Spatial-Temporal Pre-Training for Embryo Viability Prediction Using Time-Lapse Videos

Automating embryo viability prediction for in vitro fertilization (IVF) is important but challenging due to the limited availability of labeled pregnancy outcome data, as only a small fraction of embryos are labeled after transfer. Self-supervised learning (SSL) can leverage both labeled and unlabeled data to improve prediction. However, existing SSL methods for videos are not directly applicable to embryo development videos due to two challenges: (1) embryo time-lapse videos contain hundreds of frames, requiring significant GPU memory for conventional SSL; (2) the dataset contains videos with varying lengths and many outlier frames, causing traditional video alignment methods to struggle with semantic misalignment. We propose Spatial-Temporal Pre-Training (STPT) to address these challenges. STPT includes two stages: spatial and temporal. In each stage, only one encoder is trained while the other is frozen, reducing memory demands. To handle temporal misalignment, STPT avoids frame-by-frame alignment across videos. The spatial stage learns from alignments within each video and its temporally consistent augmentations. The temporal stage then models relationships between video embeddings. Our method efficiently handles long videos and temporal variability. On 23,027 time-lapse videos (3,286 labeled), STPT achieves the highest AUC of 0.635 (95% CI: 0.632-0.638) compared to baselines, with limited computational resources.