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Sep 15

When VLMs 'Fix' Students: Identifying and Penalizing Over-Correction in the Evaluation of Multi-line Handwritten Math OCR

Accurate transcription of handwritten mathematics is crucial for educational AI systems, yet current benchmarks fail to evaluate this capability properly. Most prior studies focus on single-line expressions and rely on lexical metrics such as BLEU, which fail to assess the semantic reasoning across multi-line student solutions. In this paper, we present the first systematic study of multi-line handwritten math Optical Character Recognition (OCR), revealing a critical failure mode of Vision-Language Models (VLMs): over-correction. Instead of faithfully transcribing a student's work, these models often "fix" errors, thereby hiding the very mistakes an educational assessment aims to detect. To address this, we propose PINK (Penalized INK-based score), a semantic evaluation metric that leverages a Large Language Model (LLM) for rubric-based grading and explicitly penalizes over-correction. Our comprehensive evaluation of 15 state-of-the-art VLMs on the FERMAT dataset reveals substantial ranking reversals compared to BLEU: models like GPT-4o are heavily penalized for aggressive over-correction, whereas Gemini 2.5 Flash emerges as the most faithful transcriber. Furthermore, human expert studies show that PINK aligns significantly better with human judgment (55.0% preference over BLEU's 39.5%), providing a more reliable evaluation framework for handwritten math OCR in educational settings.

  • 5 authors
·
May 25

FailureSensorIQ: A Multi-Choice QA Dataset for Understanding Sensor Relationships and Failure Modes

We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.

  • 6 authors
·
Jun 3, 2025 1

FinCriticalED: A Visual Benchmark for Financial Fact-Level OCR Evaluation

We introduce FinCriticalED (Financial Critical Error Detection), a visual benchmark for evaluating OCR and vision language models on financial documents at the fact level. Financial documents contain visually dense and table heavy layouts where numerical and temporal information is tightly coupled with structure. In high stakes settings, small OCR mistakes such as sign inversion or shifted dates can lead to materially different interpretations, while traditional OCR metrics like ROUGE and edit distance capture only surface level text similarity. \ficriticaled provides 500 image-HTML pairs with expert annotated financial facts covering over seven hundred numerical and temporal facts. It introduces three key contributions. First, it establishes the first fact level evaluation benchmark for financial document understanding, shifting evaluation from lexical overlap to domain critical factual correctness. Second, all annotations are created and verified by financial experts with strict quality control over signs, magnitudes, and temporal expressions. Third, we develop an LLM-as-Judge evaluation pipeline that performs structured fact extraction and contextual verification for visually complex financial documents. We benchmark OCR systems, open source vision language models, and proprietary models on FinCriticalED. Results show that although the strongest proprietary models achieve the highest factual accuracy, substantial errors remain in visually intricate numerical and temporal contexts. Through quantitative evaluation and expert case studies, FinCriticalED provides a rigorous foundation for advancing visual factual precision in financial and other precision critical domains.

  • 13 authors
·
Nov 18, 2025

VeriLLMed: Interactive Visual Debugging of Medical Large Language Models with Knowledge Graphs

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

  • 10 authors
·
Apr 24

Towards Expert-Level Medical Question Answering with Large Language Models

Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.

  • 31 authors
·
May 16, 2023 2

HDEE: Heterogeneous Domain Expert Ensemble

Training dense LLMs requires enormous amounts of data and centralized compute, which introduces fundamental bottlenecks and ever-growing costs for large models. Several studies aim to reduce this dependency on centralization by reducing the communication overhead of training dense models. Taking this idea of reducing communication overhead to a natural extreme, by training embarrassingly parallelizable ensembles of small independent experts, has been shown to outperform large dense models trained in traditional centralized settings. However, existing studies do not take into account underlying differences amongst data domains and treat them as monolithic, regardless of their underlying complexity, size, or distribution. In this paper, we explore the effects of introducing heterogeneity to these ensembles of domain expert models. Specifically, by allowing models within the ensemble to vary in size--as well as the number of training steps taken depending on the training data's domain--we study the effect heterogeneity has on these ensembles when evaluated against domains included in, and excluded from, the training set. We use the same compute budget to train heterogeneous ensembles and homogeneous baselines for comparison. We show that the heterogeneous ensembles achieve the lowest perplexity scores in 20 out of the 21 data domains used in the evaluation. Our code is available at https://github.com/gensyn-ai/hdee.

Gensyn Gensyn
·
Feb 26, 2025

From Beginner to Expert: Modeling Medical Knowledge into General LLMs

Recently, large language model (LLM) based artificial intelligence (AI) systems have demonstrated remarkable capabilities in natural language understanding and generation. However, these models face a significant challenge when it comes to sensitive applications, such as reasoning over medical knowledge and answering medical questions in a physician-like manner. Prior studies attempted to overcome this challenge by increasing the model size (>100B) to learn more general medical knowledge, while there is still room for improvement in LLMs with smaller-scale model sizes (<100B). In this work, we start from a pre-trained general LLM model (AntGLM-10B) and fine-tune it from a medical beginner towards a medical expert (called AntGLM-Med-10B), which leverages a 3-stage optimization procedure, i.e., general medical knowledge injection, medical domain instruction tuning, and specific medical task adaptation. Our contributions are threefold: (1) We specifically investigate how to adapt a pre-trained general LLM in medical domain, especially for a specific medical task. (2) We collect and construct large-scale medical datasets for each stage of the optimization process. These datasets encompass various data types and tasks, such as question-answering, medical reasoning, multi-choice questions, and medical conversations. (3) Specifically for multi-choice questions in the medical domain, we propose a novel Verification-of-Choice approach for prompting engineering, which significantly enhances the reasoning ability of LLMs. Remarkably, by combining the above approaches, our AntGLM-Med-10B model can outperform the most of LLMs on PubMedQA, including both general and medical LLMs, even when these LLMs have larger model size.

  • 17 authors
·
Dec 2, 2023

CHIME: LLM-Assisted Hierarchical Organization of Scientific Studies for Literature Review Support

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

  • 8 authors
·
Jul 22, 2024

Anomalous Frame Detection Using VLM-Based Description Comparison for Extracting Expert-Specific Actions and Contextual Decision-Making Scenes with Intra-Video Self-Similarity

Maintenance of critical infrastructures, such as railways and power plants, is essential for ensuring operational safety and reliability. However, the declining number of skilled maintenance workers highlights the need to transfer expert know-how to less experienced workers. Previous studies have attempted to extract candidates of expert knowledge by comparing videos of manual-based work with those of expert workers, mainly focusing on differences in observable actions. However, expert know-how is often embedded not only in actions but also in contextual decision-making during task execution. This paper proposes a method that detects anomalous frames between two task videos to automatically extract candidate scenes containing expert-specific actions and contextual decision-making scenes. The method generates frame-wise visual descriptions using a vision-language model (VLM). Expert-specific actions are extracted based on frame similarities computed from description comparisons between two videos, while contextual decision-making scenes are extracted using segment similarities derived from intra-video self-similarity of the descriptions. In simulated distribution board maintenance experiments involving 27 task scenarios, the proposed method achieved extraction rates of 65% for action candidates and 61% for decision-scene candidates, improving over conventional methods that achieved 59% and 33%, respectively. These results demonstrate the effectiveness of the proposed approach in discovering candidate scenes containing expert know-how.

  • 2 authors
·
Jul 23

Expert-level vision-language foundation model for real-world radiology and comprehensive evaluation

Radiology is a vital and complex component of modern clinical workflow and covers many tasks. Recently, vision-language (VL) foundation models in medicine have shown potential in processing multimodal information, offering a unified solution for various radiology tasks. However, existing studies either pre-trained VL models on natural data or did not fully integrate vision-language architecture and pretraining, often neglecting the unique multimodal complexity in radiology images and their textual contexts. Additionally, their practical applicability in real-world scenarios remains underexplored. Here, we present RadFound, a large and open-source vision-language foundation model tailored for radiology, that is trained on the most extensive dataset of over 8.1 million images and 250,000 image-text pairs, covering 19 major organ systems and 10 imaging modalities. To establish expert-level multimodal perception and generation capabilities, RadFound introduces an enhanced vision encoder to capture intra-image local features and inter-image contextual information, and a unified cross-modal learning design tailored to radiology. To fully assess the models' capability, we construct a benchmark, RadVLBench, including radiology interpretation tasks like medical vision-language question-answering, as well as text generation tasks ranging from captioning to report generation. We also propose a human evaluation framework. When evaluated on the real-world benchmark involving three representative modalities, 2D images (chest X-rays), multi-view images (mammograms), and 3D images (thyroid CT scans), RadFound significantly outperforms other VL foundation models on both quantitative metrics and human evaluation. In summary, the development of RadFound represents an advancement in radiology generalists, demonstrating broad applicability potential for integration into clinical workflows.

