Daily Papers

The growth of Generative Artificial Intelligence (GenAI) has shifted disinformation production from manual fabrication to automated, large-scale manipulation. This article presents findings from the first wave of a longitudinal expert perception survey (N=21) involving AI researchers, policymakers, and disinformation specialists. It examines the perceived severity of multimodal threats -- text, image, audio, and video -- and evaluates current mitigation strategies. Results indicate that while deepfake video presents immediate "shock" value, large-scale text generation poses a systemic risk of "epistemic fragmentation" and "synthetic consensus," particularly in the political domain. The survey reveals skepticism about technical detection tools, with experts favoring provenance standards and regulatory frameworks despite implementation barriers. GenAI disinformation research requires reproducible methods. The current challenge is measurement: without standardized benchmarks and reproducibility checklists, tracking or countering synthetic media remains difficult. We propose treating information integrity as an infrastructure with rigor in data provenance and methodological reproducibility.

Evaluating the quality of synthetic data remains a key challenge for ensuring privacy and utility in data-driven research. In this work, we present an evaluation framework that quantifies how well synthetic data replicates original distributional properties while ensuring privacy. The proposed approach employs a holdout-based benchmarking strategy that facilitates quantitative assessment through low- and high-dimensional distribution comparisons, embedding-based similarity measures, and nearest-neighbor distance metrics. The framework supports various data types and structures, including sequential and contextual information, and enables interpretable quality diagnostics through a set of standardized metrics. These contributions aim to support reproducibility and methodological consistency in benchmarking of synthetic data generation techniques. The code of the framework is available at https://github.com/mostly-ai/mostlyai-qa.

Reasoning has emerged as the next major frontier for language models (LMs), with rapid advances from both academic and industrial labs. However, this progress often outpaces methodological rigor, with many evaluations relying on benchmarking practices that lack transparency, robustness, or statistical grounding. In this work, we conduct a comprehensive empirical study and find that current mathematical reasoning benchmarks are highly sensitive to subtle implementation choices - including decoding parameters, random seeds, prompt formatting, and even hardware and software-framework configurations. Performance gains reported in recent studies frequently hinge on unclear comparisons or unreported sources of variance. To address these issues, we propose a standardized evaluation framework with clearly defined best practices and reporting standards. Using this framework, we reassess recent methods and find that reinforcement learning (RL) approaches yield only modest improvements - far below prior claims - and are prone to overfitting, especially on small-scale benchmarks like AIME24. In contrast, supervised finetuning (SFT) methods show consistently stronger generalization. To foster reproducibility, we release all code, prompts, and model outputs, for reasoning benchmarks, establishing more rigorous foundations for future work.

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.

Consistently checking the statistical significance of experimental results is one of the mandatory methodological steps to address the so-called "reproducibility crisis" in deep reinforcement learning. In this tutorial paper, we explain how the number of random seeds relates to the probabilities of statistical errors. For both the t-test and the bootstrap confidence interval test, we recall theoretical guidelines to determine the number of random seeds one should use to provide a statistically significant comparison of the performance of two algorithms. Finally, we discuss the influence of deviations from the assumptions usually made by statistical tests. We show that they can lead to inaccurate evaluations of statistical errors and provide guidelines to counter these negative effects. We make our code available to perform the tests.

In this paper, we summarize the current state of the field of NLP & Law with a specific focus on recent technical and substantive developments. To support our analysis, we construct and analyze a nearly complete corpus of more than six hundred NLP & Law related papers published over the past decade. Our analysis highlights several major trends. Namely, we document an increasing number of papers written, tasks undertaken, and languages covered over the course of the past decade. We observe an increase in the sophistication of the methods which researchers deployed in this applied context. Slowly but surely, Legal NLP is beginning to match not only the methodological sophistication of general NLP but also the professional standards of data availability and code reproducibility observed within the broader scientific community. We believe all of these trends bode well for the future of the field, but many questions in both the academic and commercial sphere still remain open.

Large Language Models, particularly decoder-only generative models such as GPT, are increasingly used to automate Software Engineering tasks. These models are primarily guided through natural language prompts, making prompt engineering a critical factor in system performance and behavior. Despite their growing role in SE research, prompt-related decisions are rarely documented in a systematic or transparent manner, hindering reproducibility and comparability across studies. To address this gap, we conducted a two-phase empirical study. First, we analyzed nearly 300 papers published at the top-3 SE conferences since 2022 to assess how prompt design, testing, and optimization are currently reported. Second, we surveyed 105 program committee members from these conferences to capture their expectations for prompt reporting in LLM-driven research. Based on the findings, we derived a structured guideline that distinguishes essential, desirable, and exceptional reporting elements. Our results reveal significant misalignment between current practices and reviewer expectations, particularly regarding version disclosure, prompt justification, and threats to validity. We present our guideline as a step toward improving transparency, reproducibility, and methodological rigor in LLM-based SE research.

Background: Agent skills are increasingly deployed as modular, reusable capability units in AI agent systems. Medical research agent skills require safeguards beyond general-purpose evaluation, including scientific integrity, methodological validity, reproducibility, and boundary safety. This study developed and preliminarily evaluated a domain-specific audit framework for medical research agent skills, with a focus on reliability against expert review. Methods: We developed MedSkillAudit (skill-auditor@1.0), a layered framework assessing skill release readiness before deployment. We evaluated 75 skills across five medical research categories (15 per category). Two experts independently assigned a quality score (0-100), an ordinal release disposition (Production Ready / Limited Release / Beta Only / Reject), and a high-risk failure flag. System-expert agreement was quantified using ICC(2,1) and linearly weighted Cohen's kappa, benchmarked against the human inter-rater baseline. Results: The mean consensus quality score was 72.4 (SD = 13.0); 57.3% of skills fell below the Limited Release threshold. MedSkillAudit achieved ICC(2,1) = 0.449 (95% CI: 0.250-0.610), exceeding the human inter-rater ICC of 0.300. System-consensus score divergence (SD = 9.5) was smaller than inter-expert divergence (SD = 12.4), with no directional bias (Wilcoxon p = 0.613). Protocol Design showed the strongest category-level agreement (ICC = 0.551); Academic Writing showed a negative ICC (-0.567), reflecting a structural rubric-expert mismatch. Conclusions: Domain-specific pre-deployment audit may provide a practical foundation for governing medical research agent skills, complementing general-purpose quality checks with structured audit workflows tailored to scientific use cases.

Concerns about reproducibility in artificial intelligence (AI) have emerged, as researchers have reported unsuccessful attempts to directly reproduce published findings in the field. Replicability, the ability to affirm a finding using the same procedures on new data, has not been well studied. In this paper, we examine both reproducibility and replicability of a corpus of 16 papers on table structure recognition (TSR), an AI task aimed at identifying cell locations of tables in digital documents. We attempt to reproduce published results using codes and datasets provided by the original authors. We then examine replicability using a dataset similar to the original as well as a new dataset, GenTSR, consisting of 386 annotated tables extracted from scientific papers. Out of 16 papers studied, we reproduce results consistent with the original in only four. Two of the four papers are identified as replicable using the similar dataset under certain IoU values. No paper is identified as replicable using the new dataset. We offer observations on the causes of irreproducibility and irreplicability. All code and data are available on Codeocean at https://codeocean.com/capsule/6680116/tree.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

Combating bias in NLP requires bias measurement. Bias measurement is almost always achieved by using lexicons of seed terms, i.e. sets of words specifying stereotypes or dimensions of interest. This reproducibility study focuses on the original authors' main claim that the rationale for the construction of these lexicons needs thorough checking before usage, as the seeds used for bias measurement can themselves exhibit biases. The study aims to evaluate the reproducibility of the quantitative and qualitative results presented in the paper and the conclusions drawn thereof. We reproduce most of the results supporting the original authors' general claim: seed sets often suffer from biases that affect their performance as a baseline for bias metrics. Generally, our results mirror the original paper's. They are slightly different on select occasions, but not in ways that undermine the paper's general intent to show the fragility of seed sets.

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at two levels: First, using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks related to publications indexed in PubMed Central. We identified such notebooks by mining the articles full text, locating them on GitHub and re-running them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. Second, this study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over two years. Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles, 22578 notebooks were written in Python, including 15817 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 10388 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

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.

Quantifying bias in retrieval functions through document retrievability scores is vital for assessing recall-oriented retrieval systems. However, many studies investigating retrieval model bias lack validation of their query generation methods as accurate representations of retrievability for real users and their queries. This limitation results from the absence of established criteria for query generation in retrievability assessments. Typically, researchers resort to using frequent collocations from document corpora when no query log is available. In this study, we address the issue of reproducibility and seek to validate query generation methods by comparing retrievability scores generated from artificially generated queries to those derived from query logs. Our findings demonstrate a minimal or negligible correlation between retrievability scores from artificial queries and those from query logs. This suggests that artificially generated queries may not accurately reflect retrievability scores as derived from query logs. We further explore alternative query generation techniques, uncovering a variation that exhibits the highest correlation. This alternative approach holds promise for improving reproducibility when query logs are unavailable.

In recent years, significant progress has been made in solving challenging problems across various domains using deep reinforcement learning (RL). Reproducing existing work and accurately judging the improvements offered by novel methods is vital to sustaining this progress. Unfortunately, reproducing results for state-of-the-art deep RL methods is seldom straightforward. In particular, non-determinism in standard benchmark environments, combined with variance intrinsic to the methods, can make reported results tough to interpret. Without significance metrics and tighter standardization of experimental reporting, it is difficult to determine whether improvements over the prior state-of-the-art are meaningful. In this paper, we investigate challenges posed by reproducibility, proper experimental techniques, and reporting procedures. We illustrate the variability in reported metrics and results when comparing against common baselines and suggest guidelines to make future results in deep RL more reproducible. We aim to spur discussion about how to ensure continued progress in the field by minimizing wasted effort stemming from results that are non-reproducible and easily misinterpreted.

