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Jan 6

AutoEval-Video: An Automatic Benchmark for Assessing Large Vision Language Models in Open-Ended Video Question Answering

We propose a novel and challenging benchmark, AutoEval-Video, to comprehensively evaluate large vision-language models in open-ended video question answering. The comprehensiveness of AutoEval-Video is demonstrated in two aspects: 1) AutoEval-Video constructs open-ended video-questions across 9 skill dimensions, addressing capabilities of perception, comprehension, and generation. 2) AutoEval-Video contains newly collected videos that cover over 40 distinct themes. To efficiently evaluate responses to the open-ended questions, we employ an LLM-based evaluation approach, but instead of merely providing a reference answer, we annotate unique evaluation rules for every single instance (video-question pair). To maximize the robustness of these rules, we develop a novel adversarial annotation mechanism. By using instance-specific rules as prompt, GPT-4, as an automatic evaluator, can achieve a stable evaluation accuracy of around 97.0\%, comparable to the 94.9\% - 97.5\% accuracy of a human evaluator. Furthermore, we assess the performance of eight large vision-language models on AutoEval-Video. Among them, GPT-4V(ision) significantly outperforms other models, achieving an accuracy of 32.2\%. However, there is still substantial room for improvement compared to human accuracy of 72.8\%. By conducting an extensive case study, we uncover several drawbacks of GPT-4V, such as limited temporal and dynamic comprehension, and overly general responses. Code is available at https://github.com/Xiuyuan-Chen/AutoEval-Video{magentahttps://github.com/Xiuyuan-Chen/AutoEval-Video}.

  • 4 authors
·
Nov 24, 2023

R2RGEN: Real-to-Real 3D Data Generation for Spatially Generalized Manipulation

Towards the aim of generalized robotic manipulation, spatial generalization is the most fundamental capability that requires the policy to work robustly under different spatial distribution of objects, environment and agent itself. To achieve this, substantial human demonstrations need to be collected to cover different spatial configurations for training a generalized visuomotor policy via imitation learning. Prior works explore a promising direction that leverages data generation to acquire abundant spatially diverse data from minimal source demonstrations. However, most approaches face significant sim-to-real gap and are often limited to constrained settings, such as fixed-base scenarios and predefined camera viewpoints. In this paper, we propose a real-to-real 3D data generation framework (R2RGen) that directly augments the pointcloud observation-action pairs to generate real-world data. R2RGen is simulator- and rendering-free, thus being efficient and plug-and-play. Specifically, given a single source demonstration, we introduce an annotation mechanism for fine-grained parsing of scene and trajectory. A group-wise augmentation strategy is proposed to handle complex multi-object compositions and diverse task constraints. We further present camera-aware processing to align the distribution of generated data with real-world 3D sensor. Empirically, R2RGen substantially enhances data efficiency on extensive experiments and demonstrates strong potential for scaling and application on mobile manipulation.

  • 7 authors
·
Oct 9, 2025 2

Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?

Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair - generating structurally valid molecular alternatives with reduced toxicity - has not yet been systematically defined or benchmarked. To fill this gap, we introduce ToxiMol, the first benchmark task for general-purpose Multimodal Large Language Models (MLLMs) focused on molecular toxicity repair. We construct a standardized dataset covering 11 primary tasks and 560 representative toxic molecules spanning diverse mechanisms and granularities. We design a prompt annotation pipeline with mechanism-aware and task-adaptive capabilities, informed by expert toxicological knowledge. In parallel, we propose an automated evaluation framework, ToxiEval, which integrates toxicity endpoint prediction, synthetic accessibility, drug-likeness, and structural similarity into a high-throughput evaluation chain for repair success. We systematically assess nearly 30 mainstream general-purpose MLLMs and design multiple ablation studies to analyze key factors such as evaluation criteria, candidate diversity, and failure attribution. Experimental results show that although current MLLMs still face significant challenges on this task, they begin to demonstrate promising capabilities in toxicity understanding, semantic constraint adherence, and structure-aware molecule editing.