  • 9 authors
·
Sep 24, 2024

Zhongjing: Enhancing the Chinese Medical Capabilities of Large Language Model through Expert Feedback and Real-world Multi-turn Dialogue

Recent advances in Large Language Models (LLMs) have achieved remarkable breakthroughs in understanding and responding to user intents. However, their performance lag behind general use cases in some expertise domains, such as Chinese medicine. Existing efforts to incorporate Chinese medicine into LLMs rely on Supervised Fine-Tuning (SFT) with single-turn and distilled dialogue data. These models lack the ability for doctor-like proactive inquiry and multi-turn comprehension and cannot align responses with experts' intentions. In this work, we introduce Zhongjing, the first Chinese medical LLaMA-based LLM that implements an entire training pipeline from continuous pre-training, SFT, to Reinforcement Learning from Human Feedback (RLHF). Additionally, we construct a Chinese multi-turn medical dialogue dataset of 70,000 authentic doctor-patient dialogues, CMtMedQA, which significantly enhances the model's capability for complex dialogue and proactive inquiry initiation. We also define a refined annotation rule and evaluation criteria given the unique characteristics of the biomedical domain. Extensive experimental results show that Zhongjing outperforms baselines in various capacities and matches the performance of ChatGPT in some abilities, despite the 100x parameters. Ablation studies also demonstrate the contributions of each component: pre-training enhances medical knowledge, and RLHF further improves instruction-following ability and safety. Our code, datasets, and models are available at https://github.com/SupritYoung/Zhongjing.

  • 7 authors
·
Aug 7, 2023

Accelerating Scientific Research with Gemini: Case Studies and Common Techniques

Recent advances in large language models (LLMs) have opened new avenues for accelerating scientific research. While models are increasingly capable of assisting with routine tasks, their ability to contribute to novel, expert-level mathematical discovery is less understood. We present a collection of case studies demonstrating how researchers have successfully collaborated with advanced AI models, specifically Google's Gemini-based models (in particular Gemini Deep Think and its advanced variants), to solve open problems, refute conjectures, and generate new proofs across diverse areas in theoretical computer science, as well as other areas such as economics, optimization, and physics. Based on these experiences, we extract common techniques for effective human-AI collaboration in theoretical research, such as iterative refinement, problem decomposition, and cross-disciplinary knowledge transfer. While the majority of our results stem from this interactive, conversational methodology, we also highlight specific instances that push beyond standard chat interfaces. These include deploying the model as a rigorous adversarial reviewer to detect subtle flaws in existing proofs, and embedding it within a "neuro-symbolic" loop that autonomously writes and executes code to verify complex derivations. Together, these examples highlight the potential of AI not just as a tool for automation, but as a versatile, genuine partner in the creative process of scientific discovery.

  • 34 authors
·
Feb 3 2

Seeing What You Said: Talking Face Generation Guided by a Lip Reading Expert

Talking face generation, also known as speech-to-lip generation, reconstructs facial motions concerning lips given coherent speech input. The previous studies revealed the importance of lip-speech synchronization and visual quality. Despite much progress, they hardly focus on the content of lip movements i.e., the visual intelligibility of the spoken words, which is an important aspect of generation quality. To address the problem, we propose using a lip-reading expert to improve the intelligibility of the generated lip regions by penalizing the incorrect generation results. Moreover, to compensate for data scarcity, we train the lip-reading expert in an audio-visual self-supervised manner. With a lip-reading expert, we propose a novel contrastive learning to enhance lip-speech synchronization, and a transformer to encode audio synchronically with video, while considering global temporal dependency of audio. For evaluation, we propose a new strategy with two different lip-reading experts to measure intelligibility of the generated videos. Rigorous experiments show that our proposal is superior to other State-of-the-art (SOTA) methods, such as Wav2Lip, in reading intelligibility i.e., over 38% Word Error Rate (WER) on LRS2 dataset and 27.8% accuracy on LRW dataset. We also achieve the SOTA performance in lip-speech synchronization and comparable performances in visual quality.

  • 5 authors
·
Mar 29, 2023

CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison

Large, labeled datasets have driven deep learning methods to achieve expert-level performance on a variety of medical imaging tasks. We present CheXpert, a large dataset that contains 224,316 chest radiographs of 65,240 patients. We design a labeler to automatically detect the presence of 14 observations in radiology reports, capturing uncertainties inherent in radiograph interpretation. We investigate different approaches to using the uncertainty labels for training convolutional neural networks that output the probability of these observations given the available frontal and lateral radiographs. On a validation set of 200 chest radiographic studies which were manually annotated by 3 board-certified radiologists, we find that different uncertainty approaches are useful for different pathologies. We then evaluate our best model on a test set composed of 500 chest radiographic studies annotated by a consensus of 5 board-certified radiologists, and compare the performance of our model to that of 3 additional radiologists in the detection of 5 selected pathologies. On Cardiomegaly, Edema, and Pleural Effusion, the model ROC and PR curves lie above all 3 radiologist operating points. We release the dataset to the public as a standard benchmark to evaluate performance of chest radiograph interpretation models. The dataset is freely available at https://stanfordmlgroup.github.io/competitions/chexpert .

  • 20 authors
·
Jan 21, 2019

Can AI agents conduct open-ended AI research? Early evidence from two case studies

Forecasts of explosive AI progress hinge on AI agents automating AI research. But evidence on whether agents can carry out open-ended AI research is thin. Current evaluations either test agents on narrow, verifiable tasks, which excludes open-ended research, or submit AI-generated papers to blind peer review, which is overstretched, stochastic, and suffers from poor review quality. We introduce a third way to measure progress towards AI R\&D automation. An agent takes on the central, open-ended research question of a high-quality unpublished paper, and the paper's original authors grade its output. We call these shadow evaluations. We ran shadow evaluations on two unpublished NeurIPS 2026 submissions, giving frontier agents six days and thousands of dollars of compute. The agents completed all of the engineering without human help, yet could not make substantial progress towards answering the research questions. As a result, both papers were unambiguously rejected by the authors. We identify five recurring failure modes: poor judgment about the bar for publishable research, uncreative responses to shortcomings in the research design, ineffective backtracking from dead ends, poor resource awareness, and instruction drift. A robustness check with a second model and scaffold reproduced these failures. We release the expert reviews, survey responses, agent repositories, and logs. Our results provide early evidence that today's agents can do the engineering of AI research, but struggle with critical parts of the research lifecycle.

  • 24 authors
·
Jul 28 1

GLaVE-Cap: Global-Local Aligned Video Captioning with Vision Expert Integration

Video detailed captioning aims to generate comprehensive video descriptions to facilitate video understanding. Recently, most efforts in the video detailed captioning community have been made towards a local-to-global paradigm, which first generates local captions from video clips and then summarizes them into a global caption. However, we find this paradigm leads to less detailed and contextual-inconsistent captions, which can be attributed to (1) no mechanism to ensure fine-grained captions, and (2) weak interaction between local and global captions. To remedy the above two issues, we propose GLaVE-Cap, a Global-Local aligned framework with Vision Expert integration for Captioning, which consists of two core modules: TrackFusion enables comprehensive local caption generation, by leveraging vision experts to acquire cross-frame visual prompts, coupled with a dual-stream structure; while CaptionBridge establishes a local-global interaction, by using global context to guide local captioning, and adaptively summarizing local captions into a coherent global caption. Besides, we construct GLaVE-Bench, a comprehensive video captioning benchmark featuring 5X more queries per video than existing benchmarks, covering diverse visual dimensions to facilitate reliable evaluation. We further provide a training dataset GLaVE-1.2M containing 16K high-quality fine-grained video captions and 1.2M related question-answer pairs. Extensive experiments on four benchmarks show that our GLaVE-Cap achieves state-of-the-art performance. Besides, the ablation studies and student model analyses further validate the effectiveness of the proposed modules and the contribution of GLaVE-1.2M to the video understanding community. The source code, model weights, benchmark, and dataset will be open-sourced.

  • 7 authors
·
Sep 14, 2025

Least-Loaded Expert Parallelism: Load Balancing An Imbalanced Mixture-of-Experts

Mixture-of-Experts (MoE) models are typically pre-trained with explicit load-balancing constraints to ensure statistically balanced expert routing. Despite this, we observe that even well-trained MoE models exhibit significantly imbalanced routing. This behavior is arguably natural-and even desirable - as imbalanced routing allows models to concentrate domain-specific knowledge within a subset of experts. Expert parallelism (EP) is designed to scale MoE models by distributing experts across multiple devices, but with a less-discussed assumption of balanced routing. Under extreme imbalance, EP can funnel a disproportionate number of tokens to a small number of experts, leading to compute- and memory-bound failures on overloaded devices during post-training or inference, where explicit load balancing is often inapplicable. We propose Least-Loaded Expert Parallelism (LLEP), a novel EP algorithm that dynamically reroutes excess tokens and associated expert parameters from overloaded devices to underutilized ones. This ensures that all devices complete their workloads within the minimum collective latency while respecting memory constraints. Across different model scales, LLEP achieves up to 5x speedup and 4x reduction in peak memory usage compared to standard EP. This enables faster and higher-throughput post-training and inference, with ~1.9x faster for gpt-oss-120b. We support our method with extensive theoretical analysis and comprehensive empirical evaluations, including ablation studies. These results illuminate key trade-offs and enable a principled framework for hardware-specific hyper-parameter tuning to achieve optimal performance.