Assessing the reproducibility of social science papers is essential for promoting rigor in research processes, but manual assessment is costly. With recent advances in agentic AI systems (i.e., AI agents), we seek to evaluate their capability to automate this process. However, existing benchmarks for reproducing research papers (1) focus solely on reproducing results using provided code and data without assessing their consistency with the paper, (2) oversimplify real-world scenarios, and (3) lack necessary diversity in data formats and programming languages. To address these issues, we introduce REPRO-Bench, a collection of 112 task instances, each representing a social science paper with a publicly available reproduction report. The agents are tasked with assessing the reproducibility of the paper based on the original paper PDF and the corresponding reproduction package. REPRO-Bench features end-to-end evaluation tasks on the reproducibility of social science papers with complexity comparable to real-world assessments. We evaluate three representative AI agents on REPRO-Bench, with the best-performing agent achieving an accuracy of only 21.4%. Building on our empirical analysis, we develop REPRO-Agent, which improves the highest accuracy achieved by existing agents by 71%. We conclude that more advanced AI agents should be developed to automate real-world reproducibility assessment. REPRO-Bench is publicly available at https://github.com/uiuc-kang-lab/REPRO-Bench.

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.

Sentiments about the reproducibility of cited papers in downstream literature offer community perspectives and have shown as a promising signal of the actual reproducibility of published findings. To train effective models to effectively predict reproducibility-oriented sentiments and further systematically study their correlation with reproducibility, we introduce the CC30k dataset, comprising a total of 30,734 citation contexts in machine learning papers. Each citation context is labeled with one of three reproducibility-oriented sentiment labels: Positive, Negative, or Neutral, reflecting the cited paper's perceived reproducibility or replicability. Of these, 25,829 are labeled through crowdsourcing, supplemented with negatives generated through a controlled pipeline to counter the scarcity of negative labels. Unlike traditional sentiment analysis datasets, CC30k focuses on reproducibility-oriented sentiments, addressing a research gap in resources for computational reproducibility studies. The dataset was created through a pipeline that includes robust data cleansing, careful crowd selection, and thorough validation. The resulting dataset achieves a labeling accuracy of 94%. We then demonstrated that the performance of three large language models significantly improves on the reproducibility-oriented sentiment classification after fine-tuning using our dataset. The dataset lays the foundation for large-scale assessments of the reproducibility of machine learning papers. The CC30k dataset and the Jupyter notebooks used to produce and analyze the dataset are publicly available at https://github.com/lamps-lab/CC30k .

The past two decades have witnessed the rapid development of personalized recommendation techniques. Despite significant progress made in both research and practice of recommender systems, to date, there is a lack of a widely-recognized benchmarking standard in this field. Many existing studies perform model evaluations and comparisons in an ad-hoc manner, for example, by employing their own private data splits or using different experimental settings. Such conventions not only increase the difficulty in reproducing existing studies, but also lead to inconsistent experimental results among them. This largely limits the credibility and practical value of research results in this field. To tackle these issues, we present an initiative project (namely BARS) aiming for open benchmarking for recommender systems. In comparison to some earlier attempts towards this goal, we take a further step by setting up a standardized benchmarking pipeline for reproducible research, which integrates all the details about datasets, source code, hyper-parameter settings, running logs, and evaluation results. The benchmark is designed with comprehensiveness and sustainability in mind. It covers both matching and ranking tasks, and also enables researchers to easily follow and contribute to the research in this field. This project will not only reduce the redundant efforts of researchers to re-implement or re-run existing baselines, but also drive more solid and reproducible research on recommender systems. We would like to call upon everyone to use the BARS benchmark for future evaluation, and contribute to the project through the portal at: https://openbenchmark.github.io/BARS.

Reproducibility in scientific work has been becoming increasingly important in research communities such as machine learning, natural language processing, and computer vision communities due to the rapid development of the research domains supported by recent advances in deep learning. In this work, we present a significantly upgraded version of torchdistill, a modular-driven coding-free deep learning framework significantly upgraded from the initial release, which supports only image classification and object detection tasks for reproducible knowledge distillation experiments. To demonstrate that the upgraded framework can support more tasks with third-party libraries, we reproduce the GLUE benchmark results of BERT models using a script based on the upgraded torchdistill, harmonizing with various Hugging Face libraries. All the 27 fine-tuned BERT models and configurations to reproduce the results are published at Hugging Face, and the model weights have already been widely used in research communities. We also reimplement popular small-sized models and new knowledge distillation methods and perform additional experiments for computer vision tasks.

The literature has witnessed an emerging interest in AI agents for automated assessment of scientific papers. Existing benchmarks focus primarily on the computational aspect of this task, testing agents' ability to reproduce or replicate research outcomes when having access to the code and data. This setting, while foundational, (1) fails to capture the inconsistent availability of new data for replication as opposed to reproduction, and (2) lacks ground-truth diversity by focusing only on reproducible papers, thereby failing to evaluate an agent's ability to identify non-replicable research. Furthermore, most benchmarks only evaluate outcomes rather than the replication process. In response, we introduce ReplicatorBench, an end-to-end benchmark, including human-verified replicable and non-replicable research claims in social and behavioral sciences for evaluating AI agents in research replication across three stages: (1) extraction and retrieval of replication data; (2) design and execution of computational experiments; and (3) interpretation of results, allowing a test of AI agents' capability to mimic the activities of human replicators in real world. To set a baseline of AI agents' capability, we develop ReplicatorAgent, an agentic framework equipped with necessary tools, like web search and iterative interaction with sandboxed environments, to accomplish tasks in ReplicatorBench. We evaluate ReplicatorAgent across four underlying large language models (LLMs), as well as different design choices of programming language and levels of code access. Our findings reveal that while current LLM agents are capable of effectively designing and executing computational experiments, they struggle with retrieving resources, such as new data, necessary to replicate a claim. All code and data are publicly available at https://github.com/CenterForOpenScience/llm-benchmarking.

Medical systematic reviews can be very costly and resource intensive. We explore how Large Language Models (LLMs) can support and be trained to perform literature screening when provided with a detailed set of selection criteria. Specifically, we instruction tune LLaMA and Guanaco models to perform abstract screening for medical systematic reviews. Our best model, Bio-SIEVE, outperforms both ChatGPT and trained traditional approaches, and generalises better across medical domains. However, there remains the challenge of adapting the model to safety-first scenarios. We also explore the impact of multi-task training with Bio-SIEVE-Multi, including tasks such as PICO extraction and exclusion reasoning, but find that it is unable to match single-task Bio-SIEVE's performance. We see Bio-SIEVE as an important step towards specialising LLMs for the biomedical systematic review process and explore its future developmental opportunities. We release our models, code and a list of DOIs to reconstruct our dataset for 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.

Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.

In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible, rerunning and verifying experiments is usually hard due to a lack of standards. Therefore, reusing existing scientific data processing code from state-of-the-art research is hard as well. This is why we introduce CLAIMED, which has a proven track record in scientific research for addressing the repeatability and reusability issues in modern data-driven science. CLAIMED is a framework to build reusable operators and scalable scientific workflows by supporting the scientist to draw from previous work by re-composing workflows from existing libraries of coarse-grained scientific operators. Although various implementations exist, CLAIMED is programming language, scientific library, and execution environment agnostic.

Rigorous and reproducible evaluation is critical for assessing the state of the art and for guiding scientific advances in Artificial Intelligence. Evaluation is challenging in practice due to several reasons, including benchmark saturation, lack of transparency in methods used for measurement, development challenges in extracting measurements for generative tasks, and, more generally, the extensive number of capabilities required for a well-rounded comparison across models. We make three contributions to alleviate the above challenges. First, we present Eureka, an open-source framework for standardizing evaluations of large foundation models beyond single-score reporting and rankings. Second, we introduce Eureka-Bench as an extensible collection of benchmarks testing capabilities that (i) are still challenging for state-of-the-art models and (ii) represent fundamental but overlooked language and multimodal capabilities. The inherent space for improvement in non-saturated benchmarks enables us to discover meaningful differences between models at a capability level. Third, using Eureka, we conduct an analysis of 12 state-of-the-art models, providing in-depth insights into failure understanding and model comparison, which can be leveraged to plan targeted improvements. In contrast to recent trends in reports and leaderboards showing absolute rankings and claims for one model or another to be the best, our analysis shows that there is no such best model. Different models have different strengths, but there are models that appear more often than others as best performers for some capabilities. Despite the recent improvements, current models still struggle with several fundamental capabilities including detailed image understanding, benefiting from multimodal input when available rather than fully relying on language, factuality and grounding for information retrieval, and over refusals.

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.

Tool-augmented large language models have advanced from single-turn question answering to deep research workflows that iteratively plan queries, invoke external tools, and synthesize information to address complex information needs. Evaluating such workflows presents a fundamental challenge: reliance on live APIs introduces non-determinism, as tool invocations may yield different results across runs due to temporal drift, rate limiting, and evolving backend states. This variance undermines reproducibility and invalidates cross-system comparisons. We present ScholarGym, a simulation environment for reproducible evaluation of deep research workflows on academic literature. The environment decouples workflow components into query planning, tool invocation, and relevance assessment, enabling fine-grained analysis of each stage under controlled conditions. Built on a static corpus of 570K papers with deterministic retrieval, ScholarGym provides 2,536 queries with expert-annotated ground truth. Experiments across diverse backbone models reveal how reasoning capabilities, planning strategies, and selection mechanisms interact over iterative refinement.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

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.

