than from explicit labels. Fifteen model-variant configurations from eight model families were evaluated under four experimental conditions that varied data representation, prompt clarity, and signal strength, with five trajectories per condition. Outputs were scored against deterministic ground truth using the Jaccard index and assessed through a framework that combines mean score (ms), coefficient of variation (CV), exploratory cross-condition significance tests, and Business utility, a risk-adjusted metric that we propose to summarise quality and repeatability in a single operational measure. The results show that most configurations are not reliable enough for autonomous EDA use, even when their average scores appear acceptable. GPT-5.4 with extra-high reasoning effort achieved the strongest overall profile, with an experiment-averaged ms of 0.8748 and an experiment-averaged Business utility of 0.6952, while the next-best configurations lost substantially more utility after variability discounting. Our findings suggest that evaluation of EDA agents should treat average quality, repeatability, and condition sensitivity as complementary dimensions of operational trustworthiness.

Virtual Cell Modeling (VCM) requires models that not only predict perturbation responses, but also support targeted revision when predictions fail. Current LLM-assisted modeling workflows face a refinement-routing problem: prediction discrepancies are observed through executable implementations, but the relevant revision may involve the modeling assumption, representation design, implementation, or task constraint. Without structured feedback propagation across these levels, iterative refinement may repair code while failing to revise the assumption responsible for the discrepancy. We propose CellScientist, a dual-space hierarchical framework that couples a high-level hypothesis space with a low-level executable implementation space. CellScientist represents modeling decisions as structured states, realizes them as admissible programs under task and interface constraints, and routes execution discrepancies back to targeted hypothesis or implementation updates. This enables a closed Hypothesis -> Implementation -> Hypothesis loop where failures become structured signals for model refinement rather than debugging events. Across morphology and transcriptomic benchmarks, with additional single-cell perturbation evaluations, the final executable models selected by CellScientist improve over reference baselines under fixed split and evaluation protocols, while the workflow produces auditable refinement traces.

Metaphor is pervasive in everyday language, yet token-level computational identification of metaphor-related words in Chinese under the MIPVU framework remains under-explored relative to English. This paper presents a reproducible multi-architecture baseline for token-level metaphor identification on the PSU Chinese Metaphor Corpus (PSU CMC), the only widely available MIPVU-annotated Chinese corpus. We systematically compare three model families: (i) encoder fine-tuning with Chinese RoBERTa-wwm-ext-large; (ii) MelBERT adapted to Chinese using a newly constructed basic-meaning resource derived from the Modern Chinese Dictionary, 7th edition (MCD7), comprising 74,823 entries with 71.51% PSU CMC vocabulary coverage; and (iii) Qwen3.5-9B fine-tuned with QLoRA as an instruction-tuned generative baseline. Across five fixed seeds, MelBERT MIP-only achieves the strongest performance at 0.7281 +/- 0.0050 test positive F1, marginally above MelBERT Full (0.7270 +/- 0.0069) and clearly above plain RoBERTa (0.7142 +/- 0.0121). The Qwen QLoRA generative configuration trails encoder baselines by approximately 11 F1 points (0.6157 +/- 0.0113). Three findings merit attention: (1) the SPV channel of MelBERT does not contribute reliable positive signal in Chinese, consistent with the dominance of conventional metaphor; (2) the Qwen-encoder gap is concentrated in recall, reflecting the discrete-commitment limitation of generative output; (3) several Qwen task formulations fail due to format design rather than model capacity. We release all split manifests, per-seed outputs, the MCD7 basic-meaning embedding pipeline, and training scripts to serve as a common reference for future Chinese metaphor identification research.

Research artifacts are widely shared to support reproducibility, and artifact evaluation (AE) has become common at many leading conferences. However, AE mainly checks whether artifacts work as claimed and can be reproduced. It does not aim at spotting or mitigitating potential security risks. Since these artifacts are publicly released and reused, they may unintentionally create opportunities for misuse and raise concerns about safe and responsible sharing. We study 1,388 research artifacts published between 2023 and 2025 at the top-4 security conferences, perform static analysis, and obtain 132,431 candidate security findings. We propose a taxonomy for context-aware security assessment and examine the findings to filter false positives and identify findings that represent plausible context-dependent security risks. We find that 44.80% of the reviewed findings are security-relevant. To support scalable analysis, we present SAFE (Security-Aware Framework for Artifact Evaluation), an autonomous framework that assesses tool-reported findings based on code semantics, execution context, and practical exploitability. SAFE achieves 94.40% accuracy and a 93.60% F1-score in distinguishing security-relevant from non-security findings, and 92.40% accuracy and an 81.10% F1-score in classifying security-risk types. Overall, our results show that context-aware security assessment is a practical complement to existing AE processes and can support safer and more responsible research artifact sharing. The source code for SAFE is available at: https://github.com/nanda-rani/SAFE