LLM Interactive Optimization of Open Source Python Libraries -- Case Studies and Generalization

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

  • 1 authors
·
Dec 8, 2023

The Benefits of Vulnerability Discovery and Bug Bounty Programs: Case Studies of Chromium and Firefox

Recently, bug-bounty programs have gained popularity and become a significant part of the security culture of many organizations. Bug-bounty programs enable organizations to enhance their security posture by harnessing the diverse expertise of crowds of external security experts (i.e., bug hunters). Nonetheless, quantifying the benefits of bug-bounty programs remains elusive, which presents a significant challenge for managing them. Previous studies focused on measuring their benefits in terms of the number of vulnerabilities reported or based on the properties of the reported vulnerabilities, such as severity or exploitability. However, beyond these inherent properties, the value of a report also depends on the probability that the vulnerability would be discovered by a threat actor before an internal expert could discover and patch it. In this paper, we present a data-driven study of the Chromium and Firefox vulnerability-reward programs. First, we estimate the difficulty of discovering a vulnerability using the probability of rediscovery as a novel metric. Our findings show that vulnerability discovery and patching provide clear benefits by making it difficult for threat actors to find vulnerabilities; however, we also identify opportunities for improvement, such as incentivizing bug hunters to focus more on development releases. Second, we compare the types of vulnerabilities that are discovered internally vs. externally and those that are exploited by threat actors. We observe significant differences between vulnerabilities found by external bug hunters, internal security teams, and external threat actors, which indicates that bug-bounty programs provide an important benefit by complementing the expertise of internal teams, but also that external hunters should be incentivized more to focus on the types of vulnerabilities that are likely to be exploited by threat actors.

  • 5 authors
·
Feb 23, 2023

AgentGen: Enhancing Planning Abilities for Large Language Model based Agent via Environment and Task Generation

Large Language Model (LLM) based agents have garnered significant attention and are becoming increasingly popular. Furthermore, planning ability is a crucial component of an LLM-based agent, involving interaction with the environment and executing actions to complete a planning task, which generally entails achieving a desired goal from an initial state. This paper investigates enhancing the planning abilities of LLMs through instruction tuning, referred to as agent training. Recent studies have demonstrated that utilizing expert-level trajectory for instruction-tuning LLMs effectively enhances their planning capabilities. However, existing work primarily focuses on synthesizing trajectories from manually designed planning tasks and environments. The labor-intensive nature of creating these environments and tasks impedes the generation of sufficiently varied and extensive trajectories. To address this limitation, this paper explores the automated synthesis of diverse environments and a gradual range of planning tasks, from easy to difficult. We introduce a framework, AgentGen, that leverages LLMs first to generate environments and subsequently generate planning tasks conditioned on these environments. Specifically, to improve environmental diversity, we propose using an inspiration corpus composed of various domain-specific text segments as the context for synthesizing environments. Moreover, to increase the difficulty diversity of generated planning tasks, we propose a bidirectional evolution method, Bi-Evol, that evolves planning tasks from easier and harder directions to synthesize a task set with a smoother difficulty curve. The evaluation results derived from AgentBoard show that AgentGen greatly improves LLMs' planning ability, e.g., the AgentGen instruction-tuned Llama-3 8B surpasses GPT-3.5 in overall performance. Moreover, in certain tasks, it even outperforms GPT-4.

  • 9 authors
·
Aug 1, 2024

AdaMoE: Token-Adaptive Routing with Null Experts for Mixture-of-Experts Language Models

Mixture of experts (MoE) has become the standard for constructing production-level large language models (LLMs) due to its promise to boost model capacity without causing significant overheads. Nevertheless, existing MoE methods usually enforce a constant top-k routing for all tokens, which is arguably restrictive because various tokens (e.g., "<EOS>" vs. "apple") may require various numbers of experts for feature abstraction. Lifting such a constraint can help make the most of limited resources and unleash the potential of the model for downstream tasks. In this sense, we introduce AdaMoE to realize token-adaptive routing for MoE, where different tokens are permitted to select a various number of experts. AdaMoE makes minimal modifications to the vanilla MoE with top-k routing -- it simply introduces a fixed number of null experts, which do not consume any FLOPs, to the expert set and increases the value of k. AdaMoE does not force each token to occupy a fixed number of null experts but ensures the average usage of the null experts with a load-balancing loss, leading to an adaptive number of null/true experts used by each token. AdaMoE exhibits a strong resemblance to MoEs with expert choice routing while allowing for trivial auto-regressive modeling. AdaMoE is easy to implement and can be effectively applied to pre-trained (MoE-)LLMs. Extensive studies show that AdaMoE can reduce average expert load (FLOPs) while achieving superior performance. For example, on the ARC-C dataset, applying our method to fine-tuning Mixtral-8x7B can reduce FLOPs by 14.5% while increasing accuracy by 1.69%.

  • 5 authors
·
Jun 19, 2024

EasyOmnimatte: Taming Pretrained Inpainting Diffusion Models for End-to-End Video Layered Decomposition

Existing video omnimatte methods typically rely on slow, multi-stage, or inference-time optimization pipelines that fail to fully exploit powerful generative priors, producing suboptimal decompositions. Our key insight is that, if a video inpainting model can be finetuned to remove the foreground-associated effects, then it must be inherently capable of perceiving these effects, and hence can also be finetuned for the complementary task: foreground layer decomposition with associated effects. However, although naïvely finetuning the inpainting model with LoRA applied to all blocks can produce high-quality alpha mattes, it fails to capture associated effects. Our systematic analysis reveals this arises because effect-related cues are primarily encoded in specific DiT blocks and become suppressed when LoRA is applied across all blocks. To address this, we introduce EasyOmnimatte, the first unified, end-to-end video omnimatte method. Concretely, we finetune a pretrained video inpainting diffusion model to learn dual complementary experts while keeping its original weights intact: an Effect Expert, where LoRA is applied only to effect-sensitive DiT blocks to capture the coarse structure of the foreground and associated effects, and a fully LoRA-finetuned Quality Expert learns to refine the alpha matte. During sampling, Effect Expert is used for denoising at early, high-noise steps, while Quality Expert takes over at later, low-noise steps. This design eliminates the need for two full diffusion passes, significantly reducing computational cost without compromising output quality. Ablation studies validate the effectiveness of this Dual-Expert strategy. Experiments demonstrate that EasyOmnimatte sets a new state-of-the-art for video omnimatte and enables various downstream tasks, significantly outperforming baselines in both quality and efficiency.

  • 3 authors
·
Dec 25, 2025

Do LLMs Align Human Values Regarding Social Biases? Judging and Explaining Social Biases with LLMs

Large language models (LLMs) can lead to undesired consequences when misaligned with human values, especially in scenarios involving complex and sensitive social biases. Previous studies have revealed the misalignment of LLMs with human values using expert-designed or agent-based emulated bias scenarios. However, it remains unclear whether the alignment of LLMs with human values differs across different types of scenarios (e.g., scenarios containing negative vs. non-negative questions). In this study, we investigate the alignment of LLMs with human values regarding social biases (HVSB) in different types of bias scenarios. Through extensive analysis of 12 LLMs from four model families and four datasets, we demonstrate that LLMs with large model parameter scales do not necessarily have lower misalignment rate and attack success rate. Moreover, LLMs show a certain degree of alignment preference for specific types of scenarios and the LLMs from the same model family tend to have higher judgment consistency. In addition, we study the understanding capacity of LLMs with their explanations of HVSB. We find no significant differences in the understanding of HVSB across LLMs. We also find LLMs prefer their own generated explanations. Additionally, we endow smaller language models (LMs) with the ability to explain HVSB. The generation results show that the explanations generated by the fine-tuned smaller LMs are more readable, but have a relatively lower model agreeability.

