SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics (opens in new tab)

Spatially resolved transcriptomic (SRT) data requires spatial domain identification to enable tissue microenvironment-specific downstream analyses. Here we present SPEAK (Spatial Prompting with Expert-Aligned Knowledge), a large language model (LLM) -based method to identify spatial domains from SRT data by taking advantage of the prior knowledge from both LLM and human experts. SPEAK constructs a spatial context prompt for each cell/spot based on cell types and marker genes of its neighborin...