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Poster
in
Workshop: 2nd Generative AI for Biology Workshop

Spatial Cell-Guided Pretraining for Scalable Spatial Transcriptomics Foundation Model

Jing Gong · Yixuan Wang · Nicholas Ho · Xingyi Cheng · Le Song · Eric Xing

Keywords: [ Cell ] [ Tissue ] [ LLM ]


Abstract:

Single-cell spatial transcriptomics enables high-resolution insights into tissue organization and cell-cell interactions, yet poses significant computational and modeling challenges due to its scale and complexity. Here we introduce AIDO.Tissue, a spatially-informed pretraining framework. The design employs multiple cells as input and an asymmetric encoder-decoder architecture, making it effectively encodes cross-cell dependencies while scaling to large data. Systematic evaluation shows that our method scales with neighboring size and achieves state-of-the-art performance across diverse downstream tasks, including spatial cell type classification, cell niche type prediction and cell density estimation. These results highlight the importance of multi-scale spatial context in building general-purpose foundation models for tissue-level understanding.

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