  • 2 authors
·
Sep 16, 2025

Counting Ability of Large Language Models and Impact of Tokenization

Transformers, the backbone of modern large language models (LLMs), face inherent architectural limitations that impede their reasoning capabilities. Unlike recurrent networks, Transformers lack recurrent connections, confining them to constant-depth computation. This restriction places them in the complexity class TC^0, making them theoretically incapable of solving tasks that demand increasingly deep reasoning as input length grows. Counting, a fundamental component of many reasoning tasks, also requires reasoning depth to grow linearly to be performed inductively. While previous studies have established the upper limits of counting ability in Transformer-based expert models (i.e., models specifically trained for counting tasks), these findings do not directly extend to general-purpose LLMs due to differences in reasoning mechanisms. Recent work has highlighted how Chain of Thought (CoT) reasoning can help alleviate some of the architectural limitations of Transformers in counting tasks. However, little attention has been paid to the role of tokenization in these models. Unlike expert models that often use character-level tokenization, LLMs typically rely on byte-level (BPE) tokenizers, which fundamentally alters the way reasoning is processed. Our work investigates the impact of tokenization on the counting abilities of LLMs, uncovering substantial performance variations based on input tokenization differences. We provide both theoretical and experimental analyses, offering insights into how tokenization choices can undermine models' theoretical computability, thereby inspiring the design of new tokenization methods to enhance reasoning in LLMs.

  • 3 authors
·
Oct 25, 2024 2

LLM-as-a-Judge in Healthcare: A Scoping Analysis of Applications, Methods, and Human Alignment

Large language models (LLMs) are increasingly deployed across healthcare applications, including clinical documentation, diagnostic reasoning, medicine recommendation, and medical education. Their outputs are largely unstructured clinical text, which is difficult to reliably evaluate at scale. LLM-as-a-Judge, in which an LLM evaluates another system's output against task-specific criteria, offers a scalable alternative and is increasingly used in clinical evaluation, yet its validity in healthcare remains underexamined. Existing reviews focus on general-purpose LLM evaluation or on risk framework, rather than systematically characterizing how LLM-as-a-Judge is applied in healthcare and how well their judgments align with human experts. We therefore conduct a PRISMA-guided comprehensive review of LLM-as-a-Judge applications in healthcare, searching five databases for studies published between January 2023 and February 2026. After screening 541 records, 134 studies meet the eligibility and are coded by health scenario, judge configuration, technical approach, and validation design. LLM-as-a-Judge is concentrated in clinical decision support, clinical natural language processing (NLP), medical knowledge and question answering (QA), and medical communication. OpenAI models are the most frequently used judges, and prompt engineering appears in nearly all studies, with ensemble, multi-agent, and retrieval-augmented designs as common extensions. Among studies reporting human validation, LLM judges often show moderate to strong alignment with expert judgments, although reliability varies substantially across tasks. Overall, this review positions LLM-as-a-Judge as a promising framework for scalable healthcare AI evaluation, while emphasizing that its clinical value depends on model design and rigorous validation.

  • 12 authors
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May 23

CodeCytos: AI-assisted spatial molecular imaging analysis via code-augmented agent action space

Conventional tissue image analysis software provides foundational capabilities for cellular analysis, including segmentation, basic morphological feature extraction, and spatial organization analysis. However, these tools often require manual intervention and are not well integrated with code-driven automation, limiting efficiency and scalability for complex spatial tissue studies. In addition, they offer limited flexibility for custom analyses, as they typically support only a fixed set of pre-implemented spatial cellular features. To address these limitations, we propose CodeCytos, a coding-based reasoning agent framework that enables dynamic, programmable interaction with spatial molecular imaging data to improve automation and customization. CodeCytos is designed to streamline the exploration of custom spatial cellular features and adapt to diverse research needs. We demonstrate its utility through case studies on four expert-curated datasets from distinct tissue types: frontal cortex, non-small-cell lung cancer, pancreas, and tonsil. We evaluate CodeCytos under a realistic minimal prompt setting, where bioscientists pose simple questions without task-specific instructions or contextual information about spatial cellular analysis, and benchmark multiple LLM backbones with strong coding capabilities. We further show that incorporating tailored, domain-agnostic few-shot in-context coding-reasoning examples (randomly sampled demonstrations outside the spatial analysis domain) can substantially improve performance without requiring costly, expert-crafted in-domain demonstrations. Overall, CodeCytos outperforms baseline approaches, highlighting the potential of code-action agents to assist with custom feature exploration in spatial molecular imaging and to accelerate biomarker discovery.

SurgWound-Bench: A Benchmark for Surgical Wound Diagnosis

Surgical site infection (SSI) is one of the most common and costly healthcare-associated infections and and surgical wound care remains a significant clinical challenge in preventing SSIs and improving patient outcomes. While recent studies have explored the use of deep learning for preliminary surgical wound screening, progress has been hindered by concerns over data privacy and the high costs associated with expert annotation. Currently, no publicly available dataset or benchmark encompasses various types of surgical wounds, resulting in the absence of an open-source Surgical-Wound screening tool. To address this gap: (1) we present SurgWound, the first open-source dataset featuring a diverse array of surgical wound types. It contains 697 surgical wound images annotated by 3 professional surgeons with eight fine-grained clinical attributes. (2) Based on SurgWound, we introduce the first benchmark for surgical wound diagnosis, which includes visual question answering (VQA) and report generation tasks to comprehensively evaluate model performance. (3) Furthermore, we propose a three-stage learning framework, WoundQwen, for surgical wound diagnosis. In the first stage, we employ five independent MLLMs to accurately predict specific surgical wound characteristics. In the second stage, these predictions serve as additional knowledge inputs to two MLLMs responsible for diagnosing outcomes, which assess infection risk and guide subsequent interventions. In the third stage, we train a MLLM that integrates the diagnostic results from the previous two stages to produce a comprehensive report. This three-stage framework can analyze detailed surgical wound characteristics and provide subsequent instructions to patients based on surgical images, paving the way for personalized wound care, timely intervention, and improved patient outcomes.

  • 9 authors
·
Aug 20, 2025

Microbial Genetic Algorithm-based Black-box Attack against Interpretable Deep Learning Systems

Deep learning models are susceptible to adversarial samples in white and black-box environments. Although previous studies have shown high attack success rates, coupling DNN models with interpretation models could offer a sense of security when a human expert is involved, who can identify whether a given sample is benign or malicious. However, in white-box environments, interpretable deep learning systems (IDLSes) have been shown to be vulnerable to malicious manipulations. In black-box settings, as access to the components of IDLSes is limited, it becomes more challenging for the adversary to fool the system. In this work, we propose a Query-efficient Score-based black-box attack against IDLSes, QuScore, which requires no knowledge of the target model and its coupled interpretation model. QuScore is based on transfer-based and score-based methods by employing an effective microbial genetic algorithm. Our method is designed to reduce the number of queries necessary to carry out successful attacks, resulting in a more efficient process. By continuously refining the adversarial samples created based on feedback scores from the IDLS, our approach effectively navigates the search space to identify perturbations that can fool the system. We evaluate the attack's effectiveness on four CNN models (Inception, ResNet, VGG, DenseNet) and two interpretation models (CAM, Grad), using both ImageNet and CIFAR datasets. Our results show that the proposed approach is query-efficient with a high attack success rate that can reach between 95% and 100% and transferability with an average success rate of 69% in the ImageNet and CIFAR datasets. Our attack method generates adversarial examples with attribution maps that resemble benign samples. We have also demonstrated that our attack is resilient against various preprocessing defense techniques and can easily be transferred to different DNN models.

  • 5 authors
·
Jul 12, 2023

Alt-MoE:A Scalable Framework for Bidirectional Multimodal Alignment and Efficient Knowledge Integration

Multimodal learning has advanced significantly by aligning different modalities within shared latent spaces, enabling tasks such as cross-modal understanding and generation. Current alignment strategies in multimodal learning primarily include direct alignment using pre-trained or unified encoders and single-directional alignment via modality-specific connectors. Direct alignment struggles to fully leverage rich intra-modal knowledge, often requiring extensive training data to achieve cross-modal representation. Meanwhile, single-directional alignment methods, despite leveraging pre-trained knowledge, restrict task adaptability and hinder the model's ability to capture bidirectional relationships, leading to incomplete knowledge fusion and underutilization of complementary modality-specific information. To address these limitations, we introduce Alt-MoE, a scalable multimodal alignment framework that employs a mixture of experts (MoE) model as a multi-directional connector across modalities. By utilizing a sequential alternating one-way alignment strategy, Alt-MoE iteratively refines the model to achieve bidirectional alignment. Alt-MoE operates in latent space, enabling efficient vector pre-storage and real-time retrieval via MoE, optimizing large-scale data processing. Extensive empirical studies demonstrate that Alt-MoE achieves competitive performance on cross-modal retrieval and visual question answering by integrating diverse modality-specific knowledge, generalizing to unseen data, and easily scaling to new tasks and modalities through dynamic adjustment of MoE capacity and expert activation.

