Samuel Stevens

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.

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.

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.

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.

Samuel Stevens, Yu Su

Pre-trained language models (PLMs) like BERT are being used for almost all language-related tasks, but interpreting their behavior still remains a significant challenge and many important questions remain largely unanswered. In this work, we re-purpose a sentence editing dataset, where faithful high-quality human rationales can be automatically extracted and compared with extracted model rationales, as a new testbed for interpretability. This enables us to conduct a systematic investigation on an array of questions regarding PLMs' interpretability, including the role of pre-training procedure, comparison of rationale extraction methods, and different layers in the PLM. The investigation generates new insights, for example, contrary to the common understanding, we find that attention weights correlate well with human rationales and work better than gradient-based saliency in extracting model rationales. Both the dataset and code are available at https://github.com/samuelstevens/sentence-editing-interpretability to facilitate future interpretability research.

Samuel Stevens, Wei-Lun Chao, Tanya Berger-Wolf et al. · microsoft-research

To truly understand vision models, we must not only interpret their learned features but also validate these interpretations through controlled experiments. Current approaches either provide interpretable features without the ability to test their causal influence, or enable model editing without interpretable controls. We present a unified framework using sparse autoencoders (SAEs) that bridges this gap, allowing us to discover human-interpretable visual features and precisely manipulate them to test hypotheses about model behavior. By applying our method to state-of-the-art vision models, we reveal key differences in the semantic abstractions learned by models with different pre-training objectives. We then demonstrate the practical usage of our framework through controlled interventions across multiple vision tasks. We show that SAEs can reliably identify and manipulate interpretable visual features without model re-training, providing a powerful tool for understanding and controlling vision model behavior. We provide code, demos and models on our project website: https://osu-nlp-group.github.io/SAE-V.

Samuel Stevens, Emily Wenger, Cathy Li et al.

Learning with Errors (LWE) is a hard math problem underlying recently standardized post-quantum cryptography (PQC) systems for key exchange and digital signatures. Prior work proposed new machine learning (ML)-based attacks on LWE problems with small, sparse secrets, but these attacks require millions of LWE samples to train on and take days to recover secrets. We propose three key methods -- better preprocessing, angular embeddings and model pre-training -- to improve these attacks, speeding up preprocessing by $25\times$ and improving model sample efficiency by $10\times$. We demonstrate for the first time that pre-training improves and reduces the cost of ML attacks on LWE. Our architecture improvements enable scaling to larger-dimension LWE problems: this work is the first instance of ML attacks recovering sparse binary secrets in dimension $n=1024$, the smallest dimension used in practice for homomorphic encryption applications of LWE where sparse binary secrets are proposed.

Jianyang Gu, Samuel Stevens, Elizabeth G Campolongo et al. · microsoft-research

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Samuel Stevens, S M Rayeed, Jenna Kline

The practical application of AI tools for specific computer vision tasks relies on the "small-data regime" of hundreds to thousands of labeled samples. This small-data regime is vital for applications requiring expensive expert annotations, such as ecological monitoring, medical diagnostics or industrial quality control. We find, however, that computer vision research has ignored the small data regime as evaluations increasingly focus on zero- and few-shot learning. We use the Natural World Tasks (NeWT) benchmark to compare multi-modal large language models (MLLMs) and vision-only methods across varying training set sizes. MLLMs exhibit early performance plateaus, while vision-only methods improve throughout the small-data regime, with performance gaps widening beyond 10 training examples. We provide the first comprehensive comparison between these approaches in small-data contexts and advocate for explicit small-data evaluations in AI research to better bridge theoretical advances with practical deployments.

Ziheng Zhang, Xinyue Ma, Arpita Chowdhury et al.

This work investigates descriptive captions as an additional source of supervision for biological multimodal foundation models. Images and captions can be viewed as complementary samples from the latent morphospace of a species, each capturing certain biological traits. Incorporating captions during training encourages alignment with this shared latent structure, emphasizing potentially diagnostic characters while suppressing spurious correlations. The main challenge, however, lies in obtaining faithful, instance-specific captions at scale. This requirement has limited the utilization of natural language supervision in organismal biology compared with many other scientific domains. We complement this gap by generating synthetic captions with multimodal large language models (MLLMs), guided by Wikipedia-derived visual information and taxon-tailored format examples. These domain-specific contexts help reduce hallucination and yield accurate, instance-based descriptive captions. Using these captions, we train BioCAP (i.e., BioCLIP with Captions), a biological foundation model that captures rich semantics and achieves strong performance in species classification and text-image retrieval. These results demonstrate the value of descriptive captions beyond labels in bridging biological images with multimodal foundation models.

Jenna Kline, Samuel Stevens, Guy Maalouf et al.

Real-time wildlife detection in drone imagery supports critical ecological and conservation monitoring. However, standard detection models like YOLO often fail to generalize across locations and struggle with rare species, limiting their use in automated drone deployments. We present MMLA, a novel multi-environment, multi-species, low-altitude drone dataset collected across three sites (Ol Pejeta Conservancy and Mpala Research Centre in Kenya, and The Wilds in Ohio), featuring six species (zebras, giraffes, onagers, and African wild dogs). The dataset contains 811K annotations from 37 high-resolution videos. Baseline YOLO models show performance disparities across locations while fine-tuning YOLOv11m on MMLA improves mAP50 to 82%, a 52-point gain over baseline. Our results underscore the need for diverse training data to enable robust animal detection in autonomous drone systems.