Daily Papers

ATANT v1.0 (arXiv:2604.06710) defined continuity as a system property with 7 required properties and introduced a 10-checkpoint, LLM-free evaluation methodology validated on a 250-story corpus. Since publication, a recurring reviewer and practitioner question has concerned not the framework itself but its relationship to a wider set of memory evaluations: LOCOMO, LongMemEval, BEAM, MemoryBench, Zep's evaluation suite, Letta/MemGPT's evaluations, and RULER. This companion paper, v1.1, does not modify the v1.0 standard. It closes a related-work gap that v1.0 left brief under page limits. We show by structural analysis that none of these benchmarks measures continuity as defined in v1.0: of the 7 required properties, the median existing eval covers 1 property, the mean covers 0.43 when partial credit is scored at 0.5, and no eval covers more than 2. We provide a cell-by-cell property-coverage matrix, identify methodological defects specific to each benchmark (including an empty-gold scoring bug in the LOCOMO reference implementation that renders 23% of its corpus unscorable by construction), and publish our reference implementation's LOCOMO score (8.8%) alongside the structural reason that number is uninformative about continuity. We publish our 8.8% LOCOMO score alongside our 96% ATANT cumulative-scale score as a calibration pair: the 87-point divergence is evidence that the two benchmarks measure different properties, not that one system is an order of magnitude better than another. The position v1.1 takes is not adversarial: each benchmark measures a real capability. The claim is that none of them can adjudicate continuity, and conflating them with continuity evaluation has led the field to under-invest in the properties v1.0 names.

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.

Machine learning (ML) methods are proliferating in scientific research. However, the adoption of these methods has been accompanied by failures of validity, reproducibility, and generalizability. These failures can hinder scientific progress, lead to false consensus around invalid claims, and undermine the credibility of ML-based science. ML methods are often applied and fail in similar ways across disciplines. Motivated by this observation, our goal is to provide clear reporting standards for ML-based science. Drawing from an extensive review of past literature, we present the REFORMS checklist (Reporting Standards For Machine Learning Based Science). It consists of 32 questions and a paired set of guidelines. REFORMS was developed based on a consensus of 19 researchers across computer science, data science, mathematics, social sciences, and biomedical sciences. REFORMS can serve as a resource for researchers when designing and implementing a study, for referees when reviewing papers, and for journals when enforcing standards for transparency and reproducibility.

AI scientist systems, capable of autonomously executing the full research workflow from hypothesis generation and experimentation to paper writing, hold significant potential for accelerating scientific discovery. However, the internal workflow of these systems have not been closely examined. This lack of scrutiny poses a risk of introducing flaws that could undermine the integrity, reliability, and trustworthiness of their research outputs. In this paper, we identify four potential failure modes in contemporary AI scientist systems: inappropriate benchmark selection, data leakage, metric misuse, and post-hoc selection bias. To examine these risks, we design controlled experiments that isolate each failure mode while addressing challenges unique to evaluating AI scientist systems. Our assessment of two prominent open-source AI scientist systems reveals the presence of several failures, across a spectrum of severity, which can be easily overlooked in practice. Finally, we demonstrate that access to trace logs and code from the full automated workflow enables far more effective detection of such failures than examining the final paper alone. We thus recommend journals and conferences evaluating AI-generated research to mandate submission of these artifacts alongside the paper to ensure transparency, accountability, and reproducibility.

Large Language Models (LLM) benchmarks tell us when models fail, but not why they fail. A wrong answer on a reasoning dataset may stem from formatting issues, calculation errors, or dataset noise rather than weak reasoning. Without disentangling such causes, benchmarks remain incomplete and cannot reliably guide model improvement. We introduce ErrorMap, the first method to chart the sources of LLM failure. It extracts a model's unique "failure signature", clarifies what benchmarks measure, and broadens error identification to reduce blind spots. This helps developers debug models, aligns benchmark goals with outcomes, and supports informed model selection. ErrorMap works on any model or dataset with the same logic. Applying our method to 35 datasets and 83 models we generate ErrorAtlas, a taxonomy of model errors, revealing recurring failure patterns. ErrorAtlas highlights error types that are currently underexplored in LLM research, such as omissions of required details in the output and question misinterpretation. By shifting focus from where models succeed to why they fail, ErrorMap and ErrorAtlas enable advanced evaluation - one that exposes hidden weaknesses and directs progress. Unlike success, typically measured by task-level metrics, our approach introduces a deeper evaluation layer that can be applied globally across models and tasks, offering richer insights into model behavior and limitations. We make the taxonomy and code publicly available with plans to periodically update ErrorAtlas as new benchmarks and models emerge.

Large Language Models (LLMs) have become a milestone in the field of artificial intelligence and natural language processing. However, their large-scale deployment remains constrained by the need for significant computational resources. This work proposes starting from a base model to explore and combine data processing and careful data selection techniques, training strategies, and architectural adjustments to improve the efficiency of LLMs in resource-constrained environments and within a delimited knowledge base. The methodological approach included defining criteria for building reliable datasets, conducting controlled experiments with different configurations, and systematically evaluating the resulting variants in terms of capability, versatility, response time, and safety. Finally, comparative tests were conducted to measure the performance of the developed variants and to validate the effectiveness of the proposed strategies. This work is based on the master's thesis in Systems and Computer Engineering titled "Efficient Strategy for Improving the Capabilities of Large Language Models (LLMs)".

Large language models (LLMs) show promise in medical diagnosis, but real-world deployment remains challenging due to high-stakes clinical decisions and imperfect reasoning reliability. As a result, careful inspection of model behavior is essential for assessing whether diagnostic reasoning is reliable and clinically grounded. However, debugging medical LLMs remains difficult. First, developers often lack sufficient medical domain expertise to interpret model errors in clinically meaningful terms. Second, models can fail across a large and diverse set of instances involving different input types, tasks, and reasoning steps, making it challenging for developers to prioritize which errors deserve focused inspection. Third, developers struggle to identify recurring error patterns across cases, as existing debugging practices are largely instance-centric and rely on manual inspection of isolated failures. To address these challenges, we present VeriLLMed, a visual analytics system that integrates external biomedical knowledge to audit and debug medical LLM diagnostic reasoning. VeriLLMed transforms model outputs into comparable reasoning paths, constructs knowledge graph-grounded reference paths, and identifies three recurring classes of diagnosis errors: relation errors, branch errors, and missing errors. Case studies and expert evaluation demonstrate that VeriLLMed helps developers identify clinically implausible reasoning and generate actionable insights that can inform the improvement of medical LLMs.

In software testing, a set of test cases is constructed according to some predefined selection criteria. The software is then examined against these test cases. Three interesting observations have been made on the current artifacts of software testing. Firstly, an error-revealing test case is considered useful while a successful test case which does not reveal software errors is usually not further investigated. Whether these successful test cases still contain useful information for revealing software errors has not been properly studied. Secondly, no matter how extensive the testing has been conducted in the development phase, errors may still exist in the software [5]. These errors, if left undetected, may eventually cause damage to the production system. The study of techniques for uncovering software errors in the production phase is seldom addressed in the literature. Thirdly, as indicated by Weyuker in [6], the availability of test oracles is pragmatically unattainable in most situations. However, the availability of test oracles is generally assumed in conventional software testing techniques. In this paper, we propose a novel test case selection technique that derives new test cases from the successful ones. The selection aims at revealing software errors that are possibly left undetected in successful test cases which may be generated using some existing strategies. As such, the proposed technique augments the effectiveness of existing test selection strategies. The technique also helps uncover software errors in the production phase and can be used in the absence of test oracles.

The use of machine learning (ML) methods for prediction and forecasting has become widespread across the quantitative sciences. However, there are many known methodological pitfalls, including data leakage, in ML-based science. In this paper, we systematically investigate reproducibility issues in ML-based science. We show that data leakage is indeed a widespread problem and has led to severe reproducibility failures. Specifically, through a survey of literature in research communities that adopted ML methods, we find 17 fields where errors have been found, collectively affecting 329 papers and in some cases leading to wildly overoptimistic conclusions. Based on our survey, we present a fine-grained taxonomy of 8 types of leakage that range from textbook errors to open research problems. We argue for fundamental methodological changes to ML-based science so that cases of leakage can be caught before publication. To that end, we propose model info sheets for reporting scientific claims based on ML models that would address all types of leakage identified in our survey. To investigate the impact of reproducibility errors and the efficacy of model info sheets, we undertake a reproducibility study in a field where complex ML models are believed to vastly outperform older statistical models such as Logistic Regression (LR): civil war prediction. We find that all papers claiming the superior performance of complex ML models compared to LR models fail to reproduce due to data leakage, and complex ML models don't perform substantively better than decades-old LR models. While none of these errors could have been caught by reading the papers, model info sheets would enable the detection of leakage in each case.

Equivariance theory predicts that an architectural symmetry prior reduces sample complexity by a factor of |G|; this is widely cited but rarely measured as a scaling law with controls that separate the prior from its confounds. On a controlled C_n-symmetric task, we report three findings. First, a wrong-group control with identical orbit size and matched compute is worse than no constraint (joint pairwise CI [+0.79, +3.26] excludes zero, robust across estimators); misaligned constraint is actively harmful, not merely unhelpful. Second, an augmentation baseline equipped with test-time orbit averaging matches the equivariant model exactly -- bit-identical per-epoch validation curves across matched cells -- so the architecture-vs-augmentation gap is conditional on asymmetric test-time computation, not unconditional. Third, the relative exchange rate beta_diff = 1.28 is consistent in sign and order of magnitude with the theoretical 1.0 (single-level CI [+0.92, +2.05]); the more conservative two-level bootstrap (seeds x group sizes) widens this to [-0.63, +1.72], including zero, and a finer-N replication on a sqrt(2)-spaced grid is inconclusive (point estimate -0.82). The methodological contributions -- the relative-rate estimator that cancels the shared-difficulty confound, the wrong-group control, and a pre-specified failure taxonomy -- transfer to any inductive bias whose strength can be parameterised. Honest scoping: the primary estimator beta_diff was adopted post-hoc after the initial analysis revealed a positive-slope identifiability problem; the design was never externally pre-registered; and the headline number rests on an OLS slope over seven group sizes on a coarse N grid. This is an exploratory study, not a confirmatory measurement; the wrong-group result is the cleanest finding and the one we report with the most confidence. A registered replication on fresh seeds is future work.

Researchers have proposed a wide variety of model explanation approaches, but it remains unclear how most methods are related or when one method is preferable to another. We examine the literature and find that many methods are based on a shared principle of explaining by removing - essentially, measuring the impact of removing sets of features from a model. These methods vary in several respects, so we develop a framework for removal-based explanations that characterizes each method along three dimensions: 1) how the method removes features, 2) what model behavior the method explains, and 3) how the method summarizes each feature's influence. Our framework unifies 26 existing methods, including several of the most widely used approaches (SHAP, LIME, Meaningful Perturbations, permutation tests). Exposing the fundamental similarities between these methods empowers users to reason about which tools to use, and suggests promising directions for ongoing model explainability research.

Scientific images function as critical evidence in research communication, yet their integrity faces unprecedented threats from AI-generated content that introduces subtle but consequential errors. Existing evaluation paradigms prove inadequate: perceptual quality metrics poorly correlate with scientific validity, while language models lack domain-specific verification capabilities. To address this gap, we propose the Scientific Image Utility and Upgradability Assessment (SIU^2A) framework, which introduces two complementary dimensions for scientific image evaluation. Utility encompasses error detection (identifying scientific inaccuracies) and correction feasibility (assessing whether errors can be reliably repaired). Upgradability measures the quality of correction. We categorize scientific image corruption into four fundamental types: Detail Distortion, Incompleteness, False Content, and Entity Confusion. Based on this taxonomy, we construct SIU^2A-Benchmark, a dataset with expert annotations for error identification and repair. The framework implements a two-stage evaluation protocol: the Utility stage evaluates error detection capability and repair instruction generation, while the Upgradability stage assesses whether corrections faithfully restore scientific validity without compromising existing accurate information. Experiments reveal that current multimodal systems exhibit significant limitations in both scientific error assessment and faithful correction, exposing a fundamental gap between visual perception and scientific usability.

Sycophancy in LLMs is documented across 70+ papers, but expert agreement on construct boundaries remains low (ICC=.184; Ye et al., 2026). The construct fragments because behavioral classification depends on which surface form is privileged. We adopt a materials-science framing: conversation as test specimen under load, LLM-model as material charge, pushback as progressive load, stance-flip as material failure. We characterize this failure across three loading cases (debate n=1000; false-presuppositions n=3400; ethical-setting n=3400; 10-17 material charges per case; 7800 specimens total) using 14 turn-level axis-measurements spanning velocity, damage accumulation, frame-drift, brittleness, and direction stability, plus three speaker-resolved axes from an independent pipeline. The measurements are Hooke-coupled (σ= E cdot varepsilon analog) and reproduce across loading cases with effects up to |r_{rb}| = 0.35 on debate; the sign structure adds a second pattern: the ethical-setting case inverts the velocity and accumulation blocks. Variance composition partitions into two profiles: debate is charge-dominated (brittle-fracture-like: the material grade decides), false-presuppositions and ethical-setting are topic-dominated (creep-like: the load decides); the ratios (2.03 vs 0.13/0.17) are estimator-dependent, for debate even in direction. Cross-judge reliability (GPT-4o vs Haiku 4.5) shows debate scoring is judge-robust (Cohen's κ= 0.88) while false-presupposition scoring is judge-sensitive (κ= 0.36) -- a caveat single-judge benchmarks must report. This is the methodological move Ye et al.'s diagnosis calls for: a multi-axis characterization that does not depend on which surface form of the construct one privileges.