  • 11 authors
·
Sep 9, 2024

Investigating Transfer Learning in Multilingual Pre-trained Language Models through Chinese Natural Language Inference

Multilingual transformers (XLM, mT5) have been shown to have remarkable transfer skills in zero-shot settings. Most transfer studies, however, rely on automatically translated resources (XNLI, XQuAD), making it hard to discern the particular linguistic knowledge that is being transferred, and the role of expert annotated monolingual datasets when developing task-specific models. We investigate the cross-lingual transfer abilities of XLM-R for Chinese and English natural language inference (NLI), with a focus on the recent large-scale Chinese dataset OCNLI. To better understand linguistic transfer, we created 4 categories of challenge and adversarial tasks (totaling 17 new datasets) for Chinese that build on several well-known resources for English (e.g., HANS, NLI stress-tests). We find that cross-lingual models trained on English NLI do transfer well across our Chinese tasks (e.g., in 3/4 of our challenge categories, they perform as well/better than the best monolingual models, even on 3/5 uniquely Chinese linguistic phenomena such as idioms, pro drop). These results, however, come with important caveats: cross-lingual models often perform best when trained on a mixture of English and high-quality monolingual NLI data (OCNLI), and are often hindered by automatically translated resources (XNLI-zh). For many phenomena, all models continue to struggle, highlighting the need for our new diagnostics to help benchmark Chinese and cross-lingual models. All new datasets/code are released at https://github.com/huhailinguist/ChineseNLIProbing.

  • 8 authors
·
Jun 7, 2021

Pair Programming with Large Language Models for Sampling and Estimation of Copulas

Without writing a single line of code by a human, an example Monte Carlo simulation based application for stochastic dependence modeling with copulas is developed using a state-of-the-art large language model (LLM) fine-tuned for conversations. This includes interaction with ChatGPT in natural language and using mathematical formalism, which, under careful supervision by a human-expert, led to producing a working code in MATLAB, Python and R for sampling from a given copula model, evaluation of the model's density, performing maximum likelihood estimation, optimizing the code for parallel computing for CPUs as well as for GPUs, and visualization of the computed results. In contrast to other emerging studies that assess the accuracy of LLMs like ChatGPT on tasks from a selected area, this work rather investigates ways how to achieve a successful solution of a standard statistical task in a collaboration of a human-expert and artificial intelligence (AI). Particularly, through careful prompt engineering, we separate successful solutions generated by ChatGPT from unsuccessful ones, resulting in a comprehensive list of related pros and cons. It is demonstrated that if the typical pitfalls are avoided, we can substantially benefit from collaborating with an AI partner. For example, we show that if ChatGPT is not able to provide a correct solution due to a lack of or incorrect knowledge, the human-expert can feed it with the correct knowledge, e.g., in the form of mathematical theorems and formulas, and make it to apply the gained knowledge in order to provide a solution that is correct. Such ability presents an attractive opportunity to achieve a programmed solution even for users with rather limited knowledge of programming techniques.

  • 1 authors
·
Mar 31, 2023

StuGPTViz: A Visual Analytics Approach to Understand Student-ChatGPT Interactions

The integration of Large Language Models (LLMs), especially ChatGPT, into education is poised to revolutionize students' learning experiences by introducing innovative conversational learning methodologies. To empower students to fully leverage the capabilities of ChatGPT in educational scenarios, understanding students' interaction patterns with ChatGPT is crucial for instructors. However, this endeavor is challenging due to the absence of datasets focused on student-ChatGPT conversations and the complexities in identifying and analyzing the evolutional interaction patterns within conversations. To address these challenges, we collected conversational data from 48 students interacting with ChatGPT in a master's level data visualization course over one semester. We then developed a coding scheme, grounded in the literature on cognitive levels and thematic analysis, to categorize students' interaction patterns with ChatGPT. Furthermore, we present a visual analytics system, StuGPTViz, that tracks and compares temporal patterns in student prompts and the quality of ChatGPT's responses at multiple scales, revealing significant pedagogical insights for instructors. We validated the system's effectiveness through expert interviews with six data visualization instructors and three case studies. The results confirmed StuGPTViz's capacity to enhance educators' insights into the pedagogical value of ChatGPT. We also discussed the potential research opportunities of applying visual analytics in education and developing AI-driven personalized learning solutions.

  • 7 authors
·
Jul 17, 2024

A Threshold Exceedance Framework for CBRN Uplift Evaluation in Frontier Language Models

As frontier language models advance, policymakers and model developers need methods for assessing whether model access materially increases a non-expert actor's ability to plan high-consequence Chemical, Biological, Radiological, or Nuclear (CBRN) misuse relative to public tools alone. Existing CBRN evaluations differ in non-expert definitions, threat scope, baselines, scoring rubrics, and decision rules, making results difficult to compare across studies. We introduce a Threshold Exceedance Criteria (TEC) framework that decomposes an uplift study into independently executable components: determining non-expert participant eligibility, defining the CBRN threat scope for the study, and statistically estimating material uplift. We then operationalize the TEC framework in a large-scale empirical study using a design that determines two forms of uplift: generative (where a model assists plan creation from scratch) and revisionist (where a model assists refinement of an existing plan). The study produced attack plans across the CBRN domains, which we evaluated through subject-matter-expert review to estimate generative and revisionist uplift. Applying the framework, our empirical study revealed domain heterogeneity: under this controlled pre-release evaluation, model-assisted plans sometimes received expert-equivalent instructional ratings, but confirmed material uplift was limited to the radiological domain. These findings informed mitigation and deployment-governance decisions rather than characterizing deployed model behavior. We conclude with methodological lessons for future CBRN uplift evaluations, emphasizing prespecified criteria, explicit baselines, separation of generative and revisionist estimates, and careful distinction between preliminary screening signals and confirmed risk determinations.

  • 11 authors
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Jul 12

Historical Backtesting for Scientific Question Discovery: A Protocol and Astronomy Pilot

Systems that generate scientific research questions are evaluated today by expert scores, LLM-as-judge ratings, or curated case studies -- all subjective, none falsifiable. We formalize historical backtesting as an alternative: a system generates questions from a corpus frozen at a historical cutoff, the questions are frozen before any access to later literature, and a temporally isolated future corpus then determines whether each question was subsequently answered, partially addressed, independently posed, or ignored, and whether its underlying premise was supported or refuted. The protocol is model-agnostic: any system that emits frozen questions can be scored. We release reproducible astronomy instances with temporally isolated corpora, frozen questions, auditable labels, four reference baselines, and a submission interface. Two findings result. First, evidence-structure-first generation outperforms LLM-only prompting: across a generator decomposition crossed with a four-cutoff stress test (2010-2024, 798 judged questions) whose last window postdates model training, LLM-only generation shows memorized relevance without specific foresight, while a generator using no model weights at all finds questions whose premises the future refutes in every era. Second, a seven-rater agreement study (two blinded human annotators, five judge models, 90 items) indicts the outcome taxonomy rather than the judge: two careful humans agree at kappa = 0.17, every judge model agrees with the professional annotator as well or better (0.17-0.26), and frontier models agree with one another at 0.60 -- certifying an LLM judge by model-model agreement would have overstated its reliability threefold. A prospective instance -- 200 questions frozen 2026-08-17, scored 2027-2030 -- is released so the central claims become contamination-free tests that time itself will grade.

  • 1 authors
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Aug 16

Claw AI Lab: An Autonomous Multi-Agent Research Team

We present Claw AI Lab, a lab-native autonomous research platform that advances automated research from a hidden prompt-to-paper pipeline into an interactive AI laboratory. Rather than centering the system around a single agent or a fixed serial workflow, we allow users to instantiate a full research team from one prompt, with customizable roles, collaborative workflows, real-time monitoring, artifact inspection, and rollback/resume control through a unified dashboard. The platform also supports distinct research modes for exploration, multi-agent discussion, and reproduction, making autonomous research substantially more steerable and laboratory-like in practice. A key practical contribution of Claw AI Lab lies in its Claw-Code Harness, which connects local codebases, datasets, and checkpoints to runnable experiments and feeds execution artifacts back into the research loop. As a result, the harness improves not only execution integration, but also experimental completion and result integrity: experiments are easier to inspect, iterate on, and faithfully transfer into final papers, reducing common failure modes such as partial runs and malformed result reporting. In our internal evaluation on five AI research case studies, using AutoResearchClaw as the baseline, Claw AI Lab is consistently preferred by AI expert judges on idea novelty, experiment completeness, and paper presentation quality. We view Claw AI Lab as an early step toward a new paradigm: autonomous research as usable, interactive, and reliability-aware scientific infrastructure.

