Charles V. Stewart

Dipanjyoti Paul, Arpita Chowdhury, Xinqi Xiong et al. · microsoft-research

We present a novel usage of Transformers to make image classification interpretable. Unlike mainstream classifiers that wait until the last fully connected layer to incorporate class information to make predictions, we investigate a proactive approach, asking each class to search for itself in an image. We realize this idea via a Transformer encoder-decoder inspired by DEtection TRansformer (DETR). We learn "class-specific" queries (one for each class) as input to the decoder, enabling each class to localize its patterns in an image via cross-attention. We name our approach INterpretable TRansformer (INTR), which is fairly easy to implement and exhibits several compelling properties. We show that INTR intrinsically encourages each class to attend distinctively; the cross-attention weights thus provide a faithful interpretation of the prediction. Interestingly, via "multi-head" cross-attention, INTR could identify different "attributes" of a class, making it particularly suitable for fine-grained classification and analysis, which we demonstrate on eight datasets. Our code and pre-trained models are publicly accessible at the Imageomics Institute GitHub site: https://github.com/Imageomics/INTR.

Zheda Mai, Arpita Chowdhury, Ping Zhang et al. · microsoft-research

Fine-tuning is arguably the most straightforward way to tailor a pre-trained model (e.g., a foundation model) to downstream applications, but it also comes with the risk of losing valuable knowledge the model had learned in pre-training. For example, fine-tuning a pre-trained classifier capable of recognizing a large number of classes to master a subset of classes at hand is shown to drastically degrade the model's accuracy in the other classes it had previously learned. As such, it is hard to further use the fine-tuned model when it encounters classes beyond the fine-tuning data. In this paper, we systematically dissect the issue, aiming to answer the fundamental question, "What has been damaged in the fine-tuned model?" To our surprise, we find that the fine-tuned model neither forgets the relationship among the other classes nor degrades the features to recognize these classes. Instead, the fine-tuned model often produces more discriminative features for these other classes, even if they were missing during fine-tuning! {What really hurts the accuracy is the discrepant logit scales between the fine-tuning classes and the other classes}, implying that a simple post-processing calibration would bring back the pre-trained model's capability and at the same time unveil the feature improvement over all classes. We conduct an extensive empirical study to demonstrate the robustness of our findings and provide preliminary explanations underlying them, suggesting new directions for future theoretical analysis. Our code is available at https://github.com/OSU-MLB/Fine-Tuning-Is-Fine-If-Calibrated.

Samuel Stevens, Jiaman Wu, Matthew J Thompson et al. · microsoft-research

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks and find that BioCLIP consistently and substantially outperforms existing baselines (by 16% to 17% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. https://imageomics.github.io/bioclip has models, data and code.

Cheng-Hao Tu, Hong-You Chen, Zheda Mai et al. · microsoft-research

We propose a learning problem involving adapting a pre-trained source model to the target domain for classifying all classes that appeared in the source data, using target data that covers only a partial label space. This problem is practical, as it is unrealistic for the target end-users to collect data for all classes prior to adaptation. However, it has received limited attention in the literature. To shed light on this issue, we construct benchmark datasets and conduct extensive experiments to uncover the inherent challenges. We found a dilemma -- on the one hand, adapting to the new target domain is important to claim better performance; on the other hand, we observe that preserving the classification accuracy of classes missing in the target adaptation data is highly challenging, let alone improving them. To tackle this, we identify two key directions: 1) disentangling domain gradients from classification gradients, and 2) preserving class relationships. We present several effective solutions that maintain the accuracy of the missing classes and enhance the overall performance, establishing solid baselines for holistic transfer of pre-trained models with partial target data.

Mohannad Elhamod, Mridul Khurana, Harish Babu Manogaran et al.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Veikka Immonen, Ekaterina Nepovinnykh, Tuomas Eerola et al.

Image-based re-identification of animal individuals allows gathering of information such as migration patterns of the animals over time. This, together with large image volumes collected using camera traps and crowdsourcing, opens novel possibilities to study animal populations. For many species, the re-identification can be done by analyzing the permanent fur, feather, or skin patterns that are unique to each individual. In this paper, we address the re-identification by combining two types of pattern similarity metrics: 1) pattern appearance similarity obtained by pattern feature aggregation and 2) geometric pattern similarity obtained by analyzing the geometric consistency of pattern similarities. The proposed combination allows to efficiently utilize both the local and global pattern features, providing a general re-identification approach that can be applied to a wide variety of different pattern types. In the experimental part of the work, we demonstrate that the method achieves promising re-identification accuracies for Saimaa ringed seals and whale sharks.