Large language model systems are increasingly deployed as agentic workflows that interleave reasoning, tool use, memory, and iterative refinement. These systems are effective at producing answers, but they often rely on implicit conversational state, making it difficult to preserve stable work products, isolate irrelevant updates, or propagate changes through intermediate artifacts. We introduce execution lineage: an execution model in which AI-native work is represented as a directed acyclic graph (DAG) of artifact-producing computations with explicit dependencies, stable intermediate boundaries, and identity-based replay. The goal is not to make the model a better one-shot writer, but to make evolving AI-generated work maintainable under change. We compare execution-lineage replay against loop-centric update baselines on two controlled policy-memo update tasks. In an unrelated-branch update, DAG replay preserved the final memo exactly in all runs, with zero churn and zero unrelated-branch contamination, while loop baselines regenerated the memo and frequently imported unrelated context. In an intermediate-artifact edit, all systems reflected the new constraint in the final memo, but only DAG replay achieved perfect upstream preservation, downstream propagation, unaffected-artifact preservation, and cross-artifact consistency. These results show that final answer quality and maintained-state quality are distinct. Strong loop baselines can remain competitive at producing polished final outputs when the task is a bounded synthesis/update problem and all current sources fit in context, but immediate task success can mask partial state inconsistency that may compound over future revisions. Execution lineage provides stronger guarantees about what should change, what should remain stable, and how work evolves across revisions.

Reproducing and comparing deep research agents today is hard: the same backbone evaluated on the same benchmark can report different accuracies across papers because the harness and tool registry differ, and integrating a new model into a comparable evaluation surface costs weeks of model-specific engineering. These are symptoms of a broader reproducibility problem in deep research agent research. Here, we introduce BioMedArena, an open-source toolkit that addresses this reproducibility gap and provides an arena for comparing deep research agents under a shared evaluation environment. BioMedArena decouples six layers of biomedical agent evaluation -- benchmark loading, tool exposure, tool selection, harness mode, context management, and scoring -- and exposes 166 biomedical benchmarks and 75 biomedical tools across 9 functional families. Adding a new model, benchmark, or tool can be accomplished with a few-line provider adapter. Beyond evaluation infrastructure, BioMedArena ships a library of high-quality reference components: 6 agent harnesses (including our proposed Mutual-Evolve) and 6 context-management strategies, any of which can be equipped on any backbone. Equipping these components substantially improves all 12 backbones; on each of 8 representative biomedical benchmarks, the best equipped backbone surpasses prior state-of-the-art (SOTA), by 15.01 percentage points on average. The toolkit, configurations, and per-task traces are available at https://github.com/AI-in-Health/BioMedArena.

Frontier AI safety claims - published assertions that a highly capable general-purpose model is below a threshold of concern, adequately mitigated, or suitable for release - increasingly shape model deployment, governance, and public trust. Yet the artefacts needed to evaluate them are routinely withheld, producing an evidential inversion: the most consequential claims in AI safety are often the least reproducible. This position paper argues that NeurIPS should require reproducibility standards for papers making such claims, treating non-reproducibility not as a transparency preference but as an evaluation-methodology failure. The 2026 International AI Safety Report [Bengio et al., 2026] concludes that reliable pre-deployment safety testing has become harder to conduct and that models now distinguish test from deployment contexts; the 2025 Foundation Model Transparency Index [Wan et al., 2025] reports a sector-average transparency score of 40/100 with no major developer adequately disclosing train-test overlap; contemporaneous measurement-theory work shows that attack-success-rate comparisons across systems are often founded on low-validity measurements [Chouldechova et al., 2025]. We propose a three-tier disclosure framework, distinguishing public, controlled, and claim-restricted disclosure, paired with a mandatory claim inventory, scope statements, and a phased implementation path with graduated sanctions. The framework treats secrecy and openness as endpoints of a spectrum, with controlled review (via a federated colloquium of qualified secure-review hosts) covering claims whose artefacts cannot be released publicly, and right-scaling claims whose artefacts cannot be reviewed even confidentially. The standard the community applies to its most consequential claims should be at least as high as the standard it applies to its least.