Meta-learning researchers face two fundamental issues in their empirical work: prototyping and reproducibility. Researchers are prone to make mistakes when prototyping new algorithms and tasks because modern meta-learning methods rely on unconventional functionalities of machine learning frameworks. In turn, reproducing existing results becomes a tedious endeavour -- a situation exacerbated by the lack of standardized implementations and benchmarks. As a result, researchers spend inordinate amounts of time on implementing software rather than understanding and developing new ideas. This manuscript introduces learn2learn, a library for meta-learning research focused on solving those prototyping and reproducibility issues. learn2learn provides low-level routines common across a wide-range of meta-learning techniques (e.g. meta-descent, meta-reinforcement learning, few-shot learning), and builds standardized interfaces to algorithms and benchmarks on top of them. In releasing learn2learn under a free and open source license, we hope to foster a community around standardized software for meta-learning research.

As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a `DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment.

Reproducibility and replicability are critical pillars of empirical research, particularly in machine learning, where they depend not only on the availability of models, but also on the datasets used to train and evaluate those models. In this paper, we introduce the Construction Industry Steel Ordering List (CISOL) dataset, which was developed with a focus on transparency to ensure reproducibility, replicability, and extensibility. CISOL provides a valuable new research resource and highlights the importance of having diverse datasets, even in niche application domains such as table extraction in civil engineering. CISOL is unique in that it contains real-world civil engineering documents from industry, making it a distinctive contribution to the field. The dataset contains more than 120,000 annotated instances in over 800 document images, positioning it as a medium-sized dataset that provides a robust foundation for Table Structure Recognition (TSR) and Table Detection (TD) tasks. Benchmarking results show that CISOL achieves 67.22 mAP@0.5:0.95:0.05 using the YOLOv8 model, outperforming the TSR-specific TATR model. This highlights the effectiveness of CISOL as a benchmark for advancing TSR, especially in specialized domains.

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).

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

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.

Hyperparameter optimization (HPO) is a core problem for the machine learning community and remains largely unsolved due to the significant computational resources required to evaluate hyperparameter configurations. As a result, a series of recent related works have focused on the direction of transfer learning for quickly fine-tuning hyperparameters on a dataset. Unfortunately, the community does not have a common large-scale benchmark for comparing HPO algorithms. Instead, the de facto practice consists of empirical protocols on arbitrary small-scale meta-datasets that vary inconsistently across publications, making reproducibility a challenge. To resolve this major bottleneck and enable a fair and fast comparison of black-box HPO methods on a level playing field, we propose HPO-B, a new large-scale benchmark in the form of a collection of meta-datasets. Our benchmark is assembled and preprocessed from the OpenML repository and consists of 176 search spaces (algorithms) evaluated sparsely on 196 datasets with a total of 6.4 million hyperparameter evaluations. For ensuring reproducibility on our benchmark, we detail explicit experimental protocols, splits, and evaluation measures for comparing methods for both non-transfer, as well as, transfer learning HPO.

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

High-quality datasets are fundamental to training and evaluating machine learning models, yet their creation-especially with accurate human annotations-remains a significant challenge. Many dataset paper submissions lack originality, diversity, or rigorous quality control, and these shortcomings are often overlooked during peer review. Submissions also frequently omit essential details about dataset construction and properties. While existing tools such as datasheets aim to promote transparency, they are largely descriptive and do not provide standardized, measurable methods for evaluating data quality. Similarly, metadata requirements at conferences promote accountability but are inconsistently enforced. To address these limitations, this position paper advocates for the integration of systematic, rubric-based evaluation metrics into the dataset review process-particularly as submission volumes continue to grow. We also explore scalable, cost-effective methods for synthetic data generation, including dedicated tools and LLM-as-a-judge approaches, to support more efficient evaluation. As a call to action, we introduce DataRubrics, a structured framework for assessing the quality of both human- and model-generated datasets. Leveraging recent advances in LLM-based evaluation, DataRubrics offers a reproducible, scalable, and actionable solution for dataset quality assessment, enabling both authors and reviewers to uphold higher standards in data-centric research. We also release code to support reproducibility of LLM-based evaluations at https://github.com/datarubrics/datarubrics.

Misinformation in healthcare, from vaccine hesitancy to unproven treatments, poses risks to public health and trust in medical systems. While machine learning and natural language processing have advanced automated fact-checking, validating biomedical claims remains uniquely challenging due to complex terminology, the need for domain expertise, and the critical importance of grounding in scientific evidence. We introduce CER (Combining Evidence and Reasoning), a novel framework for biomedical fact-checking that integrates scientific evidence retrieval, reasoning via large language models, and supervised veracity prediction. By integrating the text-generation capabilities of large language models with advanced retrieval techniques for high-quality biomedical scientific evidence, CER effectively mitigates the risk of hallucinations, ensuring that generated outputs are grounded in verifiable, evidence-based sources. Evaluations on expert-annotated datasets (HealthFC, BioASQ-7b, SciFact) demonstrate state-of-the-art performance and promising cross-dataset generalization. Code and data are released for transparency and reproducibility: https://github.com/PRAISELab-PicusLab/CER

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.

Listwise rerankers based on large language models (LLM) are the zero-shot state-of-the-art. However, current works in this direction all depend on the GPT models, making it a single point of failure in scientific reproducibility. Moreover, it raises the concern that the current research findings only hold for GPT models but not LLM in general. In this work, we lift this pre-condition and build for the first time effective listwise rerankers without any form of dependency on GPT. Our passage retrieval experiments show that our best list se reranker surpasses the listwise rerankers based on GPT-3.5 by 13% and achieves 97% effectiveness of the ones built on GPT-4. Our results also show that the existing training datasets, which were expressly constructed for pointwise ranking, are insufficient for building such listwise rerankers. Instead, high-quality listwise ranking data is required and crucial, calling for further work on building human-annotated listwise data resources.

This article aims to provide the information retrieval community with some reflections on recent advances in retrieval learning by analyzing the reproducibility of image-text retrieval models. Due to the increase of multimodal data over the last decade, image-text retrieval has steadily become a major research direction in the field of information retrieval. Numerous researchers train and evaluate image-text retrieval algorithms using benchmark datasets such as MS-COCO and Flickr30k. Research in the past has mostly focused on performance, with multiple state-of-the-art methodologies being suggested in a variety of ways. According to their assertions, these techniques provide improved modality interactions and hence more precise multimodal representations. In contrast to previous works, we focus on the reproducibility of the approaches and the examination of the elements that lead to improved performance by pretrained and nonpretrained models in retrieving images and text. To be more specific, we first examine the related reproducibility concerns and explain why our focus is on image-text retrieval tasks. Second, we systematically summarize the current paradigm of image-text retrieval models and the stated contributions of those approaches. Third, we analyze various aspects of the reproduction of pretrained and nonpretrained retrieval models. To complete this, we conducted ablation experiments and obtained some influencing factors that affect retrieval recall more than the improvement claimed in the original paper. Finally, we present some reflections and challenges that the retrieval community should consider in the future. Our source code is publicly available at https://github.com/WangFei-2019/Image-text-Retrieval.

Click-through rate (CTR) prediction is a critical task for many applications, as its accuracy has a direct impact on user experience and platform revenue. In recent years, CTR prediction has been widely studied in both academia and industry, resulting in a wide variety of CTR prediction models. Unfortunately, there is still a lack of standardized benchmarks and uniform evaluation protocols for CTR prediction research. This leads to non-reproducible or even inconsistent experimental results among existing studies, which largely limits the practical value and potential impact of their research. In this work, we aim to perform open benchmarking for CTR prediction and present a rigorous comparison of different models in a reproducible manner. To this end, we ran over 7,000 experiments for more than 12,000 GPU hours in total to re-evaluate 24 existing models on multiple datasets and settings. Surprisingly, our experiments show that with sufficient hyper-parameter search and model tuning, many deep models have smaller differences than expected. The results also reveal that making real progress on the modeling of CTR prediction is indeed a very challenging research task. We believe that our benchmarking work could not only allow researchers to gauge the effectiveness of new models conveniently but also make them fairly compare with the state of the arts. We have publicly released the benchmarking code, evaluation protocols, and hyper-parameter settings of our work to promote reproducible research in this field.

Efficient experiment reproduction is critical to accelerating progress in artificial intelligence. However, the inherent complexity of method design and training procedures presents substantial challenges for automation. Notably, reproducing experiments often requires implicit domain-specific knowledge not explicitly documented in the original papers. To address this, we introduce the paper lineage algorithm, which identifies and extracts implicit knowledge from the relevant references cited by the target paper. Building on this idea, we propose AutoReproduce, a multi-agent framework capable of automatically reproducing experiments described in research papers in an end-to-end manner. AutoReproduce enhances code executability by generating unit tests alongside the reproduction process. To evaluate the reproduction capability, we construct ReproduceBench, a benchmark annotated with verified implementations, and introduce novel evaluation metrics to assess both the reproduction and execution fidelity. Experimental results demonstrate that AutoReproduce outperforms the existing strong agent baselines on all five evaluation metrics by a peak margin of over 70%. In particular, compared to the official implementations, AutoReproduce achieves an average performance gap of 22.1% on 89.74% of the executable experiment runs. The code will be available at https://github.com/AI9Stars/AutoReproduce.

Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful biomedical hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.

