51: STIFT: Spatiotemporal Transcriptomics Integration by Spatially Informed Multi-Timepoint Bridging

Music City Center 

Recent advances in spatial transcriptomics have highlighted the need for integrating spatial transcriptomics data across multiple developmental and regenerative stages. We present STIFT (SpatioTemporal Integration Framework for Transcriptomics), a three-component framework combining developmental spatiotemporal optimal transport, spatiotemporal graph construction, and triplet-informed graph attention autoencoder (GATE) specifically designed for integrating spatiotemporal transcriptomics data. STIFT efficiently processes large-scale 2D and 3D spatiotemporal trancriptomics data while preserving temporal patterns and biological structures, enabling batch effect removal, spatial domain identification, trajectory inference and exploration of developmental dynamics. Applied to axolotl brain regeneration, mouse embryonic development, and 3D planarian regeneration datasets, STIFT efficiently removes batch effects and achieves clear spatial domain identification while preserving temporal developmental patterns and biological variations across hundreds of thousands of spots, demonstrating its effectiveness and specificity in integrating spatiotemporal transcriptomics data.

spatial transcriptomics

spatiotemporal data integration

graph attention autoencoder

developmental biology 

Section on Statistics in Genomics and Genetics