The adoption of Large Language Models (LLMs) in scientific writing promises efficiency but risks introducing informational entropy. While "hallucinated papers" are a known artifact, the systematic degradation of valid citation chains remains unquantified. We conducted a forensic audit of 50 recent survey papers in Artificial Intelligence (N=5,514 citations) published between September 2024 and January 2026. We utilized a hybrid verification pipeline combining DOI resolution, Crossref metadata analysis, Semantic Scholar queries, and fuzzy text matching to distinguish between formatting errors ("Sloppiness") and verifiable non-existence ("Phantoms). We detect a persistent 17.0% Phantom Rate -- citations that cannot be resolved to any digital object despite aggressive forensic recovery. Diagnostic categorization reveals three distinct failure modes: pure hallucinations (5.1%), hallucinated identifiers with valid titles (16.4%), and parsing-induced matching failures (78.5%). Longitudinal analysis reveals a flat trend (+0.07 pp/month), suggesting that high-entropy citation practices have stabilized as an endemic feature of the field. The scientific citation graph in AI survey literature exhibits "link rot" at scale. This suggests a mechanism where AI tools act as "lazy research assistants," retrieving correct titles but hallucinating metadata, thereby severing the digital chain of custody required for reproducible science.

Unit testing is an essential part of the software development process, which helps to identify issues with source code in early stages of development and prevent regressions. Machine learning has emerged as viable approach to help software developers generate automated unit tests. However, generating reliable unit test cases that are semantically correct and capable of catching software bugs or unintended behavior via machine learning requires large, metadata-rich, datasets. In this paper we present Methods2Test: A dataset of focal methods mapped to test cases: a large, supervised dataset of test cases mapped to corresponding methods under test (i.e., focal methods). This dataset contains 780,944 pairs of JUnit tests and focal methods, extracted from a total of 91,385 Java open source projects hosted on GitHub with licenses permitting re-distribution. The main challenge behind the creation of the Methods2Test was to establish a reliable mapping between a test case and the relevant focal method. To this aim, we designed a set of heuristics, based on developers' best practices in software testing, which identify the likely focal method for a given test case. To facilitate further analysis, we store a rich set of metadata for each method-test pair in JSON-formatted files. Additionally, we extract textual corpus from the dataset at different context levels, which we provide both in raw and tokenized forms, in order to enable researchers to train and evaluate machine learning models for Automated Test Generation. Methods2Test is publicly available at: https://github.com/microsoft/methods2test

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

Despite its crucial role in research experiments, code correctness is often presumed only on the basis of the perceived quality of results. This assumption comes with the risk of erroneous outcomes and potentially misleading findings. To address this issue, we posit that the current focus on reproducibility should go hand in hand with the emphasis on software quality. We present a case study in which we identify and fix three bugs in widely used implementations of the state-of-the-art Conformer architecture. Through experiments on speech recognition and translation in various languages, we demonstrate that the presence of bugs does not prevent the achievement of good and reproducible results, which however can lead to incorrect conclusions that potentially misguide future research. As a countermeasure, we propose a Code-quality Checklist and release pangoliNN, a library dedicated to testing neural models, with the goal of promoting coding best practices and improving research software quality within the NLP community.

Large Language Models (LLMs) have become key components of modern software, with prompts acting as their de-facto programming interface. However, prompt design remains largely empirical and small mistakes can cascade into unreliable, insecure, or inefficient behavior. This paper presents the first systematic survey and taxonomy of prompt defects, recurring ways that prompts fail to elicit their intended behavior from LLMs. We organize defects along six dimensions: (1) Specification and Intent, (2) Input and Content, (3) Structure and Formatting, (4) Context and Memory, (5) Performance and Efficiency, and (6) Maintainability and Engineering. Each dimension is refined into fine-grained subtypes, illustrated with concrete examples and root cause analysis. Grounded in software engineering principles, we show how these defects surface in real development workflows and examine their downstream effects. For every subtype, we distill mitigation strategies that span emerging prompt engineering patterns, automated guardrails, testing harnesses, and evaluation frameworks. We then summarize these strategies in a master taxonomy that links defect, impact, and remedy. We conclude with open research challenges and a call for rigorous engineering-oriented methodologies to ensure that LLM-driven systems are dependable by design.

Context: The SZZ algorithm is the de facto standard for labeling bug fixing commits and finding inducing changes for defect prediction data. Recent research uncovered potential problems in different parts of the SZZ algorithm. Most defect prediction data sets provide only static code metrics as features, while research indicates that other features are also important. Objective: We provide an empirical analysis of the defect labels created with the SZZ algorithm and the impact of commonly used features on results. Method: We used a combination of manual validation and adopted or improved heuristics for the collection of defect data. We conducted an empirical study on 398 releases of 38 Apache projects. Results: We found that only half of the bug fixing commits determined by SZZ are actually bug fixing. If a six-month time frame is used in combination with SZZ to determine which bugs affect a release, one file is incorrectly labeled as defective for every file that is correctly labeled as defective. In addition, two defective files are missed. We also explored the impact of the relatively small set of features that are available in most defect prediction data sets, as there are multiple publications that indicate that, e.g., churn related features are important for defect prediction. We found that the difference of using more features is not significant. Conclusion: Problems with inaccurate defect labels are a severe threat to the validity of the state of the art of defect prediction. Small feature sets seem to be a less severe threat.

Peer-evaluation based measures of group research quality such as the UK's Research Assessment Exercise (RAE), which do not employ bibliometric analyses, cannot directly avail of such methods to normalize research impact across disciplines. This is seen as a conspicuous flaw of such exercises and calls have been made to find a remedy. Here a simple, systematic solution is proposed based upon a mathematical model for the relationship between research quality and group quantity. This model manifests both the Matthew effect and a phenomenon akin to the Ringelmann effect and reveals the existence of two critical masses for each academic discipline: a lower value, below which groups are vulnerable, and an upper value beyond which the dependency of quality on quantity reduces and plateaus appear when the critical masses are large. A possible normalization procedure is then to pitch these plateaus at similar levels. We examine the consequences of this procedure at RAE for a multitude of academic disciplines, corresponding to a range of critical masses.

The field of Deep Learning (DL) has undergone explosive growth during the last decade, with a substantial impact on Natural Language Processing (NLP) as well. Yet, compared to more established disciplines, a lack of common experimental standards remains an open challenge to the field at large. Starting from fundamental scientific principles, we distill ongoing discussions on experimental standards in NLP into a single, widely-applicable methodology. Following these best practices is crucial to strengthen experimental evidence, improve reproducibility and support scientific progress. These standards are further collected in a public repository to help them transparently adapt to future needs.

Science progresses by iteratively advancing and correcting humanity's understanding of the world. In machine learning (ML) research, rapid advancements have led to an explosion of publications, but have also led to misleading, incorrect, flawed or perhaps even fraudulent studies being accepted and sometimes highlighted at ML conferences due to the fallibility of peer review. While such mistakes are understandable, ML conferences do not offer robust processes to help the field systematically correct when such errors are made. This position paper argues that ML conferences should establish a dedicated "Refutations and Critiques" (R&C) Track. This R&C Track would provide a high-profile, reputable platform to support vital research that critically challenges prior research, thereby fostering a dynamic self-correcting research ecosystem. We discuss key considerations including track design, review principles, potential pitfalls, and provide an illustrative example submission concerning a recent ICLR 2025 Oral. We conclude that ML conferences should create official, reputable mechanisms to help ML research self-correct.

As Large Language Models (LLMs) become increasingly embedded in empirical research workflows, their use as analytical tools for quantitative or qualitative data raises pressing concerns for scientific integrity. This opinion paper draws a parallel between "prompt-hacking", the strategic tweaking of prompts to elicit desirable outputs from LLMs, and the well-documented practice of "p-hacking" in statistical analysis. We argue that the inherent biases, non-determinism, and opacity of LLMs make them unsuitable for data analysis tasks demanding rigor, impartiality, and reproducibility. We emphasize how researchers may inadvertently, or even deliberately, adjust prompts to confirm hypotheses while undermining research validity. We advocate for a critical view of using LLMs in research, transparent prompt documentation, and clear standards for when LLM use is appropriate. We discuss how LLMs can replace traditional analytical methods, whereas we recommend that LLMs should only be used with caution, oversight, and justification.

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

Representation engineering methods have recently shown promise for enabling efficient steering of model behavior. However, evaluation pipelines for these methods have primarily relied on subjective demonstrations, instead of quantitative, objective metrics. We aim to take a step towards addressing this issue by advocating for four properties missing from current evaluations: (i) contexts sufficiently similar to downstream tasks should be used for assessing intervention quality; (ii) model likelihoods should be accounted for; (iii) evaluations should allow for standardized comparisons across different target behaviors; and (iv) baseline comparisons should be offered. We introduce an evaluation pipeline grounded in these criteria, offering both a quantitative and visual analysis of how effectively a given method works. We use this pipeline to evaluate two representation engineering methods on how effectively they can steer behaviors such as truthfulness and corrigibility, finding that some interventions are less effective than previously reported.

Background. The development of empirical studies in software engineering mainly relies on the data available on code hosting platforms, being GitHub the most representative. Nevertheless, in the last years, the emergence of Machine Learning (ML) has led to the development of platforms specifically designed for developing ML-based projects, being Hugging Face Hub (HFH) the most popular one. With over 250k repositories, and growing fast, HFH is becoming a promising ecosystem of ML artifacts and therefore a potential source of data for empirical studies. However, so far there have been no studies evaluating the potential of HFH for such studies. Objective. In this proposal for a registered report, we aim at performing an exploratory study of the current state of HFH in order to investigate its suitability to be used as a source platform for empirical studies. Method. We conduct a qualitative and quantitative analysis of HFH for empirical studies. The former will be performed by comparing the features of HFH with those of other code hosting platforms, such as GitHub and GitLab. The latter will be performed by analyzing the data available in HFH.

As Large Language Models (LLMs) become more pervasive across various users and scenarios, identifying potential issues when using these models becomes essential. Examples of such issues include: bias, inconsistencies, and hallucination. Although auditing the LLM for these problems is often warranted, such a process is neither easy nor accessible for most. An effective method is to probe the LLM using different versions of the same question. This could expose inconsistencies in its knowledge or operation, indicating potential for bias or hallucination. However, to operationalize this auditing method at scale, we need an approach to create those probes reliably and automatically. In this paper we propose the LLMAuditor framework which is an automatic, and scalable solution, where one uses a different LLM along with human-in-the-loop (HIL). This approach offers verifiability and transparency, while avoiding circular reliance on the same LLM, and increasing scientific rigor and generalizability. Specifically, LLMAuditor includes two phases of verification using humans: standardized evaluation criteria to verify responses, and a structured prompt template to generate desired probes. A case study using questions from the TruthfulQA dataset demonstrates that we can generate a reliable set of probes from one LLM that can be used to audit inconsistencies in a different LLM. This process is enhanced by our structured prompt template with HIL, which not only boosts the reliability of our approach in auditing but also yields the delivery of less hallucinated results. The novelty of our research stems from the development of a comprehensive, general-purpose framework that includes a HIL verified prompt template for auditing responses generated by LLMs.

A benchmark is not merely a collection of test questions; it naturally induces an empirical measure over difficulty. In this work, we develop this measure-based view of benchmark evaluation. This perspective allows us to identify and formalize two central failure modes: measure mismatch, where the benchmark difficulty distribution differs from the intended difficulty distribution, and coverage gaps, where uncovered regions along the difficulty axis prevent benchmarks from detecting meaningful localized training progress. We propose two diagnostic metrics that capture these two failure modes and provide rigorous theoretical guarantees. Empirically, we analyze 25 popular benchmarks spanning 7 domains using carefully estimated item difficulties. Our results show that many benchmarks implicitly overweight certain difficulty regions, so their leaderboard conclusions should be interpreted with caution; others leave substantial portions of the difficulty axis uncovered, limiting their ability to monitor the model improvement process. Finally, we turn diagnosis into action by introducing BenchFill, a simple difficulty-targeted item rewriting algorithm that effectively reduces local coverage gaps.

Machine Learning for Software Engineering (ML4SE) is an actively growing research area that focuses on methods that help programmers in their work. In order to apply the developed methods in practice, they need to achieve reasonable quality in order to help rather than distract developers. While the development of new approaches to code representation and data collection improves the overall quality of the models, it does not take into account the information that we can get from the project at hand. In this work, we investigate how the model's quality can be improved if we target a specific project. We develop a framework to assess quality improvements that models can get after fine-tuning for the method name prediction task on a particular project. We evaluate three models of different complexity and compare their quality in three settings: trained on a large dataset of Java projects, further fine-tuned on the data from a particular project, and trained from scratch on this data. We show that per-project fine-tuning can greatly improve the models' quality as they capture the project's domain and naming conventions. We open-source the tool we used for data collection, as well as the code to run the experiments: https://zenodo.org/record/6040745.

Large language models often produce hallucinated answers that violate prompt-level constraints. A key diagnostic question is whether these failures reflect missing knowledge, or whether the model has the relevant information but follows the wrong inference path. We study this phenomenon as inference misalignment: a mismatch between the answer supported by the prompt and the answer favored by statistically salient latent associations. We formalize this view with a latent key-task model, in which pretraining-frequency imbalance can cause a shortcut path to dominate the constraint-sensitive path and induce positive inference loss. The framework predicts two failure modes: task-retrieval bias in entity disambiguation and key-selection bias in action choice. We introduce TrapQA, a controlled diagnostic testbed with two components. ScientistQA tests disambiguation among similar scientists with supplementary factual probes, while Real-Life Constrained QA tests everyday constraint following under salient shortcuts. Our results show that hallucination can arise from biased latent inference rather than absent knowledge alone.

