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 here, project here.

The development of vision-language models (VLMs) is driven by large-scale and diverse multi-modal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are limited 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 additionally provided.We demonstrate the utility and accessibility of our resource by releasing BMC-CLIP, a suite of CLIP-style models continuously pre-trained on 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 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively) and stronger image-text retrieval while using 10x less compute. To foster reproducibility and collaboration, we release our codebase1,2and dataset3to the broader research community.

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 VM-CBench, setting a new standard for scalable, consistent, and reproducible VLM evaluation.

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 numerous 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 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 the 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 and code.

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/.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers’ efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs’ perception and cognition capabilities in biological image understanding. To address this gap, we introduce Micro-Bench, an expert-curated benchmark encompassing 24 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on Micro-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release Micro-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

This paper describes an experimental modular distributed manipulation system upon which one can implement a variety of control schemes. We have shown elsewhere that when one includes the nonsmooth effects of friction into a model of distributed manipulation, nonsmooth feedback laws must generally be used to control distributed manipulators. We summarize results obtained with this experimental system that confirm the validity of control schemes proposed by the authors in recent papers. We describe the control algorithms in some detail and include specifics of the experimental set-up and experimental results.