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Jul 17

When, Where, and How: Adaptive Binning for Tabular Self-Supervised Learning

Medical tabular data are ubiquitous in clinical research, but deep learning for tables remains underexplored because reliable labels often require costly expert adjudication, even though structured clinical variables are routinely available in tabular form. Self-supervised learning can leverage these unlabeled tables, and recent binning-based pretexts offer a promising inductive bias, but existing objectives fix a single global quantile discretization and apply feature-agnostic supervision. We propose Adaptive Binning, a training-adaptive discretization pretext for tabular SSL that couples discretization to learning through a feature-wise coarse-to-fine curriculum. Motivated by the spectral bias of neural networks and the principles of curriculum learning, our method progressively refines discretization per feature upon plateau detection and selects representation-aware splits to jointly improve value-space concentration and representation-space coherence. A heterogeneity-aware objective unifies categorical reconstruction with ordinal supervision for numerical features, and experiments on public medical tabular datasets under unified evaluation protocols show consistent gains for linear probing and fine-tuning without dataset-specific discretization tuning. We further introduce a medical tabular SSL benchmark with standardized protocols to support reproducible progress in this underexplored domain. Our code is available at https://github.com/labhai/Adaptive-Binning.

  • 3 authors
·
Jun 17 1

BTZSC: A Benchmark for Zero-Shot Text Classification Across Cross-Encoders, Embedding Models, Rerankers and LLMs

Zero-shot text classification (ZSC) offers the promise of eliminating costly task-specific annotation by matching texts directly to human-readable label descriptions. While early approaches have predominantly relied on cross-encoder models fine-tuned for natural language inference (NLI), recent advances in text-embedding models, rerankers, and instruction-tuned large language models (LLMs) have challenged the dominance of NLI-based architectures. Yet, systematically comparing these diverse approaches remains difficult. Existing evaluations, such as MTEB, often incorporate labeled examples through supervised probes or fine-tuning, leaving genuine zero-shot capabilities underexplored. To address this, we introduce BTZSC, a comprehensive benchmark of 22 public datasets spanning sentiment, topic, intent, and emotion classification, capturing diverse domains, class cardinalities, and document lengths. Leveraging BTZSC, we conduct a systematic comparison across four major model families, NLI cross-encoders, embedding models, rerankers and instruction-tuned LLMs, encompassing 38 public and custom checkpoints. Our results show that: (i) modern rerankers, exemplified by Qwen3-Reranker-8B, set a new state-of-the-art with macro F1 = 0.72; (ii) strong embedding models such as GTE-large-en-v1.5 substantially close the accuracy gap while offering the best trade-off between accuracy and latency; (iii) instruction-tuned LLMs at 4--12B parameters achieve competitive performance (macro F1 up to 0.67), excelling particularly on topic classification but trailing specialized rerankers; (iv) NLI cross-encoders plateau even as backbone size increases; and (v) scaling primarily benefits rerankers and LLMs over embedding models. BTZSC and accompanying evaluation code are publicly released to support fair and reproducible progress in zero-shot text understanding.

  • 1 authors
·
Mar 11

EgoVerse: An Egocentric Human Dataset for Robot Learning from Around the World

Robot learning increasingly depends on large and diverse data, yet robot data collection remains expensive and difficult to scale. Egocentric human data offer a promising alternative by capturing rich manipulation behavior across everyday environments. However, existing human datasets are often limited in scope, difficult to extend, and fragmented across institutions. We introduce EgoVerse, a collaborative platform for human data-driven robot learning that unifies data collection, processing, and access under a shared framework, enabling contributions from individual researchers, academic labs, and industry partners. The current release includes 1,362 hours (80k episodes) of human demonstrations spanning 1,965 tasks, 240 scenes, and 2,087 unique demonstrators, with standardized formats, manipulation-relevant annotations, and tooling for downstream learning. Beyond the dataset, we conduct a large-scale study of human-to-robot transfer with experiments replicated across multiple labs, tasks, and robot embodiments under shared protocols. We find that policy performance generally improves with increased human data, but that effective scaling depends on alignment between human data and robot learning objectives. Together, the dataset, platform, and study establish a foundation for reproducible progress in human data-driven robot learning. Videos and additional information can be found at https://egoverse.ai/

  • 39 authors
·
Apr 7

Give Me FP32 or Give Me Death? Challenges and Solutions for Reproducible Reasoning

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.

  • 10 authors
·
Jun 11, 2025 2

Muse: Towards Reproducible Long-Form Song Generation with Fine-Grained Style Control

Recent commercial systems such as Suno demonstrate strong capabilities in long-form song generation, while academic research remains largely non-reproducible due to the lack of publicly available training data, hindering fair comparison and progress. To this end, we release a fully open-source system for long-form song generation with fine-grained style conditioning, including a licensed synthetic dataset, training and evaluation pipelines, and Muse, an easy-to-deploy song generation model. The dataset consists of 116k fully licensed synthetic songs with automatically generated lyrics and style descriptions paired with audio synthesized by SunoV5. We train Muse via single-stage supervised finetuning of a Qwen-based language model extended with discrete audio tokens using MuCodec, without task-specific losses, auxiliary objectives, or additional architectural components. Our evaluations find that although Muse is trained with a modest data scale and model size, it achieves competitive performance on phoneme error rate, text--music style similarity, and audio aesthetic quality, while enabling controllable segment-level generation across different musical structures. All data, model weights, and training and evaluation pipelines will be publicly released, paving the way for continued progress in controllable long-form song generation research. The project repository is available at https://github.com/yuhui1038/Muse.

  • 17 authors
·
Jan 7

LLaSO: A Foundational Framework for Reproducible Research in Large Language and Speech Model

The development of Large Speech-Language Models (LSLMs) has been slowed by fragmented architectures and a lack of transparency, hindering the systematic comparison and reproducibility of research. Unlike in the vision-language domain, the LSLM field suffers from the common practice of releasing model weights without their corresponding training data and configurations. To address these critical gaps, we introduce LLaSO, the first fully open, end-to-end framework for large-scale speech-language modeling. LLaSO provides the community with three essential resources: (1) LLaSO-Align, a 12M-instance speech-text alignment corpus; (2) LLaSO-Instruct, a 13.5M-instance multi-task instruction-tuning dataset; and (3) LLaSO-Eval, a reproducible benchmark for standardized evaluation. To validate our framework, we build and release LLaSO-Base, a 3.8B-parameter reference model trained exclusively on our public data. It achieves a normalized score of 0.72, establishing a strong, reproducible baseline that surpasses comparable models. Our analysis reveals that while broader training coverage enhances performance, significant generalization gaps persist on unseen tasks, particularly in pure audio scenarios. By releasing the complete stack of data, benchmarks, and models, LLaSO establishes a foundational open standard to unify research efforts and accelerate community-driven progress in LSLMs. We release the code, dataset, pretrained models, and results in https://github.com/EIT-NLP/LLaSO.

  • 8 authors
·
Aug 21, 2025 2

$τ$-Voice: Benchmarking Full-Duplex Voice Agents on Real-World Domains

Full-duplex voice agents--systems that listen and speak simultaneously--are rapidly moving from research to production. However, existing evaluations address conversational dynamics and task completion in isolation. We introduce τ-voice, a benchmark for evaluating voice agents on grounded tasks with real-world complexity: agents must navigate complex multi-turn conversations, adhere to domain policies, and interact with the environment. The framework extends τ^2-bench into a novel voice agent benchmark combining verifiable completion of complex grounded tasks, full-duplex interaction, and realistic audio--enabling direct comparison between voice and text performance. A controllable and realistic voice user simulator provides diverse accents, realistic audio environments, and rich turn-taking dynamics; by decoupling simulation from wall-clock time, the user simulator can use the most capable LLM without real-time constraints. We evaluate task completion (pass@1) and voice interaction quality across 278 tasks: while GPT-5 (reasoning) achieves 85%, voice agents reach only 31--51% under clean conditions and 26--38% under realistic conditions with noise and diverse accents--retaining only 30--45% of text capability; qualitative analysis confirms 79--90% of failures stem from agent behavior, suggesting that observed failures primarily reflect agent behavior under our evaluation setup. τ-voice provides a reproducible testbed for measuring progress toward voice agents that are natural, conversational, and reliable.

  • 4 authors
·
Mar 13

SciVisAgentBench: A Benchmark for Evaluating Scientific Data Analysis and Visualization Agents

Recent advances in large language models (LLMs) have enabled agentic systems that translate natural language intent into executable scientific visualization (SciVis) tasks. Despite rapid progress, the community lacks a principled and reproducible benchmark for evaluating these emerging SciVis agents in realistic, multi-step analysis settings. We present SciVisAgentBench, a comprehensive and extensible benchmark for evaluating scientific data analysis and visualization agents. Our benchmark is grounded in a structured taxonomy spanning four dimensions: application domain, data type, complexity level, and visualization operation. It currently comprises 108 expert-crafted cases covering diverse SciVis scenarios. To enable reliable assessment, we introduce a multimodal outcome-centric evaluation pipeline that combines LLM-based judging with deterministic evaluators, including image-based metrics, code checkers, rule-based verifiers, and case-specific evaluators. We also conduct a validity study with 12 SciVis experts to examine the agreement between human and LLM judges. Using this framework, we evaluate representative SciVis agents and general-purpose coding agents to establish initial baselines and reveal capability gaps. SciVisAgentBench is designed as a living benchmark to support systematic comparison, diagnose failure modes, and drive progress in agentic SciVis. The benchmark is available at https://scivisagentbench.github.io/.

