GEESE: Genotype-aware End-to-End Spatio-temporal Embedding for Behavioral Phenotyping
arXiv:2605.24370v1 Announce Type: new Abstract: Behavioral phenotyping of genetic animal models currently requires labor-intensive manual feature engineering that limits reproducibility and scalability. We present GEESE, an end-to-end deep learning framework that learns behavioral representations directly from 3D pose dynamics without hand-crafted features. Using a pretrained time series foundation model, we encode movement sequences into a behavioral manifold that supports both behavior classification and genotype prediction. Evaluated across three autism-associated genetic models (CNTNAP2, CHD8, FMR1), our deep learning approach surpasses hand-crafted feature baselines in both tasks, revealing that learned representations capture genotype-specific behavioral signatures. The framework generalizes across genetic backgrounds, and an all-cohort model identifies both genetic background and genotype from movement patterns alone. We further provide HONK, an interactive intelligent tool enab