Yuhui Zhang

Alejandro Lozano, Jeffrey Nirschl, James Burgess et al. · stanford

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 μ-Bench, an expert-curated benchmark encompassing 22 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 μ-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 μ-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Takumi Nakagawa, Yutaro Sanada, Hiroki Waida et al.

Representation learning has been increasing its impact on the research and practice of machine learning, since it enables to learn representations that can apply to various downstream tasks efficiently. However, recent works pay little attention to the fact that real-world datasets used during the stage of representation learning are commonly contaminated by noise, which can degrade the quality of learned representations. This paper tackles the problem to learn robust representations against noise in a raw dataset. To this end, inspired by recent works on denoising and the success of the cosine-similarity-based objective functions in representation learning, we propose the denoising Cosine-Similarity (dCS) loss. The dCS loss is a modified cosine-similarity loss and incorporates a denoising property, which is supported by both our theoretical and empirical findings. To make the dCS loss implementable, we also construct the estimators of the dCS loss with statistical guarantees. Finally, we empirically show the efficiency of the dCS loss over the baseline objective functions in vision and speech domains.

Christopher Polzak, Alejandro Lozano, Min Woo Sun et al. · stanford

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.

Xiangyu Zhou, Qianru Wei, Yuhui Zhang

The inevitable feature deviation of synthetic aperture radar (SAR) image due to the special imaging principle (depression angle variation) leads to poor recognition accuracy, especially in few-shot learning (FSL). To deal with this problem, we propose a dense graph prototype network (DGP-Net) to eliminate the feature deviation by learning potential features, and classify by learning feature distribution. The role of the prototype in this model is to solve the problem of large distance between congeneric samples taken due to the contingency of single sampling in FSL, and enhance the robustness of the model. Experimental results on the MSTAR dataset show that the DGP-Net has good classification results for SAR images with different depression angles and the recognition accuracy of it is higher than typical FSL methods.

Anjiang Wei, Jiannan Cao, Ran Li et al. · stanford

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

Yuhui Zhang, Yuchang Su, Yiming Liu et al. · stanford

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/.

Jundong Xu, Hao Fei, Yuhui Zhang et al.

Multimodal symbolic logical reasoning, which aims to deduce new facts from multimodal input via formal logic, is critical in high-stakes applications such as autonomous driving and medical diagnosis, as its rigorous, deterministic reasoning helps prevent serious consequences. To evaluate such capabilities of current state-of-the-art vision language models (VLMs), we introduce the first benchmark MuSLR for multimodal symbolic logical reasoning grounded in formal logical rules. MuSLR comprises 1,093 instances across 7 domains, including 35 atomic symbolic logic and 976 logical combinations, with reasoning depths ranging from 2 to 9. We evaluate 7 state-of-the-art VLMs on MuSLR and find that they all struggle with multimodal symbolic reasoning, with the best model, GPT-4.1, achieving only 46.8%. Thus, we propose LogiCAM, a modular framework that applies formal logical rules to multimodal inputs, boosting GPT-4.1's Chain-of-Thought performance by 14.13%, and delivering even larger gains on complex logics such as first-order logic. We also conduct a comprehensive error analysis, showing that around 70% of failures stem from logical misalignment between modalities, offering key insights to guide future improvements. All data and code are publicly available at https://llm-symbol.github.io/MuSLR.