Reproducibility

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

High annotation reproducibility does not necessarily imply that an LLM-inferred measure captures the construct it is intended to measure. We test this distinction using a dataset from the European Commission's AI Act consultation, linking structured survey responses to free-text consultation submissions from the same stakeholders. LLM annotations of consultation submissions are highly reproducible (intraclass correlations > 0.99), yet show limited convergence with survey-reported measures of the nominal construct they were intended to approximate. Divergence between survey-and LLM-inferred text-based measures varies systematically across stakeholder groups: business associations express greater concern about AI risks in text-based consultations than in survey responses ({g} = +1.0), whereas public authorities and several nonbusiness groups show smaller or negative divergences. Divergences between scores suggest positive spatial autocorrelation across European countries (Moran's I = 0.347, p = 0.036), indicating that stakeholders from neighboring countries tend toward more similar text-based stances towards AI safety concerns. Despite divergence, survey-reported concerns remain strongly associated with support for explainability across all divergence levels. These results demonstrate that LLM annotation reproducibility can coexist with poor construct correspondence and motivate validation procedures that distinguish reproducibility, construct validity, and communication context variation when LLMs are used as measurement instruments.

Text-to-music (TTM) systems are increasingly used to generate musical audio from natural-language descriptions. Robust evaluation is therefore essential, yet reliable performance comparison remains challenging. This difficulty stems from differences in system architecture, supported conditioning information, and access mode, as well as heterogeneous and fragmented metrics that cannot be applied uniformly across systems. To address these challenges, we introduce TTM-Bench, a framework that defines a common protocol for systematic, reproducible performance benchmarking of contemporary TTM systems. It evaluates performance along two dimensions: musical-content alignment, quantified by interpretable semantic, genre, and musical-descriptor agreement scores against a common musical specification and summarized by an aggregate score; and computational efficiency, characterized by generation latency and real-time factor, alongside resource use for local models and cost for hosted services. We demonstrate the framework through a preliminary comparative case study, illustrating the complementary evidence captured by these dimensions. The results show that higher musical-content alignment does not systematically coincide with lower computational demands, highlighting the importance of assessing TTM performance through distinct, interpretable measures rather than a reductive overall indicator.

Open-source language models have a reproducibility problem. Despite releasing weights, training data, and recipes, none of them are provably reproducible due to the non-associativity of floating-point arithmetic. Deep learning frameworks often offer a deterministic execution mode, allowing reproducible operations on the same machines. Unfortunately, this determinism does not carry across hardware such that a user can verify that a released checkpoint was actually produced using the declared training recipe. This leaves room for undisclosed data, injected biases, or backdoors that existing techniques such as proof-of-learning or proof-of-training-data cannot rule out. We introduce a new tier of model transparency, fully auditable, in which every operation on every data sample during training is independently reproducible on heterogeneous commodity hardware with bitwise certainty. By imposing a definite order on the sources of training nondeterminism, GPU kernel reductions, data batch ordering across a data-parallel cluster, and inter/intra-node collective communication, we make it possible to replay any individual step of a large, distributed training run on a single piece of commodity hardware and check it against the published trajectory. Because replaying an entire run on one machine is infeasible, we support this with a collective verification scheme in which many independent auditors each certify individual steps, together covering the whole run. We release Open-1B, a model trained under this regime, together with its full pretraining dataset, every intermediate checkpoint, the training codebase, and the audit harness needed to reproduce and verify any step of its training.

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

A shopping conversation has many routes to the same cart, and a task-success rate reduces all of them to one score. We build a deterministic and reproducible e-commerce environment that precommits each trial's customer and trajectory parameters, including the persona, difficulty, target cart, and an item reveal schedule. A simulated consumer attempts to buy a target cart from the environment with assistance from the evaluated model. The environment guides the simulator's actions and records every assistant action alongside the environment state at that point. After the trial, these records allow the evaluator to assess individual parts of the conversation against the retained evidence. For example, the evaluator penalizes a search for failing to surface a target product only when the customer has already mentioned that product. We further use this evidence to apply different penalties to tool calls depending on how the assistant's actions compare with an expected tool-call set. Our environment also interacts with the simulator bidirectionally, reading its output to stop the trial when the simulator determines that the customer has become too frustrated and injecting directives in real time that specify when to explore, defer buying an item, or recall a previous exchange. This interaction creates an open-ended and verifiable simulation. Across eight open-weight agents from 20B to 35B parameters, with 160 trials per agent and 44 metrics, the resulting capability profiles distinguish under-action, over-purchase, unsupported product attributes, and poor search, all of which terminal success obscures.

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

Membership inference attacks (MIAs) are the standard tool for auditing the privacy risks of machine learning models. Given a query point, an MIA aims to determine whether that point was used to train the target model. In practice, such inference must rely on the statistical signals exposed by the model's outputs, such as confidence scores, logits, and intermediate feature representations. However, existing methods often fail to efficiently summarize and combine these statistical signals. To address this limitation, we propose Pairwise Likelihood MIA (PL-MIA), a unified method that combines a Gaussian likelihood-ratio (GLR) statistic with population calibration and the Cauchy combination test. We characterize theoretically how the GLR retains variance-contraction signals and establish conditions under which population calibration and Cauchy combination improve attack power. We obtain $p$-values from pairwise comparisons between the query point and reference points not used for training, and aggregate these continuous signals using the Cauchy combination test. This preserves the evidence strength that is discarded when each pairwise comparison is reduced to a binary vote. Extensive experiments demonstrate that PL-MIA outperforms strong baselines, improving the true positive rate (TPR) by over 25% in the critical low-false-positive regime, corroborating our theoretical findings. These results demonstrate how statistical principles can turn noisy model outputs into more powerful, calibrated, and reproducible evidence for membership privacy auditing.

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

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

Scientific figures are the interface through which research claims are inspected and reused, but final published panels rarely expose the data or plotting code that produced them. Recovering this hidden provenance from pixels is therefore underdetermined. We introduce SciFigure2Code, an AI-reconstructed benchmark that instead evaluates presentation recovery: generating editable Python programs that preserve how a scientific panel is arranged and read. Role-specialized Codex agents generate, execute, visually refine, and audit silver-standard presentation programs that capture geometry, visual hierarchy, encodings, annotations, and typography without claiming to recover original measurements or author source code. This reconstruction-and-audit protocol turns final published panels into auditable reference packages; the resulting resource contains 6,740 reviewed panels and SciFigureBench, a balanced 337-panel test set across 31 chart subtypes, five domains, and three complexity levels. Across 14 zero-shot models in image-only and caption-assisted settings, execution, multi-component layouts, axes, legends, and scientific labels remain weak. Claude Opus 4.7 achieves the highest image-only Overall score, Claude Opus 4.6 leads caption-assisted reconstruction, and two-stage plan-then-code prompting improves Overall for all four tested models. SciFigure2Code provides an auditable testbed for agents that construct editable, visually faithful scientific figure presentations.

Mobile GUI agents can execute tasks from natural-language instructions, but their evaluation remains difficult to make both realistic and reproducible. Existing benchmarks typically trade off these goals: simplified apps lack real-world mobile complexity, whereas live commercial apps introduce uncontrolled variation from recommendations, advertisements, accounts, and changing content. We propose AppSim-Bench, which addresses this trade-off through controllable simulated apps that preserve task-relevant interaction logic while supporting deterministic evaluation. Built through a coding-agent-assisted and human-verified workflow, it contains 557 tasks across 17 high-frequency Chinese and English apps. Its controllable backend data and outcome-based verification remove major sources of environmental stochasticity, enabling reproducible cross-model comparison. Evaluating 19 GUI agents, spanning general-purpose and GUI-specialized systems, we find that autonomous mobile execution remains far from solved. The best model completes only 50.27% of tasks, and 28.55% of tasks are not solved by any agent. Further analysis shows that failures concentrate in longer workflows, numerical reasoning tasks, and inefficient trajectories marked by high action overhead and budget exhaustion. Our project is available at https://github.com/Acrab-Agentic-Labs/AppSim.

