CytoWave
Orthology-aligned foundation model of single-cell genetic perturbation responses across large-scale human and mouse datasets.
Read project →AI for Science · Computational Biology · Foundation Models
Yuwei Miao
I am a Ph.D. student in Computer Science and Engineering at The University of Texas at Arlington (2022-Present). I obtain my Batcher Degree in Computer Science and Biology at The University of North Carolina at Chapel Hill (2018-2022). My research focuses on perturbation foundation models, gene function prediction, graph-based biological learning, and representation learning for large-scale biomedical data. My recent work spans orthology-aligned single-cell perturbation foundation models, theory for attention-based regression, gene sequence-to-phenotype prediction, and graph-informed learning for gene function discovery.
I am currently seeking internship opportunities for 2026 and potential full-time job positions.
Research Overview
ECA / Correlation Plateau
Theoretical and empirical analysis of optimization conflict in attention-based regression, with extrapolative correlation attention.
Read project →GenePheno
Predicting gene knockout-induced phenotype abnormalities directly from gene sequences with structured multi-loss learning.
Read project →GoBERT
Learning gene function relationships from Gene Ontology graphs using BERT-based representation learning.
Read project →UniEntrezDB
A unified database integrating Gene Ontology annotations across biological resources through the Entrez gene system.
Read project →Publications
Breaking the Correlation Plateau: On the Optimization and Capacity Limits of Attention-Based Regressors
Jingquan Yan*, Yuwei Miao*, Peiran Yu, Junzhou Huang
GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences
Yan, Jingquan*, Yuwei Miao*, Lei Yu, Yuzhi Guo, Xue Xiao, Lin Xu, Junzhou Huang
GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction
Yuwei Miao, Yuzhi Guo, Hehuan Ma, Jingquan Yan, Feng Jiang, Rui Liao, Junzhou Huang
HAGE: Hierarchical Alignment Gene-Enhanced Pathology Representation Learning with Spatial Transcriptomics
Dang, Thao M., Haiqing Li, Yuzhi Guo, Hehuan Ma, Feng Jiang, Yuwei Miao, Qifeng Zhou, Jean Gao, Junzhou Huang