Sitemap
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
Published:
This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
Portfolio item number 1
Short description of portfolio item number 1
Portfolio item number 2
Short description of portfolio item number 2
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.
Download Paper
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.
Download Paper
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: 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.
Download Paper
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.
Download Paper
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.
Download Paper
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.