arXiv subjects

Yuhui Zhang

Publications and source records attributed to Yuhui Zhang.

At least 55 records · Page 3Linked to original sources

arXiv2025

No Tokens Wasted: Leveraging Long Context in Biomedical Vision-Language Models

Embedding vision-language models (VLMs) are typically pretrained with short text windows (<77 tokens), which forces the truncation of long-format captions. Yet, the distribution of biomedical captions from large-scale open source literature reveals that a huge portion of captions far exceed 77 tokens. To this end, we investigate the impact of pretraining on long-format biomedical captions by extending the context length of text encoders in VLMs. We find that longer context (thus, enabling additional supervision provided in long-format captions) correlates with better retrieval and classification performance. Given this finding, we introduce BIOMEDICA-LongCAP, a dataset of 1M image-caption pairs enriched with context-aware descriptions from full-text articles, providing longer and additional textual supervision. Using BIOMEDICA-LongCAP, we train BMC-LongCLIP, a long-context biomedical VLM with a text encoder supporting windows of up to 512 tokens. Our model extends context capacity by 6.6x, reducing token waste from 55% to just 2.2%. On long-caption retrieval benchmarks, BMC-LongCLIP achieves up to +30% absolute gains in Recall@1 and +2% average improvements in classification, while also converging faster than short-context. Our results demonstrate that long-context modeling is a promising direction for advancing biomedical VLMs.

cs.CV↗

arXiv2025

EquiBench: Benchmarking Large Language Models' Reasoning about Program Semantics via Equivalence Checking

As large language models (LLMs) become integral to code-related tasks, a central question emerges: Do LLMs truly understand program semantics? We introduce EquiBench, a new benchmark for evaluating LLMs through equivalence checking, i.e., determining whether two programs produce identical outputs for all possible inputs. Unlike prior code generation benchmarks, this task directly tests a model's ability to reason about program semantics. EquiBench consists of 2400 program pairs across four languages and six categories. These pairs are generated through program analysis, compiler scheduling, and superoptimization, ensuring high-confidence labels, nontrivial difficulty, and full automation. We evaluate 19 state-of-the-art LLMs and find that in the most challenging categories, the best accuracies are 63.8% and 76.2%, only modestly above the 50% random baseline. Further analysis reveals that models often rely on syntactic similarity rather than exhibiting robust reasoning about program semantics, highlighting current limitations. Our code and dataset are publicly available at https://github.com/Anjiang-Wei/equibench

cs.LG↗

arXiv2025

Temporal Preference Optimization for Long-Form Video Understanding

Despite significant advancements in video large multimodal models (video-LMMs), achieving effective temporal grounding in long-form videos remains a challenge for existing models. To address this limitation, we propose Temporal Preference Optimization (TPO), a novel post-training framework designed to enhance the temporal grounding capabilities of video-LMMs through preference learning. TPO adopts a self-training approach that enables models to differentiate between well-grounded and less accurate temporal responses by leveraging curated preference datasets at two granularities: localized temporal grounding, which focuses on specific video segments, and comprehensive temporal grounding, which captures extended temporal dependencies across entire video sequences. By optimizing on these preference datasets, TPO significantly enhances temporal understanding while reducing reliance on manually annotated data. Extensive experiments on three long-form video understanding benchmarks--LongVideoBench, MLVU, and Video-MME--demonstrate the effectiveness of TPO across two state-of-the-art video-LMMs. Notably, LLaVA-Video-TPO establishes itself as the leading 7B model on the Video-MME benchmark, underscoring the potential of TPO as a scalable and efficient solution for advancing temporal reasoning in long-form video understanding. Project page: https://ruili33.github.io/tpo_website.

cs.CV↗

arXiv2025

Closing the Modality Gap for Mixed Modality Search

Mixed modality search -- retrieving information across a heterogeneous corpus composed of images, texts, and multimodal documents -- is an important yet underexplored real-world application. In this work, we investigate how contrastive vision-language models, such as CLIP, perform on the mixed modality search task. Our analysis reveals a critical limitation: these models exhibit a pronounced modality gap in the embedding space, where image and text embeddings form distinct clusters, leading to intra-modal ranking bias and inter-modal fusion failure. To address this issue, we propose GR-CLIP, a lightweight post-hoc calibration method that removes the modality gap in CLIP's embedding space. Evaluated on MixBench -- the first benchmark specifically designed for mixed modality search -- GR-CLIP improves NDCG@10 by up to 26 percentage points over CLIP, surpasses recent vision-language generative embedding models by 4 percentage points, while using 75x less compute.

cs.CV↗

arXiv2025

AttentionDrag: Exploiting Latent Correlation Knowledge in Pre-trained Diffusion Models for Image Editing