Mridul Khurana, Arka Daw, M. Maruf et al.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Arpita Chowdhury, Dipanjyoti Paul, Zheda Mai et al. · microsoft-research

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. Pre-trained 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.

Fangxun Liu, S M Rayeed, Samuel Stevens et al.

In entomology and ecology research, biologists often need to collect a large number of insects, among which beetles are the most common species. A common practice for biologists to organize beetles is to place them on trays and take a picture of each tray. Given the images of thousands of such trays, it is important to have an automated pipeline to process the large-scale data for further research. Therefore, we develop a 3-stage pipeline to detect all the beetles on each tray, sort and crop the image of each beetle, and do morphological segmentation on the cropped beetles. For detection, we design an iterative process utilizing a transformer-based open-vocabulary object detector and a vision-language model. For segmentation, we manually labeled 670 beetle images and fine-tuned two variants of a transformer-based segmentation model to achieve fine-grained segmentation of beetles with relatively high accuracy. The pipeline integrates multiple deep learning methods and is specialized for beetle image processing, which can greatly improve the efficiency to process large-scale beetle data and accelerate biological research.

Jonathan P. Crall, Charles V. Stewart, Tanya Y. Berger-Wolf et al.

We present HotSpotter, a fast, accurate algorithm for identifying individual animals against a labeled database. It is not species specific and has been applied to Grevy's and plains zebras, giraffes, leopards, and lionfish. We describe two approaches, both based on extracting and matching keypoints or "hotspots". The first tests each new query image sequentially against each database image, generating a score for each database image in isolation, and ranking the results. The second, building on recent techniques for instance recognition, matches the query image against the database using a fast nearest neighbor search. It uses a competitive scoring mechanism derived from the Local Naive Bayes Nearest Neighbor algorithm recently proposed for category recognition. We demonstrate results on databases of more than 1000 images, producing more accurate matches than published methods and matching each query image in just a few seconds.

Jenna Kline, Maksim Kholiavchenko, Samuel Stevens et al.

A comprehensive understanding of animal behavior ecology depends on scalable approaches to quantify and interpret complex, multidimensional behavioral patterns. Traditional field observations are often limited in scope, time-consuming, and labor-intensive, hindering the assessment of behavioral responses across landscapes. To address this, we present kabr-tools (Kenyan Animal Behavior Recognition Tools), an open-source package for automated multi-species behavioral monitoring. This framework integrates drone-based video with machine learning systems to extract behavioral, social, and spatial metrics from wildlife footage. Our pipeline leverages object detection, tracking, and behavioral classification systems to generate key metrics, including time budgets, behavioral transitions, social interactions, habitat associations, and group composition dynamics. Compared to ground-based methods, drone-based observations significantly improved behavioral granularity, reducing visibility loss by 15% and capturing more transitions with higher accuracy and continuity. We validate kabr-tools through three case studies, analyzing 969 behavioral sequences, surpassing the capacity of traditional methods for data capture and annotation. We found that, like Plains zebras, vigilance in Grevy's zebras decreases with herd size, but, unlike Plains zebras, habitat has a negligible impact. Plains and Grevy's zebras exhibit strong behavioral inertia, with rare transitions to alert behaviors and observed spatial segregation between Grevy's zebras, Plains zebras, and giraffes in mixed-species herds. By enabling automated behavioral monitoring at scale, kabr-tools offers a powerful tool for ecosystem-wide studies, advancing conservation, biodiversity research, and ecological monitoring.

Lasha Otarashvili, Tamilselvan Subramanian, Jason Holmberg et al.

Recent work has established the ecological importance of developing algorithms for identifying animals individually from images. Typically, a separate algorithm is trained for each species, a natural step but one that creates significant barriers to wide-spread use: (1) each effort is expensive, requiring data collection, data curation, and model training, deployment, and maintenance, (2) there is little training data for many species, and (3) commonalities in appearance across species are not exploited. We propose an alternative approach focused on training multi-species individual identification (re-id) models. We construct a dataset that includes 49 species, 37K individual animals, and 225K images, using this data to train a single embedding network for all species. Our model employs an EfficientNetV2 backbone and a sub-center ArcFace loss function with dynamic margins. We evaluate the performance of this multispecies model in several ways. Most notably, we demonstrate that it consistently outperforms models trained separately on each species, achieving an average gain of 12.5% in top-1 accuracy. Furthermore, the model demonstrates strong zero-shot performance and fine-tuning capabilities for new species with limited training data, enabling effective curation of new species through both incremental addition of data to the training set and fine-tuning without the original data. Additionally, our model surpasses the recent MegaDescriptor on unseen species, averaging an 19.2% top-1 improvement per species and showing gains across all 33 species tested. The fully-featured code repository is publicly available on GitHub, and the feature extractor model can be accessed on HuggingFace for seamless integration with wildlife re-identification pipelines. The model is already in production use for 60+ species in a large-scale wildlife monitoring system.

