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.

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.

Large pre-trained models, or foundation models, have shown impressive performance when adapted to a variety of downstream tasks, often out-performing specialized models. Hypernetworks, neural networks that generate some or all of the parameters of another neural network, have become an increasingly important technique for conditioning and generalizing implicit neural representations (INRs), which represent signals or objects such as audio or 3D shapes using a neural network. However, despite the potential benefits of incorporating foundation models in hypernetwork methods, this research direction has not been investigated, likely due to the dissimilarity of the weight generation task with other visual tasks. To address this gap, we (1) show how foundation models can improve hypernetworks with Transformer-based architectures, (2) provide an empirical analysis of the benefits of foundation models for hypernetworks through the lens of the generalizable INR task, showing that leveraging foundation models improves performance, generalizability, and data efficiency across a variety of algorithms and modalities. We also provide further analysis in examining the design space of foundation model-based hypernetworks, including examining the choice of foundation models, algorithms, and the effect of scaling foundation models.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlow, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlow 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, CellFlow 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, CellFlow 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.

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.

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.

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 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.

Despite the rapid advancements in language and image-language modeling (Hoffmann et al., 2022; Brown, 2020; Yang et al., 2024; Liu et al., 2024a; Alayrac et al., 2022; Laurençon et al., 2024a; OpenAI, 2024), the development of video Large Multimodal Models (video-LMMs) has not kept pace. Videos provide a rich, dynamic information source, capturing nuanced temporal and spatial features beyond the reach of static images. However, video-LMMs remain under-explored, hampered by unique challenges: notably higher computational demands and a broader, more complex design space compared to their image-based counterparts (Li et al., 2023a, 2025; Liu et al., 2024d; Li et al., 2024b; Xu et al., 2024a). Many fundamental questions about video-LMM design remain unanswered: How should videos be sampled? Which vision encoders yield optimal representations? What are the best practices for resampling video tokens? Early approaches primarily extended image-LMMs directly (Xu et al., 2024b; Kim et al., 2024; Wu, 2024; Zhang et al., 2024e) or with video-specific fine-tuning (Li et al., 2023a; Zhang et al., 2023; Maaz et al., 2023). Recent methods introduced diverse design choices, such as longer context windows (Zhang et al., 2024e), multi-modality mixing (Li et al., 2024a,c), agent workflows (Wang et al., 2024c), self-training (Zohar et al., 2024), and more. Despite these efforts, the impact of these design decisions on video-LMM performance is poorly understood.

Social dynamics in close human interactions pose significant challenges for Human Mesh Estimation (HME), particularly due to the complexity of physical contacts and the scarcity of training data. Addressing these challenges, we introduce a novel data generation method that utilizes Large Vision Language Models (LVLMs) to annotate contact maps which guide test-time optimization to produce paired image and pseudo-ground truth meshes. This methodology not only alleviates the annotation burden but also enables the assembly of a comprehensive dataset specifically tailored for close interactions in HME. Our Ask Pose Unite (APU) dataset, comprising over 6.2k human mesh pairs in contact covering diverse interaction types, is curated from images depicting naturalistic person-to-person scenes. We empirically show that using our dataset to train a diffusion-based contact prior, used as guidance during optimization, improves mesh estimation on unseen interactions. Our work addresses longstanding challenges of data scarcity for close interactions in HME enhancing the field's capabilities of handling complex interaction scenarios.

The performance of Large Vision Language Models (LVLMs) is dependent on the size and quality of their training datasets. Existing video instruction tuning datasets lack diversity as they are derived by prompting large language models with video captions to generate question-answer pairs, and are therefore mostly descriptive. Meanwhile, many labeled video datasets with diverse labels and supervision exist - however, we find that their integration into LVLMs is non-trivial. Herein, we present Video Self-Training with augmented Reasoning (Video-STaR), the first video self-training approach. Video-STaR allows the utilization of any labeled video dataset for video instruction tuning. In Video-STaR, an LVLM cycles between instruction generation and finetuning, which we show (I) improves general video understanding and (II) adapts LVLMs to novel downstream tasks with existing supervision. During generation, an LVLM is prompted to propose an answer. The answers are then filtered only to those that contain the original video labels, and the LVLM is then re-trained on the generated dataset. By only training on generated answers that contain the correct video labels, Video-STaR utilizes these existing video labels as weak supervision for video instruction tuning. Our results demonstrate that Video-STaR-enhanced LVLMs exhibit improved performance in (I) general video QA, where TempCompass performance improved by 10%, and (II) on downstream tasks, where Video-STaR improved Kinetics700-QA accuracy by 20% and action quality assessment on FineDiving by 15%.