  • 8 authors
·
Jun 12, 2025

I-MPN: Inductive Message Passing Network for Efficient Human-in-the-Loop Annotation of Mobile Eye Tracking Data

Comprehending how humans process visual information in dynamic settings is crucial for psychology and designing user-centered interactions. While mobile eye-tracking systems combining egocentric video and gaze signals can offer valuable insights, manual analysis of these recordings is time-intensive. In this work, we present a novel human-centered learning algorithm designed for automated object recognition within mobile eye-tracking settings. Our approach seamlessly integrates an object detector with a spatial relation-aware inductive message-passing network (I-MPN), harnessing node profile information and capturing object correlations. Such mechanisms enable us to learn embedding functions capable of generalizing to new object angle views, facilitating rapid adaptation and efficient reasoning in dynamic contexts as users navigate their environment. Through experiments conducted on three distinct video sequences, our interactive-based method showcases significant performance improvements over fixed training/testing algorithms, even when trained on considerably smaller annotated samples collected through user feedback. Furthermore, we demonstrate exceptional efficiency in data annotation processes and surpass prior interactive methods that use complete object detectors, combine detectors with convolutional networks, or employ interactive video segmentation.

  • 8 authors
·
Jun 10, 2024

Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

  • 4 authors
·
Dec 3, 2024

Graph-Based Captioning: Enhancing Visual Descriptions by Interconnecting Region Captions

Humans describe complex scenes with compositionality, using simple text descriptions enriched with links and relationships. While vision-language research has aimed to develop models with compositional understanding capabilities, this is not reflected yet in existing datasets which, for the most part, still use plain text to describe images. In this work, we propose a new annotation strategy, graph-based captioning (GBC) that describes an image using a labelled graph structure, with nodes of various types. The nodes in GBC are created using, in a first stage, object detection and dense captioning tools nested recursively to uncover and describe entity nodes, further linked together in a second stage by highlighting, using new types of nodes, compositions and relations among entities. Since all GBC nodes hold plain text descriptions, GBC retains the flexibility found in natural language, but can also encode hierarchical information in its edges. We demonstrate that GBC can be produced automatically, using off-the-shelf multimodal LLMs and open-vocabulary detection models, by building a new dataset, GBC10M, gathering GBC annotations for about 10M images of the CC12M dataset. We use GBC10M to showcase the wealth of node captions uncovered by GBC, as measured with CLIP training. We show that using GBC nodes' annotations -- notably those stored in composition and relation nodes -- results in significant performance boost on downstream models when compared to other dataset formats. To further explore the opportunities provided by GBC, we also propose a new attention mechanism that can leverage the entire GBC graph, with encouraging experimental results that show the extra benefits of incorporating the graph structure. Our datasets are released at https://huggingface.co/graph-based-captions.

  • 10 authors
·
Jul 9, 2024 1

Towards Alignment-Centric Paradigm: A Survey of Instruction Tuning in Large Language Models

Instruction tuning is a pivotal technique for aligning large language models (LLMs) with human intentions, safety constraints, and domain-specific requirements. This survey provides a comprehensive overview of the full pipeline, encompassing (i) data collection methodologies, (ii) full-parameter and parameter-efficient fine-tuning strategies, and (iii) evaluation protocols. We categorized data construction into three major paradigms: expert annotation, distillation from larger models, and self-improvement mechanisms, each offering distinct trade-offs between quality, scalability, and resource cost. Fine-tuning techniques range from conventional supervised training to lightweight approaches, such as low-rank adaptation (LoRA) and prefix tuning, with a focus on computational efficiency and model reusability. We further examine the challenges of evaluating faithfulness, utility, and safety across multilingual and multimodal scenarios, highlighting the emergence of domain-specific benchmarks in healthcare, legal, and financial applications. Finally, we discuss promising directions for automated data generation, adaptive optimization, and robust evaluation frameworks, arguing that a closer integration of data, algorithms, and human feedback is essential for advancing instruction-tuned LLMs. This survey aims to serve as a practical reference for researchers and practitioners seeking to design LLMs that are both effective and reliably aligned with human intentions.