  • 16 authors
·
Mar 30

Voice Evaluation of Reasoning Ability: Diagnosing the Modality-Induced Performance Gap

We present Voice Evaluation of Reasoning Ability (VERA), a benchmark for evaluating reasoning ability in voice-interactive systems under real-time conversational constraints. VERA comprises 2,931 voice-native episodes derived from established text benchmarks and organized into five tracks (Math, Web, Science, Long-Context, Factual). Each item is adapted for speech interaction while preserving reasoning difficulty. VERA enables direct text-voice comparison within model families and supports analysis of how architectural choices affect reliability. We assess 12 contemporary voice systems alongside strong text baselines and observe large, consistent modality gaps: on competition mathematics a leading text model attains 74.8% accuracy while its voice counterpart reaches 6.1%; macro-averaged across tracks the best text models achieve 54.0% versus 11.3% for voice. Latency-accuracy analyses reveal a low-latency plateau, where fast voice systems cluster around ~10% accuracy, while approaching text performance requires sacrificing real-time interaction. Diagnostic experiments indicate that common mitigations are insufficient. Increasing "thinking time" yields negligible gains; a decoupled cascade that separates reasoning from narration improves accuracy but still falls well short of text and introduces characteristic grounding/consistency errors. Failure analyses further show distinct error signatures across native streaming, end-to-end, and cascade designs. VERA provides a reproducible testbed and targeted diagnostics for architectures that decouple thinking from speaking, offering a principled way to measure progress toward real-time voice assistants that are both fluent and reliably reasoned.

adobe Adobe
·
Sep 30, 2025 2

GUI-360: A Comprehensive Dataset and Benchmark for Computer-Using Agents

We introduce GUI-360^circ, a large-scale, comprehensive dataset and benchmark suite designed to advance computer-using agents (CUAs). CUAs present unique challenges and is constrained by three persistent gaps: a scarcity of real-world CUA tasks, the lack of automated collection-and-annotation pipelines for multi-modal trajectories, and the absence of a unified benchmark that jointly evaluates GUI grounding, screen parsing, and action prediction. GUI-360^circ addresses these gaps with an LLM-augmented, largely automated pipeline for query sourcing, environment-template construction, task instantiation, batched execution, and LLM-driven quality filtering. The released corpus contains over 1.2M executed action steps across thousands of trajectories in popular Windows office applications, and includes full-resolution screenshots, accessibility metadata when available, instantiated goals, intermediate reasoning traces, and both successful and failed action trajectories. The dataset supports three canonical tasks, GUI grounding, screen parsing, and action prediction, and a hybrid GUI+API action space that reflects modern agent designs. Benchmarking state-of-the-art vision--language models on GUI-360^circ reveals substantial out-of-the-box shortcomings in grounding and action prediction; supervised fine-tuning and reinforcement learning yield significant gains but do not close the gap to human-level reliability. We release GUI-360^circ and accompanying code to facilitate reproducible research and accelerate progress on robust desktop CUAs. The full dataset has been made public on https://huggingface.co/datasets/vyokky/GUI-360.

microsoft Microsoft
·
Nov 6, 2025 2

OpenMixup: Open Mixup Toolbox and Benchmark for Visual Representation Learning

Mixup augmentation has emerged as a widely used technique for improving the generalization ability of deep neural networks (DNNs). However, the lack of standardized implementations and benchmarks has impeded recent progress, resulting in poor reproducibility, unfair comparisons, and conflicting insights. In this paper, we introduce OpenMixup, the first mixup augmentation codebase, and benchmark for visual representation learning. Specifically, we train 18 representative mixup baselines from scratch and rigorously evaluate them across 11 image datasets of varying scales and granularity, ranging from fine-grained scenarios to complex non-iconic scenes. We also open-source our modular codebase, including a collection of popular vision backbones, optimization strategies, and analysis toolkits, which not only supports the benchmarking but enables broader mixup applications beyond classification, such as self-supervised learning and regression tasks. Through experiments and empirical analysis, we gain observations and insights on mixup performance-efficiency trade-offs, generalization, and optimization behaviors, and thereby identify preferred choices for different needs. To the best of our knowledge, OpenMixup has facilitated several recent studies. We believe this work can further advance reproducible mixup augmentation research and thereby lay a solid ground for future progress in the community. The source code and user documents are available at https://github.com/Westlake-AI/openmixup.

  • 8 authors
·
Sep 11, 2022

LMRL Gym: Benchmarks for Multi-Turn Reinforcement Learning with Language Models

Large language models (LLMs) provide excellent text-generation capabilities, but standard prompting and generation methods generally do not lead to intentional or goal-directed agents and might necessitate considerable prompt tuning. This becomes particularly apparent in multi-turn conversations: even the best current LLMs rarely ask clarifying questions, engage in explicit information gathering, or take actions now that lead to better decisions after multiple turns. Reinforcement learning has the potential to leverage the powerful modeling capabilities of LLMs, as well as their internal representation of textual interactions, to create capable goal-directed language agents. This can enable intentional and temporally extended interactions, such as with humans, through coordinated persuasion and carefully crafted questions, or in goal-directed play through text games to bring about desired final outcomes. However, enabling this requires the community to develop stable and reliable reinforcement learning algorithms that can effectively train LLMs. Developing such algorithms requires tasks that can gauge progress on algorithm design, provide accessible and reproducible evaluations for multi-turn interactions, and cover a range of task properties and challenges in improving reinforcement learning algorithms. Our paper introduces the LMRL-Gym benchmark for evaluating multi-turn RL for LLMs, together with an open-source research framework containing a basic toolkit for getting started on multi-turn RL with offline value-based and policy-based RL methods. Our benchmark consists of 8 different language tasks, which require multiple rounds of language interaction and cover a range of tasks in open-ended dialogue and text games.

  • 8 authors
·
Nov 29, 2023

Graphic-Design-Bench: A Comprehensive Benchmark for Evaluating AI on Graphic Design Tasks

We introduce GraphicDesignBench (GDB), the first comprehensive benchmark suite designed specifically to evaluate AI models on the full breadth of professional graphic design tasks. Unlike existing benchmarks that focus on natural-image understanding or generic text-to-image synthesis, GDB targets the unique challenges of professional design work: translating communicative intent into structured layouts, rendering typographically faithful text, manipulating layered compositions, producing valid vector graphics, and reasoning about animation. The suite comprises 50 tasks organized along five axes: layout, typography, infographics, template & design semantics and animation, each evaluated under both understanding and generation settings, and grounded in real-world design templates drawn from the LICA layered-composition dataset. We evaluate a set of frontier closed-source models using a standardized metric taxonomy covering spatial accuracy, perceptual quality, text fidelity, semantic alignment, and structural validity. Our results reveal that current models fall short on the core challenges of professional design: spatial reasoning over complex layouts, faithful vector code generation, fine-grained typographic perception, and temporal decomposition of animations remain largely unsolved. While high-level semantic understanding is within reach, the gap widens sharply as tasks demand precision, structure, and compositional awareness. GDB provides a rigorous, reproducible testbed for tracking progress toward AI systems that can function as capable design collaborators. The full evaluation framework is publicly available.

  • 5 authors
·
Apr 6

Tactile MNIST: Benchmarking Active Tactile Perception

Tactile perception has the potential to significantly enhance dexterous robotic manipulation by providing rich local information that can complement or substitute for other sensory modalities such as vision. However, because tactile sensing is inherently local, it is not well-suited for tasks that require broad spatial awareness or global scene understanding on its own. A human-inspired strategy to address this issue is to consider active perception techniques instead. That is, to actively guide sensors toward regions with more informative or significant features and integrate such information over time in order to understand a scene or complete a task. Both active perception and different methods for tactile sensing have received significant attention recently. Yet, despite advancements, both fields lack standardized benchmarks. To bridge this gap, we introduce the Tactile MNIST Benchmark Suite, an open-source, Gymnasium-compatible benchmark specifically designed for active tactile perception tasks, including localization, classification, and volume estimation. Our benchmark suite offers diverse simulation scenarios, from simple toy environments all the way to complex tactile perception tasks using vision-based tactile sensors. Furthermore, we also offer a comprehensive dataset comprising 13,500 synthetic 3D MNIST digit models and 153,600 real-world tactile samples collected from 600 3D printed digits. Using this dataset, we train a CycleGAN for realistic tactile simulation rendering. By providing standardized protocols and reproducible evaluation frameworks, our benchmark suite facilitates systematic progress in the fields of tactile sensing and active perception.