Traditional point-based image editing methods rely on iterative latent optimization or geometric transformations, which are either inefficient in their processing or fail to capture the semantic relationships within the image. These methods often overlook the powerful yet underutilized image editing capabilities inherent in pre-trained diffusion models. In this work, we propose a novel one-step point-based image editing method, named AttentionDrag, which leverages the inherent latent knowledge and feature correlations within pre-trained diffusion models for image editing tasks. This framework enables semantic consistency and high-quality manipulation without the need for extensive re-optimization or retraining. Specifically, we reutilize the latent correlations knowledge learned by the self-attention mechanism in the U-Net module during the DDIM inversion process to automatically identify and adjust relevant image regions, ensuring semantic validity and consistency. Additionally, AttentionDrag adaptively generates masks to guide the editing process, enabling precise and context-aware modifications with friendly interaction. Our results demonstrate a performance that surpasses most state-of-the-art methods with significantly faster speeds, showing a more efficient and semantically coherent solution for point-based image editing tasks.

cs.CV↗

arXiv2025

CellFlux: Simulating Cellular Morphology Changes via Flow Matching

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

q-bio.QM↗

arXiv2025

Can Large Language Models Match the Conclusions of Systematic Reviews?

Systematic reviews (SR), in which experts summarize and analyze evidence across individual studies to provide insights on a specialized topic, are a cornerstone for evidence-based clinical decision-making, research, and policy. Given the exponential growth of scientific articles, there is growing interest in using large language models (LLMs) to automate SR generation. However, the ability of LLMs to critically assess evidence and reason across multiple documents to provide recommendations at the same proficiency as domain experts remains poorly characterized. We therefore ask: Can LLMs match the conclusions of systematic reviews written by clinical experts when given access to the same studies? To explore this question, we present MedEvidence, a benchmark pairing findings from 100 SRs with the studies they are based on. We benchmark 24 LLMs on MedEvidence, including reasoning, non-reasoning, medical specialist, and models across varying sizes (from 7B-700B). Through our systematic evaluation, we find that reasoning does not necessarily improve performance, larger models do not consistently yield greater gains, and knowledge-based fine-tuning degrades accuracy on MedEvidence. Instead, most models exhibit similar behavior: performance tends to degrade as token length increases, their responses show overconfidence, and, contrary to human experts, all models show a lack of scientific skepticism toward low-quality findings. These results suggest that more work is still required before LLMs can reliably match the observations from expert-conducted SRs, even though these systems are already deployed and being used by clinicians. We release our codebase and benchmark to the broader research community to further investigate LLM-based SR systems.

cs.CL↗

arXiv2025

NegVQA: Can Vision Language Models Understand Negation?

Negation is a fundamental linguistic phenomenon that can entirely reverse the meaning of a sentence. As vision language models (VLMs) continue to advance and are deployed in high-stakes applications, assessing their ability to comprehend negation becomes essential. To address this, we introduce NegVQA, a visual question answering (VQA) benchmark consisting of 7,379 two-choice questions covering diverse negation scenarios and image-question distributions. We construct NegVQA by leveraging large language models to generate negated versions of questions from existing VQA datasets. Evaluating 20 state-of-the-art VLMs across seven model families, we find that these models struggle significantly with negation, exhibiting a substantial performance drop compared to their responses to the original questions. Furthermore, we uncover a U-shaped scaling trend, where increasing model size initially degrades performance on NegVQA before leading to improvements. Our benchmark reveals critical gaps in VLMs' negation understanding and offers insights into future VLM development. Project page available at https://yuhui-zh15.github.io/NegVQA/.

cs.CL↗

arXiv2025

TULiP: Test-time Uncertainty Estimation via Linearization and Weight Perturbation

A reliable uncertainty estimation method is the foundation of many modern out-of-distribution (OOD) detectors, which are critical for safe deployments of deep learning models in the open world. In this work, we propose TULiP, a theoretically-driven post-hoc uncertainty estimator for OOD detection. Our approach considers a hypothetical perturbation applied to the network before convergence. Based on linearized training dynamics, we bound the effect of such perturbation, resulting in an uncertainty score computable by perturbing model parameters. Ultimately, our approach computes uncertainty from a set of sampled predictions. We visualize our bound on synthetic regression and classification datasets. Furthermore, we demonstrate the effectiveness of TULiP using large-scale OOD detection benchmarks for image classification. Our method exhibits state-of-the-art performance, particularly for near-distribution samples.