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

For scientific progress, we need benchmarks that test the limits of state-of-the-art models, and evaluation methods that inform us about failure cases. As models get stronger, standard benchmarks for machine translation are approaching saturation. Further, automatic translation metrics are unreliable, vulnerable to reward-hacking, and provide unactionable assessments. Even gold human evaluation is not problem-free, because it often lacks reproducibility, objectivity, and scalability. Overall, this prevents us from tracking objective progress in the field and identifying pathways for improvement. We introduce the Last Translation Benchmark, a collection of human-authored and peer-reviewed examples (texts, images, audio, videos) that break leading machine translation models. We also present a new evaluation approach: each example comes with handcrafted verification rules describing concrete failure cases on that example, therefore allowing reliable and actionable future evaluation. The Last Translation Benchmark is a live dataset that accepts ongoing contributions. The latest version is LTBv1, containing accepted contributions prior to September 1st 2026, with future releases planned as new data is continuously collected.

Dust in agriculture presents a significant challenge for autonomous agricultural machinery. Dust can impair the performance of sensors and algorithms. This work, therefore, presents a concept for a proving ground consisting of an indoor and outdoor area. The indoor area comprises a laboratory test bench where dust circulates in a closed system and a test hall where life-size objects can be placed. The outdoor area features dedicated test setups that enable reproducible data to be recorded with and without dust during real-world agriculture work. The proving ground and the setups are visualized in 3D.

Mobile robotic platforms offer a flexible alternative to fixed manipulators for non-destructive evaluation (NDE) of large aerospace structures, but their base-positioning accuracy and how that accuracy should inform deployment have not been assessed under a common, externally referenced protocol. This work presents a laser tracker-based evaluation workflow (ground truth approximately 6 micrometers) that measures the static and segmented trajectory positioning accuracy of five commercial mobile platforms (KUKA KMP-1500, KUKA KMR, MiR250, Boston Dynamics Spot, Clearpath Husky) under a common protocol. A coupled multi-corner calibration recovers the laser-to-robot transformation and reflector offsets; ordinary least squares over all poses is used, with robust estimation retained only as a blunder check. Static positioning accuracy ranged from a median of 8.2 mm (KMP-1500) to 63.5 mm (Spot), with the wheel-odometry-only Husky uncalibratable. Dynamic path following was characterised by cross-track error; the component was insensitive to temporal alignment, which ranged from 6.9 mm (KMP-1500) to 112.1 mm (Spot). Both accuracy and calibratability tracked localisation capability, from the newest LiDAR SLAM platform to map-free visual odometry. No configuration meets the 0.2 to 1.0 mm aerospace NDE tolerance from the base alone; the results are framed as a design input that sizes the supplementary sensing each platform requires: roughly one order of magnitude for the best platform and nearly two for the worst, providing a reproducible basis for platform selection rather than a feasibility claim.

LLM-based forecasting systems have improved on real-world tasks such as financial markets and sports outcomes, largely through stronger search and tool use. Many systems still ask an LLM to read all collected evidence together and produce the final forecast. We call this design Monolithic Prediction. It can obscure how individual evidence items affect the result and collapse uncertainty across competing outcomes. We propose LEAP (Likelihood Elicitation and Aggregation for Probabilistic forecasting), which reorganizes how collected evidence is used in the prediction stage. LEAP examines each evidence item separately and elicits likelihood parameters that describe its implications for the target. An explicit prior and a deterministic probabilistic model then combine these likelihoods into a posterior distribution. This procedure supports continuous, single-choice, and multi-choice forecasts while preserving reproducible evidence contributions. We build a benchmark covering forecasting, information-seeking, and browsing tasks, and evaluate LEAP on our own agent loop and several agent CLI frameworks. Given the same evidence, LEAP improves most prediction and calibration metrics across models and remains stronger under controlled comparisons of prior access, inference budget, and aggregation.

MutMem V1 introduced retention-preserving, cryptographically authorized mutation for persistent agent memory but did not provide a complete portable verification contract or clean-install reproduction path. MutMem V2 closes that publication gap without introducing a second memory engine. It specifies exact canonical bytes, domain-separated object and bundle commitments, mandatory recall-evidence membership and ordering, external trust anchors, identity epochs, revocation, authorization, request receipts, ordered disclosure, and three mutation terminal types. The released protocol contains 18 versioned object schemas, 39 recall vectors, 15 mutation vectors, and 37 closed recall failure reasons. Independent Node and Python implementations agree on verdict and primary reason for all 72 structural and cryptographic terminals; a production-conformance corpus agrees on 42/42 cases across 28 required classes. A clean Node v26.8.1 installation reaches first-boot, restart, and scheduler readiness with no experimental memories. A separately scoped 120-unit Canary experiment supports only explicit-marker traversal. Every public table regenerates from a self-hashed aggregate, and an independent verifier reconstructs the statistics and claim boundaries. Historical V1 empirical results remain historical. MutMem V2 supports claims about portable integrity, authorization, traceability, conformance, and reproducibility under stated assumptions; it does not establish semantic truth, universal robustness, or independent replication.

As agentic systems become compound systems, increasingly important decisions move above task execution itself: when should a higher-level controller preserve the strategy guiding another process, and when should it revise it? We study this meta-level control problem in a hierarchical latent reasoner whose manager can retain or replace a commitment governing lower-level computation. Across three precommitted training seeds, learned revision timing produces qualitatively different policies, ranging from an almost deterministic early clock to substantially more state conditioned schedule distributions, yet none outperforms the best forced timing policy evaluated on the same frozen checkpoint. This separates state dependence from decision value: a controller can vary its actions with internal state without turning that variation into a reproducible task-performance benefit. A deeper intervention study on the original checkpoint shows that timing itself is consequential and order-sensitive, while exhaustive enumeration reveals that a strong fixed schedule captures most of the measurable value available from timing at this decision budget. Counterfactual PERSIST/REPLAN diagnostics further show why score-level evidence can be misleading when predictability is dominated by decision position rather than within-position discrimination. Together, these results argue that learned meta-level control should be evaluated along three separate axes: whether its score depends on state, whether that dependence changes realized behavior, and whether those changes capture outcome value beyond a strong non-adaptive policy.

Passive fingerprints (intrinsic traces naturally left by generators) have been shown to enable attribution in speech deepfake detection, yet their persistence, reproducibility, and content-independence remain unverified. Moreover, no prior work distinguishes perceptible from imperceptible fingerprints, although the two have very different implications for attribution reliability. Perceptible fingerprints, such as emotional expression, are shaped by perceptual quality objectives and may change across model updates, whereas imperceptible fingerprints are not explicitly optimised by current training objectives and are rarely considered in existing dataset design or training strategies, as they have limited influence on downstream applications. We therefore propose a Perceptible-Imperceptible Passive-fingerprint Diagnostic Protocol (PIPDP) to define and separately analyze these two fingerprint types. PIPDP comprises three complementary analyses: multi-evidence fingerprint verification through residual-energy, reproducibility, and saliency analyses, perceptually transparent perturbations preserving audio quality, and prompt-driven emotion change that modifies perceptible fingerprints without model retraining. Experiments across ten speech generators and three attribution detectors show that imperceptible fingerprints provide persistent attribution cues. Perceptually transparent perturbations reduce attribution accuracy by up to 48.2% on HiggsAudioV3, whereas emotion-driven changes leave attribution largely unchanged, with only about a 1.0% accuracy variation across emotions on CosyVoice2 using w2v-bert-MLP. These results suggest that imperceptible fingerprints are more reliable for trustworthy attribution.