  • 6 authors
·
Jun 13, 2025

AndroidWorld: A Dynamic Benchmarking Environment for Autonomous Agents

Autonomous agents that execute human tasks by controlling computers can enhance human productivity and application accessibility. Yet, progress in this field will be driven by realistic and reproducible benchmarks. We present AndroidWorld, a fully functioning Android environment that provides reward signals for 116 programmatic task workflows across 20 real world Android applications. Unlike existing interactive environments, which provide a static test set, AndroidWorld dynamically constructs tasks that are parameterized and expressed in natural language in unlimited ways, thus enabling testing on a much larger and realistic suite of tasks. Reward signals are derived from the computer's system state, making them durable across task variations and extensible across different apps. To demonstrate AndroidWorld's benefits and mode of operation, we introduce a new computer control agent, M3A. M3A can complete 30.6% of the AndroidWorld's tasks, leaving ample room for future work. Furthermore, we adapt a popular desktop web agent to work on Android, which we find to be less effective on mobile, suggesting future research is needed to achieve universal, cross-domain agents. Finally, we conduct a robustness analysis by testing M3A against a range of task variations on a representative subset of tasks, demonstrating that variations in task parameters can significantly alter the complexity of a task and therefore an agent's performance, highlighting the importance of testing agents under diverse conditions. AndroidWorld and the experiments in this paper are available at https://github.com/google-research/android_world.

  • 15 authors
·
May 23, 2024

EasyTPP: Towards Open Benchmarking Temporal Point Processes

Continuous-time event sequences play a vital role in real-world domains such as healthcare, finance, online shopping, social networks, and so on. To model such data, temporal point processes (TPPs) have emerged as the most natural and competitive models, making a significant impact in both academic and application communities. Despite the emergence of many powerful models in recent years, there hasn't been a central benchmark for these models and future research endeavors. This lack of standardization impedes researchers and practitioners from comparing methods and reproducing results, potentially slowing down progress in this field. In this paper, we present EasyTPP, the first central repository of research assets (e.g., data, models, evaluation programs, documentations) in the area of event sequence modeling. Our EasyTPP makes several unique contributions to this area: a unified interface of using existing datasets and adding new datasets; a wide range of evaluation programs that are easy to use and extend as well as facilitate reproducible research; implementations of popular neural TPPs, together with a rich library of modules by composing which one could quickly build complex models. All the data and implementation can be found at https://github.com/ant-research/EasyTemporalPointProcess. We will actively maintain this benchmark and welcome contributions from other researchers and practitioners. Our benchmark will help promote reproducible research in this field, thus accelerating research progress as well as making more significant real-world impacts.

  • 12 authors
·
Jul 16, 2023

Fleming-R1: Toward Expert-Level Medical Reasoning via Reinforcement Learning

While large language models show promise in medical applications, achieving expert-level clinical reasoning remains challenging due to the need for both accurate answers and transparent reasoning processes. To address this challenge, we introduce Fleming-R1, a model designed for verifiable medical reasoning through three complementary innovations. First, our Reasoning-Oriented Data Strategy (RODS) combines curated medical QA datasets with knowledge-graph-guided synthesis to improve coverage of underrepresented diseases, drugs, and multi-hop reasoning chains. Second, we employ Chain-of-Thought (CoT) cold start to distill high-quality reasoning trajectories from teacher models, establishing robust inference priors. Third, we implement a two-stage Reinforcement Learning from Verifiable Rewards (RLVR) framework using Group Relative Policy Optimization, which consolidates core reasoning skills while targeting persistent failure modes through adaptive hard-sample mining. Across diverse medical benchmarks, Fleming-R1 delivers substantial parameter-efficient improvements: the 7B variant surpasses much larger baselines, while the 32B model achieves near-parity with GPT-4o and consistently outperforms strong open-source alternatives. These results demonstrate that structured data design, reasoning-oriented initialization, and verifiable reinforcement learning can advance clinical reasoning beyond simple accuracy optimization. We release Fleming-R1 publicly to promote transparent, reproducible, and auditable progress in medical AI, enabling safer deployment in high-stakes clinical environments.

  • 7 authors
·
Sep 18, 2025

Fleming-VL: Towards Universal Medical Visual Reasoning with Multimodal LLMs

Multimodal Large Language Models (MLLMs) have demonstrated remarkable effectiveness in various general-domain scenarios, such as visual question answering and image captioning. Recently, researchers have increasingly focused on empowering MLLMs with medical conversational abilities, which hold significant promise for clinical applications. However, medical data presents unique challenges due to its heterogeneous nature -- encompassing diverse modalities including 2D images, 3D volumetric scans, and temporal video sequences. The substantial domain gap and data format inconsistencies across these modalities have hindered the development of unified medical MLLMs. To address these challenges, we propose Fleming-VL, a unified end-to-end framework for comprehensive medical visual understanding across heterogeneous modalities. Fleming-VL tackles this problem from a data-centric perspective through three key strategies: (1) scaling up pretraining by integrating long-context data from both natural and medical-specific domains; (2) complementing fine-tuning with rare medical data, including holistic video analysis and underrepresented 2D modalities such as ultrasound and dermoscopy images; (3) extending existing evaluation frameworks to incorporate 3D volumetric and video understanding benchmarks. Through supervised fine-tuning (SFT) and group relative policy optimization (GRPO), we develop Fleming-VL in multiple model scales. Extensive experiments demonstrate that Fleming-VL achieves state-of-the-art performance across multiple benchmarks, including medical VQA, video QA, and 3D medical image understanding. We publicly release Fleming-VL to promote transparent, reproducible, and auditable progress in medical AI.

  • 5 authors
·
Nov 2, 2025

WebChoreArena: Evaluating Web Browsing Agents on Realistic Tedious Web Tasks

Powered by a large language model (LLM), a web browsing agent operates web browsers in a human-like manner and offers a highly transparent path toward automating a wide range of everyday tasks. As web agents become increasingly capable and demonstrate proficiency in general browsing tasks, a critical question emerges: Can they go beyond general browsing to robustly handle tasks that are tedious and complex, or chores that humans often avoid doing themselves? In this paper, we introduce WebChoreArena, a new fully reproducible benchmark comprising 532 carefully curated tasks designed to extend the scope of WebArena beyond general browsing to more labor-intensive and tedious tasks. WebChoreArena systematically integrates three key challenges: (i) Massive Memory tasks requiring accurate retrieval of large amounts of information in the observations, (ii) Calculation tasks demanding precise mathematical reasoning, and (iii) Long-Term Memory tasks necessitating long-term memory across multiple webpages. Built on top of the fully reproducible and widely adopted four WebArena simulation environments, WebChoreArena ensures strict reproducibility and enables fair, direct comparisons with the established WebArena benchmark, offering key insights into agent progress. Our experimental results demonstrate that as LLMs evolve, represented by GPT-4o, Claude 3.7 Sonnet, and Gemini 2.5 Pro, significant improvements in performance are observed on WebChoreArena. These findings suggest that WebChoreArena is well-suited to measure the advancement of state-of-the-art LLMs with greater clarity. Nevertheless, the results also indicate that even with Gemini 2.5 Pro, there remains substantial room for improvement compared to WebArena, highlighting the increased challenges posed by WebChoreArena.

  • 12 authors
·
Jun 2, 2025 3

OpenMMReasoner: Pushing the Frontiers for Multimodal Reasoning with an Open and General Recipe

Recent advancements in large reasoning models have fueled growing interest in extending such capabilities to multimodal domains. However, despite notable progress in visual reasoning, the lack of transparent and reproducible data curation and training strategies remains a major barrier to scalable research. In this work, we introduce OpenMMReasoner, a fully transparent two-stage recipe for multimodal reasoning spanning supervised fine-tuning (SFT) and reinforcement learning (RL). In the SFT stage, we construct an 874K-sample cold-start dataset with rigorous step-by-step validation, providing a strong foundation for reasoning capabilities. The subsequent RL stage leverages a 74K-sample dataset across diverse domains to further sharpen and stabilize these abilities, resulting in a more robust and efficient learning process. Extensive evaluations demonstrate that our training recipe not only surpasses strong baselines but also highlights the critical role of data quality and training design in shaping multimodal reasoning performance. Notably, our method achieves a 11.6% improvement over the Qwen2.5-VL-7B-Instruct baseline across nine multimodal reasoning benchmarks, establishing a solid empirical foundation for future large-scale multimodal reasoning research. We open-sourced all our codes, pipeline, and data at https://github.com/EvolvingLMMs-Lab/OpenMMReasoner.

lmms-lab LMMs-Lab
·
Nov 20, 2025 3

FCMBench-Video: Benchmarking Document Video Intelligence

Document understanding is a critical capability in financial credit review, onboarding, and remote verification, where both decision accuracy and evidence traceability matter. Compared with static document images, document videos present a temporally redundant and sequentially unfolding evidence stream, require evidence integration across frames, and preserve acquisition-process cues relevant to authenticity-sensitive and anti-fraud review. We introduce FCMBench-Video, a benchmark for document-video intelligence that evaluates document perception, temporal grounding, and evidence-grounded reasoning under realistic capture conditions. For privacy-compliant yet realistic data at scale, we organize construction as an atomic-acquisition and composition workflow that records reusable single-document clips, applies controlled degradations, and assembles long-form multi-document videos with prescribed temporal spans. FCMBench-Video is built from 495 atomic videos composed into 1,200 long-form videos paired with 11,322 expert-annotated question--answer instances, covering 28 document types over 20s--60s duration tiers and 5,960 Chinese / 5,362 English instances. Evaluations on nine recent Video-MLLMs show that FCMBench-Video provides meaningful separation across systems and capabilities: counting is the most duration-sensitive task, Cross-Document Validation and Evidence-Grounded Selection probe higher-level evidence integration, and Visual Prompt Injection provides a complementary robustness dimension. The overall score distribution is broad and approximately bell-shaped, indicating a benchmark that is neither saturated nor dominated by trivial cases. Together, these results position FCMBench-Video as a reproducible benchmark for tracking Video-MLLM progress on document-video understanding and probing capability boundaries in authenticity-sensitive credit-domain applications.