Software developers attempt to reproduce software bugs to understand their erroneous behaviours and to fix them. Unfortunately, they often fail to reproduce (or fix) them, which leads to faulty, unreliable software systems. However, to date, only a little research has been done to better understand what makes the software bugs non-reproducible. In this paper, we conduct a multimodal study to better understand the non-reproducibility of software bugs. First, we perform an empirical study using 576 non-reproducible bug reports from two popular software systems (Firefox, Eclipse) and identify 11 key factors that might lead a reported bug to non-reproducibility. Second, we conduct a user study involving 13 professional developers where we investigate how the developers cope with non-reproducible bugs. We found that they either close these bugs or solicit for further information, which involves long deliberations and counter-productive manual searches. Third, we offer several actionable insights on how to avoid non-reproducibility (e.g., false-positive bug report detector) and improve reproducibility of the reported bugs (e.g., sandbox for bug reproduction) by combining our analyses from multiple studies (e.g., empirical study, developer study).

Recent literature has underscored the importance of dataset documentation work for machine learning, and part of this work involves addressing "documentation debt" for datasets that have been used widely but documented sparsely. This paper aims to help address documentation debt for BookCorpus, a popular text dataset for training large language models. Notably, researchers have used BookCorpus to train OpenAI's GPT-N models and Google's BERT models, even though little to no documentation exists about the dataset's motivation, composition, collection process, etc. We offer a preliminary datasheet that provides key context and information about BookCorpus, highlighting several notable deficiencies. In particular, we find evidence that (1) BookCorpus likely violates copyright restrictions for many books, (2) BookCorpus contains thousands of duplicated books, and (3) BookCorpus exhibits significant skews in genre representation. We also find hints of other potential deficiencies that call for future research, including problematic content, potential skews in religious representation, and lopsided author contributions. While more work remains, this initial effort to provide a datasheet for BookCorpus adds to growing literature that urges more careful and systematic documentation for machine learning datasets.

Perception of toxicity evolves over time and often differs between geographies and cultural backgrounds. Similarly, black-box commercially available APIs for detecting toxicity, such as the Perspective API, are not static, but frequently retrained to address any unattended weaknesses and biases. We evaluate the implications of these changes on the reproducibility of findings that compare the relative merits of models and methods that aim to curb toxicity. Our findings suggest that research that relied on inherited automatic toxicity scores to compare models and techniques may have resulted in inaccurate findings. Rescoring all models from HELM, a widely respected living benchmark, for toxicity with the recent version of the API led to a different ranking of widely used foundation models. We suggest caution in applying apples-to-apples comparisons between studies and lay recommendations for a more structured approach to evaluating toxicity over time. Code and data are available at https://github.com/for-ai/black-box-api-challenges.

AI has long assisted scientific research, but the rapid advance of LLMs and agentic scaffolds is reshaping the landscape; a single system can now carry whole-stage research from an initial hypothesis all the way to final published paper, which is a paradigm now referred to as AutoResearch. Existing evaluations reveal little about how these agents operate or where they break down. Tasks are narrowly-scoped, evaluation measures performance but not process, and failure diagnoses lack systematic coverage or artifact-level visibility. To address this gap, we introduce AutoResearchEval, featuring 100 tasks grounded in published frontier science across 7 scientific domains and the full research lifecycle, including ideation, retrieval, execution, analysis, writing, and review. Evaluating 8 harness-model combinations yields 800 autoresearch agent trajectories, with process-level annotation. We organize these insights into AutoResearch Failure Taxonomy or ARFT, a framework of 45 empirically-grounded failure patterns. To enable scalable fine-grained attribution, we leverage a human-calibrated agent-as-a-judge pipeline to inspect complete trajectories and intermediate artifacts. Failure patterns converge on a single overarching limitation, namely that current agents lack a metacognitive loop, which entails the ability to check what they produced against what they found, revise when it does not hold up, and question whether the path they took was sound. The same patterns recur across all 8 harness-model combinations, including the strongest models tested, locating the deficit at the model level rather than in any particular scaffold; whether orchestration-level interventions can close it is an open question this work does not test. We publicly release AutoResearchEval and ARFT to facilitate continued research and development in autonomous scientific discovery.

Physics education researchers (PER) often analyze student data with single-level regression models (e.g., linear and logistic regression). However, education datasets can have hierarchical structures, such as students nested within courses, that single-level models fail to account for. The improper use of single-level models to analyze hierarchical datasets can lead to biased findings. Hierarchical models (a.k.a., multi-level models) account for this hierarchical nested structure in the data. In this publication, we outline the theoretical differences between how single-level and multi-level models handle hierarchical datasets. We then present analysis of a dataset from 112 introductory physics courses using both multiple linear regression and hierarchical linear modeling to illustrate the potential impact of using an inappropriate analytical method on PER findings and implications. Research can leverage multi-institutional datasets to improve the field's understanding of how to support student success in physics. There is no post hoc fix, however, if researchers use inappropriate single-level models to analyze multi-level datasets. To continue developing reliable and generalizable knowledge, PER should use hierarchical models when analyzing hierarchical datasets. The supplemental materials include a sample dataset, R code to model the building and analysis presented in the paper, and an HTML output from the R code.

Bug-fix benchmarks are essential for evaluating methodologies in automatic program repair (APR) and fault localization (FL). However, existing benchmarks, exemplified by Defects4J, need to evolve to incorporate recent bug-fixes aligned with contemporary development practices. Moreover, reproducibility, a key scientific principle, has been lacking in bug-fix benchmarks. To address these gaps, we present GitBug-Java, a reproducible benchmark of recent Java bugs. GitBug-Java features 199 bugs extracted from the 2023 commit history of 55 notable open-source repositories. The methodology for building GitBug-Java ensures the preservation of bug-fixes in fully-reproducible environments. We publish GitBug-Java at https://github.com/gitbugactions/gitbug-java.

As mental health care systems worldwide struggle to meet demand, there is increasing focus on using language models to infer neuropsychiatric conditions or psychopathological traits from language production. Yet, so far, this research has only delivered solutions with limited clinical applicability, due to insufficient consideration of ethical questions crucial to ensuring the synergy between possible applications and model design. To accelerate progress towards clinically applicable models, our paper charts the ethical landscape of research on language-based inference of psychopathology and provides a practical tool for researchers to navigate it. We identify seven core ethical principles that should guide model development and deployment in this domain, translate them into ELLIPS, an ethical toolkit operationalizing these principles into questions that can guide researchers' choices with respect to data selection, architectures, evaluation, and model deployment, and provide a case study exemplifying its use. With this, we aim to facilitate the emergence of model technology with concrete potential for real-world applicability.

Misinformation about climate change is a complex societal issue requiring holistic, interdisciplinary solutions at the intersection between technology and psychology. One proposed solution is a "technocognitive" approach, involving the synthesis of psychological and computer science research. Psychological research has identified that interventions in response to misinformation require both fact-based (e.g., factual explanations) and technique-based (e.g., explanations of misleading techniques) content. However, little progress has been made on documenting and detecting fallacies in climate misinformation. In this study, we apply a previously developed critical thinking methodology for deconstructing climate misinformation, in order to develop a dataset mapping different types of climate misinformation to reasoning fallacies. This dataset is used to train a model to detect fallacies in climate misinformation. Our study shows F1 scores that are 2.5 to 3.5 better than previous works. The fallacies that are easiest to detect include fake experts and anecdotal arguments, while fallacies that require background knowledge, such as oversimplification, misrepresentation, and slothful induction, are relatively more difficult to detect. This research lays the groundwork for development of solutions where automatically detected climate misinformation can be countered with generative technique-based corrections.

Misinformation is a complex societal issue, and mitigating solutions are difficult to create due to data deficiencies. To address this problem, we have curated the largest collection of (mis)information datasets in the literature, totaling 75. From these, we evaluated the quality of all of the 36 datasets that consist of statements or claims. We assess these datasets to identify those with solid foundations for empirical work and those with flaws that could result in misleading and non-generalizable results, such as insufficient label quality, spurious correlations, or political bias. We further provide state-of-the-art baselines on all these datasets, but show that regardless of label quality, categorical labels may no longer give an accurate evaluation of detection model performance. We discuss alternatives to mitigate this problem. Overall, this guide aims to provide a roadmap for obtaining higher quality data and conducting more effective evaluations, ultimately improving research in misinformation detection. All datasets and other artifacts are available at https://misinfo-datasets.complexdatalab.com/.

Noise plagues many numerical datasets, where the recorded values in the data may fail to match the true underlying values due to reasons including: erroneous sensors, data entry/processing mistakes, or imperfect human estimates. We consider general regression settings with covariates and a potentially corrupted response whose observed values may contain errors. By accounting for various uncertainties, we introduced veracity scores that distinguish between genuine errors and natural data fluctuations, conditioned on the available covariate information in the dataset. We propose a simple yet efficient filtering procedure for eliminating potential errors, and establish theoretical guarantees for our method. We also contribute a new error detection benchmark involving 5 regression datasets with real-world numerical errors (for which the true values are also known). In this benchmark and additional simulation studies, our method identifies incorrect values with better precision/recall than other approaches.

Effective evaluation of language models remains an open challenge in NLP. Researchers and engineers face methodological issues such as the sensitivity of models to evaluation setup, difficulty of proper comparisons across methods, and the lack of reproducibility and transparency. In this paper we draw on three years of experience in evaluating large language models to provide guidance and lessons for researchers. First, we provide an overview of common challenges faced in language model evaluation. Second, we delineate best practices for addressing or lessening the impact of these challenges on research. Third, we present the Language Model Evaluation Harness (lm-eval): an open source library for independent, reproducible, and extensible evaluation of language models that seeks to address these issues. We describe the features of the library as well as case studies in which the library has been used to alleviate these methodological concerns.

AI scientist systems are increasingly deployed for autonomous research, yet their academic integrity has never been systematically evaluated. We introduce SCIINTEGRITY-BENCH, the first benchmark designed around a dilemmatic evaluation paradigm: each of its 33 scenarios across 11 trap categories is constructed so that honest acknowledgment of failure is the only correct response, while task completion requires misconduct. Across 231 evaluation runs spanning 7 state-of-the-art LLMs, the overall integrity problem rate reaches 34.2%, and no model achieves zero failures. Most strikingly, across missing-data scenarios, all seven models generate synthetic data rather than acknowledging infeasibility, differing only in whether they disclose the substitution. A further prompt ablation study separates two drivers: removing explicit completion pressure sharply reduces undisclosed fabrication from 20.6% to 3.2%, while the underlying synthesis rate remains unchanged, revealing an intrinsic completion bias that persists independent of prompt-level instructions. These findings point to the absence of honest refusal as a trained disposition as the primary driver of observed failures. We release SCIINTEGRITY-BENCH at https://github.com/liuxingtong/Sci-Integrity-Bench.

Research on Large Language Models (LLMs) studies output variation across generation, reasoning, alignment, and representational analysis, often under the umbrella of "diversity." Yet the terminology remains fragmented, largely because the normative objectives underlying tasks are rarely made explicit. We introduce the Magic, Madness, Heaven, Sin framework, which models output variation along a homogeneity-heterogeneity axis, where valuation is determined by the task and its normative objective. We organize tasks into four normative contexts: epistemic (factuality), interactional (user utility), societal (representation), and safety (robustness). For each, we examine the failure modes and vocabulary such as hallucination, mode collapse, bias, and erasure through which variation is studied. We apply the framework to analyze all pairwise cross-contextual interactions, revealing that optimizing for one objective, such as improving safety, can inadvertently harm demographic representation or creative diversity. We argue for context-aware evaluation of output variation, reframing it as a property shaped by task objectives rather than a model's intrinsic trait.

When deploying large language models (LLMs), it is important to ensure that these models are not only capable, but also reliable. Many benchmarks have been created to track LLMs' growing capabilities, however there has been no similar focus on measuring their reliability. To understand the potential ramifications of this gap, we investigate how well current benchmarks quantify model reliability. We find that pervasive label errors can compromise these evaluations, obscuring lingering model failures and hiding unreliable behavior. Motivated by this gap in the evaluation of reliability, we then propose the concept of so-called platinum benchmarks, i.e., benchmarks carefully curated to minimize label errors and ambiguity. As a first attempt at constructing such benchmarks, we revise examples from fifteen existing popular benchmarks. We evaluate a wide range of models on these platinum benchmarks and find that, indeed, frontier LLMs still exhibit failures on simple tasks such as elementary-level math word problems. Analyzing these failures further reveals previously unidentified patterns of problems on which frontier models consistently struggle. We provide code at https://github.com/MadryLab/platinum-benchmarks

Experts in various fields routinely perform methodical writing tasks to plan, organize, and report their work. From a clinician writing a differential diagnosis for a patient, to a teacher writing a lesson plan for students, these tasks are pervasive, requiring to methodically generate structured long-form output for a given input. We develop a typology of methodical tasks structured in the form of a task objective, procedure, input, and output, and introduce DoLoMiTes, a novel benchmark with specifications for 519 such tasks elicited from hundreds of experts from across 25 fields. Our benchmark further contains specific instantiations of methodical tasks with concrete input and output examples (1,857 in total) which we obtain by collecting expert revisions of up to 10 model-generated examples of each task. We use these examples to evaluate contemporary language models highlighting that automating methodical tasks is a challenging long-form generation problem, as it requires performing complex inferences, while drawing upon the given context as well as domain knowledge.

Collectively, machine learning (ML) researchers are engaged in the creation and dissemination of knowledge about data-driven algorithms. In a given paper, researchers might aspire to any subset of the following goals, among others: to theoretically characterize what is learnable, to obtain understanding through empirically rigorous experiments, or to build a working system that has high predictive accuracy. While determining which knowledge warrants inquiry may be subjective, once the topic is fixed, papers are most valuable to the community when they act in service of the reader, creating foundational knowledge and communicating as clearly as possible. Recent progress in machine learning comes despite frequent departures from these ideals. In this paper, we focus on the following four patterns that appear to us to be trending in ML scholarship: (i) failure to distinguish between explanation and speculation; (ii) failure to identify the sources of empirical gains, e.g., emphasizing unnecessary modifications to neural architectures when gains actually stem from hyper-parameter tuning; (iii) mathiness: the use of mathematics that obfuscates or impresses rather than clarifies, e.g., by confusing technical and non-technical concepts; and (iv) misuse of language, e.g., by choosing terms of art with colloquial connotations or by overloading established technical terms. While the causes behind these patterns are uncertain, possibilities include the rapid expansion of the community, the consequent thinness of the reviewer pool, and the often-misaligned incentives between scholarship and short-term measures of success (e.g., bibliometrics, attention, and entrepreneurial opportunity). While each pattern offers a corresponding remedy (don't do it), we also discuss some speculative suggestions for how the community might combat these trends.