Humans play a vital role at every stage of AI development, from data collection and curation to model development and evaluation. However, humans often disagree with each other and sometimes with themselves over time. It is essential to take disagreement into account when building human-centered AI systems, especially in domains where it is prevalent, such as AI safety, content moderation, or sentiment analysis. Disagreement often arises from subjective human opinion and can vary with one's identity, beliefs, and social environment. Despite this, current LLM evaluation approaches frequently rely on aggregating labels (often via plurality voting) to represent consensus, thereby obscuring minority perspectives. By failing to account for human disagreement, these evaluation methods contribute to the reproducibility crisis in AI. Human feedback is also crucial for ensuring that AI systems align with human values. For these systems to be trustworthy, it is critical to ensure that they reflect diverse human values and perspectives. In this thesis proposal, we present a human-centered and perspective-aware framework for reproducible ML evaluation and AI alignment.

Background and Objective: Quality control is a prerequisite for whole-slide image analysis, yet the benchmarks on which quality-control methods are compared share four properties that make their reported differences hard to interpret: few independent slides, annotation concentrated in a minority of them, pooled ratio metrics with no closed-form standard error, and a single inherited train/test partition. We propose a reliability protocol for such benchmarks. Methods: The protocol quantifies four sources of variability - test-set sampling, training stochasticity, partition composition, and undocumented preprocessing - a claim is reportable only if it survives all four; three of the four cost minutes of compute. We apply it to an independent reconstruction of a published diffusion-based artifact detector, evaluated on the original 24-slide partition and against a supervised baseline. Results: The method's central mechanism reproduces: the auxiliary contrastive term improves pooled F1 from 0.673 to 0.688 and replicates under a second seed (+0.0156, p = 0.031; +0.0190, p = 0.005), although it acts on pen marking rather than the artifact types cited to motivate it. Its comparative claims do not: differences between design variants, and against the supervised baseline, fall inside the uncertainty of the evaluation. Four of 24 slides carry 70% of scored annotated pixels, giving an effective sample size of 6.2, and the inherited partition sits at the 7th percentile. An unreported tissue-restriction step excludes 41.4% of out-of-focus annotation against 2.6% of air bubble; such a gate is confounded with blur by construction. Conclusions: Small-cohort benchmarks support far weaker conclusions than current reporting implies. The four checks are cheap enough to accompany any evaluation on such a resource and separate reproducible effects from differences the evaluation cannot resolve.

Natural-language tasks can elicit different verdicts from protocol-following evaluators that receive the same declared information. We study aggregate disambiguation systems (ADSs). Given a task and a candidate solution, each evaluator casts a binary vote on whether the solution should be accepted, and the system aggregates the votes of a finite panel. The target is protocol reproducibility relative to an explicitly declared evaluator reference, not semantic truth. We separate fixed finite censuses, probabilistic evaluator populations, and growing-census limits, since their endpoint laws and guarantees are not interchangeable. In the population setting, we use finite samples to estimate how often a finite panel reaches the same decision as the declared evaluator population. We provide a lower confidence bound on the fraction of candidate solutions for which the disagreement probability is at most a chosen tolerance. The calculation accounts separately for sampling candidate solutions and sampling evaluators. The construction permits arbitrary dependence among columns induced by shared evaluator rows and uses exact binomial intervals at the evaluator layer and an exact one-sided binomial inversion at the generator layer. Simulations check the implementation against known population coverages and expose power limitations.

We characterise the measurement error of a free- hand consumer structured-light scanner used to derive three- dimensional geometric wound descriptors. Rigid wound-care phantoms cannot change, so every difference between repeat scans of one site is measurement error; all repeats come from a single scanner unit, nine sites and 23 scans, so this charac- terises one instrument. The 95 percent repeatability limit for reconstructed surface area is a factor of 4.8, with a confidence interval from 3.0 to 7.0, so rescanning an unchanged site can shift the reading from a 79 percent decrease to a 377 percent increase. Forty-four of 45 descriptors fall below an intraclass correlation of 0.50, and none of 248 descriptor and pipeline combinations reaches 0.75. An error budget formed by holding the analy- sis region fixed, leaving sensor and reconstruction untouched, bounds the share of variance attributable to how much surface the operator captured at 75 percent for surface area, 91 percent for hull area and 95 percent for bounding-box diagonal; only hull volume is majority instrumental, at 48 percent, so a better sensor would buy little. No wound is delineated anywhere in the chain, so the comparison against the four-week area reduction used clinically to predict healing, a ratio near 2.1, is a lower bound on the noise an unsegmented pipeline must overcome, not a measurement of wound-area reproducibility. Standardising the analysis region cuts the limit to 2.13, meeting that ratio rather than clearing it. Statistical outlier removal imposes a measured systematic area deficit near 11 percent.

Despite rapid advances in MIS, fair and reproducible comparisons of segmentation models remain challenging due to heterogeneous datasets, inconsistent evaluation protocols, and rapidly evolving architectures. In particular, comparisons often implicitly assume that model rankings are invariant to data partitioning, preprocessing, metric aggregation, uncertainty estimation, and computational constraints. The lack of extensible and unified evaluation frameworks further limits systematic investigation of new models, datasets, and training paradigms. We present MEDSEGBENCHMARKER (MSB), a configuration-driven framework for controlled benchmarking of 2D MIS. It integrates duplicate and near-duplicate image detection, group-aware data splitting, YAML study specifications, resumable training, hyperparameter optimization, cross-validation, and checkpoint-based evaluation. Rather than retaining only aggregate performance measures, MSB exports sample- and class-level pixel counts and predictions together with the evaluation context. These elementary artifacts enable post-hoc analyses without repeated inference. We demonstrate MSB in a case study involving three heterogeneous 2D datasets and multiple MIS and general-purpose vision models evaluated at 256- and 512-pixel input resolutions. Reaggregation of identical predictions changes the top-ranked architecture in three of six dataset-resolution settings, despite high rank correlations between aggregation strategies. Increasing input resolution produces model- and dataset-dependent performance gains and losses that must be considered alongside empirically measured inference complexity. These results show that seemingly minor choices in evaluation and experimental setup can affect benchmark conclusions. MSB, available at GitHub, provides a practical and extensible basis for making benchmark conditions and evaluation choices explicit and reproducible.

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

Organizations decide whom to treat under a budget and want to know what a targeting rule would have earned before deploying it. Off-policy evaluation promises this from logged data, but the deployable rule is a deterministic top-k policy: it removes all averaging over actions, so weak overlap hits the estimate directly. We benchmark six estimators across five datasets and two known-effect sweeps, and validate the mechanisms against a non-simulated paired reference. First, weak overlap is governed by logger-target action alignment, not by logging sharpness alone: what governs support is the logger's probability of the target's actions. Sharpening a logger built from the target's own score barely moves overlap over the tested range; action-level disagreement collapses it. Effective sample size ranks this risk across logging environments, but is weak at ranking candidates within the single log a practitioner holds, and its cut point does not transfer. Second, the optimizer's curse is not fixed by cross-fitting the outcome nuisance. When the rule is fit on the data used to evaluate it, cross-fitting the nuisance alone leaves the reuse bias in place and makes it worse. Honest policy-level splitting avoids the reuse by targeting the learning procedure's value -- a change of estimand, not a de-biasing of the full-sample policy. Third, propensity-estimation error is the largest degradation we measure: an out-of-fold estimate hurts IPS more than any other stress we apply, leaves doubly-robust estimation almost unchanged, and can invert the overlap diagnostic itself. Logging is synthesized and propensities floored at 0.02, so every failure occurs with bounded weights; the floor also reduces the two tuned hybrids to their untuned parents, leaving four practically distinct estimators, and all exact-value surfaces are synthetic or semi-synthetic. We release the benchmark; public data only.

