μ-Bench: A Vision-Language Benchmark for Microscopy Understanding

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 {\mu}-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 {\mu}-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 {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Towards an Improved Understanding and Utilization of Maximum Manifold Capacity Representations

Maximum Manifold Capacity Representations (MMCR) is a recent multi-view self-supervised learning (MVSSL) method that matches or surpasses other leading MVSSL methods. MMCR is intriguing because it does not fit neatly into any of the commonplace MVSSL lineages, instead originating from a statistical mechanical perspective on the linear separability of data manifolds. In this paper, we seek to improve our understanding and our utilization of MMCR. To better understand MMCR, we leverage tools from high dimensional probability to demonstrate that MMCR incentivizes alignment and uniformity of learned embeddings. We then leverage tools from information theory to show that such embeddings maximize a well-known lower bound on mutual information between views, thereby connecting the geometric perspective of MMCR to the information-theoretic perspective commonly discussed in MVSSL. To better utilize MMCR, we mathematically predict and experimentally confirm non-monotonic changes in the pretraining loss akin to double descent but with respect to atypical hyperparameters. We also discover compute scaling laws that enable predicting the pretraining loss as a function of gradients steps, batch size, embedding dimension and number of views. We then show that MMCR, originally applied to image data, is performant on multimodal image-text data. By more deeply understanding the theoretical and empirical behavior of MMCR, our work reveals insights on improving MVSSL methods.

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.