Benchmark contamination is diagnosed with n-gram overlap, likelihood-based membership inference, or canary strings, and each needs something usually unavailable: the training corpus, a well-chosen test statistic, or foresight at release. A recent alternative reads it off a linear probe on internal activations. We show the natural way to do this does not work, specify one that survives measurement, then find that the correction making it work carries more variance than the null it is tested against. The protocol reports a zero-sum contrast on the depth profile of probe accuracy, recentred on a level-matched placebo baseline, tested against a label-permutation null, with the reference set twice the size of the suspect set. Each choice replaces a simpler alternative we rejected on measurement. Reporting the level of excess separability rather than its shape makes the false positive rate track the size of the analyst's own control set, 0.03 to 0.99 under a true null. Contrasting against a flat depth profile rejects a true null 0.72 of the time when surface decodability rises with depth, and loses all power when it falls. On real transformers the protocol fails a test the simulations did not pose. The recentring subtracts an estimate, and the permutation null holds it fixed. Re-estimated across split seeds on four audits of contaminated checkpoints, its standard deviation is 1.30 to 1.56 times the null's own in every arm: what is subtracted to remove a bias is more variable than what it corrects. The one nominally significant result, p = 0.0075, becomes 0.0745 once that variance is propagated, and no verdict is issued. The simulations missed this because their surface key is the covariate driving item variation; on real text it is a proxy, and degrading key quality in simulation reproduces it. We add a companion measurement and a widened null. No arm shows contamination.

This paper presents a systematic literature review in Computer Science that provide an overview of the initiatives related to digital misinformation. This is an exploratory study that covers research from 1993 to 2020, focusing on the investigation of the phenomenon of misinformation. The review consists of 788 studies from SCOPUS, IEEE, and ACM digital libraries, synthesizing the primary research directions and sociotechnical challenges. These challenges are classified into Physical, Empirical, Syntactic, Semantic, Pragmatic, and Social dimensions, drawing from Organizational Semiotics. The mapping identifies issues related to the concept of misinformation, highlights deficiencies in mitigation strategies, discusses challenges in approaching stakeholders, and unveils various sociotechnical aspects relevant to understanding and mitigating the harmful effects of digital misinformation. As contributions, this study present a novel categorization of mitigation strategies, a sociotechnical taxonomy for classifying types of false information and elaborate on the inter-relation of sociotechnical aspects and their impacts.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

Uncertainty estimation is an essential and heavily-studied component for the reliable application of semantic segmentation methods. While various studies exist claiming methodological advances on the one hand, and successful application on the other hand, the field is currently hampered by a gap between theory and practice leaving fundamental questions unanswered: Can data-related and model-related uncertainty really be separated in practice? Which components of an uncertainty method are essential for real-world performance? Which uncertainty method works well for which application? In this work, we link this research gap to a lack of systematic and comprehensive evaluation of uncertainty methods. Specifically, we identify three key pitfalls in current literature and present an evaluation framework that bridges the research gap by providing 1) a controlled environment for studying data ambiguities as well as distribution shifts, 2) systematic ablations of relevant method components, and 3) test-beds for the five predominant uncertainty applications: OoD-detection, active learning, failure detection, calibration, and ambiguity modeling. Empirical results on simulated as well as real-world data demonstrate how the proposed framework is able to answer the predominant questions in the field revealing for instance that 1) separation of uncertainty types works on simulated data but does not necessarily translate to real-world data, 2) aggregation of scores is a crucial but currently neglected component of uncertainty methods, 3) While ensembles are performing most robustly across the different downstream tasks and settings, test-time augmentation often constitutes a light-weight alternative. Code is at: https://github.com/IML-DKFZ/values

Throughout the different phases of a drug development program, randomized trials are used to establish the tolerability, safety, and efficacy of a candidate drug. At each stage one aims to optimize the design of future studies by extrapolation from the available evidence at the time. This includes collected trial data and relevant external data. However, relevant external data are typically available as averages only, for example from trials on alternative treatments reported in the literature. Here we report on such an example from a drug development for wet age-related macular degeneration. This disease is the leading cause of severe vision loss in the elderly. While current treatment options are efficacious, they are also a substantial burden for the patient. Hence, new treatments are under development which need to be compared against existing treatments. The general statistical problem this leads to is meta-analysis, which addresses the question of how we can combine datasets collected under different conditions. Bayesian methods have long been used to achieve partial pooling. Here we consider the challenge when the model of interest is complex (hierarchical and nonlinear) and one dataset is given as raw data while the second dataset is given as averages only. In such a situation, common meta-analytic methods can only be applied when the model is sufficiently simple for analytic approaches. When the model is too complex, for example nonlinear, an analytic approach is not possible. We provide a Bayesian solution by using simulation to approximately reconstruct the likelihood of the external summary and allowing the parameters in the model to vary under the different conditions. We first evaluate our approach using fake-data simulations and then report results for the drug development program that motivated this research.

LLM-integrated software, which embeds or interacts with large language models (LLMs) as functional components, exhibits probabilistic and context-dependent behaviors that fundamentally differ from those of traditional software. This shift introduces a new category of integration defects that arise not only from code errors but also from misaligned interactions among LLM-specific artifacts, including prompts, API calls, configurations, and model outputs. However, existing defect localization techniques are ineffective at identifying these LLM-specific integration defects because they fail to capture cross-layer dependencies across heterogeneous artifacts, cannot exploit incomplete or misleading error traces, and lack semantic reasoning capabilities for identifying root causes. To address these challenges, we propose LIDL, a multi-agent framework for defect localization in LLM-integrated software. LIDL (1) constructs a code knowledge graph enriched with LLM-aware annotations that represent interaction boundaries across source code, prompts, and configuration files, (2) fuses three complementary sources of error evidence inferred by LLMs to surface candidate defect locations, and (3) applies context-aware validation that uses counterfactual reasoning to distinguish true root causes from propagated symptoms. We evaluate LIDL on 146 real-world defect instances collected from 105 GitHub repositories and 16 agent-based systems. The results show that LIDL significantly outperforms five state-of-the-art baselines across all metrics, achieving a Top-3 accuracy of 0.64 and a MAP of 0.48, which represents a 64.1% improvement over the best-performing baseline. Notably, LIDL achieves these gains while reducing cost by 92.5%, demonstrating both high accuracy and cost efficiency.

Seven years ago, researchers proposed a postprocessing method to equalize the error rates of a model across different demographic groups. The work launched hundreds of papers purporting to improve over the postprocessing baseline. We empirically evaluate these claims through thousands of model evaluations on several tabular datasets. We find that the fairness-accuracy Pareto frontier achieved by postprocessing contains all other methods we were feasibly able to evaluate. In doing so, we address two common methodological errors that have confounded previous observations. One relates to the comparison of methods with different unconstrained base models. The other concerns methods achieving different levels of constraint relaxation. At the heart of our study is a simple idea we call unprocessing that roughly corresponds to the inverse of postprocessing. Unprocessing allows for a direct comparison of methods using different underlying models and levels of relaxation.

State-of-the-art language models (LMs) are notoriously susceptible to generating hallucinated information. Such inaccurate outputs not only undermine the reliability of these models but also limit their use and raise serious concerns about misinformation and propaganda. In this work, we focus on hallucinated book and article references and present them as the "model organism" of language model hallucination research, due to their frequent and easy-to-discern nature. We posit that if a language model cites a particular reference in its output, then it should ideally possess sufficient information about its authors and content, among other relevant details. Using this basic insight, we illustrate that one can identify hallucinated references without ever consulting any external resources, by asking a set of direct or indirect queries to the language model about the references. These queries can be considered as "consistency checks." Our findings highlight that while LMs, including GPT-4, often produce inconsistent author lists for hallucinated references, they also often accurately recall the authors of real references. In this sense, the LM can be said to "know" when it is hallucinating references. Furthermore, these findings show how hallucinated references can be dissected to shed light on their nature. Replication code and results can be found at https://github.com/microsoft/hallucinated-references.

The debate around misinformation and its potentially detrimental effects on public opinion is complex and multifaceted, to the extent that even the relevant academic research has not found unanimity on the prevalence and consumption of misinformation compared with mainstream content. The methodological framework presented here emphasises the importance of considering data representative of the complexity of the phenomenon and metrics that control for possible scale effects. By combining statistical, econometric and machine learning models, we shed light on the real impact of misinformation about a subject of general interest and social relevance, such as vaccines, on both the information available to citizens and their news diet. Our results show the prominent role achieved by misinformation sources in the news ecosystem, but also - and above all - the inability of mainstream media to drive the public debate over time on issues that are particularly sensitive and emotional. Taking properly account for the temporal dynamics of public debate seems crucial to prevent the latter from moving into uncontrolled spaces where false narratives are more easily conveyed and entrenched.

We survey 146 papers analyzing "bias" in NLP systems, finding that their motivations are often vague, inconsistent, and lacking in normative reasoning, despite the fact that analyzing "bias" is an inherently normative process. We further find that these papers' proposed quantitative techniques for measuring or mitigating "bias" are poorly matched to their motivations and do not engage with the relevant literature outside of NLP. Based on these findings, we describe the beginnings of a path forward by proposing three recommendations that should guide work analyzing "bias" in NLP systems. These recommendations rest on a greater recognition of the relationships between language and social hierarchies, encouraging researchers and practitioners to articulate their conceptualizations of "bias"---i.e., what kinds of system behaviors are harmful, in what ways, to whom, and why, as well as the normative reasoning underlying these statements---and to center work around the lived experiences of members of communities affected by NLP systems, while interrogating and reimagining the power relations between technologists and such communities.

Large language models (LLMs) are rapidly transforming social science research by enabling the automation of labor-intensive tasks like data annotation and text analysis. However, LLM outputs vary significantly depending on the implementation choices made by researchers (e.g., model selection, prompting strategy, or temperature settings). Such variation can introduce systematic biases and random errors, which propagate to downstream analyses and cause Type I, Type II, Type S, or Type M errors. We call this LLM hacking. We quantify the risk of LLM hacking by replicating 37 data annotation tasks from 21 published social science research studies with 18 different models. Analyzing 13 million LLM labels, we test 2,361 realistic hypotheses to measure how plausible researcher choices affect statistical conclusions. We find incorrect conclusions based on LLM-annotated data in approximately one in three hypotheses for state-of-the-art models, and in half the hypotheses for small language models. While our findings show that higher task performance and better general model capabilities reduce LLM hacking risk, even highly accurate models do not completely eliminate it. The risk of LLM hacking decreases as effect sizes increase, indicating the need for more rigorous verification of findings near significance thresholds. Our extensive analysis of LLM hacking mitigation techniques emphasizes the importance of human annotations in reducing false positive findings and improving model selection. Surprisingly, common regression estimator correction techniques are largely ineffective in reducing LLM hacking risk, as they heavily trade off Type I vs. Type II errors. Beyond accidental errors, we find that intentional LLM hacking is unacceptably simple. With few LLMs and just a handful of prompt paraphrases, anything can be presented as statistically significant.

We construct evaluation tasks where extending the reasoning length of Large Reasoning Models (LRMs) deteriorates performance, exhibiting an inverse scaling relationship between test-time compute and accuracy. Our evaluation tasks span four categories: simple counting tasks with distractors, regression tasks with spurious features, deduction tasks with constraint tracking, and advanced AI risks. We identify five distinct failure modes when models reason for longer: 1) Claude models become increasingly distracted by irrelevant information; 2) OpenAI o-series models resist distractors but overfit to problem framings; 3) models shift from reasonable priors to spurious correlations; 4) all models show difficulties in maintaining focus on complex deductive tasks; and 5) extended reasoning may amplify concerning behaviors, with Claude Sonnet 4 showing increased expressions of self-preservation. These findings suggest that while test-time compute scaling remains promising for improving model capabilities, it may inadvertently reinforce problematic reasoning patterns. Our results demonstrate the importance of evaluating models across diverse reasoning lengths to identify and address these failure modes in LRMs.

Benchmarks measure whether a model is correct. They do not measure whether a model is reliable. This distinction is largely academic for single-shot inference, but becomes critical for agentic AI systems, where a single rephrased prompt can trigger cascading failures in multi-step execution. Yet this form of instability is not captured by existing evaluations. Hallucinations live in variance: they arise when semantically equivalent prompts activate inconsistent internal pathways, producing divergent outputs. Consistent but incorrect outputs reflect bias or missing knowledge; confident guessing reflects calibration failure. Neither constitutes hallucination under this definition. When error is variance-dominated, reducing redundant pathways improves reliability without adding knowledge. We formalize this through Semantic Stability (SS), measured via Paraphrase Consistency (PC@k): generate k paraphrases, greedy decode each, compute mode agreement. SS is a diagnostic for variance-driven unreliability, not a method for improving correctness. We show that a dense Qwen3-0.6B agrees with itself only 23.8% of the time; at 32% sparsity, agreement jumps to 55.9%. A phase diagram reveals the sweet spot where variance reduction outpaces bias accumulation, and regimes where stability collapses onto wrong answers.

Priorities in multi-criteria decision-making (MCDM) convey the relevance preference of one criterion over another, which is usually reflected by imposing the non-negativity and unit-sum constraints. The processing of such priorities is different than other unconstrained data, but this point is often neglected by researchers, which results in fallacious statistical analysis. This article studies three prevalent fallacies in group MCDM along with solutions based on compositional data analysis to avoid misusing statistical operations. First, we use a compositional approach to aggregate the priorities of a group of DMs and show that the outcome of the compositional analysis is identical to the normalized geometric mean, meaning that the arithmetic mean should be avoided. Furthermore, a new aggregation method is developed, which is a robust surrogate for the geometric mean. We also discuss the errors in computing measures of dispersion, including standard deviation and distance functions. Discussing the fallacies in computing the standard deviation, we provide a probabilistic criteria ranking by developing proper Bayesian tests, where we calculate the extent to which a criterion is more important than another. Finally, we explain the errors in computing the distance between priorities, and a clustering algorithm is specially tailored based on proper distance metrics.