  • 5 authors
·
Apr 27

MultiFinBen: A Multilingual, Multimodal, and Difficulty-Aware Benchmark for Financial LLM Evaluation

Recent advances in large language models (LLMs) have accelerated progress in financial NLP and applications, yet existing benchmarks remain limited to monolingual and unimodal settings, often over-relying on simple tasks and failing to reflect the complexity of real-world financial communication. We introduce MultiFinBen, the first multilingual and multimodal benchmark tailored to the global financial domain, evaluating LLMs across modalities (text, vision, audio) and linguistic settings (monolingual, bilingual, multilingual) on domain-specific tasks. We introduce two novel tasks, including PolyFiQA-Easy and PolyFiQA-Expert, the first multilingual financial benchmarks requiring models to perform complex reasoning over mixed-language inputs; and EnglishOCR and SpanishOCR, the first OCR-embedded financial QA tasks challenging models to extract and reason over information from visual-text financial documents. Moreover, we propose a dynamic, difficulty-aware selection mechanism and curate a compact, balanced benchmark rather than simple aggregation existing datasets. Extensive evaluation of 22 state-of-the-art models reveals that even the strongest models, despite their general multimodal and multilingual capabilities, struggle dramatically when faced with complex cross-lingual and multimodal tasks in financial domain. MultiFinBen is publicly released to foster transparent, reproducible, and inclusive progress in financial studies and applications.

  • 44 authors
·
Jun 16, 2025 3

Establishing Baselines for Photonic Quantum Machine Learning: Insights from an Open, Collaborative Initiative

The Perceval Challenge is an open, reproducible benchmark designed to assess the potential of photonic quantum computing for machine learning. Focusing on a reduced and hardware-feasible version of the MNIST digit classification task or near-term photonic processors, it offers a concrete framework to evaluate how photonic quantum circuits learn and generalize from limited data. Conducted over more than three months, the challenge attracted 64 teams worldwide in its first phase. After an initial selection, 11 finalist teams were granted access to GPU resources for large-scale simulation and photonic hardware execution through cloud service. The results establish the first unified baseline of photonic machine-learning performance, revealing complementary strengths between variational, hardware-native, and hybrid approaches. This challenge also underscores the importance of open, reproducible experimentation and interdisciplinary collaboration, highlighting how shared benchmarks can accelerate progress in quantum-enhanced learning. All implementations are publicly available in a single shared repository (https://github.com/Quandela/HybridAIQuantum-Challenge), supporting transparent benchmarking and cumulative research. Beyond this specific task, the Perceval Challenge illustrates how systematic, collaborative experimentation can map the current landscape of photonic quantum machine learning and pave the way toward hybrid, quantum-augmented AI workflows.

  • 31 authors
·
Oct 29, 2025

ArchGym: An Open-Source Gymnasium for Machine Learning Assisted Architecture Design

Machine learning is a prevalent approach to tame the complexity of design space exploration for domain-specific architectures. Using ML for design space exploration poses challenges. First, it's not straightforward to identify the suitable algorithm from an increasing pool of ML methods. Second, assessing the trade-offs between performance and sample efficiency across these methods is inconclusive. Finally, lack of a holistic framework for fair, reproducible, and objective comparison across these methods hinders progress of adopting ML-aided architecture design space exploration and impedes creating repeatable artifacts. To mitigate these challenges, we introduce ArchGym, an open-source gym and easy-to-extend framework that connects diverse search algorithms to architecture simulators. To demonstrate utility, we evaluate ArchGym across multiple vanilla and domain-specific search algorithms in designing custom memory controller, deep neural network accelerators, and custom SoC for AR/VR workloads, encompassing over 21K experiments. Results suggest that with unlimited samples, ML algorithms are equally favorable to meet user-defined target specification if hyperparameters are tuned; no solution is necessarily better than another (e.g., reinforcement learning vs. Bayesian methods). We coin the term hyperparameter lottery to describe the chance for a search algorithm to find an optimal design provided meticulously selected hyperparameters. The ease of data collection and aggregation in ArchGym facilitates research in ML-aided architecture design space exploration. As a case study, we show this advantage by developing a proxy cost model with an RMSE of 0.61% that offers a 2,000-fold reduction in simulation time. Code and data for ArchGym is available at https://bit.ly/ArchGym.

  • 11 authors
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Jun 15, 2023

Rethinking Pulmonary Embolism Segmentation: A Study of Current Approaches and Challenges with an Open Weight Model

Pulmonary Embolism (PE) is a life-threatening condition for which accurate and timely detection is critical to patient care. However, our systematic study of PE segmentation algorithms reveals concerning limitations in the current state of research. Challenges such as small and inconsistent datasets, a lack of reproducible baselines, and limited comparative evaluation across models are hindering progress in the field. In this study, we curated a densely annotated dataset comprising 490 CTPA scans, each from a unique patient (430 for training and 60 for testing). We evaluated nine widely used segmentation architectures, including both CNN- and ViT-based models, in 2D and 3D configurations, using mean Dice Similarity Coefficient (mDSC) and Average Symmetric Surface Distance (ASSD) as evaluation metrics. Furthermore, the highest-performing model was evaluated on a public dataset without fine-tuning and achieved reasonable generalization performance. Our results show that: (1) a 3D U-Net with ResNet encoding blocks remains a highly effective architecture for PE segmentation; (2) 3D models consistently outperform their 2D counterparts; (3) across all architectures, when trained and evaluated on the same datasets, model error patterns are highly consistent; and (4) distal emboli remain particularly challenging due to both task complexity and the scarcity of high-quality datasets, highlighting the need for datasets with more comprehensive and consistent distal PE coverage. To promote research reproducibility, the architecture and pretrained weights of our best-performing model are publicly available at https://github.com/mazurowski-lab/PulmonaryEmbolismSegmentation

  • 5 authors
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Apr 28

PipeMFL-240K: A Large-scale Dataset and Benchmark for Object Detection in Pipeline Magnetic Flux Leakage Imaging

Pipeline integrity is critical to industrial safety and environmental protection, with Magnetic Flux Leakage (MFL) detection being a primary non-destructive testing technology. Despite the promise of deep learning for automating MFL interpretation, progress toward reliable models has been constrained by the absence of a large-scale public dataset and benchmark, making fair comparison and reproducible evaluation difficult. We introduce PipeMFL-240K, a large-scale, meticulously annotated dataset and benchmark for complex object detection in pipeline MFL pseudo-color images. PipeMFL-240K reflects real-world inspection complexity and poses several unique challenges: (i) an extremely long-tailed distribution over 12 categories, (ii) a high prevalence of tiny objects that often comprise only a handful of pixels, and (iii) substantial intra-class variability. The dataset contains 240,320 images and 191,530 high-quality bounding-box annotations, collected from 11 pipelines spanning approximately 1,480 km. Extensive experiments are conducted with state-of-the-art object detectors to establish baselines. Results show that modern detectors still struggle with the intrinsic properties of MFL data, highlighting considerable headroom for improvement, while PipeMFL-240K provides a reliable and challenging testbed to drive future research. As the first public dataset and the first benchmark of this scale and scope for pipeline MFL inspection, it provides a critical foundation for efficient pipeline diagnostics as well as maintenance planning and is expected to accelerate algorithmic innovation and reproducible research in MFL-based pipeline integrity assessment.

  • 9 authors
·
Feb 3

FreshBrew: A Benchmark for Evaluating AI Agents on Java Code Migration

AI coding assistants are rapidly becoming integral to modern software development. A key challenge in this space is the continual need to migrate and modernize codebases in response to evolving software ecosystems. Traditionally, such migrations have relied on rule-based systems and human intervention. With the advent of powerful large language models (LLMs), AI-driven agentic frameworks offer a promising alternative-but their effectiveness has not been systematically evaluated. In this paper, we introduce FreshBrew, a novel benchmark for evaluating AI agents on project-level Java migrations, with a specific focus on measuring an agent's ability to preserve program semantics and avoid reward hacking, which we argue requires projects with high test coverage for a rigorous and reliable evaluation. We benchmark several state-of-the-art LLMs, and compare their performance against established rule-based tools. Our evaluation of AI agents on this benchmark of 228 repositories shows that the top-performing model, Gemini 2.5 Flash, can successfully migrate 52.3 percent of projects to JDK 17. Our empirical analysis reveals novel insights into the critical strengths and limitations of current agentic approaches, offering actionable insights into their real-world applicability. Our empirical study reveals failure modes of current AI agents in realistic Java modernization tasks, providing a foundation for evaluating trustworthy code-migration systems. By releasing FreshBrew, we aim to facilitate rigorous, reproducible evaluation and catalyze progress in AI-driven codebase modernization.

