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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.

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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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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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.

GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction

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

Keywords: Gene Ontology, Gene Function Prediction, Language Model

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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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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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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GAMI: Gradient-Aligned Modality Importance for Multimodal Cancer Outcome Prediction

Published in BIBM 2026, 2026

Keywords: Multi-modality Learning, Survival Prediction

Recommended citation: Xiao Hu, Yuzhi Guo, Zheng Zheng, Wenliang Zhong, Haiqing Li, Yuwei Miao, Jingquan Yan, Hehuan Ma, Yinhao Wu, Junzhou Huang. "GAMI: Gradient-Aligned Modality Importance for Multimodal Cancer Outcome Prediction." BIBM 2026.

B2P-Corr: Batch-to-Population Gradient Estimators for Non-Decomposable Correlation Losses

Published in NeurIPS 2026 (Poster, 25.7% acceptance rate), 2026

Keywords: Mini-batch Optimization, Non-decomposable Objectives, Correlation Learning

Recommended citation: Jingquan Yan, Yuwei Miao, Peiran Yu, Junzhou Huang. "B2P-Corr: Batch-to-Population Gradient Estimators for Non-Decomposable Correlation Losses." NeurIPS 2026.

CytoWave: Perturbation-Centric Pretraining for Single-Cell Response Prediction

Published in NeurIPS 2026 (Poster, 25.7% acceptance rate), 2026

Keywords: Single-cell Pretrained Model, Perturbation Prediction

Recommended citation: Yuwei Miao, Jingquan Yan, Hehuan Ma, Thao M. Dang, Lin Xu, Siyuan Zhang, Junzhou Huang. "CytoWave: Perturbation-Centric Pretraining for Single-Cell Response Prediction." NeurIPS 2026.

Decomposed Representations Mitigate the Alignment–Specificity Trade-off in Multi-Omics

Published in NeurIPS 2026 (Poster, 25.7% acceptance rate), 2026

Keywords: Multi-modality Learning, Learning with Missing Modality

Recommended citation: Thao M. Dang, Feng Jiang, Hehuan Ma, Yuzhi Guo, Jingquan Yan, Haiqing Li, Saiyang Na, Zheng Zheng, Thuc Anh Tran, Jean Gao, Junzhou Huang. "Decomposed Representations Mitigate the Alignment–Specificity Trade-off in Multi-Omics." NeurIPS 2026.

Uncertainty-Aware Multimodal Gait Representation Learning for Scoliosis Screening

Published in IEEE Transactions on Medical Imaging, 2026, 2026

Keywords: Gait Recognition, Evidential Deep Learning

Recommended citation: Haiqing Li, Jingquan Yan, Yinhao Wu, Yuzhi Guo, Hehuan Ma, Wenliang Zhong, Jean Gao, Junzhou Huang. "Uncertainty-Aware Multimodal Gait Representation Learning for Scoliosis Screening." IEEE Transactions on Medical Imaging, September 2026.

Talk 1 on Relevant Topic in Your Field

Published: March 01, 2012

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Tutorial 1 on Relevant Topic in Your Field

Published: March 01, 2013

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Talk 2 on Relevant Topic in Your Field

Published: February 01, 2014

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Conference Proceeding talk 3 on Relevant Topic in Your Field

Published: March 01, 2014

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Teaching experience 1

Undergraduate course, University 1, Department, 2014

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Teaching experience 2

Workshop, University 1, Department, 2015

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