Papers with niche identification
Identifying Cellular Niches in Spatial Transcriptomics: An Investigation into the Capabilities of Large Language Models (2025.acl-long)
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Huanhuan Wei, Xiao Luo, Hongyi Yu, Jinping Liang, Luning Yang, Lixing Lin, Alexandra Popa, Xiting Yan
| Challenge: | Spatial transcriptomic technologies allow measuring gene expression profile and spatial information of cells in tissues simultaneously. |
| Approach: | They propose a spatial transcriptomic approach to identify spatial niches using a zero-shot large language models by transforming spatial transcriptomics data into spatial context prompts. |
| Outcome: | The proposed model improves performance by leveraging gene expression of neighboring cells/spots, cell type composition, tissue information, and external knowledge. |