  • 6 authors
·
Oct 12, 2025

Physion: Evaluating Physical Prediction from Vision in Humans and Machines

While current vision algorithms excel at many challenging tasks, it is unclear how well they understand the physical dynamics of real-world environments. Here we introduce Physion, a dataset and benchmark for rigorously evaluating the ability to predict how physical scenarios will evolve over time. Our dataset features realistic simulations of a wide range of physical phenomena, including rigid and soft-body collisions, stable multi-object configurations, rolling, sliding, and projectile motion, thus providing a more comprehensive challenge than previous benchmarks. We used Physion to benchmark a suite of models varying in their architecture, learning objective, input-output structure, and training data. In parallel, we obtained precise measurements of human prediction behavior on the same set of scenarios, allowing us to directly evaluate how well any model could approximate human behavior. We found that vision algorithms that learn object-centric representations generally outperform those that do not, yet still fall far short of human performance. On the other hand, graph neural networks with direct access to physical state information both perform substantially better and make predictions that are more similar to those made by humans. These results suggest that extracting physical representations of scenes is the main bottleneck to achieving human-level and human-like physical understanding in vision algorithms. We have publicly released all data and code to facilitate the use of Physion to benchmark additional models in a fully reproducible manner, enabling systematic evaluation of progress towards vision algorithms that understand physical environments as robustly as people do.

  • 15 authors
·
Jun 19, 2022

CoInfra: A Large-Scale Cooperative Infrastructure Perception System and Dataset in Adverse Weather

We present CoInfra, a large-scale cooperative infrastructure perception system and dataset designed to advance robust multi-agent perception under real-world and adverse weather conditions. The CoInfra system includes 14 fully synchronized sensor nodes, each equipped with dual RGB cameras and a LiDAR, deployed across a shared region and operating continuously to capture all traffic participants in real-time. A robust, delay-aware synchronization protocol and a scalable system architecture that supports real-time data fusion, OTA management, and remote monitoring are provided in this paper. On the other hand, the dataset was collected in different weather scenarios, including sunny, rainy, freezing rain, and heavy snow and includes 195k LiDAR frames and 390k camera images from 8 infrastructure nodes that are globally time-aligned and spatially calibrated. Furthermore, comprehensive 3D bounding box annotations for five object classes (i.e., car, bus, truck, person, and bicycle) are provided in both global and individual node frames, along with high-definition maps for contextual understanding. Baseline experiments demonstrate the trade-offs between early and late fusion strategies, the significant benefits of HD map integration are discussed. By openly releasing our dataset, codebase, and system documentation at https://github.com/NingMingHao/CoInfra, we aim to enable reproducible research and drive progress in infrastructure-supported autonomous driving, particularly in challenging, real-world settings.

  • 12 authors
·
Jul 2, 2025

Exploration of an End-to-End Automatic Number-plate Recognition neural network for Indian datasets

Indian vehicle number plates have wide variety in terms of size, font, script and shape. Development of Automatic Number Plate Recognition (ANPR) solutions is therefore challenging, necessitating a diverse dataset to serve as a collection of examples. However, a comprehensive dataset of Indian scenario is missing, thereby, hampering the progress towards publicly available and reproducible ANPR solutions. Many countries have invested efforts to develop comprehensive ANPR datasets like Chinese City Parking Dataset (CCPD) for China and Application-oriented License Plate (AOLP) dataset for US. In this work, we release an expanding dataset presently consisting of 1.5k images and a scalable and reproducible procedure of enhancing this dataset towards development of ANPR solution for Indian conditions. We have leveraged this dataset to explore an End-to-End (E2E) ANPR architecture for Indian scenario which was originally proposed for Chinese Vehicle number-plate recognition based on the CCPD dataset. As we customized the architecture for our dataset, we came across insights, which we have discussed in this paper. We report the hindrances in direct reusability of the model provided by the authors of CCPD because of the extreme diversity in Indian number plates and differences in distribution with respect to the CCPD dataset. An improvement of 42.86% was observed in LP detection after aligning the characteristics of Indian dataset with Chinese dataset. In this work, we have also compared the performance of the E2E number-plate detection model with YOLOv5 model, pre-trained on COCO dataset and fine-tuned on Indian vehicle images. Given that the number Indian vehicle images used for fine-tuning the detection module and yolov5 were same, we concluded that it is more sample efficient to develop an ANPR solution for Indian conditions based on COCO dataset rather than CCPD dataset.

  • 3 authors
·
Jul 14, 2022

VStyle: A Benchmark for Voice Style Adaptation with Spoken Instructions

Spoken language models (SLMs) have emerged as a unified paradigm for speech understanding and generation, enabling natural human machine interaction. However, while most progress has focused on semantic accuracy and instruction following, the ability of SLMs to adapt their speaking style based on spoken instructions has received limited attention. We introduce Voice Style Adaptation (VSA), a new task that examines whether SLMs can modify their speaking style, such as timbre, prosody, or persona following natural language spoken commands. To study this task, we present VStyle, a bilingual (Chinese & English) benchmark covering four categories of speech generation: acoustic attributes, natural language instruction, role play, and implicit empathy. We also introduce the Large Audio Language Model as a Judge (LALM as a Judge) framework, which progressively evaluates outputs along textual faithfulness, style adherence, and naturalness, ensuring reproducible and objective assessment. Experiments on commercial systems and open source SLMs demonstrate that current models face clear limitations in controllable style adaptation, highlighting both the novelty and challenge of this task. By releasing VStyle and its evaluation toolkit, we aim to provide the community with a foundation for advancing human centered spoken interaction. The dataset and code are publicly available at https://junzhan2000.github.io/VStyle.github.io/{project's homepage}.

  • 14 authors
·
Sep 9, 2025 2

Computational reproducibility of Jupyter notebooks from biomedical publications

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.

  • 2 authors
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Aug 10, 2023

Scaling Reproducibility: An AI-Assisted Workflow for Large-Scale Reanalysis

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.

  • 2 authors
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Feb 17

AutoReproduce: Automatic AI Experiment Reproduction with Paper Lineage

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.

  • 9 authors
·
May 26, 2025

REPRO-Bench: Can Agentic AI Systems Assess the Reproducibility of Social Science Research?

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.

  • 6 authors
·
Jul 24, 2025

Unleashing Scientific Reasoning for Bio-experimental Protocol Generation via Structured Component-based Reward Mechanism

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.

  • 11 authors
·
Oct 17, 2025 2

PIE: Simulating Disease Progression via Progressive Image Editing

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

  • 6 authors
·
Sep 20, 2023 1

AutoLab: Can Frontier Models Solve Long-Horizon Auto Research and Engineering Tasks?

Scientific and engineering progress is fundamentally a long-horizon iterative process: proposing changes, running experiments, measuring outcomes, and continuously refining artifacts. Yet existing benchmarks for frontier models primarily evaluate either single-turn responses or short-horizon agent trajectories, failing to capture the challenges of sustained iterative improvement over extended time horizons. To address this gap, we introduce AutoLab, a new benchmark for ultra long-horizon closed-loop optimization. AutoLab consists of 36 realistic, expert-curated tasks spanning four diverse domains: system optimization, puzzle & challenge, model development, and CUDA kernel optimization. Each task begins with a correct but deliberately suboptimal baseline and challenges agents to improve it within a strict wall-clock budget. Evaluating 17 state-of-the-art models reveals the dominant predictor of success is not the quality of an agent's initial attempt, but its persistence in repeatedly benchmarking, editing, and incorporating empirical feedback. While claude-opus-4.6 exhibits strong long-horizon optimization capabilities, most frontier models, including several proprietary ones, either terminate prematurely or exhaust their budgets with minimal progress. These results underscore the importance of time awareness and persistent iteration in autonomous agents. We open-source the full benchmark, evaluation harness, and task artifacts, to accelerate research toward truly capable long-horizon agents.

  • 19 authors
·
Jun 2

ReplicatorBench: Benchmarking LLM Agents for Replicability in Social and Behavioral Sciences

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.

  • 11 authors
·
Feb 11

Eureka: Evaluating and Understanding Large Foundation Models

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.

  • 9 authors
·
Sep 13, 2024

O1 Replication Journey: A Strategic Progress Report -- Part 1

This paper introduces a pioneering approach to artificial intelligence research, embodied in our O1 Replication Journey. In response to the announcement of OpenAI's groundbreaking O1 model, we embark on a transparent, real-time exploration to replicate its capabilities while reimagining the process of conducting and communicating AI research. Our methodology addresses critical challenges in modern AI research, including the insularity of prolonged team-based projects, delayed information sharing, and the lack of recognition for diverse contributions. By providing comprehensive, real-time documentation of our replication efforts, including both successes and failures, we aim to foster open science, accelerate collective advancement, and lay the groundwork for AI-driven scientific discovery. Our research progress report diverges significantly from traditional research papers, offering continuous updates, full process transparency, and active community engagement throughout the research journey. Technologically, we proposed the journey learning paradigm, which encourages models to learn not just shortcuts, but the complete exploration process, including trial and error, reflection, and backtracking. With only 327 training samples and without any additional tricks, journey learning outperformed conventional supervised learning by over 8\% on the MATH dataset, demonstrating its extremely powerful potential. We believe this to be the most crucial component of O1 technology that we have successfully decoded. We share valuable resources including technical hypotheses and insights, cognitive exploration maps, custom-developed tools, etc at https://github.com/GAIR-NLP/O1-Journey.

