Papers by Lixing Yu
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. |
Dissecting Failure Dynamics in Large Language Model Reasoning (2026.acl-long)
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| Challenge: | Large Language Models achieve strong performance through extended inference-time deliberation, yet how their reasoning failures arise remains poorly understood. |
| Approach: | They propose a framework that probes and redirects critical transitions using uncertainty signals. |
| Outcome: | Empirical evaluations show that GUARD improves reasoning performance . GUard probes critical transitions and redirects them using uncertainty signals . |