  • 6 authors
·
Aug 23, 2025

PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

  • 12 authors
·
Jul 7, 2025 1

BTL-UI: Blink-Think-Link Reasoning Model for GUI Agent

In the field of AI-driven human-GUI interaction automation, while rapid advances in multimodal large language models and reinforcement fine-tuning techniques have yielded remarkable progress, a fundamental challenge persists: their interaction logic significantly deviates from natural human-GUI communication patterns. To fill this gap, we propose "Blink-Think-Link" (BTL), a brain-inspired framework for human-GUI interaction that mimics the human cognitive process between users and graphical interfaces. The system decomposes interactions into three biologically plausible phases: (1) Blink - rapid detection and attention to relevant screen areas, analogous to saccadic eye movements; (2) Think - higher-level reasoning and decision-making, mirroring cognitive planning; and (3) Link - generation of executable commands for precise motor control, emulating human action selection mechanisms. Additionally, we introduce two key technical innovations for the BTL framework: (1) Blink Data Generation - an automated annotation pipeline specifically optimized for blink data, and (2) BTL Reward -- the first rule-based reward mechanism that enables reinforcement learning driven by both process and outcome. Building upon this framework, we develop a GUI agent model named BTL-UI, which demonstrates consistent state-of-the-art performance across both static GUI understanding and dynamic interaction tasks in comprehensive benchmarks. These results provide conclusive empirical validation of the framework's efficacy in developing advanced GUI Agents.

  • 11 authors
·
Sep 19, 2025 3

SAM2S: Segment Anything in Surgical Videos via Semantic Long-term Tracking

Surgical video segmentation is crucial for computer-assisted surgery, enabling precise localization and tracking of instruments and tissues. Interactive Video Object Segmentation (iVOS) models such as Segment Anything Model 2 (SAM2) provide prompt-based flexibility beyond methods with predefined categories, but face challenges in surgical scenarios due to the domain gap and limited long-term tracking. To address these limitations, we construct SA-SV, the largest surgical iVOS benchmark with instance-level spatio-temporal annotations (masklets) spanning eight procedure types (61k frames, 1.6k masklets), enabling comprehensive development and evaluation for long-term tracking and zero-shot generalization. Building on SA-SV, we propose SAM2S, a foundation model enhancing SAM2 for Surgical iVOS through: (1) DiveMem, a trainable diverse memory mechanism for robust long-term tracking; (2) temporal semantic learning for instrument understanding; and (3) ambiguity-resilient learning to mitigate annotation inconsistencies across multi-source datasets. Extensive experiments demonstrate that fine-tuning on SA-SV enables substantial performance gains, with SAM2 improving by 12.99 average J\&F over vanilla SAM2. SAM2S further advances performance to 80.42 average J\&F, surpassing vanilla and fine-tuned SAM2 by 17.10 and 4.11 points respectively, while maintaining 68 FPS real-time inference and strong zero-shot generalization. Code and dataset will be released at https://jinlab-imvr.github.io/SAM2S.

MagicGUI: A Foundational Mobile GUI Agent with Scalable Data Pipeline and Reinforcement Fine-tuning

This paper presents MagicGUI, a foundational mobile GUI agent designed to address critical challenges in perception, grounding, and reasoning within real-world mobile GUI environments. The framework is underpinned by following six key components: (1) a comprehensive and accurate dataset, constructed via the scalable GUI Data Pipeline, which aggregates the largest and most diverse GUI-centric multimodal data to date from open-source repositories, automated crawling, and targeted manual annotation; (2) enhanced perception and grounding capabilities, facilitating fine-grained multimodal alignment for UI element referencing, grounding, and screen comprehension; (3) a comprehensive and unified action space, encompassing both fundamental UI operations and complex interactive intents to support human-agent interactions; (4) planning-oriented reasoning mechanisms that enable the model to decompose complex user instructions into sequential actions with explicit intermediate meta-paln reasoning; (5) an iterative two-stage training procedure, combining large-scale continue pre-training on 7.8M samples with reinforcement fine-tuning utilizing a spatially enhanced composite reward and dual filtering strategy; and (6) competitive performance on both the proprietary Magic-RICH benchmark and over a dozen public benchmarks, achieving superior performance across GUI perception and agent tasks, while demonstrating robust generalization and real-world deployment potential in practical mobile GUI scenarios, as detailed in Figure 1.