  • 11 authors
·
Oct 8, 2024

Reproducibility of the Methods in Medical Imaging with Deep Learning

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.

  • 5 authors
·
Oct 20, 2022

SciPredict: Can LLMs Predict the Outcomes of Scientific Experiments in Natural Sciences?

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

ScaleAI Scale AI
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Apr 11 1

AgentRxiv: Towards Collaborative Autonomous Research

Progress in scientific discovery is rarely the result of a single "Eureka" moment, but is rather the product of hundreds of scientists incrementally working together toward a common goal. While existing agent workflows are capable of producing research autonomously, they do so in isolation, without the ability to continuously improve upon prior research results. To address these challenges, we introduce AgentRxiv-a framework that lets LLM agent laboratories upload and retrieve reports from a shared preprint server in order to collaborate, share insights, and iteratively build on each other's research. We task agent laboratories to develop new reasoning and prompting techniques and find that agents with access to their prior research achieve higher performance improvements compared to agents operating in isolation (11.4% relative improvement over baseline on MATH-500). We find that the best performing strategy generalizes to benchmarks in other domains (improving on average by 3.3%). Multiple agent laboratories sharing research through AgentRxiv are able to work together towards a common goal, progressing more rapidly than isolated laboratories, achieving higher overall accuracy (13.7% relative improvement over baseline on MATH-500). These findings suggest that autonomous agents may play a role in designing future AI systems alongside humans. We hope that AgentRxiv allows agents to collaborate toward research goals and enables researchers to accelerate discovery.

  • 2 authors
·
Mar 23, 2025 2

Coding-agents can replicate scientific machine learning papers

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

  • 2 authors
·
Jul 9

AstaBench: Rigorous Benchmarking of AI Agents with a Scientific Research Suite

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.

  • 39 authors
·
Oct 24, 2025 1

CORE-Bench: Fostering the Credibility of Published Research Through a Computational Reproducibility Agent Benchmark

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.

  • 5 authors
·
Sep 17, 2024 2

PyGen: A Collaborative Human-AI Approach to Python Package Creation

The principles of automation and innovation serve as foundational elements for advancement in contemporary science and technology. Here, we introduce Pygen, an automation platform designed to empower researchers, technologists, and hobbyists to bring abstract ideas to life as core, usable software tools written in Python. Pygen leverages the immense power of autoregressive large language models to augment human creativity during the ideation, iteration, and innovation process. By combining state-of-the-art language models with open-source code generation technologies, Pygen has significantly reduced the manual overhead of tool development. From a user prompt, Pygen automatically generates Python packages for a complete workflow from concept to package generation and documentation. The findings of our work show that Pygen considerably enhances the researcher's productivity by enabling the creation of resilient, modular, and well-documented packages for various specialized purposes. We employ a prompt enhancement approach to distill the user's package description into increasingly specific and actionable. While being inherently an open-ended task, we have evaluated the generated packages and the documentation using Human Evaluation, LLM-based evaluation, and CodeBLEU, with detailed results in the results section. Furthermore, we documented our results, analyzed the limitations, and suggested strategies to alleviate them. Pygen is our vision of ethical automation, a framework that promotes inclusivity, accessibility, and collaborative development. This project marks the beginning of a large-scale effort towards creating tools where intelligent agents collaborate with humans to improve scientific and technological development substantially. Our code and generated examples are open-sourced at [https://github.com/GitsSaikat/Pygen]

  • 6 authors
·
Nov 12, 2024

JARVIS-Leaderboard: A Large Scale Benchmark of Materials Design Methods

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

  • 38 authors
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Jun 20, 2023

An Exploratory Literature Study on Sharing and Energy Use of Language Models for Source Code

Large language models trained on source code can support a variety of software development tasks, such as code recommendation and program repair. Large amounts of data for training such models benefit the models' performance. However, the size of the data and models results in long training times and high energy consumption. While publishing source code allows for replicability, users need to repeat the expensive training process if models are not shared. The main goal of the study is to investigate if publications that trained language models for software engineering (SE) tasks share source code and trained artifacts. The second goal is to analyze the transparency on training energy usage. We perform a snowballing-based literature search to find publications on language models for source code, and analyze their reusability from a sustainability standpoint. From 494 unique publications, we identified 293 relevant publications that use language models to address code-related tasks. Among them, 27% (79 out of 293) make artifacts available for reuse. This can be in the form of tools or IDE plugins designed for specific tasks or task-agnostic models that can be fine-tuned for a variety of downstream tasks. Moreover, we collect insights on the hardware used for model training, as well as training time, which together determine the energy consumption of the development process. We find that there are deficiencies in the sharing of information and artifacts for current studies on source code models for software engineering tasks, with 40% of the surveyed papers not sharing source code or trained artifacts. We recommend the sharing of source code as well as trained artifacts, to enable sustainable reproducibility. Moreover, comprehensive information on training times and hardware configurations should be shared for transparency on a model's carbon footprint.

  • 3 authors
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Jul 5, 2023

VeriContest: A Competitive-Programming Benchmark for Verifiable Code Generation

Large language models can generate useful code from natural language, but their outputs come without correctness guarantees. Verifiable code generation offers a path beyond testing by requiring models to produce not only executable code, but also formal specifications and machine-checkable proofs. Progress in this direction, however, is difficult to measure: existing benchmarks are often small, focus on only one part of the pipeline, lack ground-truth proofs or rigorous specification validation, or target verification settings far from mainstream software development. We present VeriContest, a benchmark of 946 competitive-programming problems from LeetCode and Codeforces for verifiable code generation in Rust with Verus. Each problem pairs a natural language description with expert-validated formal specifications, judge-accepted Rust code, Verus-checked proofs, and positive and negative test suites. VeriContest is constructed through a three-phase pipeline that scales from manually verified seed problems to semi-automated expansion with human-in-the-loop review. To further strengthen benchmark quality, we use testing as an additional quality-assurance layer for validating postcondition completeness. VeriContest supports isolated and compositional evaluation of specification generation, code generation, proof generation, and end-to-end verified program synthesis. Evaluating ten state-of-the-art models reveals a sharp gap between coding ability and verifiable code generation: the strongest model reaches 92.18% on natural-language-to-code generation, but only 48.31% on specification generation, 13.95% on proof generation, and 5.29% end-to-end. These results identify proof and specification generation as the central bottlenecks for models and establish VeriContest as a rigorous platform for measuring and training future systems that generate code with machine-checkable correctness.

  • 8 authors
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May 7

Remote Bio-Sensing: Open Source Benchmark Framework for Fair Evaluation of rPPG

rPPG (Remote photoplethysmography) is a technology that measures and analyzes BVP (Blood Volume Pulse) by using the light absorption characteristics of hemoglobin captured through a camera. Analyzing the measured BVP can derive various physiological signals such as heart rate, stress level, and blood pressure, which can be applied to various applications such as telemedicine, remote patient monitoring, and early prediction of cardiovascular disease. rPPG is rapidly evolving and attracting great attention from both academia and industry by providing great usability and convenience as it can measure biosignals using a camera-equipped device without medical or wearable devices. Despite extensive efforts and advances in this field, serious challenges remain, including issues related to skin color, camera characteristics, ambient lighting, and other sources of noise and artifacts, which degrade accuracy performance. We argue that fair and evaluable benchmarking is urgently required to overcome these challenges and make meaningful progress from both academic and commercial perspectives. In most existing work, models are trained, tested, and validated only on limited datasets. Even worse, some studies lack available code or reproducibility, making it difficult to fairly evaluate and compare performance. Therefore, the purpose of this study is to provide a benchmarking framework to evaluate various rPPG techniques across a wide range of datasets for fair evaluation and comparison, including both conventional non-deep neural network (non-DNN) and deep neural network (DNN) methods. GitHub URL: https://github.com/remotebiosensing/rppg

  • 8 authors
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Aug 17, 2023

Red Teaming for Generative AI, Report on a Copyright-Focused Exercise Completed in an Academic Medical Center

Background: Generative artificial intelligence (AI) deployment in academic medical settings raises copyright compliance concerns. Dana-Farber Cancer Institute implemented GPT4DFCI, an internal generative AI tool utilizing OpenAI models, that is approved for enterprise use in research and operations. Given (1) the exceptionally broad adoption of the tool in our organization, (2) our research mission, and (3) the shared responsibility model required to benefit from Customer Copyright Commitment in Azure OpenAI Service products, we deemed rigorous copyright compliance testing necessary. Case Description: We conducted a structured red teaming exercise in Nov. 2024, with 42 participants from academic, industry, and government institutions. Four teams attempted to extract copyrighted content from GPT4DFCI across four domains: literary works, news articles, scientific publications, and access-restricted clinical notes. Teams successfully extracted verbatim book dedications and near-exact passages through various strategies. News article extraction failed despite jailbreak attempts. Scientific article reproduction yielded only high-level summaries. Clinical note testing revealed appropriate privacy safeguards. Discussion: The successful extraction of literary content indicates potential copyrighted material presence in training data, necessitating inference-time filtering. Differential success rates across content types suggest varying protective mechanisms. The event led to implementation of a copyright-specific meta-prompt in GPT4DFCI; this mitigation has been in production since Jan. 2025. Conclusion: Systematic red teaming revealed specific vulnerabilities in generative AI copyright compliance, leading to concrete mitigation strategies. Academic medical institutions deploying generative AI should implement continuous testing protocols to ensure legal and ethical compliance.

