Publications

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Graph for LLMs

X Dai, K Guo, CH Lo, S Zeng, J Ding, D Luo… GraphGhost: Tracing Structures Behind Large Language Models - arXiv preprint arXiv:2510.08613, 2025

X Dai, CH Lo, K Guo, S Zeng, D Luo, J Tang Uncovering Graph Reasoning in Decoder-only Transformers with Circuit Tracing - Efficient Reasoning Workshop, Neurips 2025 (Spotlight)

LLMs for graph reasoning

X Dai*, K Yang*, J Revolinsky, K Guo, A Wang, B Zhang… From sequence to structure: Uncovering substructure reasoning in transformers - Neurips 2025

Y Wang, X Dai, W Fan, Y Ma. Exploring Graph Tasks with Pure LLMs: A Comprehensive Benchmark and Investigation

X Dai, H Qu, Y Shen, B Zhang, Q Wen, W Fan, D Li… How Do Large Language Models Understand Graph Patterns? A Benchmark for Graph Pattern Comprehension ICLR 2025

X Dai, Q Wen, Y Shen, H Wen, D Li, J Tang, C Shan Revisiting the Graph Reasoning Ability of Large Language Models: Case Studies in Translation, Connectivity and Shortest Path - arXiv preprint arXiv:2408.09529, 2024

Deep Learning in Single-cell

B Ouyang, C Shan, S Shen, X Dai, Q Chen, X Su… AI-powered omics-based drug pair discovery for pyroptosis therapy targeting triple-negative breast cancer. Nature Communications, 15(1), 7560. 2024

X Dai, C Shan, J Zheng, X Li, D Li Biological Factor Regulatory Neural Network. arXiv preprint arXiv:2304.04982. 2023