Turning a research idea into a complete paper requires more than text generation: the system must retrieve literature, design and execute experiments, revise claims according to evidence, produce publication-ready figures, and maintain consistency across a long generation process. We present Spark-to-Paper, an end-to-end research paper generation system implemented as thirteen composable skills inside an existing coding assistant, without requiring a separate agent platform or orchestration service. Spark-to-Paper separates model-based judgment from deterministic operations that can be directly executed and checked. It further separates experiment planning from reporting, so that required evidence is specified before results are observed and manuscript claims are revised according to measured outcomes. To improve reliability over long research trajectories, the system combines deterministic integrity checks with self-critique and bounds a failure mode we call the Self-Refutation Loop, in which repeated experiments continue to reject the original research objective. Spark-to-Paper also produces editable vector figures through programmatic plotting for experimental results and code-based reconstruction for generated method diagrams. Across eight controlled research topics, Spark-to-Paper achieves 99.5% citation validity and 96.4% figure editability. A controlled ablation increases fabrication detection from 14% for a single-pass draft to 92% with the full integrity and review stack, while adversarial review achieves 74% precision. The full system uses 11.9M tokens, costs $8.1 per manuscript, and requires 3.2 hours on average. These results show that end-to-end research paper generation can be implemented as a lightweight, composable workflow inside existing coding assistants while keeping experimental evidence central to how claims are accepted, revised, or abandoned.

Quantitative language research often depends on long chains of computational steps, yet the logic connecting those steps usually remains buried in scripts. This makes analyses harder to inspect, share, and revise than they need to be. Focusing on quantitative syntax, we present QLWF, a visual workflow platform that turns natural-language research descriptions into executable workflows through an AI assisted five-stage pipeline. In this setting, reification makes the research logic visible as a workflow, while formalization gives that workflow deterministic execution semantics. The language model is used only during construction. Execution is handled by a fixed node library and engine, which keeps the resulting workflows reproducible. QLWF also supports incremental refinement, so saved workflows can be revised by changing only the parts that need to change rather than being rebuilt from scratch. To evaluate the approach, we build a 64-task benchmark called QL-Bench from the quantitative-syntax literature. Across three runs, QLWF produces structurally valid and executable workflows for every task and reaches a mean output-plausibility rate of 98.4%, well above the prompt-based baselines. On a separate 12-task lifecycle benchmark, this refinement process succeeds in every case and uses roughly one-third of the tokens required by full regeneration. The paper also releases the node library, benchmark, workflow templates, and platform as reusable resources for quantitative-syntax research.

In fair ranked link prediction, demographic parity ($Δ_\mathrm{DP}$) is a common fairness metric. Yet, Mattos et al. (2025) argue that it fails to detect exposure bias because it ignores where links appear in the ranking. In this study, we reproduce this claim by showing that $Δ_\mathrm{DP}$ can indicate aggregate parity even when some subgroup-pair links are systematically ranked lower than others. The proposed rank-aware Normalized Discounted KL-divergence (NDKL), however, does detect such disparities. We also reproduce the effectiveness of MORAL, a post-processing method that improves exposure-based fairness while maintaining competitive utility. Beyond reproduction, we assess robustness using synthetic homophily settings, categorical sensitive attributes, and additional fairness and utility metrics, including subgroup-pair-adapted Attention-Weighted Rank Fairness (AWRF). Overall, our results show that exposure-based metrics uncover biases hidden by $Δ_\mathrm{DP}$ and that MORAL reduces these biases with minimal utility loss across diverse settings and datasets. We release a corrected, reproducible implementation at https://github.com/Floris93100/reproducing-MORAL.

We introduce Sci-VBench, a comprehensive benchmark for evaluating knowledge- and reasoning-intensive video generation across scientific domains. It contains 1,253 expert-annotated examples spanning 60 subjects across four core disciplines: Natural Science, Healthcare, Humanities & Social Sciences, and Engineering. Each example requires models to generate temporally rich videos that demand scientific reasoning and knowledge-grounded synthesis, going beyond surface-level visual plausibility. We further establish a rubric-based evaluation protocol. Our analysis shows that, under this protocol, both non-expert human evaluators and MLLM-as-Judge systems can achieve relatively high agreement with expert judgments, supporting reproducible evaluation at scale. We benchmark 16 frontier proprietary and open-source models and find that, while automatic perceptual-quality scores cluster tightly across systems, performance on Prompt Grounding and Scientific and Causal Correctness varies substantially, with a pronounced proprietary-open-source gap. These findings show that advances in visual realism have not yet translated into reliable modeling of scientific and causal dynamics.

We present a reproducibility study of XFeat, a lightweight local feature extractor and matcher designed to identify corresponding points across images efficiently on resource-constrained hardware. We re-implement the architecture based on the paper and supplementary material, re-evaluate the authors' released checkpoint alongside our re-implementation, and conduct additional architectural ablations to examine design choices that were not fully justified in the original work. This distinction between re-evaluation and reproduction is important, as the paper, supplement, and public code differ in several implementation details, including the backbone layout, fusion block, and training losses. Empirically, our reproduced models closely match and, in some cases, outperform the re-evaluated original checkpoint on MegaDepth-1500 and ScanNet-1500, supporting the main claim that XFeat provides a strong accuracy-efficiency trade-off for standard image-matching benchmarks. Our ablations provide a more nuanced view of two architectural arguments from the original paper. In particular, the parallel keypoint branch is important for semi-dense matching, but its benefit is less pronounced than originally claimed, while the evidence for the specific placement of the single skip-connection remains inconclusive. Finally, we reproduce the original downstream evaluations and find close agreement for homography estimation, while Aachen visual localization remains below the reported results, even for the released checkpoint, suggesting sensitivity to underspecified evaluation details. We then extend the analysis to zero-shot out-of-distribution and cross-modal matching across retinal, thermal-visible, and multimodal remote-sensing imagery, where XFeat remains effective in some settings but degrades sharply under severe modality shifts.

GUI agents have advanced rapidly, producing a growing body of frameworks, benchmarks, and applications. However, this growth has outpaced the maturity of the field. GUI agents remain technically brittle, incompletely engineered, and insufficiently validated for sustained real-world use. They are evolving into closed-loop software systems. Within these systems, model reasoning is coupled with interface perception, execution feedback, recovery, and human oversight. This evolution calls for a software engineering perspective that remains largely absent from existing research. We address this gap by reviewing 336 GUI-agent papers from January 2018 to April 2026. Five research questions examine the research landscape, architectures, evaluation, software lifecycle concerns, and future opportunities. Our findings show that the field has expanded sharply since 2024, while mobile and web settings remain dominant. Architectures increasingly adopt modular perceive-reason-act loops, but recovery, human escalation, safety enforcement, and auditability remain underdeveloped. This architectural imbalance extends to evaluation. Evaluations are becoming more interactive, but they remain centered on task success and are difficult to compare across protocols. More broadly, existing studies provide limited support for testing beyond benchmarks and for maintaining agents after release. Observability, privacy engineering, and systematic human oversight are also underdeveloped. Together, these findings show that capability improvements alone cannot ensure deployment readiness. Future research should connect dependable execution with lifecycle-centered testing and reproducible evaluation. It should also integrate permission and privacy controls with cost-aware, human-centered governance. This integration is necessary to build dependable, maintainable, secure, and deployable GUI-agent systems.