  • 41 authors
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Jun 26, 2025

LeanProgress: Guiding Search for Neural Theorem Proving via Proof Progress Prediction

Mathematical reasoning remains a significant challenge for Large Language Models (LLMs) due to hallucinations. When combined with formal proof assistants like Lean, these hallucinations can be eliminated through rigorous verification, making theorem proving reliable. However, even with formal verification, LLMs still struggle with long proofs and complex mathematical formalizations. While Lean with LLMs offers valuable assistance with retrieving lemmas, generating tactics, or even complete proofs, it lacks a crucial capability: providing a sense of proof progress. This limitation particularly impacts the overall development efficiency in large formalization projects. We introduce LeanProgress, a method that predicts the progress in the proof. Training and evaluating our models made on a large corpus of Lean proofs from Lean Workbook Plus and Mathlib4 and how many steps remain to complete it, we employ data preprocessing and balancing techniques to handle the skewed distribution of proof lengths. Our experiments show that LeanProgress achieves an overall prediction accuracy of 75.1\% in predicting the amount of progress and, hence, the remaining number of steps. When integrated into a best-first search framework using Reprover, our method shows a 3.8\% improvement on Mathlib4 compared to baseline performances of 41.2\%, particularly for longer proofs. These results demonstrate how proof progress prediction can enhance both automated and interactive theorem proving, enabling users to make more informed decisions about proof strategies.

  • 4 authors
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Feb 25, 2025

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

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.

  • 2 authors
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Apr 19, 2024

Serialisation Strategy Matters: How FHIR Data Format Affects LLM Medication Reconciliation

Medication reconciliation at clinical handoffs is a high-stakes, error-prone process. Large language models are increasingly proposed to assist with this task using FHIR-structured patient records, but a fundamental and largely unstudied variable is how the FHIR data is serialised before being passed to the model. We present the first systematic comparison of four FHIR serialisation strategies (Raw JSON, Markdown Table, Clinical Narrative, and Chronological Timeline) across five open-weight models (Phi-3.5-mini, Mistral-7B, BioMistral-7B, Llama-3.1-8B, Llama-3.3-70B) on a controlled benchmark of 200 synthetic patients, totalling 4,000 inference runs. We find that serialisation strategy has a large, statistically significant effect on performance for models up to 8B parameters: Clinical Narrative outperforms Raw JSON by up to 19 F1 points for Mistral-7B (r = 0.617, p < 10^{-10}). This advantage reverses at 70B, where Raw JSON achieves the best mean F1 of 0.9956. In all 20 model and strategy combinations, mean precision exceeds mean recall: omission is the dominant failure mode, with models more often missing an active medication than fabricating one, which changes how clinical safety auditing priorities should be set. Smaller models plateau at roughly 7-10 concurrent active medications, leaving polypharmacy patients, the patients most at risk from reconciliation errors, systematically underserved. BioMistral-7B, a domain-pretrained model without instruction tuning, produces zero usable output in all conditions, showing that domain pretraining alone is not sufficient for structured extraction. These results offer practical, evidence-based format recommendations for clinical LLM deployment: Clinical Narrative for models up to 8B, Raw JSON for 70B and above. The complete pipeline is reproducible on open-source tools running on an AWS g6e.xlarge instance (NVIDIA L40S, 48 GB VRAM).

  • 1 authors
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Apr 21

On Randomness in Agentic Evals

Agentic systems are evaluated on benchmarks where agents interact with environments to solve tasks. Most papers report a pass@1 score computed from a single run per task, assuming this gives a reliable performance estimate. We test this assumption by collecting 60,000 agentic trajectories on SWE-Bench-Verified, spanning three models and two scaffolds. We find substantial variance: single-run pass@1 estimates vary by 2.2 to 6.0 percentage points depending on which run is selected, with standard deviations exceeding 1.5 percentage points even at temperature 0. This variance has critical implications: reported improvements of 2--3 percentage points may reflect evaluation noise rather than genuine algorithmic progress. Through token-level analysis, we show that trajectories diverge early, often within the first few percent of tokens, and that these small differences cascade into different solution strategies. To enable reliable evaluation of agentic systems, we recommend three concrete practices: (1) estimate pass@1 from multiple independent runs per task, especially when measuring small improvements, (2) use statistical power analysis to determine the number of runs needed to detect expected effect sizes, and (3) consider metrics like pass@k (optimistic bound) and pass^k (pessimistic bound) with k>1 to better characterize the full performance envelope. While these practices increase evaluation cost, they are essential for distinguishing genuine scientific progress from statistical noise.

Geometric coherence of single-cell CRISPR perturbations reveals regulatory architecture and predicts cellular stress

Genome engineering has achieved sequence-level precision, yet predicting the transcriptomic state a cell will occupy after perturbation remains open. Single-cell CRISPR screens measure how far cells move, but effect magnitude ignores whether the cells move together. We introduce Shesha perturbation stability (S_p), which quantifies directional coherence as the mean cosine similarity between individual cell shift vectors and the mean perturbation direction. Across five CRISPR datasets (2,200+ perturbations), stability correlates with magnitude (Spearman ρ= 0.75--0.97), but discordant cases expose regulatory architecture: pleiotropic regulators such as CEBPA pay a ``geometric tax,'' producing large but incoherent shifts, while lineage-specific factors such as KLF1 produce coordinated responses. S_p and Song et al.'s perturbation-response score (PS) share partial overlap (ρ_{partial} = +0.51 after controlling for magnitude), but S_p provides significant incremental prediction of UPR pathway activation beyond both PS and magnitude (p < 10^{-18}). In a split-half reproducibility assay, S_p predicts directional reproducibility beyond magnitude (ρ_{partial} = +0.384) while PS does not (ρ_{partial} = -0.193), with the advantage consistent across all magnitude strata and both datasets. Geometric instability is independently associated with UPR activation across four datasets. S_p is implemented in the open-source shesha-geometry Python package.

  • 1 authors
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Jun 21 2

LiveFigure: Generating Editable Scientific Illustration with VLM Agents

Scientific illustrations are essential for depicting conceptual designs, methodologies, and experimental workflows in research, playing a pivotal role in communicating complex academic insights. However, creating high-quality scientific illustrations remains a labor-intensive task for human scientists. While recent generative image models have advanced prompt-based editing, the synthesis of fully editable figures remains a fundamental challenge. Valid editability involves structured transformations of graphical elements, scales, attributes, and text, rather than simple pixel-level changes. Existing models generate raster outputs that do not support manual correction or layout adjustment, limiting their utility in scientific publishing, where editable vector figures are typically required for submission. To address this challenge, we introduce LiveFigure, an agentic framework driven by VLM agents that imitates the multi-step drawing workflow of human researchers. It first plans figure blueprints by drawing inspiration from high-quality references in previous works, then generates executable scripts that produce figures via the PowerPoint interface based on skills and experience, and finally refines the outputs with targeted visual diagnostics, producing fully vectorized, editable figures that meet publication standards. Extensive experiments demonstrate that LiveFigure generates inherently editable figures, achieving 80% publication-readiness in only 17 manual edits, far surpassing the 24% rate of the strongest baseline, NanoBanana. Human preference studies further validate this advantage, with LiveFigure securing a 60% win rate against NanoBanana. Our code is available at https://github.com/tsinghua-fib-lab/LiveFigure.git.

  • 4 authors
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May 21

CC30k: A Citation Contexts Dataset for Reproducibility-Oriented Sentiment Analysis

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 .

  • 3 authors
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Nov 10, 2025 2

Agentic Agile-V: From Vibe Coding to Verified Engineering in Software and Hardware Development

Agentic AI coding systems can inspect repositories, plan implementation steps, edit files, call tools, run tests, and submit pull requests. These capabilities make software and hardware development faster in some settings, but current evidence does not support the simple claim that autonomous code generation automatically improves engineering outcomes. Controlled studies report productivity gains in some enterprise tasks, slowdowns in mature open-source work, moderate but heterogeneous meta-analytic effects, and persistent failures in repository setup, dependency handling, permission gating, and hardware verification. This paper argues that the central problem is no longer prompt engineering; it is engineering process control. It synthesizes evidence from agentic software engineering, GitHub-scale adoption studies, repository-level agent configuration, productivity trials, issue-resolution benchmarks, and hardware/RTL verification research. It proposes Agentic Agile-V, a process framework that uses Agile-V as the lifecycle backbone and a task-level SCOPE-V loop - Specify, Constrain, Orchestrate, Prove, Evolve, and Verify - to convert conversational intent into structured engineering artifacts and acceptance evidence. The paper contributes: (i) a taxonomy of minimum input artifacts for agentic software, firmware, and hardware work; (ii) a conversation-to-contract gate that separates exploratory dialogue from implementation; (iii) risk-adaptive feature, bug-fix, testing, and hardware workflows; and (iv) an evidence-bundle acceptance model for agent-generated artifacts. The paper concludes that agentic AI does not eliminate engineering discipline; it increases the value of requirements, constraints, traceability, independent verification, and human approval.

