Alyson East

Vardaan Pahuja, Samuel Stevens, Alyson East et al.

Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in large-scale ecological studies. A major bottleneck is the absence of high-quality datasets linking biological images to trait-level annotations. In this work, we demonstrate that sparse autoencoders trained on foundation-model features yield monosemantic, spatially grounded neurons that consistently activate on meaningful morphological parts. Leveraging this property, we introduce a trait annotation pipeline that localizes salient regions and uses vision-language prompting to generate interpretable trait descriptions. Using this approach, we construct Bioscan-Traits, a dataset of 80K trait annotations spanning 19K insect images from BIOSCAN-5M. Human evaluation confirms the biological plausibility of the generated morphological descriptions. We assess design sensitivity through a comprehensive ablation study, systematically varying key design choices and measuring their impact on the quality of the resulting trait descriptions. By annotating traits with a modular pipeline rather than prohibitively expensive manual efforts, we offer a scalable way to inject biologically meaningful supervision into foundation models, enable large-scale morphological analyses, and bridge the gap between ecological relevance and machine-learning practicality.

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.

Hanane Nour Moussa, Patrick Queiroz Da Silva, Daniel Adu-Ampratwum et al.

As AI tools become increasingly common for research ideation, robust evaluation is critical to ensure the validity and usefulness of generated ideas. We introduce ScholarEval, a retrieval augmented evaluation framework that assesses research ideas based on two fundamental criteria: soundness - the empirical validity of proposed methods based on existing literature, and contribution - the degree of advancement made by the idea across different dimensions relative to prior research. To evaluate ScholarEval, we introduce ScholarIdeas, the first expert-annotated dataset of multi-domain research ideas and reviews, comprised of 117 ideas across four disciplines: artificial intelligence, neuroscience, biochemistry, and ecology. Our evaluation shows that ScholarEval achieves significantly higher coverage of points mentioned in the human expert annotated rubrics in ScholarIdeas compared to all baselines. Furthermore, ScholarEval is consistently preferred over our strongest baseline o4-mini-deep-research, a reasoning and search-enabled agentic system by OpenAI, in terms of evaluation actionability, depth, and evidence support. Our large-scale user study also shows that ScholarEval significantly outperforms deep research in literature engagement, idea refinement, and usefulness. We openly release our code, dataset, and ScholarEval tool for the community to use and build on.

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.

S M Rayeed, Alyson East, Samuel Stevens et al.

Ground beetles are a highly sensitive and speciose biological indicator, making them vital for monitoring biodiversity. However, they are currently an underutilized resource due to the manual effort required by taxonomic experts to perform challenging species differentiations based on subtle morphological differences, precluding widespread applications. In this paper, we evaluate 12 vision models on taxonomic classification across four diverse, long-tailed datasets spanning over 230 genera and 1769 species, with images ranging from controlled laboratory settings to challenging field-collected (in-situ) photographs. We further explore taxonomic classification in two important real-world contexts: sample efficiency and domain adaptation. Our results show that the Vision and Language Transformer combined with an MLP head is the best performing model, with 97% accuracy at genus and 94% at species level. Sample efficiency analysis shows that we can reduce train data requirements by up to 50% with minimal compromise in performance. The domain adaptation experiments reveal significant challenges when transferring models from lab to in-situ images, highlighting a critical domain gap. Overall, our study lays a foundation for large-scale automated taxonomic classification of beetles, and beyond that, advances sample-efficient learning and cross-domain adaptation for diverse long-tailed ecological datasets.

S M Rayeed, Mridul Khurana, Alyson East et al.

Despite the ecological significance of invertebrates, global trait databases remain heavily biased toward vertebrates and plants, limiting comprehensive ecological analyses of high-diversity groups like ground beetles. Ground beetles (Coleoptera: Carabidae) serve as critical bioindicators of ecosystem health, providing valuable insights into biodiversity shifts driven by environmental changes. While the National Ecological Observatory Network (NEON) maintains an extensive collection of carabid specimens from across the United States, these primarily exist as physical collections, restricting widespread research access and large-scale analysis. To address these gaps, we present a multimodal dataset digitizing over 13,200 NEON carabids from 30 sites spanning the continental US and Hawaii through high-resolution imaging, enabling broader access and computational analysis. The dataset includes digitally measured elytra length and width of each specimen, establishing a foundation for automated trait extraction using AI. Validated against manual measurements, our digital trait extraction achieves sub-millimeter precision, ensuring reliability for ecological and computational studies. By addressing invertebrate under-representation in trait databases, this work supports AI-driven tools for automated species identification and trait-based research, fostering advancements in biodiversity monitoring and conservation.