Residential virtual power plants (VPPs) can provide grid flexibility by shifting household demand, but physical flexibility becomes dependable capacity only when residents authorize a plan and the promised response is delivered. Existing benchmarks evaluate control but omit event-specific authorization. We present EnergyBridge, a benchmark and agent framework connecting capacity reporting, household authorization, and physical execution. It combines region-specific EnergyPlus environments for Tianjin and Berlin with an LLM-based User Participation Simulator. Against 584 persona- and event-matched human role-play judgments, the LLM-based User Participation Simulator preserves method ordering with a 5.3-point mean absolute acceptance error. Across conventional controllers and agent baselines, EnergyBridge achieves the highest simulated authorization, lowest event-window energy, and the most reliable capacity commitment in both regions. We release human data and codes for reproducible human-centered grid-flexibility research: https://github.com/Agentic-Intelligence-Lab/EnergyBridge.

Khatri et al. (2026) [DOI: 10.1109/DSN-W70714.2026.00027] show that lightweight MLP probes on final-layer activations of a single 8B model (LLaMA-3.1-8B) detect harmful prompts at F1 competitive with guard models 1000x larger, using one probe per benchmark. We reproduce this pipeline end-to-end and extend it along two axes the original study leaves open. First, we test whether the result generalizes across other model architecture and scale by training identical probes on activations from models like Gemma-4-E4B, Mistral-7B-v0.3, and Qwen2-7B, using the three benchmarks (WildJailbreak, BeaverTails, AEGIS 2.0). Second, we test how much of the reported performance is affected by non-determinism during inference by repeating extraction under five random seeds and measuring the variance of F1 scores. Our results reproduce the original LLaMA model benchmarks within 0.37 percentage points of the original F1 scores (and within 0.2 points on BeaverTails). We find that the original MLP probe architecture extends to other model families with F1 scores within a point of the values reported for LLaMA-3.1-8B. Our experiments varying seed values reveal an interesting observation: final token latent vectors remained the same for all tested architectures irrespective of the seed values used.

Image-based profiling captures rich phenotypic signatures for drug discovery and functional genomics. Large public datasets like JUMP Cell Painting now provide millions of images for systematic study. However, JUMP alone occupies 115 TB, and fragmented evaluation practices make systematic comparisons of representation methods impractical for many researchers. Here we present Nahual, an open-source framework for reproducible model deployment, and JUMP-lite, a 92.0 GB subset of JUMP that is approximately 1,250-fold smaller, selected to cover genetic modalities and compound annotations and reduced via lossy JPEG XL compression. Using these resources, we benchmark five representation methods, including classical features (CellProfiler) and deep learning models (MorphEM, OpenPhenom, SubCell, DINOv2). Moderate compression broadly retains signal relative to uncompressed images. Standardized phenotypic activity and consistency metrics reveal meaningful performance differences across methods. Together, JUMP-lite and Nahual provide a foundation for accessible, reproducible benchmarking of image-based cell representations.

Giving an LLM judge more compute does not necessarily make it check more requirements. When one call must return many verdicts, some decisions become weakly grounded in the evidence, even when that call receives the same token or tool budget as a panel of separate calls. Across expert-graded research replications, legal work, and clinical-trial assessments, agreement with experts falls as the number of verdicts per call grows. We identify sharding as the intervention that mitigates this failure in model-based oversight. Sharding partitions the requirements into smaller groups, assigns each group to a separate call, and aggregates the verdicts. Against a single call with the panel's full budget, sharding improves agreement while holding the model, evidence, total budget, and per-decision budget fixed. Overall, we find that a sharded weaker judge can outperform a more capable holistic judge and match that judge even when the latter receives the panel's full budget. Additionally, we find that sharding exhibits robustness against adversaries. A best-of-N adversary can hold the underlying work fixed, vary only its presentation, and increase an overloaded judge's acceptance of genuinely unmet criteria severalfold. Wherever sharding reduces baseline error, it removes this adversarial advantage, keeping over-acceptance low even as the adversary's search widens. Sharding does not address attacks that persuade the judge separately on each criterion rather than exploiting overload. In that setting, we find that debate-style opposition on top of sharding withstands such adaptive re-optimization.

CheMLFlow is an open-source platform for building and executing end-to-end, high-throughput, and agentic workflows for scientific and technological applications. CheMLFlow targets a common bottleneck in scientific machine learning development, where researchers often need to assemble data acquisition, curation, representation, model training, validation, screening, interpretation, and reporting into a reproducible pipeline, even when their primary research contribution concerns only one stage. CheMLFlow provides modular workflow components, ready-to-run reference pipelines, standardized artifacts, and evaluation outputs that reduce orchestration overhead and support benchmarking across methods and datasets. The platform is designed to be extensible, reproducible, and automation friendly, with pluggable representations and models, deterministic splits, explicit run artifacts, batch execution, and report generation. As scientific software increasingly moves toward agent assisted experimentation, CheMLFlow's configuration driven workflows and structured outputs also provide a practical interface for coding agents to help users construct experiments, inspect results, and summarize findings under human supervision. This article describes the system architecture, core workflows, and benchmarks that reach literature performance for quantum mechanical, physicochemical and bioactivity property prediction, and use cases involving time series datasets demonstrating applications beyond molecular chemistry datasets.

Agentic code generation has shown promise in automating and accelerating software development by utilizing Large Language Models (LLMs) to generate, test, and deploy code. For engineers and scientists, such systems have the potential to accelerate the development of applied and scientific workflows while reducing barriers to entry in domains that have yet to fully realize their benefits. However, a key gap remains: existing coding agents primarily focus on code generation and do not address the entire workflow lifecycle, including deployment and sharing. As a result, users develop and stitch modules independently while managing deployment on their own. To address this gap, we propose CURATE - Composition, User-in-the-loop, Reuse, and Automated Task Execution - a novel human-in-the-loop multi-agent system that uses LLM agents to manage and develop composable workflows across their entire lifecycle. A key feature of the system is a catalog that allows for the storage and reuse of modules across workflows. Module catalogs provide a foundation that can be expanded to support FAIR principles by facilitating the sharing and reuse of curated modules and subgraphs. We demonstrate the feasibility of our system with an initial prototype using Claude Opus 4.8, comprising 6 experiments: reproducing and adapting 4 workflows derived from the SeBS-Flow benchmark suite, and automating the development and scaling of a workflow that leverages a complex mechanistic model in environmental engineering used to simulate anaerobic digestion.

Large language models can solve harder reasoning problems with more inference-time compute. The term "test-time scaling," however, covers several inference algorithms: extending deliberation along one trajectory, sampling completed candidates and aggregating them by voting or verification, and searching over partial states. These algorithms differ in statistical structure, compute requirements, and failure modes. Treating them as interchangeable under a scalar "budget," or reporting accuracy without specifying the inference protocol, makes results difficult to compare across studies. We study test-time scaling along three axes. First, we formalize it as budgeted inference over the implicit prefix tree of an autoregressive model and distinguish single-trajectory sequential scaling, leaf-level scaling with terminal reduction, and prefix-level scaling. Second, we treat the full inference system as the evaluated object and separate end-to-end performance from candidate-bank diagnostics. We introduce an evaluation profile whose coordinates and simple functionals recover or bound common repeated-sampling metrics, and require compute accounting and uncertainty estimates that match the protocol. Third, we distinguish exact replay from distributional reproducibility and state the requirements for each. We also organize open-weight reasoning models by model-side and interface mechanisms. Our empirical study covers broad knowledge, symbolic reasoning, and competition mathematics, and we publicly release 1,403,520 sampled model attempts. The project website is available at https://mohsenhariri.github.io/scorio/tts. The released datasets are Trace (https://huggingface.co/datasets/harimo/scorio-trace), Lite (https://huggingface.co/datasets/harimo/scorio-lite), Math (https://huggingface.co/buckets/harimo/scorio-math), and SuperGPQA (https://huggingface.co/buckets/harimo/scorio-gpqa).