  • 24 authors
·
Jul 19, 2025

Unveiling the Mechanisms of Explicit CoT Training: How Chain-of-Thought Enhances Reasoning Generalization

Training large language models (LLMs) with high-quality Chain-of-Thought (CoT) annotations has become a widely adopted strategy due to its significant enhancement of reasoning capabilities. To fully comprehend this approach, two questions naturally arise: (Q1) What advantages does training with CoT offer compared to training without CoT? (Q2) If there are advantages, what are the underlying mechanisms of explicit CoT training? Analyzing the advantages and mechanisms of CoT training is challenging due to the many factors involved. To address this, we conduct a detailed analysis using clear and controllable data distributions and, for the first time, reveal that CoT training offers the following advantages: (1) Training with CoT markedly improves reasoning generalization, extending it from in-distribution (ID) to both ID and out-of-distribution (OOD) scenarios, while also speeding up convergence; (2) Even when training with CoT includes a certain range of erroneous reasoning steps, it still enables the model to learn reasoning patterns, leading to systematic generalization. We further explore the underlying mechanisms from a circuit perspective: (1) The data distribution (e.g., ratio lambda and pattern) plays a crucial role in influencing the model's systematic generalization; (2) CoT training (with two-hop facts) internalizes reasoning into a two-stage generalizing circuit, where the number of stages corresponds to the explicit reasoning steps during training. Our findings elucidate the mechanisms underlying explicit CoT training and offer critical insights into tuning strategies for LLMs to achieve robust generalization.

  • 4 authors
·
Feb 7, 2025

VMBench: A Benchmark for Perception-Aligned Video Motion Generation

Video generation has advanced rapidly, improving evaluation methods, yet assessing video's motion remains a major challenge. Specifically, there are two key issues: 1) current motion metrics do not fully align with human perceptions; 2) the existing motion prompts are limited. Based on these findings, we introduce VMBench--a comprehensive Video Motion Benchmark that has perception-aligned motion metrics and features the most diverse types of motion. VMBench has several appealing properties: 1) Perception-Driven Motion Evaluation Metrics, we identify five dimensions based on human perception in motion video assessment and develop fine-grained evaluation metrics, providing deeper insights into models' strengths and weaknesses in motion quality. 2) Meta-Guided Motion Prompt Generation, a structured method that extracts meta-information, generates diverse motion prompts with LLMs, and refines them through human-AI validation, resulting in a multi-level prompt library covering six key dynamic scene dimensions. 3) Human-Aligned Validation Mechanism, we provide human preference annotations to validate our benchmarks, with our metrics achieving an average 35.3% improvement in Spearman's correlation over baseline methods. This is the first time that the quality of motion in videos has been evaluated from the perspective of human perception alignment. Additionally, we will soon release VMBench at https://github.com/GD-AIGC/VMBench, setting a new standard for evaluating and advancing motion generation models.

  • 10 authors
·
Mar 13, 2025

PyFi: Toward Pyramid-like Financial Image Understanding for VLMs via Adversarial Agents

This paper proposes PyFi, a novel framework for pyramid-like financial image understanding that enables vision language models (VLMs) to reason through question chains in a progressive, simple-to-complex manner. At the core of PyFi is PyFi-600K, a dataset comprising 600K financial question-answer pairs organized into a reasoning pyramid: questions at the base require only basic perception, while those toward the apex demand increasing levels of capability in financial visual understanding and expertise. This data is scalable because it is synthesized without human annotations, using PyFi-adv, a multi-agent adversarial mechanism under the Monte Carlo Tree Search (MCTS) paradigm, in which, for each image, a challenger agent competes with a solver agent by generating question chains that progressively probe deeper capability levels in financial visual reasoning. Leveraging this dataset, we present fine-grained, hierarchical, and comprehensive evaluations of advanced VLMs in the financial domain. Moreover, fine-tuning Qwen2.5-VL-3B and Qwen2.5-VL-7B on the pyramid-structured question chains enables these models to answer complex financial questions by decomposing them into sub-questions with gradually increasing reasoning demands, yielding average accuracy improvements of 19.52% and 8.06%, respectively, on the dataset. All resources of code, dataset and models are available at: https://github.com/AgenticFinLab/PyFi .