Alyson East, Elizabeth G. Campolongo, Luke Meyers et al.

1) Biological collections house millions of specimens with digital images increasingly available through open-access platforms. However, most imaging protocols were developed for human interpretation without considering automated analysis requirements. As computer vision applications revolutionize taxonomic identification and trait extraction, a critical gap exists between current digitization practices and computational analysis needs. This review provides the first comprehensive practical framework for optimizing biological specimen imaging for computer vision applications. 2) Through interdisciplinary collaboration between taxonomists, collection managers, ecologists, and computer scientists, we synthesized evidence-based recommendations addressing fundamental computer vision concepts and practical imaging considerations. We provide immediately actionable implementation guidance while identifying critical areas requiring community standards development. 3) Our framework encompasses ten interconnected considerations for optimizing image capture for computer vision-powered taxonomic identification and trait extraction. We translate these into practical implementation checklists, equipment selection guidelines, and a roadmap for community standards development including filename conventions, pixel density requirements, and cross-institutional protocols. 4)By bridging biological and computational disciplines, this approach unlocks automated analysis potential for millions of existing specimens and guides future digitization efforts toward unprecedented analytical capabilities.

Vardaan Pahuja, Weidi Luo, Yu Gu et al.

Camera traps are important tools in animal ecology for biodiversity monitoring and conservation. However, their practical application is limited by issues such as poor generalization to new and unseen locations. Images are typically associated with diverse forms of context, which may exist in different modalities. In this work, we exploit the structured context linked to camera trap images to boost out-of-distribution generalization for species classification tasks in camera traps. For instance, a picture of a wild animal could be linked to details about the time and place it was captured, as well as structured biological knowledge about the animal species. While often overlooked by existing studies, incorporating such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively incorporating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that transforms species classification as link prediction in a multimodal knowledge graph (KG). This framework enables the seamless integration of diverse multimodal contexts for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework enhances sample efficiency for recognizing under-represented species.

Avirath Sundaresan, Jason R. Parham, Jonathan Crall et al.

In both 2016 and 2018, a census of the highly-endangered Grevy's zebra population was enabled by the Great Grevy's Rally (GGR), a citizen science event that produces population estimates via expert and algorithmic curation of volunteer-captured images. A complementary, scalable, and long-term Grevy's population monitoring approach involves deploying camera trap networks. However, in both scenarios, a substantial majority of zebra images are not usable for individual identification due to poor in-the-wild imaging conditions; camera trap images in particular present high rates of occlusion and high spatio-temporal similarity within image bursts. Our proposed filtering pipeline incorporates animal detection, species identification, viewpoint estimation, quality evaluation, and temporal subsampling to obtain individual crops suitable for re-ID, which are subsequently curated by the LCA decision management algorithm. Our method processed images taken during GGR-16 and GGR-18 in Meru County, Kenya, into 4,142 highly-comparable annotations, requiring only 120 contrastive human decisions to produce a population estimate within 4.6% of the ground-truth count. Our method also efficiently processed 8.9M unlabeled camera trap images from 70 cameras at the Mpala Research Centre in Laikipia County, Kenya over two years into 685 encounters of 173 individuals, requiring only 331 contrastive human decisions.

Aleksandr Algasov, Ekaterina Nepovinnykh, Tuomas Eerola et al.

Recent advancements in the automatic re-identification of animal individuals from images have opened up new possibilities for studying wildlife through camera traps and citizen science projects. Existing methods leverage distinct and permanent visual body markings, such as fur patterns or scars, and typically employ one of two strategies: local features or end-to-end learning. In this study, we delve into the impact of training set size by conducting comprehensive experiments across six different methods and five animal species. While it is well known that end-to-end learning-based methods surpass local feature-based methods given a sufficient amount of good-quality training data, the challenge of gathering such datasets for wildlife animals means that local feature-based methods remain a more practical approach for many species. We demonstrate the benefits of both local feature and end-to-end learning-based approaches and show that species-specific characteristics, particularly intra-individual variance, have a notable effect on training data requirements.

Aleksandr Algasov, Ekaterina Nepovinnykh, Fedor Zolotarev et al.