  • 15 authors
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May 20

Text-driven Adaptation of Foundation Models for Few-shot Surgical Workflow Analysis

Purpose: Surgical workflow analysis is crucial for improving surgical efficiency and safety. However, previous studies rely heavily on large-scale annotated datasets, posing challenges in cost, scalability, and reliance on expert annotations. To address this, we propose Surg-FTDA (Few-shot Text-driven Adaptation), designed to handle various surgical workflow analysis tasks with minimal paired image-label data. Methods: Our approach has two key components. First, Few-shot selection-based modality alignment selects a small subset of images and aligns their embeddings with text embeddings from the downstream task, bridging the modality gap. Second, Text-driven adaptation leverages only text data to train a decoder, eliminating the need for paired image-text data. This decoder is then applied to aligned image embeddings, enabling image-related tasks without explicit image-text pairs. Results: We evaluate our approach to generative tasks (image captioning) and discriminative tasks (triplet recognition and phase recognition). Results show that Surg-FTDA outperforms baselines and generalizes well across downstream tasks. Conclusion: We propose a text-driven adaptation approach that mitigates the modality gap and handles multiple downstream tasks in surgical workflow analysis, with minimal reliance on large annotated datasets. The code and dataset will be released in https://github.com/CAMMA-public/Surg-FTDA

  • 5 authors
·
Jan 16, 2025

FPUS23: An Ultrasound Fetus Phantom Dataset with Deep Neural Network Evaluations for Fetus Orientations, Fetal Planes, and Anatomical Features

Ultrasound imaging is one of the most prominent technologies to evaluate the growth, progression, and overall health of a fetus during its gestation. However, the interpretation of the data obtained from such studies is best left to expert physicians and technicians who are trained and well-versed in analyzing such images. To improve the clinical workflow and potentially develop an at-home ultrasound-based fetal monitoring platform, we present a novel fetus phantom ultrasound dataset, FPUS23, which can be used to identify (1) the correct diagnostic planes for estimating fetal biometric values, (2) fetus orientation, (3) their anatomical features, and (4) bounding boxes of the fetus phantom anatomies at 23 weeks gestation. The entire dataset is composed of 15,728 images, which are used to train four different Deep Neural Network models, built upon a ResNet34 backbone, for detecting aforementioned fetus features and use-cases. We have also evaluated the models trained using our FPUS23 dataset, to show that the information learned by these models can be used to substantially increase the accuracy on real-world ultrasound fetus datasets. We make the FPUS23 dataset and the pre-trained models publicly accessible at https://github.com/bharathprabakaran/FPUS23, which will further facilitate future research on fetal ultrasound imaging and analysis.

  • 4 authors
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Mar 14, 2023

Automatic Image-Level Morphological Trait Annotation for Organismal Images

Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in large-scale ecological studies. A major bottleneck is the absence of high-quality datasets linking biological images to trait-level annotations. In this work, we demonstrate that sparse autoencoders trained on foundation-model features yield monosemantic, spatially grounded neurons that consistently activate on meaningful morphological parts. Leveraging this property, we introduce a trait annotation pipeline that localizes salient regions and uses vision-language prompting to generate interpretable trait descriptions. Using this approach, we construct Bioscan-Traits, a dataset of 80K trait annotations spanning 19K insect images from BIOSCAN-5M. Human evaluation confirms the biological plausibility of the generated morphological descriptions. We assess design sensitivity through a comprehensive ablation study, systematically varying key design choices and measuring their impact on the quality of the resulting trait descriptions. By annotating traits with a modular pipeline rather than prohibitively expensive manual efforts, we offer a scalable way to inject biologically meaningful supervision into foundation models, enable large-scale morphological analyses, and bridge the gap between ecological relevance and machine-learning practicality.

Omni-iEEG: A Large-Scale, Comprehensive iEEG Dataset and Benchmark for Epilepsy Research

Epilepsy affects over 50 million people worldwide, and one-third of patients suffer drug-resistant seizures where surgery offers the best chance of seizure freedom. Accurate localization of the epileptogenic zone (EZ) relies on intracranial EEG (iEEG). Clinical workflows, however, remain constrained by labor-intensive manual review. At the same time, existing data-driven approaches are typically developed on single-center datasets that are inconsistent in format and metadata, lack standardized benchmarks, and rarely release pathological event annotations, creating barriers to reproducibility, cross-center validation, and clinical relevance. With extensive efforts to reconcile heterogeneous iEEG formats, metadata, and recordings across publicly available sources, we present Omni-iEEG, a large-scale, pre-surgical iEEG resource comprising 302 patients and 178 hours of high-resolution recordings. The dataset includes harmonized clinical metadata such as seizure onset zones, resections, and surgical outcomes, all validated by board-certified epileptologists. In addition, Omni-iEEG provides over 36K expert-validated annotations of pathological events, enabling robust biomarker studies. Omni-iEEG serves as a bridge between machine learning and epilepsy research. It defines clinically meaningful tasks with unified evaluation metrics grounded in clinical priors, enabling systematic evaluation of models in clinically relevant settings. Beyond benchmarking, we demonstrate the potential of end-to-end modeling on long iEEG segments and highlight the transferability of representations pretrained on non-neurophysiological domains. Together, these contributions establish Omni-iEEG as a foundation for reproducible, generalizable, and clinically translatable epilepsy research. The project page with dataset and code links is available at omni-ieeg.github.io/omni-ieeg.

  • 12 authors
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Feb 17

HydroAgent: Formalizing Forecaster Expertise into Skill-Orchestrated Flood Forecasting Workflows

Operational flood forecasting depends on tacit forecaster expertise that is difficult to formalize, audit, and transfer. Although artificial intelligence methods have advanced flood prediction and model-error correction, most existing studies have not explicitly represented the tacit expert rules, review checkpoints, and workflow constraints that connect model outputs to operational warning decisions. To address this issue, we propose HydroAgent, a skill-orchestrated agent framework that embeds Large Language Models (LLMs) into a model-driven flood forecasting workflow, where each skill encodes explicit rules to bound LLM reasoning. We validated its effectiveness using five state-of-the-art LLMs in the South Yamhill River basin. Our results demonstrate that prior judgment captures observed peak flow and flood volume within 5% tolerance in 10 and 11 out of 14 events, with 5-fold cross-validation over 129 events yielding Pearson correlations of 0.62 and 0.84. Building on a high-baseline scheme library (average KGE 0.890), the guided scheme selection further improves KGE by 0.023-0.154, with simulated peak flow and flood volume falling within the prior judgment ranges for 14 and 13 out of 14 events. All five tested LLMs successfully execute the HydroAgent workflow with comparable judgment accuracy (40%-80%), while showing moderate performance variation and substantial cost differences. HydroAgent does not aim to replace human forecasters; instead, it translates their tacit expertise into an auditable and reproducible workflow, streamlining analytical steps and supporting more informed decision-making. This skill-orchestrated paradigm demonstrates how explicit rule boundaries can guide language model reasoning to complement physically based simulation in next-generation flood forecasting.

  • 23 authors
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Jul 26

The Ideation-Execution Gap: Execution Outcomes of LLM-Generated versus Human Research Ideas

Large Language Models (LLMs) have shown promise in accelerating the scientific research pipeline. A key capability for this process is the ability to generate novel research ideas, and prior studies have found settings in which LLM-generated research ideas were judged as more novel than human-expert ideas. However, a good idea should not simply appear to be novel, it should also result in better research after being executed. To test whether AI-generated ideas lead to better research outcomes, we conduct an execution study by recruiting 43 expert researchers to execute randomly-assigned ideas, either written by experts or generated by an LLM. Each expert spent over 100 hours implementing the idea and wrote a 4-page short paper to document the experiments. All the executed projects are then reviewed blindly by expert NLP researchers. Comparing the review scores of the same ideas before and after execution, the scores of the LLM-generated ideas decrease significantly more than expert-written ideas on all evaluation metrics (novelty, excitement, effectiveness, and overall; p < 0.05), closing the gap between LLM and human ideas observed at the ideation stage. When comparing the aggregated review scores from the execution study, we even observe that for many metrics there is a flip in rankings where human ideas score higher than LLM ideas. This ideation-execution gap highlights the limitations of current LLMs in generating truly effective research ideas and the challenge of evaluating research ideas in the absence of execution outcomes.

  • 3 authors
·
Jun 25, 2025

SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

  • 12 authors
·
Mar 13, 2022

Neural Poetry: Learning to Generate Poems using Syllables

Motivated by the recent progresses on machine learning-based models that learn artistic styles, in this paper we focus on the problem of poem generation. This is a challenging task in which the machine has to capture the linguistic features that strongly characterize a certain poet, as well as the semantics of the poet's production, that are influenced by his personal experiences and by his literary background. Since poetry is constructed using syllables, that regulate the form and structure of poems, we propose a syllable-based neural language model, and we describe a poem generation mechanism that is designed around the poet style, automatically selecting the most representative generations. The poetic work of a target author is usually not enough to successfully train modern deep neural networks, so we propose a multi-stage procedure that exploits non-poetic works of the same author, and also other publicly available huge corpora to learn syntax and grammar of the target language. We focus on the Italian poet Dante Alighieri, widely famous for his Divine Comedy. A quantitative and qualitative experimental analysis of the generated tercets is reported, where we included expert judges with strong background in humanistic studies. The generated tercets are frequently considered to be real by a generic population of judges, with relative difference of 56.25\% with respect to the ones really authored by Dante, and expert judges perceived Dante's style and rhymes in the generated text.