Academic citations are widely used for evaluating research and tracing knowledge flows. Such uses typically rely on raw citation counts and neglect variability in citation types. In particular, citations can vary in their fidelity as original knowledge from cited studies may be paraphrased, summarized, or reinterpreted, possibly wrongly, leading to variation in how much information changes from cited to citing paper. In this study, we introduce a computational pipeline to quantify citation fidelity at scale. Using full texts of papers, the pipeline identifies citations in citing papers and the corresponding claims in cited papers, and applies supervised models to measure fidelity at the sentence level. Analyzing a large-scale multi-disciplinary dataset of approximately 13 million citation sentence pairs, we find that citation fidelity is higher when authors cite papers that are 1) more recent and intellectually close, 2) more accessible, and 3) the first author has a lower H-index and the author team is medium-sized. Using a quasi-experiment, we establish the "telephone effect" - when citing papers have low fidelity to the original claim, future papers that cite the citing paper and the original have lower fidelity to the original. Our work reveals systematic differences in citation fidelity, underscoring the limitations of analyses that rely on citation quantity alone and the potential for distortion of evidence.

The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full version of PG exists to date. In fact, most PG studies so far either consider only a small number of manually selected books, leading to potential biased subsets, or employ vastly different pre-processing strategies (often specified in insufficient details), raising concerns regarding the reproducibility of published results. In order to address these shortcomings, here we present the Standardized Project Gutenberg Corpus (SPGC), an open science approach to a curated version of the complete PG data containing more than 50,000 books and more than 3 times 10^9 word-tokens. Using different sources of annotated metadata, we not only provide a broad characterization of the content of PG, but also show different examples highlighting the potential of SPGC for investigating language variability across time, subjects, and authors. We publish our methodology in detail, the code to download and process the data, as well as the obtained corpus itself on 3 different levels of granularity (raw text, timeseries of word tokens, and counts of words). In this way, we provide a reproducible, pre-processed, full-size version of Project Gutenberg as a new scientific resource for corpus linguistics, natural language processing, and information retrieval.

Misinformation in healthcare, from vaccine hesitancy to unproven treatments, poses risks to public health and trust in medical systems. While machine learning and natural language processing have advanced automated fact-checking, validating biomedical claims remains uniquely challenging due to complex terminology, the need for domain expertise, and the critical importance of grounding in scientific evidence. We introduce CER (Combining Evidence and Reasoning), a novel framework for biomedical fact-checking that integrates scientific evidence retrieval, reasoning via large language models, and supervised veracity prediction. By integrating the text-generation capabilities of large language models with advanced retrieval techniques for high-quality biomedical scientific evidence, CER effectively mitigates the risk of hallucinations, ensuring that generated outputs are grounded in verifiable, evidence-based sources. Evaluations on expert-annotated datasets (HealthFC, BioASQ-7b, SciFact) demonstrate state-of-the-art performance and promising cross-dataset generalization. Code and data are released for transparency and reproducibility: https: //github.com/PRAISELab-PicusLab/CER.

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

A Mamba state-space model trained only for next-step prediction appears to recover Granger-causal structure through a simple readout S = |W_{out} W_{in}|, with early experiments suggesting the phenomenon generalized across architectures and benefited from interventional data at p < 10^{-5}. We package the protocol used to test that claim -- standardized synthetic generators (VAR/Lorenz/CauseMe-style), three intervention semantics (do(X=c), soft-noise, random-forcing), edge-provenance cards on three real datasets, and size-matched control arms -- as a reusable falsification benchmark, and walk the claim through it in five stages. The method-level claim does not survive: (i) a plain linear bottleneck does as well or better; (ii) tuned Lasso beats the bottleneck on synthetic CauseMe-style benchmarks, and on Lorenz-96 (the only real benchmark with unambiguous ground truth) classical PCMCI and Granger lead a tight cluster in which the bottleneck trails; (iii) the headline intervention advantage is roughly 60% a sample-size confound, and the residual disappears under standard do(X=c) interventions, surviving only under a non-standard random-forcing scheme; (iv) even that residual reproduces, with a larger effect, in classical bivariate Granger -- the effect is method-agnostic. What survives is a narrow characterization result; the benchmark is the lasting artifact, and each stage above is one of its control arms.

Reporting quality is an important topic in clinical trial research articles, as it can impact clinical decisions. In this article, we test the ability of large language models to assess the reporting quality of this type of article using the Consolidated Standards of Reporting Trials (CONSORT). We create CONSORT-QA, an evaluation corpus from two studies on abstract reporting quality with CONSORT-abstract standards. We then evaluate the ability of different large generative language models (from the general domain or adapted to the biomedical domain) to correctly assess CONSORT criteria with different known prompting methods, including Chain-of-thought. Our best combination of model and prompting method achieves 85% accuracy. Using Chain-of-thought adds valuable information on the model's reasoning for completing the task.

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.

The accelerating pace of research on autoregressive generative models has produced thousands of papers, making manual literature surveys and reproduction studies increasingly impractical. We present a fully open-source, reproducible pipeline that automatically retrieves candidate documents from public repositories, filters them for relevance, extracts metadata, hyper-parameters and reported results, clusters topics, produces retrieval-augmented summaries and generates containerised scripts for re-running selected experiments. Quantitative evaluation on 50 manually-annotated papers shows F1 scores above 0.85 for relevance classification, hyper-parameter extraction and citation identification. Experiments on corpora of up to 1000 papers demonstrate near-linear scalability with eight CPU workers. Three case studies -- AWD-LSTM on WikiText-2, Transformer-XL on WikiText-103 and an autoregressive music model on the Lakh MIDI dataset -- confirm that the extracted settings support faithful reproduction, achieving test perplexities within 1--3% of the original reports.

Large language models are emerging as scientific assistants, but evaluating their ability to reason from empirical data remains challenging. Benchmarks derived from published studies and human annotations inherit publication bias, known-knowledge bias, label noise, and substantial storage requirements. We present InfiniteScienceGym, a procedurally generated benchmark of scientific repositories paired with a verifiable question-answering task. From a seed, the simulator deterministically generates a self-contained repository with realistic directory structure, files, and tabular data, and a privileged QA generator produces both answerable and unanswerable questions with exact ground truth. This makes it possible to evaluate evidence-grounded reasoning, abstention, and tool-mediated analysis in a controlled setting without distributing a large static corpus. InfiniteScienceGym complements real scientific benchmarks by targeting blind spots and failure modes that are hard to evaluate using published datasets alone. Evaluating both proprietary and open-weight models, we find that none achieve more than 45% accuracy overall, that recognizing unanswerable questions remains a major weakness, and that stronger models tend to use tools more effectively rather than simply consuming more tokens.

In natural language processing, a recently popular line of work explores how to best report the experimental results of neural networks. One exemplar publication, titled "Show Your Work: Improved Reporting of Experimental Results," advocates for reporting the expected validation effectiveness of the best-tuned model, with respect to the computational budget. In the present work, we critically examine this paper. As far as statistical generalizability is concerned, we find unspoken pitfalls and caveats with this approach. We analytically show that their estimator is biased and uses error-prone assumptions. We find that the estimator favors negative errors and yields poor bootstrapped confidence intervals. We derive an unbiased alternative and bolster our claims with empirical evidence from statistical simulation. Our codebase is at http://github.com/castorini/meanmax.

Amid mounting concern about the reliability and credibility of machine learning research, we present a principled framework for making robust and generalizable claims: the multiverse analysis. Our framework builds upon the multiverse analysis (Steegen et al., 2016) introduced in response to psychology's own reproducibility crisis. To efficiently explore high-dimensional and often continuous ML search spaces, we model the multiverse with a Gaussian Process surrogate and apply Bayesian experimental design. Our framework is designed to facilitate drawing robust scientific conclusions about model performance, and thus our approach focuses on exploration rather than conventional optimization. In the first of two case studies, we investigate disputed claims about the relative merit of adaptive optimizers. Second, we synthesize conflicting research on the effect of learning rate on the large batch training generalization gap. For the machine learning community, the multiverse analysis is a simple and effective technique for identifying robust claims, for increasing transparency, and a step toward improved reproducibility.

We have tried to reproduce the results of the paper "Natural Language Inference over Interaction Space" submitted to ICLR 2018 conference as part of the ICLR 2018 Reproducibility Challenge. Initially, we were not aware that the code was available, so we started to implement the network from scratch. We have evaluated our version of the model on Stanford NLI dataset and reached 86.38% accuracy on the test set, while the paper claims 88.0% accuracy. The main difference, as we understand it, comes from the optimizers and the way model selection is performed.

Large Language Models (LLMs) are now integral across various domains and have demonstrated impressive performance. Progress, however, rests on the premise that benchmark scores are both accurate and reproducible. We demonstrate that the reproducibility of LLM performance is fragile: changing system configuration such as evaluation batch size, GPU count, and GPU version can introduce significant difference in the generated responses. This issue is especially pronounced in reasoning models, where minor rounding differences in early tokens can cascade into divergent chains of thought, ultimately affecting accuracy. For instance, under bfloat16 precision with greedy decoding, a reasoning model like DeepSeek-R1-Distill-Qwen-7B can exhibit up to 9% variation in accuracy and 9,000 tokens difference in response length due to differences in GPU count, type, and evaluation batch size. We trace the root cause of this variability to the non-associative nature of floating-point arithmetic under limited numerical precision. This work presents the first systematic investigation into how numerical precision affects reproducibility in LLM inference. Through carefully controlled experiments across various hardware, software, and precision settings, we quantify when and how model outputs diverge. Our analysis reveals that floating-point precision -- while critical for reproducibility -- is often neglected in evaluation practices. Inspired by this, we develop a lightweight inference pipeline, dubbed LayerCast, that stores weights in 16-bit precision but performs all computations in FP32, balancing memory efficiency with numerical stability. Code is available at https://github.com/nanomaoli/llm_reproducibility.