  • 3 authors
·
Dec 11, 2025

SASVi -- Segment Any Surgical Video

Purpose: Foundation models, trained on multitudes of public datasets, often require additional fine-tuning or re-prompting mechanisms to be applied to visually distinct target domains such as surgical videos. Further, without domain knowledge, they cannot model the specific semantics of the target domain. Hence, when applied to surgical video segmentation, they fail to generalise to sections where previously tracked objects leave the scene or new objects enter. Methods: We propose SASVi, a novel re-prompting mechanism based on a frame-wise Mask R-CNN Overseer model, which is trained on a minimal amount of scarcely available annotations for the target domain. This model automatically re-prompts the foundation model SAM2 when the scene constellation changes, allowing for temporally smooth and complete segmentation of full surgical videos. Results: Re-prompting based on our Overseer model significantly improves the temporal consistency of surgical video segmentation compared to similar prompting techniques and especially frame-wise segmentation, which neglects temporal information, by at least 1.5%. Our proposed approach allows us to successfully deploy SAM2 to surgical videos, which we quantitatively and qualitatively demonstrate for three different cholecystectomy and cataract surgery datasets. Conclusion: SASVi can serve as a new baseline for smooth and temporally consistent segmentation of surgical videos with scarcely available annotation data. Our method allows us to leverage scarce annotations and obtain complete annotations for full videos of the large-scale counterpart datasets. We make those annotations publicly available, providing extensive annotation data for the future development of surgical data science models.

  • 4 authors
·
Feb 11, 2025

Zooming In on Fakes: A Novel Dataset for Localized AI-Generated Image Detection with Forgery Amplification Approach

The rise of AI-generated image editing tools has made localized forgeries increasingly realistic, posing challenges for visual content integrity. Although recent efforts have explored localized AIGC detection, existing datasets predominantly focus on object-level forgeries while overlooking broader scene edits in regions such as sky or ground. To address these limitations, we introduce BR-Gen, a large-scale dataset of 150,000 locally forged images with diverse scene-aware annotations, which are based on semantic calibration to ensure high-quality samples. BR-Gen is constructed through a fully automated Perception-Creation-Evaluation pipeline to ensure semantic coherence and visual realism. In addition, we further propose NFA-ViT, a Noise-guided Forgery Amplification Vision Transformer that enhances the detection of localized forgeries by amplifying forgery-related features across the entire image. NFA-ViT mines heterogeneous regions in images, i.e., potential edited areas, by noise fingerprints. Subsequently, attention mechanism is introduced to compel the interaction between normal and abnormal features, thereby propagating the generalization traces throughout the entire image, allowing subtle forgeries to influence a broader context and improving overall detection robustness. Extensive experiments demonstrate that BR-Gen constructs entirely new scenarios that are not covered by existing methods. Take a step further, NFA-ViT outperforms existing methods on BR-Gen and generalizes well across current benchmarks. All data and codes are available at https://github.com/clpbc/BR-Gen.

  • 8 authors
·
Apr 16, 2025

TRivia: Self-supervised Fine-tuning of Vision-Language Models for Table Recognition

Table recognition (TR) aims to transform table images into semi-structured representations such as HTML or Markdown. As a core component of document parsing, TR has long relied on supervised learning, with recent efforts dominated by fine-tuning vision-language models (VLMs) using labeled data. While VLMs have brought TR to the next level, pushing performance further demands large-scale labeled data that is costly to obtain. Consequently, although proprietary models have continuously pushed the performance boundary, open-source models, often trained with limited resources and, in practice, the only viable option for many due to privacy regulations, still lag far behind. To bridge this gap, we introduce TRivia, a self-supervised fine-tuning method that enables pretrained VLMs to learn TR directly from unlabeled table images in the wild. Built upon Group Relative Policy Optimization, TRivia automatically identifies unlabeled samples that most effectively facilitate learning and eliminates the need for human annotations through a question-answering-based reward mechanism. An attention-guided module generates diverse questions for each table image, and the ability to interpret the recognition results and answer them correctly provides feedback to optimize the TR model. This closed-loop process allows the TR model to autonomously learn to recognize, structure, and reason over tables without labeled data. Leveraging this pipeline, we present TRivia-3B, an open-sourced, compact, and state-of-the-art TR model that surpasses existing systems (e.g., Gemini 2.5 Pro, MinerU2.5) on three popular benchmarks. Model and code are released at: https://github.com/opendatalab/TRivia

  • 16 authors
·
Nov 30, 2025 2