stat.ML↗

arXiv2025

A 2D Semantic-Aware Position Encoding for Vision Transformers

Vision transformers have demonstrated significant advantages in computer vision tasks due to their ability to capture long-range dependencies and contextual relationships through self-attention. However, existing position encoding techniques, which are largely borrowed from natural language processing, fail to effectively capture semantic-aware positional relationships between image patches. Traditional approaches like absolute position encoding and relative position encoding primarily focus on 1D linear position relationship, often neglecting the semantic similarity between distant yet contextually related patches. These limitations hinder model generalization, translation equivariance, and the ability to effectively handle repetitive or structured patterns in images. In this paper, we propose 2-Dimensional Semantic-Aware Position Encoding ($\text{SaPE}^2$), a novel position encoding method with semantic awareness that dynamically adapts position representations by leveraging local content instead of fixed linear position relationship or spatial coordinates. Our method enhances the model's ability to generalize across varying image resolutions and scales, improves translation equivariance, and better aggregates features for visually similar but spatially distant patches. By integrating $\text{SaPE}^2$ into vision transformers, we bridge the gap between position encoding and perceptual similarity, thereby improving performance on computer vision tasks.

cs.CV↗

arXiv2025

Comet: Accelerating Private Inference for Large Language Model by Predicting Activation Sparsity

With the growing use of large language models (LLMs) hosted on cloud platforms to offer inference services, privacy concerns about the potential leakage of sensitive information are escalating. Secure multi-party computation (MPC) is a promising solution to protect the privacy in LLM inference. However, MPC requires frequent inter-server communication, causing high performance overhead. Inspired by the prevalent activation sparsity of LLMs, where most neuron are not activated after non-linear activation functions, we propose an efficient private inference system, Comet. This system employs an accurate and fast predictor to predict the sparsity distribution of activation function output. Additionally, we introduce a new private inference protocol. It efficiently and securely avoids computations involving zero values by exploiting the spatial locality of the predicted sparse distribution. While this computation-avoidance approach impacts the spatiotemporal continuity of KV cache entries, we address this challenge with a low-communication overhead cache refilling strategy that merges miss requests and incorporates a prefetching mechanism. Finally, we evaluate Comet on four common LLMs and compare it with six state-of-the-art private inference systems. Comet achieves a 1.87x-2.63x speedup and a 1.94x-2.64x communication reduction.

cs.CR↗

arXiv2025

Automated Generation of Challenging Multiple-Choice Questions for Vision Language Model Evaluation

The rapid development of vision language models (VLMs) demands rigorous and reliable evaluation. However, current visual question answering (VQA) benchmarks often depend on open-ended questions, making accurate evaluation difficult due to the variability in natural language responses. To address this, we introduce AutoConverter, an agentic framework that automatically converts these open-ended questions into multiple-choice format, enabling objective evaluation while reducing the costly multiple-choice question creation process. Our experiments demonstrate that AutoConverter can generate correct and challenging multiple-choice questions, with VLMs demonstrating consistently similar or lower accuracy on these questions compared to human-created ones. Using AutoConverter, we construct VMCBench, a benchmark created by transforming 20 existing VQA datasets into a unified multiple-choice format, totaling 9,018 questions. We comprehensively evaluate 33 state-of-the-art VLMs on VMCBench, setting a new standard for scalable, consistent, and reproducible VLM evaluation.

cs.CV↗

arXiv2025

DataLab: A Unified Platform for LLM-Powered Business Intelligence

Business intelligence (BI) transforms large volumes of data within modern organizations into actionable insights for informed decision-making. Recently, large language model (LLM)-based agents have streamlined the BI workflow by automatically performing task planning, reasoning, and actions in executable environments based on natural language (NL) queries. However, existing approaches primarily focus on individual BI tasks such as NL2SQL and NL2VIS. The fragmentation of tasks across different data roles and tools lead to inefficiencies and potential errors due to the iterative and collaborative nature of BI. In this paper, we introduce DataLab, a unified BI platform that integrates a one-stop LLM-based agent framework with an augmented computational notebook interface. DataLab supports various BI tasks for different data roles in data preparation, analysis, and visualization by seamlessly combining LLM assistance with user customization within a single environment. To achieve this unification, we design a domain knowledge incorporation module tailored for enterprise-specific BI tasks, an inter-agent communication mechanism to facilitate information sharing across the BI workflow, and a cell-based context management strategy to enhance context utilization efficiency in BI notebooks. Extensive experiments demonstrate that DataLab achieves state-of-the-art performance on various BI tasks across popular research benchmarks. Moreover, DataLab maintains high effectiveness and efficiency on real-world datasets from Tencent, achieving up to a 58.58% increase in accuracy and a 61.65% reduction in token cost on enterprise-specific BI tasks.

