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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
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Blog Post number 4
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Blog Post number 3
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Blog Post number 2
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Blog Post number 1
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portfolio
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publications
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.
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
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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