Benchmarking the ability of AI scientists to generate novel ideas is notoriously difficult. Existing benchmarks in this field have made progress in evaluating scientific reasoning and research replication, but often rely on synthetic tasks or retrospective targets, which may be confounded by prior exposure. We hypothesize that complex, adversarial, fast-moving real-world domains where expert practitioners independently generate observable outputs can provide a practical solution to fill this gap and evaluate the capabilities needed for AI scientists, including reasoning, novelty, and hypothesis formulation. We instantiate this framework in two structurally different domains, Formula 1 (F1), where models ideate around car design concepts for the 2026 season, and real pre-season innovations provide a ground truth, and Magic: The Gathering (MTG), where models propose decks from a recently updated card pool and are evaluated against 19 Pro Tour (PT) decklists. Across both domains, models produce plausible outputs, but few align with real-world expert solutions. In F1, the best model, GPT-5.2 matched 10 of 40 real innovations with 166 ideas proposed across runs. In MTG, the best deck from Gemini 3 Flash recovered 5 of 7 new-set cards from the third-place PT deck, and across all 108 decks, the cards models selected most often were also the cards most widely adopted by PT decks (Spearman $ρ= 0.74$, $p = 0.0003$). These results suggest that a key capability gap for AI scientists is not idea generation, but filtering, prioritization, and coherent novelty.

Agent evaluation relies almost entirely on outcome metrics such as success rate, which capture whether an agent succeeds but not how consistently it behaves. We argue that behavioral consistency across tasks is a distinct and measurable property, and we introduce the Behavioral Consistency Metric (BCM) to quantify it. BCM trains a model to predict task success from behavioral features of agent execution traces, derives a per-trajectory feature-attribution vector, and measures the mean pairwise similarity of these vectors within an agent system. Across roughly 9,000 trajectories from six language model agents on software engineering tasks, our central finding is that cross-task and within-task consistency are distinct axes that can diverge: some systems are locally reproducible, behaving similarly on repeated attempts at one task, yet globally fragmented, with no stable strategy across different tasks, while others are consistent at both scales. Prior work measures only same-task reproducibility and so cannot observe this separation. We further find that consistency is not reducible to success rate, since systems with comparable success can differ sharply in consistency, and that the frontier-versus-open-source consistency gap persists under a within-task control that holds task difficulty constant. We position BCM as a process-level reliability signal that complements outcome metrics, and we are explicit about the conditions under which it is meaningful.

Environmental time-series causal discovery requires expert decisions about method choice, conditional-independence tests, lag horizons, sample-size adequacy, multiple-testing control, and evidence interpretation. Applied inconsistently across datasets, these choices yield graphs that cannot be compared, reproduced, or audited. We present AutoCause, an open-source Python workflow that records each decision, derives defaults from an extended causal-audit module, and admits domain-informed overrides. The workflow wraps four established causal-discovery methods from three families, adds non-causal reference models, and grades links by method-count support. On 145 datasets from DGP-Atlas, TimeGraph, and a topology-derived CausalRivers reference, the methods recover complementary parts of the reference graphs. Majority-supported links are more precise than single-method links on the synthetic benchmarks but not against river topology. AutoCause converts inconsistent expert practice into an auditable, repeatable analysis; causal interpretation remains with the analyst. Available at https://github.com/marcoruizrueda/autocause.

When a repair agent runs a test and sees it pass, the result is treated as evidence about the reported defect. We measure how often that treatment is warranted. BSG-VA (buggy-state/candidate-state/gold-fix validation analysis) captures each validation command at its exact working-tree state, extracts a test-only patch, and replays the command on the original buggy code (B), the candidate state (S), and the developer gold fix (G). The captured outcome and the replay results assign every event an evidence role, from gold-aligned bug-discriminating through regression-only to misleading. Across 3,730 events in 643 rollouts on 110 tasks, 46.0% of positive comparable events carry no bug-discriminating information; 23.8% of baseline rollouts, with no feedback injected, close with a patch whose entire positive evidence base is of this kind. A three-arm experiment tests whether returning the B-replay outcome to the agent changes this pattern. Bug-contrast feedback reduces evidence-inadequate closure by 7.8 percentage points relative to an attention-matched reminder (p = 0.0029) and raises bug-discriminating evidence by 7.4 points (p = 0.011), with no detectable cost to repair success. Both estimates fall below the prespecified 10-percentage-point smallest effect size of interest, so practical magnitude remains uncertain. Roughly a third of the improvement traces to the reminder alone; across two exploratory replications, varying the scaffold and the model, the B-replay content adds a detectable increment only with gpt-5.6-sol under the unconstrained tool-use loop. BSG-VA applies post hoc to any replayable repair trajectory that preserves the required code states and execution environment. Keywords: program repair agents, validation evidence, test adequacy, large language models, software quality, controlled experiment.

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

Existing benchmarks for electrocardiogram foundation models primarily evaluate downstream predictive performance, providing limited insight into whether their internal representations can be faithfully decomposed, clinically interpreted, or reproduced across independent analyses. We introduce ECG-InterpBench, a benchmark designed to systematically evaluate the interpretability of ECG foundation-model representations. ECG-InterpBench uses sparse autoencoders as standardized measurement instruments and matches their capacity across models to enable controlled comparisons. We evaluate six frozen ECG foundation models across five standardized encoder depths, five matched dictionary widths, and three random seeds, producing a 450-cell interpretability atlas comprising 75 exactly matched six-model comparison blocks. The benchmark evaluates complementary dimensions of representation interpretability, including sparse reconstruction fidelity, single-feature accessibility and coverage of 49 clinically meaningful ECG measurements, and cross-seed feature reproducibility. The evaluation further quantifies patient-sampling uncertainty, depth- and seed-dependent variation, and sensitivity to the sparsity parameterization. The benchmark reveals that ECG foundation models exhibit distinct interpretability profiles. A matched replication on MIMIC-IV-ECG confirms that reconstruction fidelity and clinical accessibility identify different leading models. The benchmark is accompanied by executable evaluation code, standardized manifests, cell-level metrics, and reproducibility audits. ECG-InterpBench complements performance-centered ECG benchmarks by providing a capacity-controlled and reproducible framework for comparing ECG foundation models across distinct dimensions of representation interpretability.

Automated research systems use experimental scores both to deliver artifacts and to decide which ideas to retain, transfer, and pursue. Yet one run scores one implementation of an idea. Crediting that realization-level score as evidence about the parent mechanism creates the \emph{implementation lottery}, in which an idea-level conclusion depends on which plausible implementation was sampled. The mismatch is structural whenever one run updates beliefs about a mechanism. We estimate its magnitude. The \emph{Idea Reliability Audit} measures \emph{idea reliability} by validating and freezing candidate cards, sampling fresh-session implementations, using outcome-blind fidelity labels, and rerunning saved artifacts. It reports idea ICC and leave-one-implementation-out (LOO) winner reversal. Prior work generally repeats the task; we repeat the idea. Across 312 assignments on 13 tabular tasks and two coding-agent setups, implementation variance was more than five and ten times same-artifact rerun variance, respectively, and the winner from one implementation draw differed from the winner under the other-two mean in 25.6% and 43.6% of decisions. Reversal survives card-level filtering under two outcome-blind review rules. An exploratory diagnostic on three materials-regression workflows with a deterministic evaluator also finds implementation variation dominating the decomposition. These findings distinguish idea reliability from best-of-$N$ artifact utility. Before a score guides idea-level branching, transfer, or research memory, evidence should cover multiple implementations.