Scientific research relies on accurate citation for attribution and integrity, yet large language models (LLMs) introduce a new risk: fabricated references that appear plausible but correspond to no real publications. Such hallucinated citations have already been observed in submissions and accepted papers at major machine learning venues, exposing vulnerabilities in peer review. Meanwhile, rapidly growing reference lists make manual verification impractical, and existing automated tools remain fragile to noisy and heterogeneous citation formats and lack standardized evaluation. We present the first comprehensive benchmark and detection framework for hallucinated citations in scientific writing. Our multi-agent verification pipeline decomposes citation checking into claim extraction, evidence retrieval, passage matching, reasoning, and calibrated judgment to assess whether a cited source truly supports its claim. We construct a large-scale human-validated dataset across domains and define unified metrics for citation faithfulness and evidence alignment. Experiments with state-of-the-art LLMs reveal substantial citation errors and show that our framework significantly outperforms prior methods in both accuracy and interpretability. This work provides the first scalable infrastructure for auditing citations in the LLM era and practical tools to improve the trustworthiness of scientific references.

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

Accelerating scientific discovery requires the identification of which experiments would yield the best outcomes before committing resources to costly physical validation. While existing benchmarks evaluate LLMs on scientific knowledge and reasoning, their ability to predict experimental outcomes - a task where AI could significantly exceed human capabilities - remains largely underexplored. We introduce SciPredict, a benchmark comprising 405 tasks derived from recent empirical studies in 33 specialized sub-fields of physics, biology, and chemistry. SciPredict addresses two critical questions: (a) can LLMs predict the outcome of scientific experiments with sufficient accuracy? and (b) can such predictions be reliably used in the scientific research process? Evaluations reveal fundamental limitations on both fronts. Model accuracies are 14-26% and human expert performance is approx20%. Although some frontier models exceed human performance model accuracy is still far below what would enable reliable experimental guidance. Even within the limited performance, models fail to distinguish reliable predictions from unreliable ones, achieving only approx20% accuracy regardless of their confidence or whether they judge outcomes as predictable without physical experimentation. Human experts, in contrast, demonstrate strong calibration: their accuracy increases from approx5% to approx80% as they deem outcomes more predictable without conducting the experiment. SciPredict establishes a rigorous framework demonstrating that superhuman performance in experimental science requires not just better predictions, but better awareness of prediction reliability. For reproducibility all our data and code are provided at https://github.com/scaleapi/scipredict

Literature research, vital for scientific work, faces the challenge of the surging torrent of information in the vast ocean of literature exceeding researchers' processing capabilities. To address this issue, we present an automated review generation method based on Large Language Models (LLMs), aimed at overcoming efficiency bottlenecks in literature processing and reducing cognitive load. Our statistically validated evaluation framework demonstrates that the generated reviews match or exceed manual quality, offering broad applicability across research fields due to minimal domain knowledge requirements. In a case study on propane dehydrogenation (PDH) catalysts, our method swiftly analyzed 343 articles, averaging seconds per article per LLM account, producing comprehensive reviews spanning 35 topics. Extended analysis of 1041 articles provided deep insights into catalysts' composition, structure, and performance. Recognizing LLMs' hallucinations, we implemented a multi-layered quality control strategy, effectively mitigating risks and ensuring reliability, as quantitatively demonstrated through manual verification. Expert verification confirms the accuracy and citation integrity of generated reviews, demonstrating LLM hallucination risks reduced to below 0.5\% with over 95\% confidence. Released Windows application enables one-click review generation, aiding researchers in tracking advancements and recommending literature. This approach showcases LLMs' role in enhancing scientific research productivity and sets the stage for further exploration.

The advent of Deep Research agents has substantially reduced the time required for conducting extensive research tasks. However, these tasks inherently demand rigorous standards of factual accuracy and comprehensiveness, necessitating thorough evaluation before widespread adoption. In this paper, we propose ReportBench, a systematic benchmark designed to evaluate the content quality of research reports generated by large language models (LLMs). Our evaluation focuses on two critical dimensions: (1) the quality and relevance of cited literature, and (2) the faithfulness and veracity of the statements within the generated reports. ReportBench leverages high-quality published survey papers available on arXiv as gold-standard references, from which we apply reverse prompt engineering to derive domain-specific prompts and establish a comprehensive evaluation corpus. Furthermore, we develop an agent-based automated framework within ReportBench that systematically analyzes generated reports by extracting citations and statements, checking the faithfulness of cited content against original sources, and validating non-cited claims using web-based resources. Empirical evaluations demonstrate that commercial Deep Research agents such as those developed by OpenAI and Google consistently generate more comprehensive and reliable reports than standalone LLMs augmented with search or browsing tools. However, there remains substantial room for improvement in terms of the breadth and depth of research coverage, as well as factual consistency. The complete code and data will be released at the following link: https://github.com/ByteDance-BandAI/ReportBench

Lack of rigorous reproducibility and validation are major hurdles for scientific development across many fields. Materials science in particular encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with both perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard

Frontier AI agents show increasing promise as scientific research assistants, and may eventually be useful for extended, open-ended research workflows. However, in order to use agents for novel research, we must first assess the underlying faithfulness and correctness of their work. To evaluate agents as research assistants, we introduce ReplicationBench, an evaluation framework that tests whether agents can replicate entire research papers drawn from the astrophysics literature. Astrophysics, where research relies heavily on archival data and computational study while requiring little real-world experimentation, is a particularly useful testbed for AI agents in scientific research. We split each paper into tasks which require agents to replicate the paper's core contributions, including the experimental setup, derivations, data analysis, and codebase. Each task is co-developed with the original paper authors and targets a key scientific result, enabling objective evaluation of both faithfulness (adherence to original methods) and correctness (technical accuracy of results). ReplicationBench is extremely challenging for current frontier language models: even the best-performing language models score under 20%. We analyze ReplicationBench trajectories in collaboration with domain experts and find a rich, diverse set of failure modes for agents in scientific research. ReplicationBench establishes the first benchmark of paper-scale, expert-validated astrophysics research tasks, reveals insights about agent performance generalizable to other domains of data-driven science, and provides a scalable framework for measuring AI agents' reliability in scientific research.

In recent years, the intersection of Natural Language Processing (NLP) and public health has opened innovative pathways for investigating various domains, including chronic pain in textual datasets. Despite the promise of NLP in chronic pain, the literature is dispersed across various disciplines, and there is a need to consolidate existing knowledge, identify knowledge gaps in the literature, and inform future research directions in this emerging field. This review aims to investigate the state of the research on NLP-based interventions designed for chronic pain research. A search strategy was formulated and executed across PubMed, Web of Science, IEEE Xplore, Scopus, and ACL Anthology to find studies published in English between 2014 and 2024. After screening 132 papers, 26 studies were included in the final review. Key findings from this review underscore the significant potential of NLP techniques to address pressing challenges in chronic pain research. The past 10 years in this field have showcased the utilization of advanced methods (transformers like RoBERTa and BERT) achieving high-performance metrics (e.g., F1>0.8) in classification tasks, while unsupervised approaches like Latent Dirichlet Allocation (LDA) and k-means clustering have proven effective for exploratory analyses. Results also reveal persistent challenges such as limited dataset diversity, inadequate sample sizes, and insufficient representation of underrepresented populations. Future research studies should explore multimodal data validation systems, context-aware mechanistic modeling, and the development of standardized evaluation metrics to enhance reproducibility and equity in chronic pain research.

Observational studies can yield clinically actionable evidence at scale, but executing them on real-world databases is open-ended and requires coherent decisions across cohort construction, analysis, and reporting. Prior evaluations of LLM agents emphasize isolated steps or single answers, missing the integrity and internal structure of the resulting evidence bundle. To address this gap, we introduce RWE-bench, a benchmark grounded in MIMIC-IV and derived from peer-reviewed observational studies. Each task provides the corresponding study protocol as the reference standard, requiring agents to execute experiments in a real database and iteratively generate tree-structured evidence bundles. We evaluate six LLMs (three open-source, three closed-source) under three agent scaffolds using both question-level correctness and end-to-end task metrics. Across 162 tasks, task success is low: the best agent reaches 39.9%, and the best open-source model reaches 30.4%. Agent scaffolds also matter substantially, causing over 30% variation in performance metrics. Furthermore, we implement an automated cohort evaluation method to rapidly localize errors and identify agent failure modes. Overall, the results highlight persistent limitations in agents' ability to produce end-to-end evidence bundles, and efficient validation remains an important direction for future work. Code and data are available at https://github.com/somewordstoolate/RWE-bench.

The use of large language models (LLMs) in scholarly publications has grown dramatically since the launch of ChatGPT in late 2022. This usage is often undisclosed, and it can be challenging for readers and reviewers to identify human written but LLM-revised or translated text, or predominantly LLM-generated text. Given the known quality and reliability issues connected with LLM-generated text, their potential growth poses an increasing problem for research integrity, and for public trust in research. This study presents a simple and easily reproducible methodology to show the growth in the full text of published papers, across the full range of research, as indexed in the Dimensions database. It uses this to demonstrate that LLM tools are likely to have been involved in the production of more than 10% of all published papers in 2024, based on disproportionate use of specific indicative words, and draws together earlier studies to confirm that this is a plausible overall estimate. It then discusses the implications of this for the integrity of scholarly publishing, highlighting evidence that use of LLMs for text generation is still being concealed or downplayed by authors, and presents an argument that more comprehensive disclosure requirements are urgently required to address this.