cs.DB↗

arXiv2025

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset. Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally. On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

cs.CV↗

arXiv2025

MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology. Despite recent advances in multimodal large language models (MLLMs) for AI-assisted research, existing multimodal reasoning benchmarks only target up to college-level difficulty, while research-level benchmarks emphasize lower-level perception, falling short of the complex multimodal reasoning needed for scientific discovery. To bridge this gap, we introduce MicroVQA, a visual-question answering (VQA) benchmark designed to assess three reasoning capabilities vital in research workflows: expert image understanding, hypothesis generation, and experiment proposal. MicroVQA consists of 1,042 multiple-choice questions (MCQs) curated by biology experts across diverse microscopy modalities, ensuring VQA samples represent real scientific practice. In constructing the benchmark, we find that standard MCQ generation methods induce language shortcuts, motivating a new two-stage pipeline: an optimized LLM prompt structures question-answer pairs into MCQs; then, an agent-based `RefineBot' updates them to remove shortcuts. Benchmarking on state-of-the-art MLLMs reveal a peak performance of 53\%; models with smaller LLMs only slightly underperform top models, suggesting that language-based reasoning is less challenging than multimodal reasoning; and tuning with scientific articles enhances performance. Expert analysis of chain-of-thought responses shows that perception errors are the most frequent, followed by knowledge errors and then overgeneralization errors. These insights highlight the challenges in multimodal scientific reasoning, showing MicroVQA is a valuable resource advancing AI-driven biomedical research. MicroVQA is available at https://huggingface.co/datasets/jmhb/microvqa, and project page at https://jmhb0.github.io/microvqa.

cs.CV↗

arXiv2025

Video Action Differencing

How do two individuals differ when performing the same action? In this work, we introduce Video Action Differencing (VidDiff), the novel task of identifying subtle differences between videos of the same action, which has many applications, such as coaching and skill learning. To enable development on this new task, we first create VidDiffBench, a benchmark dataset containing 549 video pairs, with human annotations of 4,469 fine-grained action differences and 2,075 localization timestamps indicating where these differences occur. Our experiments demonstrate that VidDiffBench poses a significant challenge for state-of-the-art large multimodal models (LMMs), such as GPT-4o and Qwen2-VL. By analyzing failure cases of LMMs on VidDiffBench, we highlight two key challenges for this task: localizing relevant sub-actions over two videos and fine-grained frame comparison. To overcome these, we propose the VidDiff method, an agentic workflow that breaks the task into three stages: action difference proposal, keyframe localization, and frame differencing, each stage utilizing specialized foundation models. To encourage future research in this new task, we release the benchmark at https://huggingface.co/datasets/jmhb/VidDiffBench and code at http://jmhb0.github.io/viddiff.

cs.CV↗

arXiv2024

Why are Visually-Grounded Language Models Bad at Image Classification?

Image classification is one of the most fundamental capabilities of machine vision intelligence. In this work, we revisit the image classification task using visually-grounded language models (VLMs) such as GPT-4V and LLaVA. We find that existing proprietary and public VLMs, despite often using CLIP as a vision encoder and having many more parameters, significantly underperform CLIP on standard image classification benchmarks like ImageNet. To understand the reason, we explore several hypotheses concerning the inference algorithms, training objectives, and data processing in VLMs. Our analysis reveals that the primary cause is data-related: critical information for image classification is encoded in the VLM's latent space but can only be effectively decoded with enough training data. Specifically, there is a strong correlation between the frequency of class exposure during VLM training and instruction-tuning and the VLM's performance in those classes; when trained with sufficient data, VLMs can match the accuracy of state-of-the-art classification models. Based on these findings, we enhance a VLM by integrating classification-focused datasets into its training, and demonstrate that the enhanced classification performance of the VLM transfers to its general capabilities, resulting in an improvement of 11.8% on the newly collected ImageWikiQA dataset.

cs.CV↗

arXiv2024

Pre-trained Language Models Do Not Help Auto-regressive Text-to-Image Generation

Recent advances in image tokenizers, such as VQ-VAE, have enabled text-to-image generation using auto-regressive methods, similar to language modeling. However, these methods have yet to leverage pre-trained language models, despite their adaptability to various downstream tasks. In this work, we explore this gap by adapting a pre-trained language model for auto-regressive text-to-image generation, and find that pre-trained language models offer limited help. We provide a two-fold explanation by analyzing tokens from each modality. First, we demonstrate that image tokens possess significantly different semantics compared to text tokens, rendering pre-trained language models no more effective in modeling them than randomly initialized ones. Second, the text tokens in the image-text datasets are too simple compared to normal language model pre-training data, which causes the catastrophic degradation of language models' capability.

cs.CV↗