Existing individual re-identification methods often struggle with the deformable nature of animal fur or skin patterns which undergo geometric distortions due to body movement and posture changes. In this paper, we propose a geometry-aware texture mapping approach that unwarps pelage patterns, the unique markings found on an animal's skin or fur, into a canonical UV space, enabling more robust feature matching. Our method uses surface normal estimation to guide the unwrapping process while preserving the geometric consistency between the 3D surface and the 2D texture space. We focus on two challenging species: Saimaa ringed seals (Pusa hispida saimensis) and leopards (Panthera pardus). Both species have distinctive yet highly deformable fur patterns. By integrating our pattern-preserving UV mapping with existing re-identification techniques, we demonstrate improved accuracy across diverse poses and viewing angles. Our framework does not require ground truth UV annotations and can be trained in a self-supervised manner. Experiments on seal and leopard datasets show up to a 5.4% improvement in re-identification accuracy.

Zhenyang Feng, Zihe Wang, Jianyang Gu et al.

We study image segmentation in the biological domain, particularly trait segmentation from specimen images (e.g., butterfly wing stripes, beetle elytra). This fine-grained task is crucial for understanding the biology of organisms, but it traditionally requires manually annotating segmentation masks for hundreds of images per species, making it highly labor-intensive. To address this challenge, we propose a label-efficient approach, Static Segmentation by Tracking (SST), based on a key insight: while specimens of the same species exhibit natural variation, the traits of interest show up consistently. This motivates us to concatenate specimen images into a ``pseudo-video'' and reframe trait segmentation as a tracking problem. Specifically, SST generates masks for unlabeled images by propagating annotated or predicted masks from the ``pseudo-preceding'' images. Built upon recent video segmentation models, such as Segment Anything Model 2, SST achieves high-quality trait segmentation with only one labeled image per species, marking a breakthrough in specimen image analysis. To further enhance segmentation quality, we introduce a cycle-consistent loss for fine-tuning, again requiring only one labeled image. Additionally, we demonstrate the broader potential of SST, including one-shot instance segmentation in natural images and trait-based image retrieval.

Devis Tuia, Benjamin Kellenberger, Sara Beery et al.

Data acquisition in animal ecology is rapidly accelerating due to inexpensive and accessible sensors such as smartphones, drones, satellites, audio recorders and bio-logging devices. These new technologies and the data they generate hold great potential for large-scale environmental monitoring and understanding, but are limited by current data processing approaches which are inefficient in how they ingest, digest, and distill data into relevant information. We argue that machine learning, and especially deep learning approaches, can meet this analytic challenge to enhance our understanding, monitoring capacity, and conservation of wildlife species. Incorporating machine learning into ecological workflows could improve inputs for population and behavior models and eventually lead to integrated hybrid modeling tools, with ecological models acting as constraints for machine learning models and the latter providing data-supported insights. In essence, by combining new machine learning approaches with ecological domain knowledge, animal ecologists can capitalize on the abundance of data generated by modern sensor technologies in order to reliably estimate population abundances, study animal behavior and mitigate human/wildlife conflicts. To succeed, this approach will require close collaboration and cross-disciplinary education between the computer science and animal ecology communities in order to ensure the quality of machine learning approaches and train a new generation of data scientists in ecology and conservation.

Charles V. Stewart, Jason R. Parham, Jason Holmberg et al.

Hoping to stimulate new research in individual animal identification from images, we propose to formulate the problem as the human-machine Continual Curation of images and animal identities. This is an open world recognition problem, where most new animals enter the system after its algorithms are initially trained and deployed. Continual Curation, as defined here, requires (1) an improvement in the effectiveness of current recognition methods, (2) a pairwise verification algorithm that allows the possibility of no decision, and (3) an algorithmic decision mechanism that seeks human input to guide the curation process. Error metrics must evaluate the ability of recognition algorithms to identify not only animals that have been seen just once or twice but also recognize new animals not in the database. An important measure of overall system performance is accuracy as a function of the amount of human input required.

Hendrik J. Weideman, Zachary M. Jablons, Jason Holmberg et al.

We address the problem of identifying individual cetaceans from images showing the trailing edge of their fins. Given the trailing edge from an unknown individual, we produce a ranking of known individuals from a database. The nicks and notches along the trailing edge define an individual's unique signature. We define a representation based on integral curvature that is robust to changes in viewpoint and pose, and captures the pattern of nicks and notches in a local neighborhood at multiple scales. We explore two ranking methods that use this representation. The first uses a dynamic programming time-warping algorithm to align two representations, and interprets the alignment cost as a measure of similarity. This algorithm also exploits learned spatial weights to downweight matches from regions of unstable curvature. The second interprets the representation as a feature descriptor. Feature keypoints are defined at the local extrema of the representation. Descriptors for the set of known individuals are stored in a tree structure, which allows us to perform queries given the descriptors from an unknown trailing edge. We evaluate the top-k accuracy on two real-world datasets to demonstrate the effectiveness of the curvature representation, achieving top-1 accuracy scores of approximately 95% and 80% for bottlenose dolphins and humpback whales, respectively.