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.

We propose Lighthouse, a user-friendly library for reproducible video moment retrieval and highlight detection (MR-HD). Although researchers proposed various MR-HD approaches, the research community holds two main issues. The first is a lack of comprehensive and reproducible experiments across various methods, datasets, and video-text features. This is because no unified training and evaluation codebase covers multiple settings. The second is user-unfriendly design. Because previous works use different libraries, researchers set up individual environments. In addition, most works release only the training codes, requiring users to implement the whole inference process of MR-HD. Lighthouse addresses these issues by implementing a unified reproducible codebase that includes six models, three features, and five datasets. In addition, it provides an inference API and web demo to make these methods easily accessible for researchers and developers. Our experiments demonstrate that Lighthouse generally reproduces the reported scores in the reference papers. The code is available at https://github.com/line/lighthouse.

As researchers increasingly adopt LLMs as writing assistants, generating high-quality research paper introductions remains both challenging and essential. We introduce Scientific Introduction Generation (SciIG), a task that evaluates LLMs' ability to produce coherent introductions from titles, abstracts, and related works. Curating new datasets from NAACL 2025 and ICLR 2025 papers, we assess five state-of-the-art models, including both open-source (DeepSeek-v3, Gemma-3-12B, LLaMA 4-Maverick, MistralAI Small 3.1) and closed-source GPT-4o systems, across multiple dimensions: lexical overlap, semantic similarity, content coverage, faithfulness, consistency, citation correctness, and narrative quality. Our comprehensive framework combines automated metrics with LLM-as-a-judge evaluations. Results demonstrate LLaMA-4 Maverick's superior performance on most metrics, particularly in semantic similarity and faithfulness. Moreover, three-shot prompting consistently outperforms fewer-shot approaches. These findings provide practical insights into developing effective research writing assistants and set realistic expectations for LLM-assisted academic writing. To foster reproducibility and future research, we will publicly release all code and datasets.

Various benchmarks have been proposed to assess the performance of large language models (LLMs) in different coding scenarios. We refer to them as code-related benchmarks. However, there are no systematic guidelines by which such a benchmark should be developed to ensure its quality, reliability, and reproducibility. We propose How2Bench, which is comprised of a 55- 55-criteria checklist as a set of guidelines to govern the development of code-related benchmarks comprehensively. Using HOW2BENCH, we profiled 274 benchmarks released within the past decade and found concerning issues. Nearly 70% of the benchmarks did not take measures for data quality assurance; over 10% did not even open source or only partially open source. Many highly cited benchmarks have loopholes, including duplicated samples, incorrect reference codes/tests/prompts, and unremoved sensitive/confidential information. Finally, we conducted a human study involving 49 participants, which revealed significant gaps in awareness of the importance of data quality, reproducibility, and transparency.

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

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.

Null Hypothesis Significance Testing is the de facto tool for assessing effectiveness differences between Information Retrieval systems. Researchers use statistical tests to check whether those differences will generalise to online settings or are just due to the samples observed in the laboratory. Much work has been devoted to studying which test is the most reliable when comparing a pair of systems, but most of the IR real-world experiments involve more than two. In the multiple comparisons scenario, testing several systems simultaneously may inflate the errors committed by the tests. In this paper, we use a new approach to assess the reliability of multiple comparison procedures using simulated and real TREC data. Experiments show that Wilcoxon plus the Benjamini-Hochberg correction yields Type I error rates according to the significance level for typical sample sizes while being the best test in terms of statistical power.

As LLMs are deployed in high-stakes settings, users must judge the correctness of individual responses, often relying on model-generated justifications such as reasoning chains or explanations. Yet, no standard measure exists for whether these justifications help users distinguish correct answers from incorrect ones. We formalize this idea as error verifiability and propose v_{bal}, a balanced metric that measures whether justifications enable raters to accurately assess answer correctness, validated against human raters who show high agreement. We find that neither common approaches, such as post-training and model scaling, nor more targeted interventions recommended improve verifiability. We introduce two methods that succeed at improving verifiability: reflect-and-rephrase (RR) for mathematical reasoning and oracle-rephrase (OR) for factual QA, both of which improve verifiability by incorporating domain-appropriate external information. Together, our results establish error verifiability as a distinct dimension of response quality that does not emerge from accuracy improvements alone and requires dedicated, domain-aware methods to address.

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.

The development of large language models (LLMs) depends on trustworthy evaluation. However, most current evaluations rely on public benchmarks, which are prone to data contamination issues that significantly compromise fairness. Previous researches have focused on constructing dynamic benchmarks to address contamination. However, continuously building new benchmarks is costly and cyclical. In this work, we aim to tackle contamination by analyzing the mechanisms of contaminated models themselves. Through our experiments, we discover that the overestimation of contaminated models is likely due to parameters acquiring shortcut solutions in training. We further propose a novel method for identifying shortcut neurons through comparative and causal analysis. Building on this, we introduce an evaluation method called shortcut neuron patching to suppress shortcut neurons. Experiments validate the effectiveness of our approach in mitigating contamination. Additionally, our evaluation results exhibit a strong linear correlation with MixEval, a recently released trustworthy benchmark, achieving a Spearman coefficient (rho) exceeding 0.95. This high correlation indicates that our method closely reveals true capabilities of the models and is trustworthy. We conduct further experiments to demonstrate the generalizability of our method across various benchmarks and hyperparameter settings. Code: https://github.com/GaryStack/Trustworthy-Evaluation

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

We introduce a new -- currently 42 gigabyte -- ``living'' dataset of phone images of dog feces, annotated with manually drawn or AI-assisted polygon labels. There are 6k full resolution images and 4k detailed polygon annotations. The collection and annotation of images started in late 2020 and the dataset grows by roughly 1GB a month. We train VIT and MaskRCNN baseline models to explore the difficulty of the dataset. The best model achieves a pixelwise average precision of 0.858 on a 691-image validation set and 0.847 on a small independently captured 30-image contributor test set. The most recent snapshot of dataset is made publicly available through three different distribution methods: one centralized (Girder) and two decentralized (IPFS and BitTorrent). We study of the trade-offs between distribution methods and discuss the feasibility of each with respect to reliably sharing open scientific data. The code to reproduce the experiments is hosted on GitHub, and the data is published under the Creative Commons Attribution 4.0 International license. Model weights are made publicly available with the dataset. Experimental hardware, time, energy, and emissions are quantified.

We test whether Large Language Models (LLMs) can be used to simulate human participants in social-science studies. To do this, we run replications of 14 studies from the Many Labs 2 replication project with OpenAI's text-davinci-003 model, colloquially known as GPT3.5. Based on our pre-registered analyses, we find that among the eight studies we could analyse, our GPT sample replicated 37.5% of the original results and 37.5% of the Many Labs 2 results. However, we were unable to analyse the remaining six studies due to an unexpected phenomenon we call the "correct answer" effect. Different runs of GPT3.5 answered nuanced questions probing political orientation, economic preference, judgement, and moral philosophy with zero or near-zero variation in responses: with the supposedly "correct answer." In one exploratory follow-up study, we found that a "correct answer" was robust to changing the demographic details that precede the prompt. In another, we found that most but not all "correct answers" were robust to changing the order of answer choices. One of our most striking findings occurred in our replication of the Moral Foundations Theory survey results, where we found GPT3.5 identifying as a political conservative in 99.6% of the cases, and as a liberal in 99.3% of the cases in the reverse-order condition. However, both self-reported 'GPT conservatives' and 'GPT liberals' showed right-leaning moral foundations. Our results cast doubts on the validity of using LLMs as a general replacement for human participants in the social sciences. Our results also raise concerns that a hypothetical AI-led future may be subject to a diminished diversity-of-thought.

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".

Generative search engines directly generate responses to user queries, along with in-line citations. A prerequisite trait of a trustworthy generative search engine is verifiability, i.e., systems should cite comprehensively (high citation recall; all statements are fully supported by citations) and accurately (high citation precision; every cite supports its associated statement). We conduct human evaluation to audit four popular generative search engines -- Bing Chat, NeevaAI, perplexity.ai, and YouChat -- across a diverse set of queries from a variety of sources (e.g., historical Google user queries, dynamically-collected open-ended questions on Reddit, etc.). We find that responses from existing generative search engines are fluent and appear informative, but frequently contain unsupported statements and inaccurate citations: on average, a mere 51.5% of generated sentences are fully supported by citations and only 74.5% of citations support their associated sentence. We believe that these results are concerningly low for systems that may serve as a primary tool for information-seeking users, especially given their facade of trustworthiness. We hope that our results further motivate the development of trustworthy generative search engines and help researchers and users better understand the shortcomings of existing commercial systems.

With an increasing number of replication studies performed in psychological science, the question of how to evaluate the outcome of a replication attempt deserves careful consideration. Bayesian approaches allow to incorporate uncertainty and prior information into the analysis of the replication attempt by their design. The Replication Bayes Factor, introduced by Verhagen & Wagenmakers (2014), provides quantitative, relative evidence in favor or against a successful replication. In previous work by Verhagen & Wagenmakers (2014) it was limited to the case of t-tests. In this paper, the Replication Bayes Factor is extended to F-tests in multi-group, fixed-effect ANOVA designs. Simulations and examples are presented to facilitate the understanding and to demonstrate the usefulness of this approach. Finally, the Replication Bayes Factor is compared to other Bayesian and frequentist approaches and discussed in the context of replication attempts. R code to calculate Replication Bayes factors and to reproduce the examples in the paper is available at https://osf.io/jv39h/.

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)".

