We present a simple approach to make pre-trained Vision Transformers (ViTs) interpretable for fine-grained analysis, aiming to identify and localize the traits that distinguish visually similar categories, such as bird species. Pretrained ViTs, such as DINO, have demonstrated remarkable capabilities in extracting localized, discriminative features. However, saliency maps like Grad-CAM often fail to identify these traits, producing blurred, coarse heatmaps that highlight entire objects instead. We propose a novel approach, Prompt Class Attention Map (Prompt-CAM), to address this limitation. Prompt-CAM learns class-specific prompts for a pre-trained ViT and uses the corresponding outputs for classification. To correctly classify an image, the true-class prompt must attend to unique image patches not present in other classes’ images (i.e., traits). As a result, the true class’s multi-head attention maps reveal traits and their locations. Implementation-wise, Prompt-CAM is almost a "free lunch," requiring only a modification to the prediction head of Visual Prompt Tuning (VPT). This makes Prompt-CAM easy to train and apply, in stark contrast to other interpretable methods that require designing specific models and training processes. Extensive empirical studies on a dozen datasets from various domains (e.g., birds, fishes, insects, fungi, flowers, food, and cars) validate the superior interpretation capability of Prompt-CAM. The source code and demo are available at https://github.com/Imageomics/Prompt_CAM.

We introduce Fish-Visual Trait Analysis (Fish-Vista), the first organismal image dataset designed for the analysis of visual traits of aquatic species directly from images using machine learning and computer vision methods. Fish-Vista contains 69,269 annotated images spanning 4,316 fish species, curated and organized to serve three downstream tasks: species classification, trait identification, and trait segmentation. Our work makes two key contributions. First, we provide a fully reproducible data processing pipeline to process fish images sourced from various museum collections, contributing to the advancement of AI in biodiversity science. We annotate the images with carefully curated labels from biological databases and manual annotations to create an AI-ready dataset of visual traits. Second, our work offers fertile grounds for researchers to develop novel methods for a variety of problems in computer vision such as handling long-tailed distributions, out-of-distribution generalization, learning with weak labels, explainable AI, and segmenting small objects. Dataset and code for Fish-Vista are available at https://github.com/Imageomics/Fish-Vista

A grand challenge in biology is to discover evolutionary traits---features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of image repositories in biology, there is a tremendous opportunity to discover evolutionary traits directly from images in the form of a hierarchy of prototypes. However, current prototype-based methods are mostly designed to operate over a flat structure of classes and face several challenges in discovering hierarchical prototypes, including the issue of learning over-specific prototypes at internal nodes. To overcome these challenges, we introduce the framework of Hierarchy aligned Commonality through Prototypical Networks (HComP-Net). The key novelties in HComP-Net include a novel over-specificity loss to avoid learning over-specific prototypes, a novel discriminative loss to ensure prototypes at an internal node are absent in the contrasting set of species with different ancestry, and a novel masking module to allow for the exclusion of over-specific prototypes at higher levels of the tree without hampering classification performance. We empirically show that HComP-Net learns prototypes that are accurate, semantically consistent, and generalizable to unseen species in comparison to baselines. Our code is publicly accessible at Imageomics Institute Github site: https://github.com/Imageomics/HComPNet.

Validating claims from misinformation is a highly challenging task that involves understanding how each factual assertion within the claim relates to a set of trusted source materials. Existing approaches often make coarse-grained predictions but fail to identify the specific aspects of the claim that are troublesome and the specific evidence relied upon. In this paper, we introduce a method and new benchmark for this challenging task. Our method predicts the fine-grained logical relationship of each aspect of the claim from a set of multimodal documents, which include text, image(s), video(s), and audio(s). We also introduce a new benchmark (M^3DC) of claims requiring multimodal multidocument reasoning, which we construct using a novel claim synthesis technique. Experiments show that our approach significantly outperforms state-of-the-art baselines on this challenging task on two benchmarks while providing finer-grained predictions, explanations, and evidence.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of $12$ state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of $469K$ question-answer pairs involving $30K$ images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images.