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.

With the rise of medical foundation models and the growing availability of imaging data, scalable pretraining techniques offer a promising way to identify imaging biomarkers predictive of future disease risk. While current self-supervised methods for 3D medical imaging models capture local structural features like organ morphology, they fail to link pixel biomarkers with long-term health outcomes due to a missing context problem. Current approaches lack the temporal context necessary to identify biomarkers correlated with disease progression, as they rely on supervision derived only from images and concurrent text descriptions. To address this, we introduce time-to-event pretraining, a pretraining framework for 3D medical imaging models that leverages large-scale temporal supervision from paired, longitudinal electronic health records (EHRs). Using a dataset of 18,945 CT scans (4.2 million 2D images) and time-to-event distributions across thousands of EHR-derived tasks, our method improves outcome prediction, achieving an average AUROC increase of 23.7% and a 29.4% gain in Harrell’s C-index across 8 benchmark tasks. Importantly, these gains are achieved without sacrificing diagnostic classification performance. This study lays the foundation for integrating longitudinal EHR and 3D imaging data to advance clinical risk prediction.

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/.

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. MedAlign is provided under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

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 work presents the design of a control trajec-tory algorithm based on Barrier Lyapunov functions (BLF) for a class of third-order electro-mechanical systems. The method considers unknown control gains and uncertain plant parame-ters, a common problem in control engineering applications. In order to deal with the uncertain parameters, this study proposes a backstepping adaptive strategy applying Nussbaum functions to know the sign of the control gains. The BLF imposes partial constraints to keep the trajectories of the system inside a safe operation set. The proposed controller is tested in a virtual one-link robotic manipulator including actuator dynamics to develop an adequate trajectory tracking. The maximum tracking error norm was 0.02, which fulfilled the maximum constrained bound of 0.5.

This work deals with the design of a millimetric electrospinning device (MED) controlled with the implemen-tation of a sliding mode controller taking into account states constraints or constraint sliding mode controller (CSM C). The proposed MED is integrated by two cartesian robots with two (injector system) and three (collector system) degrees of freedom, respectively. These two cartesian robots work in a coordinated manner to regulate the deposition processes for the generation of polymeric micro and nanofibers. This strategy addresses one of the most common problems of classic MEDs, guaranteeing that the fibers are deposited in a specific zone (aiming to create 3D polymeric structures). The suggested CSM C successfully restricts the motions of the MED to a predefined working space that led to the production of aligned polymer fibers, ensuring the convergence of the tracking error to the sliding surface in finite-time, while the state constraints are satisfied. Experimental results validate the effectiveness of the proposed CSMC by using the least mean square evaluation of the tracking error and the integral of the control signal. The evaluation is also done following a comparative analysis concerning the performance forced with respect to a state feedback form. The evaluation confirmed the effectiveness of the CDMC strategy compared to the state feedback form.