  • 3 authors
·
Aug 23, 2019

Hadith computational science in the age of large language models: a critical narrative review

We examine how hadith computational science is being reshaped by transformer models, retrieval-grounded pipelines, and large language models (LLMs). Recent reviews document growth in the literature, but they do not yet provide a critical account of which advances are methodologically robust, which remain benchmark-bound, and which unresolved problems still limit scholarly use. We address this gap through a critical narrative review that combines critique of existing reviews, paper-level appraisal of representative original studies, and synthesis of Islamic scholar and domain-expert perspectives on authenticity, authority, and responsible use. We find uneven progress. Data resources have expanded, segmentation tasks have matured, narrator and source-verification problems are better formalized, and LLM-assisted workflows now support corpus-scale enrichment, multilingual access, and grounded evaluation. At the same time, progress remains constrained by narrow corpora, weak benchmark comparability, synthetic-to-real transfer gaps, narrator identity resolution, preprocessing fragility, limited reproducibility, and sparse expert-grounded validation. We show that important gaps lie beyond dominant benchmarks: non-canonical and obscure corpora, commentary and explanatory literature, cross-source links with Qur'an and seerah, and fiqh-facing evidence support. We argue that hadith computation should be assessed less as isolated model performance than as an evidence infrastructure problem requiring knowledge integration, provenance, and expert supervision. On this basis, we define a research agenda for making the field methodologically stronger and more useful to Islamic scholarship.

  • 2 authors
·
Jun 17 2

Evaluating Language Models for Mathematics through Interactions

The standard methodology of evaluating large language models (LLMs) based on static pairs of inputs and outputs is insufficient for developing assistants: this kind of assessments fails to take into account the essential interactive element in their deployment, and therefore limits how we understand language model capabilities. We introduce CheckMate, an adaptable prototype platform for humans to interact with and evaluate LLMs. We conduct a study with CheckMate to evaluate three language models~(InstructGPT, ChatGPT, and GPT-4) as assistants in proving undergraduate-level mathematics, with a mixed cohort of participants from undergraduate students to professors of mathematics. We release the resulting interaction and rating dataset, MathConverse. By analysing MathConverse, we derive a preliminary taxonomy of human behaviours and uncover that despite a generally positive correlation, there are notable instances of divergence between correctness and perceived helpfulness in LLM generations, amongst other findings. Further, we identify useful scenarios and existing issues of GPT-4 in mathematical reasoning through a series of case studies contributed by expert mathematicians. We conclude with actionable takeaways for ML practitioners and mathematicians: models which communicate uncertainty, respond well to user corrections, are more interpretable and concise may constitute better assistants; interactive evaluation is a promising way to continually navigate the capability of these models; humans should be aware of language models' algebraic fallibility, and for that reason discern where they should be used.

  • 14 authors
·
Jun 2, 2023

Align, Reason and Learn: Enhancing Medical Vision-and-Language Pre-training with Knowledge

Medical vision-and-language pre-training (Med-VLP) has received considerable attention owing to its applicability to extracting generic vision-and-language representations from medical images and texts. Most existing methods mainly contain three elements: uni-modal encoders (i.e., a vision encoder and a language encoder), a multi-modal fusion module, and pretext tasks, with few studies considering the importance of medical domain expert knowledge and explicitly exploiting such knowledge to facilitate Med-VLP. Although there exist knowledge-enhanced vision-and-language pre-training (VLP) methods in the general domain, most require off-the-shelf toolkits (e.g., object detectors and scene graph parsers), which are unavailable in the medical domain. In this paper, we propose a systematic and effective approach to enhance Med-VLP by structured medical knowledge from three perspectives. First, considering knowledge can be regarded as the intermediate medium between vision and language, we align the representations of the vision encoder and the language encoder through knowledge. Second, we inject knowledge into the multi-modal fusion model to enable the model to perform reasoning using knowledge as the supplementation of the input image and text. Third, we guide the model to put emphasis on the most critical information in images and texts by designing knowledge-induced pretext tasks. To perform a comprehensive evaluation and facilitate further research, we construct a medical vision-and-language benchmark including three tasks. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on all downstream tasks. Further analyses explore the effects of different components of our approach and various settings of pre-training.

  • 3 authors
·
Sep 15, 2022

A foundation model for human-AI collaboration in medical literature mining

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

  • 23 authors
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Jan 27, 2025

DEER: A Benchmark for Evaluating Deep Research Agents on Expert Report Generation

Recent advances in large language models have enabled deep research systems that generate expert-level reports through multi-step reasoning and evidence-based synthesis. However, evaluating such reports remains challenging: report quality is multifaceted, making it difficult to determine what to assess and by what criteria; LLM-based judges may miss errors that require domain expertise to identify; and because deep research relies on retrieved evidence, report-wide claim verification is also necessary. To address these issues, we propose DEER, a benchmark for evaluating expert-level deep research reports. DEER systematizes evaluation criteria with an expert-developed taxonomy (7 dimensions, 25 subdimensions) operationalized as 101 fine-grained rubric items. We also provide task-specific Expert Evaluation Guidance to support LLM-based judging. Alongside rubric-based assessment, we propose a claim verification architecture that verifies both cited and uncited claims and quantifies evidence quality. Experiments show that while current deep research systems can produce structurally plausible reports that cite external evidence, there is room for improvement in fulfilling expert-level user requests and achieving logical completeness. Beyond simple performance comparisons, DEER makes system strengths and limitations interpretable and provides diagnostic signals for improvement.

LG-AI-Research LG AI Research
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Dec 19, 2025 1

ResearchQA: Evaluating Scholarly Question Answering at Scale Across 75 Fields with Survey-Mined Questions and Rubrics

Evaluating long-form responses to research queries heavily relies on expert annotators, restricting attention to areas like AI where researchers can conveniently enlist colleagues. Yet, research expertise is widespread: survey articles synthesize knowledge distributed across the literature. We introduce ResearchQA, a resource for evaluating LLM systems by distilling survey articles from 75 research fields into 21K queries and 160K rubric items. Each rubric, derived jointly with queries from survey sections, lists query-specific answer evaluation criteria, i.e., citing papers, making explanations, and describing limitations. Assessments by 31 Ph.D. annotators in 8 fields indicate 96% of queries support Ph.D. information needs and 87% of rubric items should be addressed in system responses by a sentence or more. Using our rubrics, we are able to construct an automatic pairwise judge obtaining 74% agreement with expert judgments. We leverage ResearchQA to analyze competency gaps in 18 systems in over 7.6K pairwise evaluations. No parametric or retrieval-augmented system we evaluate exceeds 70% on covering rubric items, and the highest-ranking agentic system shows 75% coverage. Error analysis reveals that the highest-ranking system fully addresses less than 11% of citation rubric items, 48% of limitation items, and 49% of comparison items. We release our data to facilitate more comprehensive multi-field evaluations.

  • 4 authors
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Aug 30, 2025

Accelerating Social Science Research via Agentic Hypothesization and Experimentation

Data-driven social science research is inherently slow, relying on iterative cycles of observation, hypothesis generation, and experimental validation. While recent data-driven methods promise to accelerate parts of this process, they largely fail to support end-to-end scientific discovery. To address this gap, we introduce EXPERIGEN, an agentic framework that operationalizes end-to-end discovery through a Bayesian optimization inspired two-phase search, in which a Generator proposes candidate hypotheses and an Experimenter evaluates them empirically. Across multiple domains, EXPERIGEN consistently discovers 2-4x more statistically significant hypotheses that are 7-17 percent more predictive than prior approaches, and naturally extends to complex data regimes including multimodal and relational datasets. Beyond statistical performance, hypotheses must be novel, empirically grounded, and actionable to drive real scientific progress. To evaluate these qualities, we conduct an expert review of machine-generated hypotheses, collecting feedback from senior faculty. Among 25 reviewed hypotheses, 88 percent were rated moderately or strongly novel, 70 percent were deemed impactful and worth pursuing, and most demonstrated rigor comparable to senior graduate-level research. Finally, recognizing that ultimate validation requires real-world evidence, we conduct the first A/B test of LLM-generated hypotheses, observing statistically significant results with p less than 1e-6 and a large effect size of 344 percent.