Among chess opening positions that a strong engine judges essentially equal (Stockfish 18 evaluation within 10 centipawns of zero, depth-stable) and that humans actually reach on Lichess (October 2025; 1,661 positions, 16.1M occurrences), human results are not balanced. Positions carry outcome skews, each the gap between its games' actual results and what the players' ratings predict, whose directions are stable properties of the naturally-reached position: some positions favour White, others Black. These skews reproduce across three re-partitions -- disjoint player-account sets (primary), time, and disjoint rating bands -- and on an out-of-sample month eight months later. On the primary split, each position's skew is measured once in each account group, and the replication slope asks how well one measurement predicts the other after removing rating and opening-family effects: one means undiminished carry-over; zero, no linear relation. We find 0.69 (family-clustered 95% CI [0.65, 0.74]), rising to 0.94 on the most-popular, best-measured positions. The slope's value depends on the position mix. Existence is the invariant claim: it survives every tighter evaluation band, search depth, calibration, and popularity cutoff we test, and replicates within blitz and rapid separately. The typical skew is small (median $|δ| \approx 0.018$, about two percentage points of White score), yet it reproduces, position by position, across disjoint accounts. At these positions the disfavoured side also thinks longer. Even where the evaluation is most confident, it is not a sufficient statistic for human outcomes. The result is observational, and the causal question is left to a pre-registered randomised companion study.

Medical world models offer a framework for extending medical artificial intelligence beyond static prediction by representing evolving patient states and modelling how they change over time and in response to clinical interventions. This Review defines the conceptual boundaries, technical foundations, application domains, and evidence requirements of the field through a structured narrative synthesis with reproducible evidence mapping. We screened 1,455 unique records and assembled a corpus of 98 sources, including 14 studies that met a strict empirical definition of a medical world model. The field is organised around four capabilities: patient state representation, temporal dynamics modelling, intervention-conditioned simulation, and clinician-supervised planning. Evidence spans medical imaging, longitudinal electronic health records, treatment response modelling, physiological and multimodal state modelling, ultrasound and surgical interaction, and population and health-system simulation; clinical digital twins are treated as a cross-cutting integration framework. Current studies provide early evidence of technical feasibility for trajectory forecasting and comparison of candidate interventions, but most remain retrospective, task-specific, or preclinical. The evidence base is further limited by incomplete longitudinal intervention data, inconsistent action semantics, limited causal identifiability, long-horizon error accumulation, inadequate uncertainty estimation, and limited external validation. Clinical translation will therefore depend on precise intervention representations, robust causal and mechanistic grounding, calibrated trajectory-level uncertainty, safety-constrained planning, and prospective multicentre validation against clinically meaningful endpoints.

Digital phenotyping (DP) using smartphones and wearable devices has shown considerable potential for mental health monitoring. However, progress remains difficult to evaluate due to heterogeneous datasets, inconsistent preprocessing pipelines. In this work, we present a reproducible benchmark built upon the Neurai-VN dataset, a high-resolution, multimodal dataset comprising passive sensing and active assessment from wearable and smartphone devices, collected from 100 Vietnamese adults over two weeks. We define four binary classification tasks evaluated using standardized subject-wise cross-validation. Representative linear, tree-based, and neural baseline models are evaluated systematically across predefined feature-group configurations. Mean subject-level F1 scores across five cross-validation folds reached 0.71 for Healthy Control vs. Depression and Healthy Control vs. Clinical, while Healthy Control vs. Anxiety and Depression vs. Anxiety achieved 0.69 and 0.56, respectively. These baseline results provide reproducible baselines for future research on multimodal DP for mental health classification tasks.

Contrastive decoding (CD) has been proposed as a training-free strategy for mitigating object hallucinations in multimodal large language models (MLLMs), with reported gains on benchmarks such as POPE. However, recent work has questioned whether these gains reflect genuine improvements in visual grounding. In this study, we reproduce and extend the findings of "The Mirage of Performance Gains: Why Contrastive Decoding Fails to Mitigate Object Hallucinations in MLLMs." Specifically, we test the claim that CD induces a unidirectional output distribution shift in discriminative datasets and examine its generalizability across datasets. We also verify that the adaptive plausibility constraint (APC) reduces sampling to greedy search on both discriminative and generative benchmarks. Beyond reproduction, we rigorously study the effects of CD across generative and discriminative datasets. We conduct several experiments that provide additional insights: we analyze the logit distributions induced by different CD strategies on generative datasets, propose a proxy method and compare its performance against CD techniques, and investigate how hallucination signals propagate through each layer of the expert and amateur models. Experimental results across MME, POPE, and CHAIR using LLaVA and Qwen validate the original claims and show that the apparent improvements from CD are often spurious and do not consistently translate into stronger visual grounding for reducing hallucinations. These findings challenge the effectiveness of current contrastive decoding strategies and motivate the development of more reliable approaches for mitigating hallucinations in MLLMs.

Large language models increasingly solve scientific-computing tasks, but executable feedback from one problem rarely becomes durable capability on subsequent problems. We study scientific-computing experience consolidation: converting verified runtime experience into transferable procedural knowledge and persistent model improvement. This setting presents two challenges: trajectory-derived artifacts may encode source-specific repairs rather than cross-task computational mechanisms; and a weaker target model may be unable to operationalize an otherwise valid abstract procedure - an abstraction-execution gap. We introduce SciConsolidate, which contrasts verified successes and failures to induce cross-task procedures, selects them through a development-validation gate, and uses failure-informed, answer-free query synthesis to expand the consolidation data without requiring pre-existing reference answers. Because the target model may not directly execute these abstractions, a stronger model concretizes them into executable code supervision for standard, procedure-free SFT; a matched no-procedure teacher branch isolates the value of procedural guidance. On SciCode, runtime procedure injection improves Qwen3.6-27B by +3.85/+6.26 sub-step/main-problem points, but yields almost no aggregate main-problem gain for Qwen3.5-9B, providing operational evidence of the abstraction-execution gap. After procedure-guided concretization, the 9B student improves under procedure-free deployment by +3.89/+6.25 points over the no-procedure SFT control and by +5.62/+11.25 over the original 9B model. These results establish an experience-to-capability pathway for scientific computing and provide a practical starting point for scaling self-improving scientific assistance.

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

Enterprise AI programmes stall at a rate that is widely quoted and poorly explained. This paper measures the mechanism. Six document-heavy workflows of the kind performed daily in regulated financial services were run across four model families and three tool configurations, three times each, producing 5,093 scored output elements across 72 configurations. Each configuration was assessed twice: against a demonstration bar, being a single correct run on a single case, and against a production bar requiring sustained accuracy, reproducibility across repeats, verifiable attribution, and a confidence signal that carries information. 57 of 72 configurations cleared the demonstration bar and 32 cleared the production bar, a survival rate of 56.1%. The paper then computes the review burden each configuration imposes, estimated out of sample rather than with hindsight. A tool that states no confidence requires review of 100% of its output, because it offers a reviewer no basis for triage. Requiring the tool to cite its sources and state a confidence reduces that to 49% while holding the residual error tolerance in 17 of 20 configurations. Adding a self-verification pass costs 2.3 times the latency of the plain configuration, reaches 44%, and is the only configuration that fails to hold the error tolerance. The practical implication is that the value of an AI workflow is set less by how often it is right than by how much of it a human must still check, and that the second property is measurable and rarely measured.

