Title: Automatic Image-Level Morphological Trait Annotation for Organismal Images
Primary area: datasets and benchmarks
Keywords: morphological traits, morphological trait annotation, ecology, trait description generation

Abstract: 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 expert-validated trait annotations spanning 19K insect images from BIOSCAN-5M. Human evaluation confirms the biological plausibility of the generated morphological descriptions. When used to fine-tune BioCLIP, a biologically grounded vision-language model, Bioscan-Traits improves zero-shot species classification on the in-the-wild Insects benchmark, underscoring the value of trait-level supervision for enhancing model generalization.

TL;DR: We develop a trait annotation pipeline that leverages sparse autoencoders to generate interpretable morphological trait descriptions from ecological images.