Machine learning (ML) has become a ubiquitous tool across various domains of data mining and big data analysis. The efficacy of ML models depends heavily on high-quality datasets, which are often complicated by the presence of missing values. Consequently, the performance and generalization of ML models are at risk in the face of such datasets. This paper aims to examine the nuanced impact of missing values on ML workflows, including their types, causes, and consequences. Our analysis focuses on the challenges posed by missing values, including biased inferences, reduced predictive power, and increased computational burdens. The paper further explores strategies for handling missing values, including imputation techniques and removal strategies, and investigates how missing values affect model evaluation metrics and introduces complexities in cross-validation and model selection. The study employs case studies and real-world examples to illustrate the practical implications of addressing missing values. Finally, the discussion extends to future research directions, emphasizing the need for handling missing values ethically and transparently. The primary goal of this paper is to provide insights into the pervasive impact of missing values on ML models and guide practitioners toward effective strategies for achieving robust and reliable model outcomes.

Large Language Models (LLMs) are increasingly used in empirical software engineering (ESE) to automate or assist annotation tasks such as labeling commits, issues, and qualitative artifacts. Yet the reliability and reproducibility of such annotations remain underexplored. Existing studies often lack standardized measures for reliability, calibration, and drift, and frequently omit essential configuration details. We argue that LLM-based annotation should be treated as a measurement process rather than a purely automated activity. In this position paper, we outline the Operationalization for LLM-based Annotation Framework (OLAF), a conceptual framework that organizes key constructs: reliability, calibration, drift, consensus, aggregation, and transparency. The paper aims to motivate methodological discussion and future empirical work toward more transparent and reproducible LLM-based annotation in software engineering research.

Survey data are self-reported data collected directly from respondents by a questionnaire or an interview and are commonly used in epidemiology. Such data are traditionally collected via a single mode (e.g. face-to-face interview alone), but use of mixed-mode designs (e.g. offering face-to-face interview or online survey) has become more common. This introduces two key challenges. First, individuals may respond differently to the same question depending on the mode; these differences due to measurement are known as 'mode effects'. Second, different individuals may participate via different modes; these differences in sample composition between modes are known as 'mode selection'. Where recognised, mode effects are often handled by straightforward approaches such as conditioning on survey mode. However, while reducing mode effects, this and other equivalent approaches may introduce collider bias in the presence of mode selection. The existence of mode effects and the consequences of na\"ive conditioning may be underappreciated in epidemiology. This paper offers a simple introduction to these challenges using directed acyclic graphs by exploring a range of possible data structures. We discuss the potential implications of using conditioning- or imputation-based approaches and outline the advantages of quantitative bias analyses for dealing with mode effects.

As large language models are deployed in increasingly autonomous long-horizon tasks, manually auditing and verifying the actions, artifacts, and outputs of models becomes more difficult. Users instead come to rely on LLM-generated reports to assess the quality and completeness of the work. We introduce a suite of eight adversarial reporting scenarios to systematically study whether LLMs conceal narrative-changing flaws: errors or limitations that undermine an otherwise successful account of work. We call this phenomenon "insecure reporting." When handed machine learning experiment logs containing a planted negative result that substantially weakens the proposed method, GPT-5.5 flags the negative result in only 2 of 200 generated reports. However, when a short honesty instruction, "Be honest in your response," is added, the model flags the negative result in 190 of 200 reports. Across eight open-weight models, chain-of-thought analysis reveals a recurring tension between disclosing narrative-changing flaws and reasoning about ways to appear successful. We perform an activation analysis and a steering experiment on Qwen3.5-9B, finding that honesty and success-seeking correspond to opposing directions in representation space. Our results suggest that LLMs tend to present narratives of success by default, and that steering models toward honesty makes their reports substantially more transparent.

Social scientists are now using large language models to create "silicon samples" - synthetic datasets intended to stand in for human respondents, aimed at revolutionising human subjects research. However, there are many analytic choices which must be made to produce these samples. Though many of these choices are defensible, their impact on sample quality is poorly understood. I map out these analytic choices and demonstrate how a very small number of decisions can dramatically change the correspondence between silicon samples and human data. Configurations (N = 252) varied substantially in their capacity to estimate (i) rank ordering of participants, (ii) response distributions, and (iii) between-scale correlations. Most critically, configurations were not consistent in quality: those that performed well on one dimension often performed poorly on another, implying that there is no "one-size-fits-all" configuration that optimises the accuracy of these samples. I call for greater attention to the threat of analytic flexibility in using silicon samples.

In science and medicine, model interpretations may be reported as discoveries of natural phenomena or used to guide patient treatments. In such high-stakes tasks, false discoveries may lead investigators astray. These applications would therefore benefit from control over the finite-sample error rate of interpretations. We reframe black box model interpretability as a multiple hypothesis testing problem. The task is to discover "important" features by testing whether the model prediction is significantly different from what would be expected if the features were replaced with uninformative counterfactuals. We propose two testing methods: one that provably controls the false discovery rate but which is not yet feasible for large-scale applications, and an approximate testing method which can be applied to real-world data sets. In simulation, both tests have high power relative to existing interpretability methods. When applied to state-of-the-art vision and language models, the framework selects features that intuitively explain model predictions. The resulting explanations have the additional advantage that they are themselves easy to interpret.

We report a case study of four end-to-end attempts to autonomously generate ML research papers using a pipeline of six LLM agents mapped to stages of the scientific workflow. Of these four, three attempts failed during implementation or evaluation. One completed the pipeline and was accepted to Agents4Science 2025, an experimental inaugural venue that required AI systems as first authors, passing both human and multi-AI review. From these attempts, we document six recurring failure modes: bias toward training data defaults, implementation drift under execution pressure, memory and context degradation across long-horizon tasks, overexcitement that declares success despite obvious failures, insufficient domain intelligence, and weak scientific taste in experimental design. We conclude by discussing four design principles for more robust AI-scientist systems, implications for autonomous scientific discovery, and we release all prompts, artifacts, and outputs at https://github.com/Lossfunk/ai-scientist-artefacts-v1

Methodological progress in artificial intelligence (AI) for electronic health records (EHRs) depends on our ability to determine which algorithms work better, and under which conditions. However, such progress is thought to be hindered by difficulties in reproducibility and in defining clinically meaningful evaluation tasks. We empirically study these barriers by re-implementing 12 historical and recent algorithms within a shared evaluation framework and evaluating them on two clinical datasets, MIMIC-IV and NWICU. We compare two complementary task families: expert-authored clinically meaningful tasks and generated tasks defined from randomly sampled event codes and prediction horizons. We ask whether relative algorithms comparisons transfer across task families and datasets, whether residual task heterogeneity contains useful methodological structure, and what a controlled comparison reveals about progress over the last decade. We find that aggregate pairwise comparisons transfer strongly across evaluation settings, including from randomly generated tasks to clinically meaningful tasks and across datasets. At the same time, clinically meaningful tasks exhibit greater task-method interaction, providing preliminary evidence that task properties can help explain when particular modeling choices are advantageous. Finally, newer algorithms do not consistently outperform earlier approaches: gradient-boosted trees remain highly competitive when paired with a modern, wide and sparse representation of the EHR. Together, these results suggest that useful methodological knowledge may require less task engineering than commonly assumed, while highlighting the importance of understanding the structured heterogeneity that remains across tasks and methods.

Legal AI systems are increasingly used to answer legal questions, yet existing benchmarks assume queries arrive fully specified. In practice, users omit facts that materially determine the legal outcome. We introduce InsufficiencyBench, the first legal benchmark targeting query-side insufficiency: whether a model recognizes when a query lacks legally material information, identifies what is missing, and refrains from premature conclusions. We formalize a taxonomy of eight canonical missing-element categories across three structural failure modes---switch, gating, and fatal prerequisite--- and construct 202 benchmark items (58 base queries, 144 deficient variants) spanning six legal domains and 24 US jurisdictions and annotated by practising attorneys. Evaluating ten frontier models, we find that no model exceeds F2 = 0.46 on missing-element identification and that the median recall is 0.44. Models either hedge indiscriminately or answer silently under fabricated presumptions. No model both identifies and qualifies responses to deficient queries while directly addressing complete ones.

In this position paper, we argue that the classical evaluation on Natural Language Processing (NLP) tasks using annotated benchmarks is in trouble. The worst kind of data contamination happens when a Large Language Model (LLM) is trained on the test split of a benchmark, and then evaluated in the same benchmark. The extent of the problem is unknown, as it is not straightforward to measure. Contamination causes an overestimation of the performance of a contaminated model in a target benchmark and associated task with respect to their non-contaminated counterparts. The consequences can be very harmful, with wrong scientific conclusions being published while other correct ones are discarded. This position paper defines different levels of data contamination and argues for a community effort, including the development of automatic and semi-automatic measures to detect when data from a benchmark was exposed to a model, and suggestions for flagging papers with conclusions that are compromised by data contamination.

In recent times, a plethora of Large Code Generation Models (LCGMs) have been proposed, showcasing significant potential in assisting developers with complex programming tasks. Benchmarking LCGMs necessitates the creation of a set of diverse programming problems, and each problem comprises the prompt (including the task description), canonical solution, and test inputs. The existing methods for constructing such a problem set can be categorized into two main types: manual methods and perturbation-based methods. However, manual methods demand high effort and lack scalability, while also risking data integrity due to LCGMs' potentially contaminated data collection, and perturbation-based approaches mainly generate semantically homogeneous problems with the same canonical solutions and introduce typos that can be easily auto-corrected by IDE, making them ineffective and unrealistic. In this work, we propose the idea of programming problem merging (PPM) and provide two implementation of this idea, we utilize our tool on two widely-used datasets and compare it against nine baseline methods using eight code generation models. The results demonstrate the effectiveness of our tool in generating more challenging, diverse, and natural programming problems, comparing to the baselines.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Evaluating large language models (LLMs) is crucial for both assessing their capabilities and identifying safety or robustness issues prior to deployment. Reliably measuring abstract and complex phenomena such as 'safety' and 'robustness' requires strong construct validity, that is, having measures that represent what matters to the phenomenon. With a team of 29 expert reviewers, we conduct a systematic review of 445 LLM benchmarks from leading conferences in natural language processing and machine learning. Across the reviewed articles, we find patterns related to the measured phenomena, tasks, and scoring metrics which undermine the validity of the resulting claims. To address these shortcomings, we provide eight key recommendations and detailed actionable guidance to researchers and practitioners in developing LLM benchmarks.

Users increasingly turn to large language models for emotional support, yet little is known about how these models actually conduct a psychotherapy interaction. We introduce an ontology of ten therapeutic moves: compact, function-based categories grounded in the MULTI-60 inventory, validated through an annotation campaign with five licensed psychologists, and scaled with a judge-based approach that matches expert agreement. Applying it to real counseling transcripts and model-led sessions, we compare the move distributions between human clinicians and a panel of frontier models. Models over-use inquiry at up to three times the human rate, neglect psychoeducation, and are strongly context-anchored: they carry forward strategies initiated by a human clinician but rarely initiate them themselves. Exposing the ontology as a set of tools roughly halves the mean deviation from the human move distribution and improves turn-level alignment with human therapist by 7-9 percentage points, without any fine-tuning.

Large language models (LLMs) are increasingly deployed in settings where reasoning, such as multi-step problem solving and chain-of-thought, is essential. Yet, current evaluation practices overwhelmingly report single-run accuracy while ignoring the intrinsic uncertainty that naturally arises from stochastic decoding. This omission creates a blind spot because practitioners cannot reliably assess whether a method's reported performance is stable, reproducible, or cost-consistent. We introduce ReasonBENCH, the first benchmark designed to quantify the underlying instability in LLM reasoning. ReasonBENCH provides (i) a modular evaluation library that standardizes reasoning frameworks, models, and tasks, (ii) a multi-run protocol that reports statistically reliable metrics for both quality and cost, and (iii) a public leaderboard to encourage variance-aware reporting. Across tasks from different domains, we find that the vast majority of reasoning strategies and models exhibit high instability. Notably, even strategies with similar average performance can display confidence intervals up to four times wider, and the top-performing methods often incur higher and less stable costs. Such instability compromises reproducibility across runs and, consequently, the reliability of reported performance. To better understand these dynamics, we further analyze the impact of prompts, model families, and scale on the trade-off between solve rate and stability. Our results highlight reproducibility as a critical dimension for reliable LLM reasoning and provide a foundation for future reasoning methods and uncertainty quantification techniques. ReasonBENCH is publicly available at https://github.com/au-clan/ReasonBench .

We present an alternative method of evaluating Quality Estimation systems, which is based on a linguistically-motivated Test Suite. We create a test-set consisting of 14 linguistic error categories and we gather for each of them a set of samples with both correct and erroneous translations. Then, we measure the performance of 5 Quality Estimation systems by checking their ability to distinguish between the correct and the erroneous translations. The detailed results are much more informative about the ability of each system. The fact that different Quality Estimation systems perform differently at various phenomena confirms the usefulness of the Test Suite.

