LLM

RegFM: an interpretable context-aware foundation model for human transcriptional regulation

Zijing Gao, Yining Sun, Haochen Wang, Rui Jiang^*, Qiao Liu^*. bioRxiv, 2026.

Zijing Gao, Yining Sun, Haochen Wang, Rui Jiang, Qiao Liu

RegFM: an interpretable context-aware foundation model for human transcriptional regulation

Conditional Attribute Estimation with Autoregressive Sequence Models

Erica Stutz, Giacomo Marino, Daniella Meeker, Qiao Liu, and Andrew J. Loza^*. arXiv, 2026.

Erica Stutz, Giacomo Marino, Daniella Meeker, Qiao Liu, Andrew J. Loza

Conditional Attribute Estimation with Autoregressive Sequence Models

Leveraging genomic foundation models to identify genotype-brain-clinical pathways in Alzheimer's disease

Qiao Liu^†,*, Zhaoyang Zhang^†, Haochen Wang, Heping Zhang, Hongtu Zhu, Lexin Li^*, Wing Hung Wong^*. medRxiv, 2026.

Qiao Liu, Zhaoyang Zhang, Haochen Wang, Heping Zhang, Hongtu Zhu, Lexin Li, Wing Hung Wong

Leveraging genomic foundation models to identify genotype-brain-clinical pathways in Alzheimer's disease

Application of LLMs/Transformer-Based Models for Metabolite Annotation in Metabolomics

Yijiang Liu, Feifan Zhang, Yifei Ge, Qiao Liu, Siyu He, and Xiaotao Shen^*. Health and Metabolism, 2025.

Yijiang Liu, Feifan Zhang, Yifei Ge, Qiao Liu, Siyu He, Xiaotao Shen

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

Zijing Gao^†, Qiao Liu^†,*, Wanwen Zeng, Rui Jiang^*, Wing Hung Wong^*. Genome Biology, 2024.

Zijing Gao, Qiao Liu, Wanwen Zeng, Rui Jiang, Wing Hung Wong

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics