Publications

You can also find my articles on my Google Scholar profile.

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

Published in AAAI 2026 (Oral, top 25% accepted), 2026

Keywords: Phenotype Prediction, Gene Ontology, Multi-label Classification, Explainable AI, Label Correlation

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

Published in ICLR 2026 (Poster, 28% acceptance rate), 2026

Keywords: Joint Optimization, Correlation Learning, Attention Mechanism, Regression Model

Recommended citation: Jingquan Yan, Yuwei Miao, Peiran Yu, Junzhou Huang. "Breaking the Correlation Plateau: On the Optimization and Capacity Limits of Attention-Based Regressors." ICLR 2026.
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GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction

Published in AAAI 2025 (Poster, 23.4% acceptance rate), 2025

Keywords: Language Model, Gene Ontology

Recommended citation: 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.
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Efficient Uncertainty-Aware Multiple Instance Regression

Published in Under Review, 2025

Keywords: Multi-instance Learning, Pathology Image, Uncertainty, Survival Regression

Recommended citation: 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

Published in Preprint: arXiv:2412.12688, 2024

Authors: Yuwei Miao, Yuzhi Guo, Hehuan Ma, Jingquan Yan, Feng Jiang, Weizhi An, Jean Gao, Junzhou Huang

Recommended citation: 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.
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Self-Interpretable Time Series Prediction with Counterfactual Explanations

Published in ICML 2023 (Oral, top 8% accepted), 2023

Keywords: Bayesian Deep Learning, Causal Inference, Time Series, Healthcare, Explainable AI

Recommended citation: Jingquan Yan, Hao Wang. "Self-Interpretable Time Series Prediction with Counterfactual Explanations." ICML 2023 Oral.
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HiddenVis: a Hidden State Visualization Toolkit to Visualize and Interpret Deep Learning Models for Time Series Data

Published in Preprint: bioRxiv 2020.12.11.422030, 2020

Authors: Jingquan Yan, Ruichen Rong, Guanghua Xiao, Xiaowei Zhan

Recommended citation: 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.