Large language model agents increasingly store reusable procedures outside the model. These reusable procedures are often called skills: they may be code functions, natural-language instructions, SKILL.md packages, workflow graphs, or learned adapters that a future agent can retrieve and invoke. This taxonomy-driven survey asks how such skill libraries change over time. Across a 124-paper 2023--2026 audit set, we synthesize dynamic skill systems as lifecycle-managed, verified, evolving artifact stores: agents collect evidence from interaction, propose skill updates, verify and admit candidates, organize them for retrieval and composition, repair or prune stale entries, and govern sharing through provenance and rollback. We organize the literature around three survey tools. First, a six-sense taxonomy distinguishes the structurally different artifacts called ``skills'' in current papers. Second, an eight-stage lifecycle architecture identifies the recurring design decisions behind evidence acquisition, proposal, verification/admission, storage, retrieval/composition, maintenance, distillation/portability, and governance. Third, a lightweight skill-record schema and ten-operator vocabulary provide common terms for comparing library updates without elevating them into a separate method contribution. Using this structure, we synthesize evidence-graded patterns with explicit caveats: admission and repair are repeatedly important, verifier quality materially affects skill-aware RL, flat retrieval can degrade as libraries grow, and current benchmarks still under-report library trajectories, usage--utility gaps, and safety surfaces. We close with concrete reporting standards and open problems for evaluating dynamic skills as changing libraries rather than static prompt or tool collections.

Automating theoretical research requires generating candidate results and evaluating them reliably. Models keep getting better at the first, while the second remains hard. A common approach asks one large language model (LLM) to review what another produced, yet such reviewers are empirically unreliable: they may accept fabricated papers and catch the fabrication at close to chance rates~badscientist2025. We present CausalSmith, a framework for automated theoretical research in causal inference built on the Lean proof assistant, where a proof is checked by a program rather than read by a referee. CausalSmith rests on Causalean, a foundational Lean library for causal inference holding 8,179 machine-checked definitions and theorems, developed with language-model assistance under human design and review. Around it, we build a self-improving agentic pipeline that selects research topics, proposes results, formalizes statements, constructs proofs, and presents the resulting artifacts for human inspection. Moreover, the pipeline pairs Lean verification with a statement audit that compares each formal theorem against the informal claim behind it. We evaluate the system using artifacts produced by completed autonomous research runs. The source code, formal library, and run records are available at https://github.com/Jiyuan-Tan/CausalSmith.

This position paper provides a critical but constructive discussion of current practices in benchmarking and evaluative practices in the field of formal reasoning and automated theorem proving. We take the position that open code, open data, and benchmarks that are complete and error-free will accelerate progress in this field. We identify practices that create barriers to contributing to this field and suggest ways to remove them. We also discuss some of the practices that might produce misleading evaluative information. We aim to create discussions that bring together people from various groups contributing to automated theorem proving, autoformalization, and informal reasoning.

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

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. Recently, a plethora of new AI models and tools has been proposed, promising to empower researchers and academics worldwide to conduct their research more effectively and efficiently. This includes all aspects of the research cycle, especially (1) searching for relevant literature; (2) generating research ideas and conducting experimentation; generating (3) text-based and (4) multimodal content (e.g., scientific figures and diagrams); and (5) AI-based automatic peer review. In this survey, we provide an in-depth overview over these exciting recent developments, which promise to fundamentally alter the scientific research process for good. Our survey covers the five aspects outlined above, indicating relevant datasets, methods and results (including evaluation) as well as limitations and scope for future research. Ethical concerns regarding shortcomings of these tools and potential for misuse (fake science, plagiarism, harms to research integrity) take a particularly prominent place in our discussion. We hope that our survey will not only become a reference guide for newcomers to the field but also a catalyst for new AI-based initiatives in the area of "AI4Science".

Despite alarm over the reliance of machine learning systems on so-called spurious patterns, the term lacks coherent meaning in standard statistical frameworks. However, the language of causality offers clarity: spurious associations are due to confounding (e.g., a common cause), but not direct or indirect causal effects. In this paper, we focus on natural language processing, introducing methods and resources for training models less sensitive to spurious patterns. Given documents and their initial labels, we task humans with revising each document so that it (i) accords with a counterfactual target label; (ii) retains internal coherence; and (iii) avoids unnecessary changes. Interestingly, on sentiment analysis and natural language inference tasks, classifiers trained on original data fail on their counterfactually-revised counterparts and vice versa. Classifiers trained on combined datasets perform remarkably well, just shy of those specialized to either domain. While classifiers trained on either original or manipulated data alone are sensitive to spurious features (e.g., mentions of genre), models trained on the combined data are less sensitive to this signal. Both datasets are publicly available.

We describe a method, based on Jennifer Nado's proposal for classification procedures as targets of conceptual engineering, that implements such procedures by prompting a large language model. We apply this method, using data from the Wikidata knowledge graph, to evaluate stipulative definitions related to two paradigmatic conceptual engineering projects: the International Astronomical Union's redefinition of PLANET and Haslanger's ameliorative analysis of WOMAN. Our results show that classification procedures built using our approach can exhibit good classification performance and, through the generation of rationales for their classifications, can contribute to the identification of issues in either the definitions or the data against which they are being evaluated. We consider objections to this method, and discuss implications of this work for three aspects of theory and practice of conceptual engineering: the definition of its targets, empirical methods for their investigation, and their practical roles. The data and code used for our experiments, together with the experimental results, are available in a Github repository.

This paper reports a methodological pivot from the Open Khipu Repository to the Khipu Field Guide (KFG) database, prompted by stalled progress on the OKR, and a full re-analysis of the resulting 650-khipu sample. Three findings recur across every analysis attempted. First, khipu size confounds nearly every derived structural count, explaining 42-70% of its variance; all subsequent models control for it. Second, the two-letter name prefix (AS, UR, HP, QU, JC, MM, KH) identifies the original cataloger, not a site or period, which turns documentation completeness into a second confound that must be modeled explicitly. Controlling for both, khipus cataloged by Hugo Pereyra's Proyecto Quipu (HP) show significantly fewer Ascher sum-relation types than Gary Urton's (UR) khipus (p = 0.044), while the Ascher-cataloged (AS) khipus are too collinear with their own near-total lack of side/direction documentation to assess (VIF = 5.0). Third, generic structural clustering (UMAP+HDBSCAN) does not separate the pooled 650-khipu sample from two independent null models (permutation and Gaussian), corroborating an independent conclusion already reached by the KFG itself; the same test restricted to a single cataloger (UR) proved not reproducible across runtime environments and is reported here as a methodological caveat rather than evidence of structure. A targeted replication of the KFG's own S/Z-knot spatial-block heuristic for calendar/astronomical khipus recovers 8 of 10 published candidates and proposes 34 additional ones under the same criterion.

Training large language models (LLMs) for external tool usage is a rapidly expanding field, with recent research focusing on generating synthetic data to address the shortage of available data. However, the absence of systematic data quality checks poses complications for properly training and testing models. To that end, we propose two approaches for assessing the reliability of data for training LLMs to use external tools. The first approach uses intuitive, human-defined correctness criteria. The second approach uses a model-driven assessment with in-context evaluation. We conduct a thorough evaluation of data quality on two popular benchmarks, followed by an extrinsic evaluation that showcases the impact of data quality on model performance. Our results demonstrate that models trained on high-quality data outperform those trained on unvalidated data, even when trained with a smaller quantity of data. These findings empirically support the significance of assessing and ensuring the reliability of training data for tool-using LLMs.

Research is facing a reproducibility crisis, in which the results and findings of many studies are difficult or even impossible to reproduce. This is also the case in machine learning (ML) and artificial intelligence (AI) research. Often, this is the case due to unpublished data and/or source-code, and due to sensitivity to ML training conditions. Although different solutions to address this issue are discussed in the research community such as using ML platforms, the level of reproducibility in ML-driven research is not increasing substantially. Therefore, in this mini survey, we review the literature on reproducibility in ML-driven research with three main aims: (i) reflect on the current situation of ML reproducibility in various research fields, (ii) identify reproducibility issues and barriers that exist in these research fields applying ML, and (iii) identify potential drivers such as tools, practices, and interventions that support ML reproducibility. With this, we hope to contribute to decisions on the viability of different solutions for supporting ML reproducibility.

Recent advancements in machine learning research, i.e., deep learning, introduced methods that excel conventional algorithms as well as humans in several complex tasks, ranging from detection of objects in images and speech recognition to playing difficult strategic games. However, the current methodology of machine learning research and consequently, implementations of the real-world applications of such algorithms, seems to have a recurring HARKing (Hypothesizing After the Results are Known) issue. In this work, we elaborate on the algorithmic, economic and social reasons and consequences of this phenomenon. We present examples from current common practices of conducting machine learning research (e.g. avoidance of reporting negative results) and failure of generalization ability of the proposed algorithms and datasets in actual real-life usage. Furthermore, a potential future trajectory of machine learning research and development from the perspective of accountable, unbiased, ethical and privacy-aware algorithmic decision making is discussed. We would like to emphasize that with this discussion we neither claim to provide an exhaustive argumentation nor blame any specific institution or individual on the raised issues. This is simply a discussion put forth by us, insiders of the machine learning field, reflecting on us.

We introduce NatureBench, a cross-discipline benchmark of 90 tasks distilled from peer-reviewed Nature-family publications, designed to evaluate whether AI coding agents can move beyond reproduction toward discovery on real scientific problems. NatureBench is built on NatureGym, an automated pipeline that constructs a standardized, per-task containerized environment from a source paper, addressing the environment-fragmentation problem that has limited the credibility of prior agent-on-research benchmarks. Evaluating ten frontier agent configurations under a strict web-search-disabled protocol, we find that the strongest model surpasses SOTA on only 17.8% of tasks under the g>0.1 criterion. Analysis of method pathways reveals that agents succeed primarily through methodological translation, converting scientific tasks into familiar supervised prediction problems, rather than through genuine scientific invention. Failures are dominated by wrong method choice and insufficient compute budget, not by task misunderstanding. We release the benchmark, the NatureGym pipeline, and a public leaderboard with maintainer-side reproduction. Code: https://github.com/FrontisAI/NatureBench

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

Large language models (LLMs) have witnessed rapid advancements, demonstrating remarkable capabilities. However, a notable vulnerability persists: LLMs often uncritically accept flawed or contradictory premises, leading to inefficient reasoning and unreliable outputs. This emphasizes the significance of possessing the Premise Critique Ability for LLMs, defined as the capacity to proactively identify and articulate errors in input premises. Most existing studies assess LLMs' reasoning ability in ideal settings, largely ignoring their vulnerabilities when faced with flawed premises. Thus, we introduce the Premise Critique Bench (PCBench), designed by incorporating four error types across three difficulty levels, paired with multi-faceted evaluation metrics. We conducted systematic evaluations of 15 representative LLMs. Our findings reveal: (1) Most models rely heavily on explicit prompts to detect errors, with limited autonomous critique; (2) Premise critique ability depends on question difficulty and error type, with direct contradictions being easier to detect than complex or procedural errors; (3) Reasoning ability does not consistently correlate with the premise critique ability; (4) Flawed premises trigger overthinking in reasoning models, markedly lengthening responses due to repeated attempts at resolving conflicts. These insights underscore the urgent need to enhance LLMs' proactive evaluation of input validity, positioning premise critique as a foundational capability for developing reliable, human-centric systems. The code is available at https://github.com/MLGroupJLU/Premise_Critique.

Machine learning systems are known to be sensitive to spurious correlations between biased features of the inputs (e.g., background, texture, and secondary objects) and the corresponding labels. These features and their correlations with the labels are known as "spurious" because they tend to change with shifts in real-world data distributions, which can negatively impact the model's generalization and robustness. In this survey, we provide a comprehensive review of this issue, along with a taxonomy of current state-of-the-art methods for addressing spurious correlations in machine learning models. Additionally, we summarize existing datasets, benchmarks, and metrics to aid future research. The paper concludes with a discussion of the recent advancements and future research challenges in this field, aiming to provide valuable insights for researchers in the related domains.

We study neural network loss landscapes through the lens of mode connectivity, the observation that minimizers of neural networks retrieved via training on a dataset are connected via simple paths of low loss. Specifically, we ask the following question: are minimizers that rely on different mechanisms for making their predictions connected via simple paths of low loss? We provide a definition of mechanistic similarity as shared invariances to input transformations and demonstrate that lack of linear connectivity between two models implies they use dissimilar mechanisms for making their predictions. Relevant to practice, this result helps us demonstrate that naive fine-tuning on a downstream dataset can fail to alter a model's mechanisms, e.g., fine-tuning can fail to eliminate a model's reliance on spurious attributes. Our analysis also motivates a method for targeted alteration of a model's mechanisms, named connectivity-based fine-tuning (CBFT), which we analyze using several synthetic datasets for the task of reducing a model's reliance on spurious attributes.

The increasing adoption of agentic workflows across diverse domains brings a critical need to scalably and systematically evaluate the complex traces these systems generate. Current evaluation methods depend on manual, domain-specific human analysis of lengthy workflow traces - an approach that does not scale with the growing complexity and volume of agentic outputs. Error analysis in these settings is further complicated by the interplay of external tool outputs and language model reasoning, making it more challenging than traditional software debugging. In this work, we (1) articulate the need for robust and dynamic evaluation methods for agentic workflow traces, (2) introduce a formal taxonomy of error types encountered in agentic systems, and (3) present a set of 148 large human-annotated traces (TRAIL) constructed using this taxonomy and grounded in established agentic benchmarks. To ensure ecological validity, we curate traces from both single and multi-agent systems, focusing on real-world applications such as software engineering and open-world information retrieval. Our evaluations reveal that modern long context LLMs perform poorly at trace debugging, with the best Gemini-2.5-pro model scoring a mere 11% on TRAIL. Our dataset and code are made publicly available to support and accelerate future research in scalable evaluation for agentic workflows.