  • 1 authors
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May 18

Sibyl-AutoResearch: Autonomous Research Needs Self-Evolving Trial-and-Error Harnesses, Not Paper Generators

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

  • 6 authors
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May 20

ACES: Automatic Cohort Extraction System for Event-Stream Datasets

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.

  • 4 authors
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Jun 28, 2024

Emergent Collaborative Deliberation in Multi-Model AI Systems: A BFT-Derived Protocol for Epistemic Synthesis

We present the Consilium Protocol, a Byzantine Fault Tolerance-derived architecture for structured multi-model AI deliberation that treats inter-model disagreement as epistemic signal rather than error. The protocol assigns engineered cognitive personas to language models -- separating what a model is from how it reasons -- and introduces an In-Sample/Out-of-Sample validation framework adapted from quantitative finance to distinguish training-data consensus from empirically grounded conclusions. Across 1,478 deliberation sessions spanning 32 topics in 10 domain categories, we demonstrate that (1) the cognitive persona, not the underlying model, determines epistemic behavior: free edge-inference models costing 0.0002 USD per batch produced comparable analytical output to frontier models costing 10.69 USD; (2) RLHF alignment training creates measurable, domain-specific epistemic blind spots -- contested policy topics exhibit 12.3 percentage points less adversarial challenge than settled science topics, and AI safety topics show asymmetric bias (Δ=11.6%) where models challenge claims that AI is dangerous far more vigorously than claims that AI risk is overstated; (3) the protocol exhibits no directional bias of its own (immigration Δ=2.3%, renewables Δ=1.2%); and (4) out-of-sample evidence retrieval validated 239 claims with 100% evidence retrieval and surfaced 167 blind-spot discoveries invisible to training-data deliberation. Run-to-run reproducibility across randomized modeltimespersona assignments averages pm2.2% standard deviation. Total cost for the complete battery including all overhead: 217 USD. We release the protocol specification under MIT license to enable independent verification.

  • 1 authors
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Mar 26

The Model Openness Framework: Promoting Completeness and Openness for Reproducibility, Transparency, and Usability in Artificial Intelligence

Generative AI (GAI) offers unprecedented opportunities for research and innovation, but its commercialization has raised concerns about transparency, reproducibility, and safety. Many open GAI models lack the necessary components for full understanding and reproducibility, and some use restrictive licenses whilst claiming to be ``open-source''. To address these concerns, we propose the Model Openness Framework (MOF), a ranked classification system that rates machine learning models based on their completeness and openness, following principles of open science, open source, open data, and open access. The MOF requires specific components of the model development lifecycle to be included and released under appropriate open licenses. This framework aims to prevent misrepresentation of models claiming to be open, guide researchers and developers in providing all model components under permissive licenses, and help individuals and organizations identify models that can be safely adopted without restrictions. By promoting transparency and reproducibility, the MOF combats ``openwashing'' practices and establishes completeness and openness as primary criteria alongside the core tenets of responsible AI. Wide adoption of the MOF will foster a more open AI ecosystem, benefiting research, innovation, and adoption of state-of-the-art models.

  • 6 authors
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Mar 20, 2024

SARM: Stage-Aware Reward Modeling for Long Horizon Robot Manipulation

Large-scale robot learning has recently shown promise for enabling robots to perform complex tasks by integrating perception, control, and language understanding. Yet, it struggles with long-horizon, contact-rich manipulation such as deformable object handling, where demonstration quality is inconsistent. Reward modeling offers a natural solution: by providing grounded progress signals, it transforms noisy demonstrations into stable supervision that generalizes across diverse trajectories. We introduce a stage-aware, video-based reward modeling framework that jointly predicts high-level task stages and fine-grained progress. Reward labels are automatically derived from natural language subtask annotations, ensuring consistent progress estimation across variable-length demonstrations. This design overcomes frame-index labeling, which fails in variable-duration tasks like folding a T-shirt. Our reward model demonstrates robustness to variability, generalization to out-of-distribution settings, and strong utility for policy training. Building on it, we propose Reward-Aligned Behavior Cloning (RA-BC), which filters high-quality data and reweights samples by reward. Experiments show the reward model alone outperforms baselines on validation and real robot rollouts. Integrated into RA-BC, our approach achieves 83% success on folding T-shirts from the flattened state and 67% from the crumpled state -- far surpassing vanilla behavior cloning, which attains only 8% and 0% success. Overall, our results highlight reward modeling as a key enabler for scalable, annotation-efficient, and robust imitation learning in long-horizon manipulation.

  • 6 authors
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Sep 29, 2025

Enhancing Automated Paper Reproduction via Prompt-Free Collaborative Agents

Automated paper reproduction has emerged as a promising approach to accelerate scientific research, employing multi-step workflow frameworks to systematically convert academic papers into executable code. However, existing frameworks often lack mechanisms to verify and refine the outputs at each generation step, or rely heavily on manually designed prompts for self-refinement, which limits their adaptability and scalability. To address these limitations, we propose a prompt-free collaborative agent framework that automatically enhances the quality of paper-to-code generation. Our approach employs two collaborative agents: a verification agent that examines whether the outputs at each step satisfy the requirements specified in the corresponding system prompt, and a refinement agent that revises the outputs based on the identified issues. Unlike previous methods that require human experts to craft specific refinement prompts for each step, our framework achieves automatic verification and improvement by leveraging only the original system prompts. We integrate our collaborative agents into the Paper2Code framework and conduct comprehensive experiments on PaperBench Code-Dev and Paper2CodeBench datasets. Experimental results demonstrate that our approach significantly improves the accuracy and completeness of reproduced code, achieving performance gains of approximately 15\% and 13\%, respectively, compared to the baseline without our agents. Furthermore, comparative experiments against Self-Refine validate the robustness and consistency of our prompt-free approach across different datasets.

  • 4 authors
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Dec 2, 2025

Open RL Benchmark: Comprehensive Tracked Experiments for Reinforcement Learning

In many Reinforcement Learning (RL) papers, learning curves are useful indicators to measure the effectiveness of RL algorithms. However, the complete raw data of the learning curves are rarely available. As a result, it is usually necessary to reproduce the experiments from scratch, which can be time-consuming and error-prone. We present Open RL Benchmark, a set of fully tracked RL experiments, including not only the usual data such as episodic return, but also all algorithm-specific and system metrics. Open RL Benchmark is community-driven: anyone can download, use, and contribute to the data. At the time of writing, more than 25,000 runs have been tracked, for a cumulative duration of more than 8 years. Open RL Benchmark covers a wide range of RL libraries and reference implementations. Special care is taken to ensure that each experiment is precisely reproducible by providing not only the full parameters, but also the versions of the dependencies used to generate it. In addition, Open RL Benchmark comes with a command-line interface (CLI) for easy fetching and generating figures to present the results. In this document, we include two case studies to demonstrate the usefulness of Open RL Benchmark in practice. To the best of our knowledge, Open RL Benchmark is the first RL benchmark of its kind, and the authors hope that it will improve and facilitate the work of researchers in the field.

  • 33 authors
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Feb 5, 2024

StructAgent: Harness Long-horizon Digital Agents with Unified Causal Structure

Recent advances in large language models (LLMs) and vision-language models (VLMs) have enabled increasingly capable digital agents for computer use. However, real-world tasks are often long-horizon and involve evolving contexts containing accumulated observations, intermediate edits, failed attempts, and partially completed executions. Existing agents typically operate over raw interaction history, making task progress difficult to interpret, verify, and recover, which ultimately limits reliable long-horizon execution. In this paper, we argue that addressing this challenge requires explicitly structuring both the agent's state and workflow around a unified causal representation of task progress. We present StructAgent, a state-centered framework that introduces a unified state for maintaining compact, verifiable task progress and a structured workflow that regulates progress through verifier-backed state transitions. Building on this design, StructAgent further enables explicit progress checkpointing, evidence-driven task completion, targeted failure recovery, and tool-supported execution, while ensuring that all progress updates remain grounded in verification. Extensive experiments demonstrate that StructAgent consistently improves a wide range of LLM and VLM backbones on long-horizon computer-use tasks. On OSWorld-Verified, it improves Qwen3.5-9B from 27.0\% to 46.9\% success rate and Qwen3.5-27B from 31.6\% to 62.2\%, while achieving a new open-source state of the art of 78.9\% with MiniMax-M3. Moreover, the same framework generalizes beyond desktop environments to Minecraft, demonstrating the generality of our design.

  • 6 authors
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Jul 12