Recent advances in large language models (LLMs) have driven growing interest in using LLMs to automate test generation. Prior work commonly evaluates generated test suites using proxy metrics such as code coverage and mutation score. However, studies by Inozemtseva et al. and Papadakis et al. show that, for human-written tests, correlations among coverage, mutation, and real-bug detection can largely vanish once test suite size is controlled, raising concerns about the validity of evaluations based on proxy metrics. It also remains unclear whether these conclusions carry over to LLM-generated tests, given that prevailing LLM-based test-generation workflows differ substantially from traditional approaches. In this paper, we conduct a large-scale replication study of these two prior works using a wide range of test suites generated by a diverse set of LLMs, and re-examine the relationships among coverage, mutation, and real-bug detection effectiveness. Our findings diverge substantially from prior results. We show that the usefulness of coverage and mutation is highly context-dependent: in regression-style settings where the code provided to the LLM can be reasonably assumed bug-free, these metrics can provide meaningful signals when comparing across models; in another common scenario where the code-under-test may already be buggy and the goal is to expose the bug within the code-under-test, they no longer serve as reliable indicators. We also find little evidence that test suite size is a dominant confounder for correlations among coverage, mutation, and real-bug detection for LLM-generated tests. Based on these findings, we discuss how to interpret results from prior studies and provide actionable guidance for evaluating LLM-based test generation.

Efficient processing is becoming increasingly important in infrared remote sensing, where satellite constellations produce large volumes of observations under constrained detector resolution, power, and downlink bandwidth. Multi-frame super-resolution (MFSR) offers a software-based route to spatial enhancement, but its evaluation in infrared sensing remains fragmented across private datasets and ad-hoc protocols. Existing benchmarks do not explicitly capture the thermal contrast, sensor noise, weak texture, and platform-induced frame-to-frame variation that characterize infrared video. We introduce IR275K, a curated benchmark containing 594 infrared video sequences and 275,196 frames. It provides sequence-level train/validation/test splits and a reproducible X4 evaluation protocol. As an initial architectural probe, we further evaluate CGMamba, a lightweight state-space model with 10.90M parameters and 112.14G FLOPs. CGMamba combines 2D rotary position encoding (2DRoPE) with center-guided cross-Mamba (CGCM) fusion for implicit multi-frame reconstruction. It achieves 33.19dB PSNR, outperforming infrared single-image super-resolution references by 0.35--0.52dB at substantially lower computational cost. Ablation results show that removing 2D~RoPE from CGCM causes a 1.53dB drop and severe grid-like artifacts. This indicates that explicit spatial anchoring is critical for stabilizing SSM-based cross-frame gating under infrared conditions. IR275K provides a reproducible foundation for accuracy--efficiency evaluation of infrared MFSR methods, while the architectural analysis offers a concrete starting point for spatially aware SSM design under resource-constrained infrared sensing. Dataset and evaluation resources are available at: https://github.com/InfraRecon7/IR275K.

LLM-based database agents show promise, but differing task scopes, testbeds, and metrics hinder comparison. We identify four gaps between evaluation and production operations: live-environment fidelity (multi-turn read-write interaction with a running database); observation-space scale and complexity (causal diagnosis across thousands of time series, business logs, and concurrent activity); solution-space openness (multiple remediations with different operational trade-offs); and scenario complexity and coverage (faults cascading across internal mechanisms and operational domains). We present DBA-Bench, a benchmark addressing these gaps through production fidelity, outcome-first evaluation, and controlled scenario reproducibility. It uses instrumented PostgreSQL environments with active workloads, persistent state, and multi-source observations; defines success by measurable recovery or fault elimination under safety constraints; and restores snapshots with scenario-specific checks before each run. The benchmark contains 106 scenarios across seven task domains, with two public difficulty labels based on reference-path diagnostic depth and environmental complexity. We evaluate nine baseline groups, including six foundation-model systems, two GPT-5.5-backed database agents, and a Human DBA reference. Across 848 automated runs, Diagnosis, Outcome, and Safe Pass rates are 32.7%, 19.6%, and 12.4%; the best automated baseline reaches 17.9% Safe Pass versus 93.4% for the Human DBA reference. Automated Safe Pass falls from 19.6% on Easy scenarios to 7.6% on Hard scenarios, underscoring the difficulty of safe end-to-end remediation.

Prior classical-ML learning-curve work fits power laws to tree, linear, and kernel models on tabular data, but at small scale: typically one curve, one team, a handful of cells. We present a distributed classroom-scale replication: 127 graduate students each ran a fixed protocol on 3 assigned datasets, drawn from 18 tabular classification and regression datasets and 6 model families (Boosting, Random Forest, SVM, Linear/Logistic, Ridge, Lasso), yielding 11,536 training runs and 1,648 fitted power-law curves of the form error(N) = a N^(-b) + c. Three findings. (1) Power laws fit: R^2 > 0.8 on 77.7% of cells, with tree ensembles dominating at full data (Boosting 50% of datasets, RandomForest 33%; linear models underperform on classification). (2) Approximate shared exponents within a model family: for 5 of 6 families, a single family-level exponent predicts each family's cross-dataset curves nearly as well as per-dataset exponents (R^2 gap < 0.011), though AIC favors the unconstrained fit and curve collapse is partial (32-58% of points within +/-0.5 dex). We frame this as approximate predictive compressibility, not dataset-independent universality; Lasso fails outright (negative control) and Ridge is fragile under leave-one-dataset-out. (3) Replicator-implementation variance: with random_state=42 fixed, independent re-implementations of the same protocol still differ by mean CV(b) = 0.144 on the fitted exponent -- not seed variance, but the spread induced by unconstrained parts of the protocol (preprocessing, encoding, missing-value handling). We release the aggregated curves, per-cell fits, and a practical data-requirement table for N* to reach target error 0.15.

Large language models (LLMs) show promise in code generation, but their capabilities to produce correct, synthesizable hardware description language (HDL) code still remain to be properly benchmarked. Existing evaluations are primarily relying on pass@k metrics and lack proper end-to-end toolchain validation. This paper presents a reproducible benchmarking platform that evaluates open-source LLMs on Verilog RTL generation across 50 curated tasks consisting of combinational, sequential, finite state machine (FSM), and mixed designs. The pipeline consisting of constrained prompting, post-processing, and semantic-aware iterative refinement with waveform analysis, formal equivalence verification, and Abstract Syntax Tree (AST)-based repair validates the generated code via Verilator compilation and Icarus Verilog simulation. Across the 12 benchmarks and the 1,610 total runs evaluating three models of different sizes (Llama-3-8B, StarCoder2-7B, and TinyLlama-1.1B), the pipeline improved syntax validity from 0% to a 70.43% average and simulation pass rate to 51.8% across three open-source models. Most notably TinyLlama (1.1B parameters) achieved the highest individual syntax validity at 80.0%, with functional correctness comparable to the 8B model. The platform and dataset are open-source, enabling reproducible evaluation of generative AI for hardware design workflows.

Preprocessing blood glucose time-series data is a critical yet often overlooked step in developing data-driven methods for diabetes management, particularly for type 1 diabetes. The lack of standardized preprocessing workflows and evaluation protocols hinders reproducibility and complicates fair comparison across studies. These challenges are further exacerbated by data-sharing restrictions, as privacy and licensing constraints often prevent the redistribution of preprocessed medical datasets. To address these limitations, we present GlucoTune, a comprehensive and extensible framework for reproducible experimentation with blood glucose time-series data. The framework standardizes the entire experimental workflow, from preprocessing to model evaluation, enabling reproducible experiments directly from the original datasets. Reproducible preprocessing is achieved through configurable pipelines defined in portable YAML configuration files, ensuring consistent data handling without distributing sensitive preprocessed data. Beyond preprocessing, GlucoTune provides a unified interface for implementing, training, and evaluating blood glucose prediction models. The framework integrates public datasets through standardized wrappers and provides a curated collection of state-of-the-art blood glucose prediction and general time-series forecasting methods, while remaining readily extensible to additional datasets, preprocessing strategies, and forecasting models. To promote transparent and consistent evaluation, GlucoTune includes a benchmarking leaderboard that reports results across datasets, preprocessing configurations, and forecasting methods, enabling systematic comparison of experimental settings. We demonstrate the effectiveness of GlucoTune through comprehensive experiments and assess its usability in a user study.