CV

Education

Ph.D. in Computer Science and Engineering, University of Texas at Arlington (Expected 2028) — GPA: 4.0/4.0
Computer Science, Rutgers University (2021–2023) — GPA: 4.0/4.0
M.S. in Electrical Engineering, University of Southern California (2019–2021) — GPA: 3.94/4.0
B.E. in Communication Engineering, University of Science and Technology Beijing (2015–2019) — GPA: 3.66/4.0
- Dissertation: “Complex Aviation Mobile Services Link Aggregation with Hidden Markov Model” — University Excellent Student Paper Award (top 3%)

Publications

GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences

Jingquan Yan, Yuwei Miao, Lei Yu, Yuzhi Guo, Xue Xiao, Lin Xu, Junzhou Huang. "GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences." AAAI 2026 Oral.

Breaking the Correlation Plateau: On the Optimization and Capacity Limits of Attention-Based Regressors

Jingquan Yan, Yuwei Miao, Peiran Yu, Junzhou Huang. "Breaking the Correlation Plateau: On the Optimization and Capacity Limits of Attention-Based Regressors." ICLR 2026.

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. "GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction." AAAI 2025.

Efficient Uncertainty-Aware Multiple Instance Regression

Jingquan Yan, Yuwei Miao, Thao M. Dang, Junzhou Huang. "Efficient Uncertainty-Aware Multiple Instance Regression." Under Review.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers

Yuwei Miao, Yuzhi Guo, Hehuan Ma, Jingquan Yan, Feng Jiang, Weizhi An, Jean Gao, Junzhou Huang. "UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers." arXiv:2412.12688.

Self-Interpretable Time Series Prediction with Counterfactual Explanations

Jingquan Yan, Hao Wang. "Self-Interpretable Time Series Prediction with Counterfactual Explanations." ICML 2023 Oral.

HiddenVis: a Hidden State Visualization Toolkit to Visualize and Interpret Deep Learning Models for Time Series Data

Jingquan Yan, Ruichen Rong, Guanghua Xiao, Xiaowei Zhan. "HiddenVis: a Hidden State Visualization Toolkit to Visualize and Interpret Deep Learning Models for Time Series Data." bioRxiv 2020.12.11.422030.

Research Interests

Trustworthy and Interpretable AI: Explainability and uncertainty quantification in AI systems
Correlation Learning: Learning and exploiting label and feature correlations in modern machine learning
AI4Science: Applications of deep learning in healthcare (time-series, pathology data) and biology (genetic data)

Services

Reviewer: ICLR, CVPR, NeurIPS, AAAI, WACV, ACML