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Despite strong performance on existing benchmarks, it remains unclear whether large language models can reason over genuinely novel scientific information. Most evaluations score end-to-end RAG pipelines, where reasoning is confounded with retrieval and toolchain choices, and the signal is further contaminated by parametric memorization and open-web volatility. We introduce DeR2, a controlled deep-research sandbox that isolates document-grounded reasoning while preserving core difficulties of deep search: multi-step synthesis, denoising, and evidence-based conclusion making. DeR2 decouples evidence access from reasoning via four regimes--Instruction-only, Concepts (gold concepts without documents), Related-only (only relevant documents), and Full-set (relevant documents plus topically related distractors)--yielding interpretable regime gaps that operationalize retrieval loss vs. reasoning loss and enable fine-grained error attribution. To prevent parametric leakage, we apply a two-phase validation that requires parametric failure without evidence while ensuring oracle-concept solvability. To ensure reproducibility, each instance provides a frozen document library (drawn from 2023-2025 theoretical papers) with expert-annotated concepts and validated rationales. Experiments across a diverse set of state-of-the-art foundation models reveal substantial variation and significant headroom: some models exhibit mode-switch fragility, performing worse with the Full-set than with Instruction-only, while others show structural concept misuse, correctly naming concepts but failing to execute them as procedures.

We report on the curation of several publicly available datasets for age and gender prediction. Furthermore, we present experiments to predict age and gender with models based on a pre-trained wav2vec 2.0. Depending on the dataset, we achieve an MAE between 7.1 years and 10.8 years for age, and at least 91.1% ACC for gender (female, male, child). Compared to a modelling approach built on handcrafted features, our proposed system shows an improvement of 9% UAR for age and 4% UAR for gender. To make our findings reproducible, we release the best performing model to the community as well as the sample lists of the data splits.

Despite its importance to experimental design, statistical power (the probability that, given a real effect, an experiment will reject the null hypothesis) has largely been ignored by the NLP community. Underpowered experiments make it more difficult to discern the difference between statistical noise and meaningful model improvements, and increase the chances of exaggerated findings. By meta-analyzing a set of existing NLP papers and datasets, we characterize typical power for a variety of settings and conclude that underpowered experiments are common in the NLP literature. In particular, for several tasks in the popular GLUE benchmark, small test sets mean that most attempted comparisons to state of the art models will not be adequately powered. Similarly, based on reasonable assumptions, we find that the most typical experimental design for human rating studies will be underpowered to detect small model differences, of the sort that are frequently studied. For machine translation, we find that typical test sets of 2000 sentences have approximately 75% power to detect differences of 1 BLEU point. To improve the situation going forward, we give an overview of best practices for power analysis in NLP and release a series of notebooks to assist with future power analyses.

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.

We introduce ResearchGym, a benchmark and execution environment for evaluating AI agents on end-to-end research. To instantiate this, we repurpose five oral and spotlight papers from ICML, ICLR, and ACL. From each paper's repository, we preserve the datasets, evaluation harness, and baseline implementations but withhold the paper's proposed method. This results in five containerized task environments comprising 39 sub-tasks in total. Within each environment, agents must propose novel hypotheses, run experiments, and attempt to surpass strong human baselines on the paper's metrics. In a controlled evaluation of an agent powered by GPT-5, we observe a sharp capability--reliability gap. The agent improves over the provided baselines from the repository in just 1 of 15 evaluations (6.7%) by 11.5%, and completes only 26.5% of sub-tasks on average. We identify recurring long-horizon failure modes, including impatience, poor time and resource management, overconfidence in weak hypotheses, difficulty coordinating parallel experiments, and hard limits from context length. Yet in a single run, the agent surpasses the solution of an ICML 2025 Spotlight task, indicating that frontier agents can occasionally reach state-of-the-art performance, but do so unreliably. We additionally evaluate proprietary agent scaffolds including Claude Code (Opus-4.5) and Codex (GPT-5.2) which display a similar gap. ResearchGym provides infrastructure for systematic evaluation and analysis of autonomous agents on closed-loop research.

Reproducibility remains a significant challenge in machine learning (ML) for healthcare. In this field, datasets, model pipelines, and even task/cohort definitions are often private, leading to a significant barrier in sharing, iterating, and understanding ML results on electronic health record (EHR) datasets. In this paper, we address a significant part of this problem by introducing the Automatic Cohort Extraction System for Event-Stream Datasets (ACES). This tool is designed to simultaneously simplify the development of task/cohorts for ML in healthcare and enable the reproduction of these cohorts, both at an exact level for single datasets and at a conceptual level across datasets. To accomplish this, ACES provides (1) a highly intuitive and expressive configuration language for defining both dataset-specific concepts and dataset-agnostic inclusion/exclusion criteria, and (2) a pipeline to automatically extract patient records that meet these defined criteria from real-world data. ACES can be automatically applied to any dataset in either the Medical Event Data Standard (MEDS) or EventStreamGPT (ESGPT) formats, or to *any* dataset for which the necessary task-specific predicates can be extracted in an event-stream form. ACES has the potential to significantly lower the barrier to entry for defining ML tasks, redefine the way researchers interact with EHR datasets, and significantly improve the state of reproducibility for ML studies in this modality. ACES is available at https://github.com/justin13601/aces.

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

The Massive Text Embedding Benchmark (MTEB) has become a standard evaluation platform for text embedding models. While previous work has established the core benchmark methodology, this paper focuses on the engineering aspects that ensure MTEB's continued reproducibility and extensibility. We present our approach to maintaining robust continuous integration pipelines that validate dataset integrity, automate test execution, and assess benchmark results' generalizability. We detail the design choices that collectively enhance reproducibility and usability. Furthermore, we discuss our strategies for handling community contributions and extending the benchmark with new tasks and datasets. These engineering practices have been instrumental in scaling MTEB to become more comprehensive while maintaining quality and, ultimately, relevance to the field. Our experiences offer valuable insights for benchmark maintainers facing similar challenges in ensuring reproducibility and usability in machine learning evaluation frameworks. The MTEB repository is available at: https://github.com/embeddings-benchmark/mteb

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.

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.

Evaluations are critical for understanding the capabilities of large language models (LLMs). Fundamentally, evaluations are experiments; but the literature on evaluations has largely ignored the literature from other sciences on experiment analysis and planning. This article shows researchers with some training in statistics how to think about and analyze data from language model evaluations. Conceptualizing evaluation questions as having been drawn from an unseen super-population, we present formulas for analyzing evaluation data, measuring differences between two models, and planning an evaluation experiment. We make a number of specific recommendations for running language model evaluations and reporting experiment results in a way that minimizes statistical noise and maximizes informativeness.

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.

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.

Limited large-scale evaluations exist for facilitation strategies of online discussions due to significant costs associated with human involvement. An effective solution is synthetic discussion simulations using Large Language Models (LLMs) to create initial pilot experiments. We propose a simple, generalizable, LLM-driven methodology to prototype the development of LLM facilitators, and produce high-quality synthetic data without human involvement. We use our methodology to test whether current facilitation strategies can improve the performance of LLM facilitators. We find that, while LLM facilitators significantly improve synthetic discussions, there is no evidence that the application of more elaborate facilitation strategies proposed in modern Social Science research lead to further improvements in discussion quality, compared to more basic approaches. Additionally, we find that small LLMs (such as Mistral Nemo 12B) can perform comparably to larger models (such as LLaMa 70B), and that special instructions must be used for instruction-tuned models to induce toxicity in synthetic discussions. We confirm that each component of our methodology contributes substantially to high quality data via an ablation study. We release an open-source framework, "SynDisco" (pip install syndisco), which implements our methodology. We also release the "Virtual Moderation Dataset" (https://paperswithcode.com/dataset/vmd), a large, publicly available dataset containing LLM-generated and LLM-annotated discussions using multiple open-source LLMs.

Recent advances have made long-form report-generating systems widely available. This has prompted evaluation frameworks that use LLM-as-judge protocols and claim verification, along with meta-evaluation frameworks that seek to validate these methods. Many of the meta-evaluations estimate an evaluation quality's by comparing its assessments against human pairwise preferences. Prior work, however, suggests that human pairwise preference may be overly simplistic and can fail to capture nuances of expert expectations. We conduct a case study in meta-evaluation for long-form QA benchmarks using ScholarQA-CS2, a benchmark designed for assessing retrieval-augmented deep-research QA in the scientific domain. We comprehensively validate the benchmark through human pairwise preference judgments, then critically examine the strengths, weaknesses, and confounders of this approach. We show that pairwise preference rankings are best suited for system-level evaluation, while explicit metric-wise annotations and expert annotators are critical for reliable metric-level assessment, with subjectivity remaining a key challenge. Based on our findings, we offer practical guidelines for designing future meta-evaluations that better align evaluation methods, annotator expertise, and reporting practices. By surfacing these methodological challenges, we aim to advance evaluation standards for deep-research systems.

We present the system description for our submission towards the Key Point Analysis Shared Task at ArgMining 2021. Track 1 of the shared task requires participants to develop methods to predict the match score between each pair of arguments and keypoints, provided they belong to the same topic under the same stance. We leveraged existing state of the art pre-trained language models along with incorporating additional data and features extracted from the inputs (topics, key points, and arguments) to improve performance. We were able to achieve mAP strict and mAP relaxed score of 0.872 and 0.966 respectively in the evaluation phase, securing 5th place on the leaderboard. In the post evaluation phase, we achieved a mAP strict and mAP relaxed score of 0.921 and 0.982 respectively. All the codes to generate reproducible results on our models are available on Github.