Reservoir characterization workflows increasingly rely on image-based and machine-learning/deep learning or even generative AI approaches, but openly available geological image datasets suitable for reproducible benchmarking remain limited. Here we describe a high-resolution dataset of reservoir-property image slices derived from the Groningen static geological model. The dataset contains aligned two-dimensional PNG images representing facies, porosity, permeability, and water saturation, generated from three-dimensional reservoir grids and prepared for downstream visualization, segmentation, and image-to-image translation tasks. In addition to the deposited original image corpus, we provide an archived software workflow for reproducing augmentation, mask generation, paired-image construction, and example baseline experiments. The resource is designed to support benchmarking of geological image analysis methods and the study of cross-domain relationships among reservoir properties. By separating the fixed image dataset from the reproducible processing workflow, this work provides a transparent foundation for reuse in geoscience, reservoir modeling, and machine-learning applications.

Recent advances in de novo protein binder design have enabled increasing experimental validation, yet reported in silico metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We introduce ProtDBench, a standardized and throughput-aware evaluation framework for protein binder design. ProtDBench defines unified benchmark tasks, evaluation protocols, and success criteria, enabling systematic analysis of how evaluation design influences observed performance. Using a large wet-lab annotated dataset, we analyze commonly used structure prediction models as evaluation verifiers, revealing substantial verifier-dependent bias and limited agreement under identical filtering protocols. We then benchmark representative open-source generative binder design methods across ten diverse protein targets under a fixed evaluation protocol. Beyond per-sequence success rates, ProtDBench incorporates throughput-aware metrics based on a fixed 24-hour budget, as well as cluster-level success criteria to account for structural diversity. Together, these results expose systematic differences induced by filtering rules, success definitions, and throughput-aware evaluation between computational efficiency, success rate, and structural diversity. Overall, ProtDBench provides a fair and reproducible evaluation pipeline that supports systematic and controlled comparison of protein binder design methods under realistic evaluation settings.

Scientific peer review increasingly struggles to assess reproducibility at the scale and complexity of modern research output. Evaluating reproducibility requires reconstructing experimental dependencies, methodological choices, data flows, and result-generating procedures, which often exceeds what human reviewers can provide. Agentic Reproducibility Assessment (ARA) formalizes reproducibility assessment as a structured reasoning task over scientific documents. Given a paper, ARA extracts a directed workflow graph linking sources, methods, experiments, and outputs, then evaluates its reconstructability using structural and content-based scores for reproducibility assessments. Experiments on 213 ReScience C articles - the largest cross-domain benchmark of human-validated computational reproducibility studies considered to date - demonstrate ARA's generalizability and consistent workflow reconstruction and assessment across LLMs, model temperatures, and scientific domains. ARA achieves ~61% accuracy on three benchmarks, and the highest accuracy reported on ReproBench (60.71% vs. 36.84%) and GoldStandardDB (61.68% vs. 43.56%), highlighting its potential to complement human review at scale and enabling next-generation peer review. Code and Data available: https://github.com/AndresLaverdeMarin/agentic_reproducibility_assessment.

Automated research agents increasingly generate code, retrieve literature, and draft scientific artifacts, but they often fail to verify whether generated experiments execute correctly or whether cited sources support generated claims. We present AutoResearch, an execution-grounded multi-agent framework for reliable research workflow automation. AutoResearch couples sandboxed Python/PyTorch execution, iterative code repair, citation verification, claim-support auditing, decision control, and structured \LaTeX{} artifact generation. The system treats runtime errors, citation-verification failures, and review-agent feedback as practical filtering signals for generated research artifacts. In controlled evaluations on HumanEval, MBPP, a SciCode subset, citation-validation tasks, claim-support auditing, and small end-to-end workflow stress tests, AutoResearch improves execution success, citation validity, local claim support, and workflow completion relative to directly comparable baselines. Code-oriented agents are reported separately as partial comparisons. AutoResearch is intended as a reliability-oriented research assistant, not as a fully autonomous scientist or a standalone manuscript-quality benchmark. Source Code: https://github.com/raja21068/AutoResearch