FATE-MAP predicts teratogenicity and human gastrulation failure modes by integrating deep learning and mechanistic modeling

Gastrulation, a critical developmental stage involving germ layer specification and axes formation, is a major point of failure in human development, contributing to pregnancy loss and congenital malformations. However, due to ethical constraints and anatomical differences in animal models, the failure modes underlying human gastrulation remain poorly understood. To elucidate these failure modes, we introduce FATE-MAP (Failure Analysis and Trajectory Evaluation via Mechanistic-AI Prediction), an integrated platform that combines high-throughput perturbations of human 2D gastruloids with quantitative phenotypic mapping, predictive deep learning, and mechanistic morphogen modeling. Analyzing over 2000 drug-treated human 2D gastruloids, we mapped a phenotypic morphospace that separates canonical patterning, in which primitive-streak fates are correctly specified and radially organized, from failure modes, defined as departures from this organization and marked by a loss of a required fate and/or radial symmetry. To predict and interpret patterning outcomes, FATE-MAP combines a transformer linking chemical structure to phenotype with PDE simulations of morphogen transport and cell fate specification, and projects both outputs onto the experimentally defined morphospace. Applying this framework, we flagged two clinical molecules as potential teratogens and identified two parameters, cell density and SOX2 stability, that form orthogonal morphospace axes along which canonically patterned gastruloids systematically vary. FATE-MAP thus provides a roadmap for decoding human developmental trajectories and accelerating safe therapeutic discovery.