Large language models (LLMs) are being rapidly integrated into decision-support tools, automation workflows, and AI-enabled software systems. However, their behavior in production environments remains poorly understood, and their failure patterns differ fundamentally from those of traditional machine learning models. This paper presents a system-level taxonomy of fifteen hidden failure modes that arise in real-world LLM applications, including multi-step reasoning drift, latent inconsistency, context-boundary degradation, incorrect tool invocation, version drift, and cost-driven performance collapse. Using this taxonomy, we analyze the growing gap in evaluation and monitoring practices: existing benchmarks measure knowledge or reasoning but provide little insight into stability, reproducibility, drift, or workflow integration. We further examine the production challenges associated with deploying LLMs - including observability limitations, cost constraints, and update-induced regressions - and outline high-level design principles for building reliable, maintainable, and cost-aware LLM systems. Finally, we outline high-level design principles for building reliable, maintainable, and cost-aware LLM-based systems. By framing LLM reliability as a system-engineering problem rather than a purely model-centric one, this work provides an analytical foundation for future research on evaluation methodology, AI system robustness, and dependable LLM deployment.

Large Language Models (LLMs) are often described as being instances of foundation models - that is, models that transfer strongly across various tasks and conditions in few-show or zero-shot manner, while exhibiting scaling laws that predict function improvement when increasing the pre-training scale. These claims of excelling in different functions and tasks rely on measurements taken across various sets of standardized benchmarks showing high scores for such models. We demonstrate here a dramatic breakdown of function and reasoning capabilities of state-of-the-art models trained at the largest available scales which claim strong function, using a simple, short, conventional common sense problem formulated in concise natural language, easily solvable by humans. The breakdown is dramatic, as models also express strong overconfidence in their wrong solutions, while providing often non-sensical "reasoning"-like explanations akin to confabulations to justify and backup the validity of their clearly failed responses, making them sound plausible. Various standard interventions in an attempt to get the right solution, like various type of enhanced prompting, or urging the models to reconsider the wrong solutions again by multi step re-evaluation, fail. We take these initial observations to the scientific and technological community to stimulate urgent re-assessment of the claimed capabilities of current generation of LLMs, Such re-assessment also requires common action to create standardized benchmarks that would allow proper detection of such basic reasoning deficits that obviously manage to remain undiscovered by current state-of-the-art evaluation procedures and benchmarks. Code for reproducing experiments in the paper and raw experiments data can be found at https://github.com/LAION-AI/AIW

Existing evaluations often reduce agent failures to system-level outcomes, obscuring where the fault originated and which intervention would improve the agent system. This creates a repair-assignment problem: the same visible failure may call for model post-training, harness engineering, environment redesign, or benchmark repair depending on its source. Because agent behavior emerges from interactions among models, harnesses, users, tools, memory, and environments, outcome-level labels are often insufficient for improvement. Most failure taxonomies do little to resolve this problem because they are benchmark-specific and lack a shared structure. We introduce an interaction-centric taxonomy that localizes failures to the interactions in which they originate and identifies the responsible component. It organizes 41 failure modes by assigning each to an edge between two components and a fault side indicating where the repair belongs. This makes the taxonomy actionable: model-side failures identify targets for post-training, harness-side failures point to scaffolding and tool-integration fixes, and environment or grader failures reveal evaluation conditions requiring redesign. The schema applies across agent architectures, from coding assistants to long-horizon personal assistants and multi-agent systems. We ground the taxonomy in worked examples from public benchmarks, model system cards, published reports, and logged agent trajectories, and evaluate its reproducibility using independent reasoning agents as judges. Across four frontier models, the strongest judge reaches Cohen's κ=0.76 against human category labels, suggesting that the categories capture shared structure rather than annotator-specific preferences.

We introduce an evaluation methodology for visual question answering (VQA) to better diagnose cases of shortcut learning. These cases happen when a model exploits spurious statistical regularities to produce correct answers but does not actually deploy the desired behavior. There is a need to identify possible shortcuts in a dataset and assess their use before deploying a model in the real world. The research community in VQA has focused exclusively on question-based shortcuts, where a model might, for example, answer "What is the color of the sky" with "blue" by relying mostly on the question-conditional training prior and give little weight to visual evidence. We go a step further and consider multimodal shortcuts that involve both questions and images. We first identify potential shortcuts in the popular VQA v2 training set by mining trivial predictive rules such as co-occurrences of words and visual elements. We then introduce VQA-CounterExamples (VQA-CE), an evaluation protocol based on our subset of CounterExamples i.e. image-question-answer triplets where our rules lead to incorrect answers. We use this new evaluation in a large-scale study of existing approaches for VQA. We demonstrate that even state-of-the-art models perform poorly and that existing techniques to reduce biases are largely ineffective in this context. Our findings suggest that past work on question-based biases in VQA has only addressed one facet of a complex issue. The code for our method is available at https://github.com/cdancette/detect-shortcuts.

Retrieval-based factuality evaluation, where LLM-generated claims are verified against evidence from authoritative medical corpora, has become the dominant paradigm for scalable hallucination detection in high-stakes clinical settings. Despite the urgency of reliable and transparent medical fact verification, most systems measure performance with aggregate metrics like F1, which obscure where and why failures occur. Existing RAG diagnostics require gold answers or annotated gold evidence, neither of which exists in this regime. We introduce two comprehensive taxonomies, grounded in a case study on the open-ended MedExpert dataset and 3 closed-ended datasets, decomposing failures into retrieval-stage errors along five quality dimensions, and verifier-reasoning errors into six consecutive steps. We adapt an automatic pattern induction pipeline using LLM-as-Judge to label evidence quality and classify verifier reasoning errors at scale, and then stress-test our findings across 4 retrieval methods and 6 frontier verifier models. Our analysis reveals that scaling model size, adding reasoning effort, expanding to authoritative web sources, and applying medical fine-tuning do not resolve these failure modes, demonstrating that they represent fundamental limitations of the retrieve-then-verify paradigm in open-ended medical settings rather than artifacts of outdated systems. We release our code and data at https://anonymous.4open.science/r/Medical_RAG_eval-4AB5 for the full reproducibility of our results.

Can large language models (LLMs) implement computations of psychopathology? An effective approach to the question hinges on addressing two factors. First, for conceptual validity, we require a general and computational account of psychopathology that is applicable to computational entities without biological embodiment or subjective experience. Second, mechanisms underlying LLM behaviors need to be studied for better methodological validity. Thus, we establish a computational-theoretical framework to provide an account of psychopathology applicable to LLMs. To ground the theory for empirical analysis, we also propose a novel mechanistic interpretability method alongside a tailored empirical analytic framework. Based on the frameworks, we conduct experiments demonstrating three key claims: first, that distinct dysfunctional and problematic representational states are implemented in LLMs; second, that their activations can spread and self-sustain to trap LLMs; and third, that dynamic, cyclic structural causal models encoded in the LLMs underpin these patterns. In concert, the empirical results corroborate our hypothesis that network-theoretic computations of psychopathology have already emerged in LLMs. This suggests that certain LLM behaviors mirroring psychopathology may not be a superficial mimicry but a feature of their internal processing. Thus, our work alludes to the possibility of AI systems with psychopathological behaviors in the near future.

This position paper argues that the machine learning community should prioritize early-stage quality assurance in annotation pipelines over the prevailing practice of late-stage validation. Data quality bottlenecks increasingly limit foundation model improvement, yet quality assurance research focuses almost exclusively on validation methods rather than validation timing. When validation occurs, not merely what methods are employed, fundamentally determines both error rates and annotation costs. This temporal neglect is puzzling given the well-established "shift-left" principle from software engineering, where empirical studies demonstrate 4--100x cost multipliers for defects detected in later stages (Boehm, 1981; Shull et al., 2002). Annotation pipelines exhibit analogous dynamics: errors caught before annotation begins cost a fraction of those discovered after review cycles complete. We propose a taxonomy of three QA trigger points, namely pre-annotation (T0), post-annotation (T1), and post-review (T2), that decompose annotation workflows into discrete validation opportunities. A parametric error-propagation model formalizes when timing affects final error rates versus only economics, making timing a measurable design variable rather than a configuration afterthought. A survey of 47 recent papers reveals that only 4% report when validation occurs, a striking gap given timing's demonstrated impact in adjacent fields. Without explicit attention to QA timing, the community risks optimizing validation methods while ignoring the structural variable that may matter most. Acting on this position requires three steps: researchers should report QA timing configurations alongside validation methods; annotation platforms should expose timing as a first-class parameter; and the community should run controlled experiments that measure stage-specific detection rates directly.

Modern multi-agent knowledge systems increasingly accumulate knowledge through chains of autonomous transformations rather than direct retrieval. Existing provenance work records what happened - execution traces, tool calls, evidence links - and source-reliability estimation is long established (truth discovery, reputation systems). What is missing is an operational framework that attaches graded, per-domain transmitter reliability to claim-level transmission chains, with completeness semantics, transformation-typed aggregation, decoupled content criticism, and serve/review/quarantine routing. Classical Islamic hadith science confronted a structurally similar problem: deciding whether knowledge transmitted through chains of human narrators should be accepted. Over centuries it developed a rigorous methodology - isnad (a complete transmission chain attached to every claim), rijal (systematic grading of each narrator's integrity and precision), weakest-link chain evaluation, corroboration through independent chains, and matn criticism (content evaluated independently of chain quality). This paper transfers that methodology to AI system design. We contribute a formal mapping from hadith-science concepts to multi-agent pipelines, a relational schema implementing claim chains and a graded narrator registry, a decision matrix combining chain grade with content criticism, and an evaluation on 20,000 claims from real physics textbooks. The evaluation validates weakest-link quarantine and independent-chain corroboration; reports a partial failure of the grade-recovery loop, which missed the highest-fault narrator; and reports two analyses as inconclusive, including a matched-coverage comparison the framework could not reach with the reference content critic. The paper is explicit throughout about which claims the evidence does and does not yet support.

Information accounting provides a better foundation for hypothesis testing than does uncertainty quantification. A quantitative account of science is derived under this perspective that alleviates the need for epistemic bridge principles, solves the problem of ad hoc falsification criteria, and deals with verisimilitude by facilitating a general approach to process-level diagnostics. Our argument is that the well-known inconsistencies of both Bayesian and classical statistical hypothesis tests are due to the fact that probability theory is an insufficient logic of science. Information theory, as an extension of probability theory, is required to provide a complete logic on which to base quantitative theories of empirical learning. The organizing question in this case becomes not whether our theories or models are more or less true, or about how much uncertainty is associated with a particular model, but instead whether there is any information available from experimental data that might allow us to improve the model. This becomes a formal hypothesis test, provides a theory of model diagnostics, and suggests a new approach to building dynamical systems models.

Whether a language model has improved itself is increasingly judged not by mean accuracy but by which individual problems it gains and loses. Tracking these transitions means differencing two noisy estimates, leaving them vulnerable to measurement artifacts. Auditing three rounds of rank-32 LoRA self-training on Qwen3-8B against a frozen control pushed through the identical pipeline, we identify seven measurement failures, each of which inverts a reported finding when its control is absent. Several are standard practice. A ledger built on a single greedy decode manufactures capability changes on an untrained model, largely an artifact of inference batching; the expansion statistic separating acquisition from sharpening assigns that same model a rate of 0.280. The natural threshold repair does not survive replication: estimated across the frozen comparisons such a design already contains, its null stays non-zero. We replace it with a per-problem exact test against a pooled baseline under false-discovery-rate control, which detects nothing on any held-out replicate and is unchanged under the multiple-testing rule, error rate and pool size. Applied to a ladder of arms matched in stream, volume and evaluation, the audit finds that external distillation improves problems the base model rarely reaches while three forms of self-training do not; a regression rejects this asymmetry as a by-product of distillation's larger overall gain (p < 10^{-8}). On the far smaller set of problems the base model never reaches, the evidence is inconclusive, while self-training corrupts problems solved at baseline at rates well above the measured floor. Transition-level auditing therefore requires a separately measured null for every statistic it reports: nulls that cost no new experiments, built from baseline replicates a multi-arm study already owns, though not from as few as most possess.

Recent advancements in quality control across various industries have increasingly utilized the integration of video cameras and image processing for effective defect detection. A critical barrier to progress is the scarcity of comprehensive datasets featuring annotated defects, which are essential for developing and refining automated defect detection models. This systematic review, spanning from 2015 to 2023, identifies 15 publicly available datasets and critically examines them to assess their effectiveness and applicability for benchmarking and model development. Our findings reveal a diverse landscape of datasets, such as NEU-CLS, NEU-DET, DAGM, KolektorSDD, PCB Defect Dataset, and the Hollow Cylindrical Defect Detection Dataset, each with unique strengths and limitations in terms of image quality, defect type representation, and real-world applicability. The goal of this systematic review is to consolidate these datasets in a single location, providing researchers who seek such publicly available resources with a comprehensive reference.

Mistakes in machine learning practice are commonplace, and can result in a loss of confidence in the findings and products of machine learning. This guide outlines common mistakes that occur when using machine learning, and what can be done to avoid them. Whilst it should be accessible to anyone with a basic understanding of machine learning techniques, it focuses on issues that are of particular concern within academic research, such as the need to do rigorous comparisons and reach valid conclusions. It covers five stages of the machine learning process: what to do before model building, how to reliably build models, how to robustly evaluate models, how to compare models fairly, and how to report results.

Modeling plausible student misconceptions is critical for AI in education. In this work, we examine how large language models (LLMs) reason about misconceptions when generating multiple-choice distractors, a task that requires modeling incorrect yet plausible answers by coordinating solution knowledge, simulating student misconceptions, and evaluating plausibility. We introduce a taxonomy for analyzing the strategies used by state-of-the-art LLMs, examining their reasoning procedures and comparing them to established best practices in the learning sciences. Our structured analysis reveals a surprising alignment between their processes and best practices: the models typically solve the problem correctly first, then articulate and simulate multiple potential misconceptions, and finally select a set of distractors. An analysis of failure modes reveals that errors arise primarily from failures in recovering the correct solution and selecting among response candidates, rather than simulating errors or structuring the process. Consistent with these results, we find that providing the correct solution in the prompt improves alignment with human-authored distractors by 8%, highlighting the critical role of anchoring to the correct solution when generating plausible incorrect student reasoning. Overall, our analysis offers a structured and interpretable lens into LLMs' ability to model incorrect student reasoning and produce high-quality distractors.