  • 8 authors
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Feb 7

Super Research: Answering Highly Complex Questions with Large Language Models through Super Deep and Super Wide Research

While Large Language Models (LLMs) have demonstrated proficiency in Deep Research or Wide Search, their capacity to solve highly complex questions-those requiring long-horizon planning, massive evidence gathering, and synthesis across heterogeneous sources-remains largely unexplored. We introduce Super Research, a task for complex autonomous research tasks that integrates (i) structured decomposition into a research plan, (ii) super wide retrieval for diverse perspectives, and (iii) super deep investigation to resolve uncertainties through iterative queries. To evaluate this capability, we curated a benchmark of 300 expert-written questions across diverse domains, each requiring up to 100+ retrieval steps and 1,000+ web pages to reconcile conflicting evidence. Super Research produces verifiable reports with fine-grained citations and intermediate artifacts (e.g., outlines and tables) to ensure traceable reasoning. Furthermore, we present a graph-anchored auditing protocol that evaluates Super Research along five dimensions: Coverage, Logical Consistency, Report Utility, Objectivity and Citation Health. While super-complex questions may be infrequent in standard applications, Super Research serves as a critical ceiling evaluation and stress test for LLM capabilities. A model's proficiency within Super Research acts as a powerful proxy for its general research competence; success here suggests the robustness necessary to navigate nearly any subordinate research task. Leaderboard is available at: https://cnsdqd-dyb.github.io/Super-Research-Benchmark/

  • 8 authors
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Mar 2

Transitive Expert Error and Routing Problems in Complex AI Systems

Domain expertise enhances judgment within boundaries but creates systematic vulnerabilities specifically at borders. We term this Transitive Expert Error (TEE), distinct from Dunning-Kruger effects, requiring calibrated expertise as precondition. Mechanisms enabling reliable within-domain judgment become liabilities when structural similarity masks causal divergence. Two core mechanisms operate: structural similarity bias causes experts to overweight surface features (shared vocabulary, patterns, formal structure) while missing causal architecture differences; authority persistence maintains confidence across competence boundaries through social reinforcement and metacognitive failures (experts experience no subjective uncertainty as pattern recognition operates smoothly on familiar-seeming inputs.) These mechanism intensify under three conditions: shared vocabulary masking divergent processes, social pressure for immediate judgment, and delayed feedback. These findings extend to AI routing architectures (MoE systems, multi-model orchestration, tool-using agents, RAG systems) exhibiting routing-induced failures (wrong specialist selected) and coverage-induced failures (no appropriate specialist exists). Both produce a hallucination phenotype: confident, coherent, structurally plausible but causally incorrect outputs at domain boundaries. In human systems where mechanisms are cognitive black boxes; AI architectures make them explicit and addressable. We propose interventions: multi-expert activation with disagreement detection (router level), boundary-aware calibration (specialist level), and coverage gap detection (training level). TEE has detectable signatures (routing patterns, confidence-accuracy dissociations, domain-inappropriate content) enabling monitoring and mitigation. What remains intractable in human cognition becomes addressable through architectural design.

  • 1 authors
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Jan 6

Deep literature reviews: an application of fine-tuned language models to migration research

This paper presents a hybrid framework for literature reviews that augments traditional bibliometric methods with large language models (LLMs). By fine-tuning open-source LLMs, our approach enables scalable extraction of qualitative insights from large volumes of research content, enhancing both the breadth and depth of knowledge synthesis. To improve annotation efficiency and consistency, we introduce an error-focused validation process in which LLMs generate initial labels and human reviewers correct misclassifications. Applying this framework to over 20000 scientific articles about human migration, we demonstrate that a domain-adapted LLM can serve as a "specialist" model - capable of accurately selecting relevant studies, detecting emerging trends, and identifying critical research gaps. Notably, the LLM-assisted review reveals a growing scholarly interest in climate-induced migration. However, existing literature disproportionately centers on a narrow set of environmental hazards (e.g., floods, droughts, sea-level rise, and land degradation), while overlooking others that more directly affect human health and well-being, such as air and water pollution or infectious diseases. This imbalance highlights the need for more comprehensive research that goes beyond physical environmental changes to examine their ecological and societal consequences, particularly in shaping migration as an adaptive response. Overall, our proposed framework demonstrates the potential of fine-tuned LLMs to conduct more efficient, consistent, and insightful literature reviews across disciplines, ultimately accelerating knowledge synthesis and scientific discovery.

  • 3 authors
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Apr 17, 2025

On the limits and opportunities of AI reviewers: Reviewing the reviews of Nature-family papers with 45 expert scientists

With the advancement of AI capabilities, AI reviewers are beginning to be deployed in scientific peer review, yet their capability and credibility remain in question: many scientists simply view them as probabilistic systems without the expertise to evaluate research, while other researchers are more optimistic about their readiness without concrete evidence. Understanding what AI reviewers do well, where they fall short, and what challenges remain is essential. However, existing evaluations of AI reviewers have focused on whether their verdicts match human verdicts (e.g., score alignment, acceptance prediction), which is insufficient to characterize their capabilities and limits. In this paper, we close this gap through a large-scale expert annotation study, in which 45 domain scientists in Physical, Biological, and Health Sciences spent 469 hours rating 2,960 individual criticisms (each targeting one specific aspect of a paper) from human-written and AI-generated reviews of 82 Nature-family papers on correctness, significance, and sufficiency of evidence. On a composite of all three dimensions, a reviewing agent powered by GPT-5.2 scores above each paper's top-rated human reviewer (60.0% vs. 48.2%, p = 0.009), while all three AI reviewers (including Gemini 3.0 Pro and Claude Opus 4.5) exceed the lowest-rated human across every dimension. AI reviewers' accurate criticisms are also more often rated significant and well-evidenced, and surface a distinct 26% of issues no human raises. However, AI reviewers overlap far more than humans do (21% vs. 3% for cross-reviewer pairs), and exhibit 16 recurring weaknesses humans do not share, such as limited subfield knowledge, lack of long context management over multiple files, and overly critical stance on minor issues. Overall, our results position current AI reviewers as complements to, not substitutes for, human reviewers.

Decade of Natural Language Processing in Chronic Pain: A Systematic Review

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

  • 1 authors
·
Dec 19, 2024

Personalized Auto-Research: Towards a True AI Co-Scientist

AI co-scientists that generate hypotheses, retrieve related work, design experiments, execute code, and draft full papers are beginning to change how research is carried out. Despite this rapid progress, state-of-the-art systems remain researcher-agnostic: given a research goal, they optimize novelty, validity, or reviewer score while ignoring the individual scientist who will use the output. This overlooks a fundamental fact about research, namely, that what counts as novel, valuable, or feasible depends on the researcher, including their prior work, methodological repertoire, and the collaborators and communities in which they are embedded. In this work, we introduce the problem of personalized auto-research, which conditions every stage of the research process on a representation of the individual researcher. We argue that personalization is not a convenience layer, but rather the fundamental property that allows an AI system to serve as a genuine co-scientist rather than a generic instrument. To address this problem, we propose a general and flexible framework that threads a graph-grounded researcher context through retrieval, hypothesis search, experimentation, writing, and review. The framework consists of three fundamental components: (i) graph-grounded researcher representations, (ii) personalization across the full research pipeline, and (iii) evaluation grounded in the individual. Notably, we highlight a one-size-fits-all failure mode where distinct researchers issuing the same goal receive essentially the same research, erasing the tacit knowledge through which novel ideas arise. Finally, we discuss fundamental open problems and challenges.

  • 8 authors
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Aug 13 2

Large Language Model Hacking: Quantifying the Hidden Risks of Using LLMs for Text Annotation

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

  • 7 authors
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Sep 10, 2025 3

Is Deep Research Reliable? Misleading Knowledge Induces False Conclusions

Deep Research agents extend LLM-based assistants into long-horizon workflows involving planning, retrieval, evidence synthesis, and report generation, yet their reliability in open information environments remains underexplored. A key concern is whether apparently credible but factually misleading knowledge encountered in such environments can propagate through these workflows and be adopted as false conclusions in final reports. To study this failure mode, we introduce MisKnow-Agent, a framework for constructing and validating misleading knowledge for Deep Research tasks. MisKnow-Agent generates misleading instances with controllable authority levels and styles, yielding 5,933 quality-controlled instances built on DeepResearch Benchmark tasks. Extensive experiments across open-source and closed-source Deep Research agents show that even limited exposure to misleading knowledge can induce false-conclusion adoption in final reports, revealing a broad reliability vulnerability in current Deep Research agents. Although search-enabled verifier models consistently identify the retained instances as misleading during focused corpus validation, the same instances can still be adopted during long-horizon research, revealing a disconnect between focused verification and workflow-level evidence use. Finally, we evaluate pre- and post-research defenses, both individually and in combination, finding that all three configurations mitigate but do not fully prevent false-conclusion adoption. Our findings suggest that reliable Deep Research requires evidence verification and correction capabilities at both the model and framework levels, beyond improvements in planning, retrieval, evidence integration, or report-generation abilities.

  • 4 authors
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Jul 22 2