The increasing adoption of large language models (LLMs) has been accompanied by growing concerns regarding their reliability and trustworthiness. As a result, a growing body of research focuses on evidence-based text generation with LLMs, aiming to link model outputs to supporting evidence to ensure traceability and verifiability. However, the field is fragmented due to inconsistent terminology, isolated evaluation practices, and a lack of unified benchmarks. To bridge this gap, we systematically analyze 134 papers, introduce a unified taxonomy of evidence-based text generation with LLMs, and investigate 300 evaluation metrics across seven key dimensions. Thereby, we focus on approaches that use citations, attribution, or quotations for evidence-based text generation. Building on this, we examine the distinctive characteristics and representative methods in the field. Finally, we highlight open challenges and outline promising directions for future work.

We consider the problem of automatically generating a narrative biomedical evidence summary from multiple trial reports. We evaluate modern neural models for abstractive summarization of relevant article abstracts from systematic reviews previously conducted by members of the Cochrane collaboration, using the authors conclusions section of the review abstract as our target. We enlist medical professionals to evaluate generated summaries, and we find that modern summarization systems yield consistently fluent and relevant synopses, but that they are not always factual. We propose new approaches that capitalize on domain-specific models to inform summarization, e.g., by explicitly demarcating snippets of inputs that convey key findings, and emphasizing the reports of large and high-quality trials. We find that these strategies modestly improve the factual accuracy of generated summaries. Finally, we propose a new method for automatically evaluating the factuality of generated narrative evidence syntheses using models that infer the directionality of reported findings.

Recent advancements in large language models (LLMs) have shown promise in generating novel research ideas. However, these ideas often face challenges related to feasibility and expected effectiveness. This paper explores how augmenting LLMs with relevant data during the idea generation process can enhance the quality of generated ideas. We introduce two ways of incorporating data: (1) providing metadata during the idea generation stage to guide LLMs toward feasible directions, and (2) adding automatic validation during the idea selection stage to assess the empirical plausibility of hypotheses within ideas. We conduct experiments in the social science domain, specifically with climate negotiation topics, and find that metadata improves the feasibility of generated ideas by 20%, while automatic validation improves the overall quality of selected ideas by 7%. A human study shows that LLM-generated ideas, along with their related data and validation processes, inspire researchers to propose research ideas with higher quality. Our work highlights the potential of data-driven research idea generation, and underscores the practical utility of LLM-assisted ideation in real-world academic settings.

The development of robust safety benchmarks for large language models requires open, reproducible datasets that can measure both appropriate refusal of harmful content and potential over-restriction of legitimate scientific discourse. We present an open-source dataset and testing framework for evaluating LLM safety mechanisms across mainly controlled substance queries, analyzing four major models' responses to systematically varied prompts. Our results reveal distinct safety profiles: Claude-3.5-sonnet demonstrated the most conservative approach with 73% refusals and 27% allowances, while Mistral attempted to answer 100% of queries. GPT-3.5-turbo showed moderate restriction with 10% refusals and 90% allowances, and Grok-2 registered 20% refusals and 80% allowances. Testing prompt variation strategies revealed decreasing response consistency, from 85% with single prompts to 65% with five variations. This publicly available benchmark enables systematic evaluation of the critical balance between necessary safety restrictions and potential over-censorship of legitimate scientific inquiry, while providing a foundation for measuring progress in AI safety implementation. Chain-of-thought analysis reveals potential vulnerabilities in safety mechanisms, highlighting the complexity of implementing robust safeguards without unduly restricting desirable and valid scientific discourse.

With the advent of large language models (LLMs) like GPT-3, a natural question is the extent to which these models can be utilized for source code optimization. This paper presents methodologically stringent case studies applied to well-known open source python libraries pillow and numpy. We find that contemporary LLM ChatGPT-4 (state September and October 2023) is surprisingly adept at optimizing energy and compute efficiency. However, this is only the case in interactive use, with a human expert in the loop. Aware of experimenter bias, we document our qualitative approach in detail, and provide transcript and source code. We start by providing a detailed description of our approach in conversing with the LLM to optimize the _getextrema function in the pillow library, and a quantitative evaluation of the performance improvement. To demonstrate qualitative replicability, we report further attempts on another locus in the pillow library, and one code locus in the numpy library, to demonstrate generalization within and beyond a library. In all attempts, the performance improvement is significant (factor up to 38). We have also not omitted reporting of failed attempts (there were none). We conclude that LLMs are a promising tool for code optimization in open source libraries, but that the human expert in the loop is essential for success. Nonetheless, we were surprised by how few iterations were required to achieve substantial performance improvements that were not obvious to the expert in the loop. We would like bring attention to the qualitative nature of this study, more robust quantitative studies would need to introduce a layer of selecting experts in a representative sample -- we invite the community to collaborate.

Retractions play a vital role in maintaining scientific integrity, yet systematic studies of retractions in computer science and other STEM fields remain scarce. We present WithdrarXiv, the first large-scale dataset of withdrawn papers from arXiv, containing over 14,000 papers and their associated retraction comments spanning the repository's entire history through September 2024. Through careful analysis of author comments, we develop a comprehensive taxonomy of retraction reasons, identifying 10 distinct categories ranging from critical errors to policy violations. We demonstrate a simple yet highly accurate zero-shot automatic categorization of retraction reasons, achieving a weighted average F1-score of 0.96. Additionally, we release WithdrarXiv-SciFy, an enriched version including scripts for parsed full-text PDFs, specifically designed to enable research in scientific feasibility studies, claim verification, and automated theorem proving. These findings provide valuable insights for improving scientific quality control and automated verification systems. Finally, and most importantly, we discuss ethical issues and take a number of steps to implement responsible data release while fostering open science in this area.

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.

We explore the ability of GPT-4 to perform ad-hoc schema based information extraction from scientific literature. We assess specifically whether it can, with a basic prompting approach, replicate two existing material science datasets, given the manuscripts from which they were originally manually extracted. We employ materials scientists to perform a detailed manual error analysis to assess where the model struggles to faithfully extract the desired information, and draw on their insights to suggest research directions to address this broadly important task.

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.

AI agents hold the potential to revolutionize scientific productivity by automating literature reviews, replicating experiments, analyzing data, and even proposing new directions of inquiry; indeed, there are now many such agents, ranging from general-purpose "deep research" systems to specialized science-specific agents, such as AI Scientist and AIGS. Rigorous evaluation of these agents is critical for progress. Yet existing benchmarks fall short on several fronts: they (1) fail to provide holistic, product-informed measures of real-world use cases such as science research; (2) lack reproducible agent tools necessary for a controlled comparison of core agentic capabilities; (3) do not account for confounding variables such as model cost and tool access; (4) do not provide standardized interfaces for quick agent prototyping and evaluation; and (5) lack comprehensive baseline agents necessary to identify true advances. In response, we define principles and tooling for more rigorously benchmarking agents. Using these, we present AstaBench, a suite that provides the first holistic measure of agentic ability to perform scientific research, comprising 2400+ problems spanning the entire scientific discovery process and multiple scientific domains, and including many problems inspired by actual user requests to deployed Asta agents. Our suite comes with the first scientific research environment with production-grade search tools that enable controlled, reproducible evaluation, better accounting for confounders. Alongside, we provide a comprehensive suite of nine science-optimized classes of Asta agents and numerous baselines. Our extensive evaluation of 57 agents across 22 agent classes reveals several interesting findings, most importantly that despite meaningful progress on certain individual aspects, AI remains far from solving the challenge of science research assistance.

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research.

Existing benchmarks fail to capture a crucial aspect of intelligence: physical reasoning, the integrated ability to combine domain knowledge, symbolic reasoning, and understanding of real-world constraints. To address this gap, we introduce PhyX: the first large-scale benchmark designed to assess models capacity for physics-grounded reasoning in visual scenarios. PhyX includes 3K meticulously curated multimodal questions spanning 6 reasoning types across 25 sub-domains and 6 core physics domains: thermodynamics, electromagnetism, mechanics, modern physics, optics, and wave\&acoustics. In our comprehensive evaluation, even state-of-the-art models struggle significantly with physical reasoning. GPT-4o, Claude3.7-Sonnet, and GPT-o4-mini achieve only 32.5\%, 42.2\%, and 45.8\% accuracy respectively-performance gaps exceeding 29\% compared to human experts. Our analysis exposes critical limitations in current models: over-reliance on memorized disciplinary knowledge, excessive dependence on mathematical formulations, and surface-level visual pattern matching rather than genuine physical understanding. We provide in-depth analysis through fine-grained statistics, detailed case studies, and multiple evaluation paradigms to thoroughly examine physical reasoning capabilities. To ensure reproducibility, we implement a compatible evaluation protocol based on widely-used toolkits such as VLMEvalKit, enabling one-click evaluation.

AI holds promise for transforming scientific processes, including hypothesis generation. Prior work on hypothesis generation can be broadly categorized into theory-driven and data-driven approaches. While both have proven effective in generating novel and plausible hypotheses, it remains an open question whether they can complement each other. To address this, we develop the first method that combines literature-based insights with data to perform LLM-powered hypothesis generation. We apply our method on five different datasets and demonstrate that integrating literature and data outperforms other baselines (8.97\% over few-shot, 15.75\% over literature-based alone, and 3.37\% over data-driven alone). Additionally, we conduct the first human evaluation to assess the utility of LLM-generated hypotheses in assisting human decision-making on two challenging tasks: deception detection and AI generated content detection. Our results show that human accuracy improves significantly by 7.44\% and 14.19\% on these tasks, respectively. These findings suggest that integrating literature-based and data-driven approaches provides a comprehensive and nuanced framework for hypothesis generation and could open new avenues for scientific inquiry.

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.

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 .