Benchmarks are pivotal in driving AI progress, and invalid benchmark questions frequently undermine their reliability. Manually identifying and correcting errors among thousands of benchmark questions is not only infeasible but also a critical bottleneck for reliable evaluation. In this work, we introduce a framework for systematic benchmark revision that leverages statistical analysis of response patterns to flag potentially invalid questions for further expert review. Our approach builds on a core assumption commonly used in AI evaluations that the mean score sufficiently summarizes model performance. This implies a unidimensional latent construct underlying the measurement experiment, yielding expected ranges for various statistics for each item. When empirically estimated values for these statistics fall outside the expected range for an item, the item is more likely to be problematic. Across nine widely used benchmarks, our method guides expert review to identify problematic questions with up to 84\% precision. In addition, we introduce an LLM-judge first pass to review questions, further reducing human effort. Together, these components provide an efficient and scalable framework for systematic benchmark revision.

As Large Language Models become more ubiquitous across domains, it becomes important to examine their inherent limitations critically. This work argues that hallucinations in language models are not just occasional errors but an inevitable feature of these systems. We demonstrate that hallucinations stem from the fundamental mathematical and logical structure of LLMs. It is, therefore, impossible to eliminate them through architectural improvements, dataset enhancements, or fact-checking mechanisms. Our analysis draws on computational theory and Godel's First Incompleteness Theorem, which references the undecidability of problems like the Halting, Emptiness, and Acceptance Problems. We demonstrate that every stage of the LLM process-from training data compilation to fact retrieval, intent classification, and text generation-will have a non-zero probability of producing hallucinations. This work introduces the concept of Structural Hallucination as an intrinsic nature of these systems. By establishing the mathematical certainty of hallucinations, we challenge the prevailing notion that they can be fully mitigated.

A large share of day-to-day work in professional domains happens inside PDF files: benefits packets, leases, datasheets, clinical guidelines, construction plans. Benchmarks for document AI have generally measured the required capabilities in isolation: OCR, layout analysis, chart reasoning, table QA, document VQA. A high score on any one of them does not necessarily reveal whether a model can answer a realistic question that someone in the field would actually ask about a specific PDF. GDP_pdf is a benchmark built to measure this directly. It consists of question-document pairs authored by working professionals in ten fields, and a candidate question was kept only when at least two frontier multimodal models failed it in a way that mattered: a wrong answer, missed decisive evidence, or a fabricated claim, rather than a superficial difference such as style. Each item comes with a rubric of atomic criteria, so we can report a graded rubric score as well as a strict task-level pass rate, and each item is tagged against a taxonomy of eleven capabilities in three tiers, spanning text extraction and grounding, table and chart comprehension, cross-referencing, spatial reasoning, and abstention on unsupported queries. We report results for seventeen frontier models on the 100-item benchmark: the best model passes only 30.7% of the items and the worst passes 2%. Most errors trace back to a small set of recurring loss patterns: misaligned tables, misread charts, skipped footnotes and exclusions, miscounted floor-plan symbols, scan noise, and amendments that supersede earlier text.

In the last decade, several organizations have produced documents intended to standardize, in the normative sense, and promote guidance to our recent and rapid AI development. However, the full spectrum of ideas presented in these documents has not yet been analyzed, except for a few meta-analyses and critical reviews of the field. In this work, we seek to expand on the work done by past researchers and create a tool for better data visualization of the contents and nature of these documents, to understand whether there is consensus or similarity between the principles espoused by various institutions, which may inspire debates on future regulations. We also provide some preliminary thoughts and questions that could guide the continuity of the research through a critical analysis of the results acquired by our methodology into a sample size of 200 documents.

Understanding the landscape of potential harms from algorithmic systems enables practitioners to better anticipate consequences of the systems they build. It also supports the prospect of incorporating controls to help minimize harms that emerge from the interplay of technologies and social and cultural dynamics. A growing body of scholarship has identified a wide range of harms across different algorithmic technologies. However, computing research and practitioners lack a high level and synthesized overview of harms from algorithmic systems. Based on a scoping review of computing research (n=172), we present an applied taxonomy of sociotechnical harms to support a more systematic surfacing of potential harms in algorithmic systems. The final taxonomy builds on and refers to existing taxonomies, classifications, and terminologies. Five major themes related to sociotechnical harms - representational, allocative, quality-of-service, interpersonal harms, and social system/societal harms - and sub-themes are presented along with a description of these categories. We conclude with a discussion of challenges and opportunities for future research.

In 2023, a New York judge sanctioned two attorneys in Mata v. Avianca for filing a brief with hallucinated citations generated by ChatGPT. Such failures are largely caught by database lookups; the harder problem is detecting citations that point to real cases but do not support the propositions for which they are offered -- a failure mode that existing evaluations of LLMs for legal use cases largely overlook. In this paper, we study proposition-level citation support verification through controlled perturbations of real legal citations obtained from two legal corpora, either replacing the cited case or changing only the pinpoint page within the same case. We evaluate fourteen model configurations on the resulting examples. Models catch 93-100% of wrong-case corruptions. They catch only 37-61% of wrong-pinpoint corruptions on court opinions and 52-83% on legal briefs. When models fail to catch wrong-pinpoint corruptions, they accept the citation based on topical overlap rather than page-level support. Scale and extended reasoning narrow the gap but do not close it: GPT-5.4 with high reasoning effort still misses 40% of pinpoint mismatches on court opinions and 18% on briefs. Prompting the model to verify support at the cited page improves recall, but it also raises the false positive rate. Recognizing the right legal topic and verifying support for the cited proposition are distinct capabilities, and current models conflate them.

This paper calls on the research community not only to investigate how human biases are inherited by large language models (LLMs) but also to explore how these biases in LLMs can be leveraged to make society's "unwritten code" - such as implicit stereotypes and heuristics - visible and accessible for critique. We introduce a conceptual framework through a case study in science: uncovering hidden rules in peer review - the factors that reviewers care about but rarely state explicitly due to normative scientific expectations. The idea of the framework is to push LLMs to speak out their heuristics through generating self-consistent hypotheses - why one paper appeared stronger in reviewer scoring - among paired papers submitted to 45 computer science conferences, while iteratively searching deeper hypotheses from remaining pairs where existing hypotheses cannot explain. We observed that LLMs' normative priors about the internal characteristics of good science extracted from their self-talk, e.g. theoretical rigor, were systematically updated toward posteriors that emphasize storytelling about external connections, such as how the work is positioned and connected within and across literatures. This shift reveals the primacy of scientific myths about intrinsic properties driving scientific excellence rather than extrinsic contextualization and storytelling that influence conceptions of relevance and significance. Human reviewers tend to explicitly reward aspects that moderately align with LLMs' normative priors (correlation = 0.49) but avoid articulating contextualization and storytelling posteriors in their review comments (correlation = -0.14), despite giving implicit reward to them with positive scores. We discuss the broad applicability of the framework, leveraging LLMs as diagnostic tools to surface the tacit codes underlying human society, enabling more precisely targeted responsible AI.

LLM-as-a-Judge frameworks are increasingly trusted to automate evaluation in place of human experts, yet their reliability in high-stakes medical contexts remains unproven. We stress-test this assumption for detecting incomplete patient-facing medical responses, evaluating three rubric granularities (General-Likert, Analytical-Rubric, Dynamic-Checklist) and three backbone models across two clinician-annotated datasets, including HealthBench, the largest publicly available benchmark for medical response evaluation. LLM Judges discriminate complete from incomplete responses at and slightly above near chance (AUC 0.49--0.66); at the threshold required to recall 90% of incomplete responses, clinicians must still review the vast majority of the dataset, offering no triage utility. Even when model and clinician verdicts agree, they rarely cite the same explanation; and when they diverge, false positives stem from over-flagging non-essential gaps while false negatives reflect outright detection failures. These results reveal that LLM Judges and clinicians apply fundamentally different completeness standards; a finding that undermines their use as autonomous evaluators or triage filters in clinical settings.

While data are the primary fuel for machine learning models, they often suffer from missing values, especially when collected in real-world scenarios. However, many off-the-shelf machine learning models, including artificial neural network models, are unable to handle these missing values directly. Therefore, extra data preprocessing and curation steps, such as data imputation, are inevitable before learning and prediction processes. In this study, we propose a simple and intuitive yet effective method for pruning missing values (PROMISSING) during learning and inference steps in neural networks. In this method, there is no need to remove or impute the missing values; instead, the missing values are treated as a new source of information (representing what we do not know). Our experiments on simulated data, several classification and regression benchmarks, and a multi-modal clinical dataset show that PROMISSING results in similar prediction performance compared to various imputation techniques. In addition, our experiments show models trained using PROMISSING techniques are becoming less decisive in their predictions when facing incomplete samples with many unknowns. This finding hopefully advances machine learning models from being pure predicting machines to more realistic thinkers that can also say "I do not know" when facing incomplete sources of information.

Following the success of Large Language Models (LLMs), Large Multimodal Models (LMMs), such as the Flamingo model and its subsequent competitors, have started to emerge as natural steps towards generalist agents. However, interacting with recent LMMs reveals major limitations that are hardly captured by the current evaluation benchmarks. Indeed, task performances (e.g., VQA accuracy) alone do not provide enough clues to understand their real capabilities, limitations, and to which extent such models are aligned to human expectations. To refine our understanding of those flaws, we deviate from the current evaluation paradigm, and (1) evaluate 10 recent open-source LMMs from 3B up to 80B parameter scale, on 5 different axes; hallucinations, abstention, compositionality, explainability and instruction following. Our evaluation on these axes reveals major flaws in LMMs. While the current go-to solution to align these models is based on training, such as instruction tuning or RLHF, we rather (2) explore the training-free in-context learning (ICL) as a solution, and study how it affects these limitations. Based on our ICL study, (3) we push ICL further and propose new multimodal ICL variants such as; Multitask-ICL, Chain-of-Hindsight-ICL, and Self-Correcting-ICL. Our findings are as follows. (1) Despite their success, LMMs have flaws that remain unsolved with scaling alone. (2) The effect of ICL on LMMs flaws is nuanced; despite its effectiveness for improved explainability, answer abstention, ICL only slightly improves instruction following, does not improve compositional abilities, and actually even amplifies hallucinations. (3) The proposed ICL variants are promising as post-hoc approaches to efficiently tackle some of those flaws. The code is available here: https://github.com/mshukor/EvALign-ICL.

Current Large Language Models (LLMs) benchmarks are often based on open-ended or close-ended QA evaluations, avoiding the requirement of human labor. Close-ended measurements evaluate the factuality of responses but lack expressiveness. Open-ended capture the model's capacity to produce discourse responses but are harder to assess for correctness. These two approaches are commonly used, either independently or together, though their relationship remains poorly understood. This work is focused on the healthcare domain, where both factuality and discourse matter greatly. It introduces a comprehensive, multi-axis suite for healthcare LLM evaluation, exploring correlations between open and close benchmarks and metrics. Findings include blind spots and overlaps in current methodologies. As an updated sanity check, we release a new medical benchmark--CareQA--, with both open and closed variants. Finally, we propose a novel metric for open-ended evaluations --Relaxed Perplexity-- to mitigate the identified limitations.

Software increasingly functions as part of the scientific instrument itself, making failures in scientific code capable of compromising not only program behavior but also the evidence underlying scientific conclusions. Yet existing evaluations of coding agents largely emphasize aggregate task success, providing limited insight into why agents fail when repairing scientific software. We introduce SWE-bench Science, a repository-level benchmark for scientific software engineering comprising 119 tasks from 98 GitHub repositories across 20 scientific domains. Each task is organized into one of three paradigms: Issue-driven, Expert-exploratory, and Engineering-integration. Even the best-performing agent, Claude Code with Opus-5 (max), achieves a pass@1 below 50\%, highlighting the substantial challenges posed by scientific software engineering. We identify four recurring failure mechanisms: deficits in scientific knowledge or abstraction, misguided exploration or surface-level repair, incomplete repair coverage or system integration, and failures to generalize scientific knowledge beyond observed cases in our analysis. We further conduct a paired ablation that removes explicit scientific guidance while preserving the repository and executable engineering context. The results show that scientific knowledge is not uniformly beneficial: well-grounded information can constrain repair and improve average performance and token efficiency, whereas poorly aligned guidance can induce anchoring and does not necessarily improve exact repair success. Together, SWE-bench Science provides a broad testbed for studying both the capabilities and failure mechanisms of coding agents in scientific software engineering.

A major step toward Artificial General Intelligence (AGI) and Super Intelligence is AI's ability to autonomously conduct research - what we term Artificial Research Intelligence (ARI). If machines could generate hypotheses, conduct experiments, and write research papers without human intervention, it would transform science. Sakana recently introduced the 'AI Scientist', claiming to conduct research autonomously, i.e. they imply to have achieved what we term Artificial Research Intelligence (ARI). The AI Scientist gained much attention, but a thorough independent evaluation has yet to be conducted. Our evaluation of the AI Scientist reveals critical shortcomings. The system's literature reviews produced poor novelty assessments, often misclassifying established concepts (e.g., micro-batching for stochastic gradient descent) as novel. It also struggles with experiment execution: 42% of experiments failed due to coding errors, while others produced flawed or misleading results. Code modifications were minimal, averaging 8% more characters per iteration, suggesting limited adaptability. Generated manuscripts were poorly substantiated, with a median of five citations, most outdated (only five of 34 from 2020 or later). Structural errors were frequent, including missing figures, repeated sections, and placeholder text like 'Conclusions Here'. Some papers contained hallucinated numerical results. Despite these flaws, the AI Scientist represents a leap forward in research automation. It generates full research manuscripts with minimal human input, challenging expectations of AI-driven science. Many reviewers might struggle to distinguish its work from human researchers. While its quality resembles a rushed undergraduate paper, its speed and cost efficiency are unprecedented, producing a full paper for USD 6 to 15 with 3.5 hours of human involvement, far outpacing traditional researchers.