Artificial Intelligence and Quantitative Pathology
- Contrastive Learning Enhances Fairness in Pathology Artificial Intelligence Systems.
Shih-Yen Lin*, Pei-Chen Tsai*, Fang-Yi Su*, Chun-Yen Chen, Fuchen Li, Junhan Zhao, Yuk Yeung Ho, Tsung-Lu Michael Lee, Elizabeth Healey, Po-Jen Lin, Ting-Wan Kao, Dmytro Vremenko, Thomas Roetzer-Pejrimovsky, Lynette Sholl, Deborah Dillon, Nancy U. Lin, David Meredith, Keith L. Ligon, Ying-Chun Lo, Nipon Chaisuriya, David J. Cook, Adelheid Woehrer, Jeffrey Meyerhardt, Shuji Ogino, MacLean P. Nasrallah, Jeffrey A. Golden, Sabina Signoretti, Jung-Hsien Chiang, Kun-Hsing Yu
Cell Reports Medicine. 2025 Dec 16;6(12):102527. [Pubmed] [Codes]
- Uncertainty-Aware Ensemble of Foundation Models Differentiates Glioblastoma from Its Mimics.
Junhan Zhao*, Shih-Yen Lin*, Raphaël Attias, Liza Mathews, Christian Engel, Guillaume Larghero, Dmytro Vremenko, Ting-Wan Kao, Tsung-Hua Lee, Yu-Hsuan Wang, Cheng Che Tsai, Eliana Marostica, Ying-Chun Lo, David Meredith, Keith L. Ligon, Omar Arnaout, Thomas Roetzer-Pejrimovsky, Shih-Chieh Lin, Natalie N.C. Shih, Nipon Chaisuriya, David J. Cook, Jung-Hsien Chiang, Chia-Jen Liu, Adelheid Woehrer, Jeffrey A. Golden, MacLean P. Nasrallah, Kun-Hsing Yu.
Nature Communications. 2025 Sep 29;16(1):8341. [Pubmed] [Codes]
- A Pathology Foundation Model for Cancer Diagnosis and Prognostic Prediction.
Xiyue Wang*, Junhan Zhao*, Eliana Marostica, Wei Yuan, Jietian Jin, Jiayu Zhang, Ruijiang Li, Hongping Tang, Kanran Wang, Yu Li, Fang Wang, Yulong Peng, Junyou Zhu, Jing Zhang, Christopher R. Jackson, Jun Zhang, Deborah Dillon, Nancy U. Lin, Lynette Sholl, Thomas Denize, David Meredith, Keith L. Ligon, Sabina Signoretti, Shuji Ogino, Jeffrey A. Golden, MacLean P. Nasrallah, Xiao Han, Sen Yang, Kun-Hsing Yu.
Nature. 2024 Oct;634(8035):970-978. [Pubmed] [Codes]
- Artificial Intelligence in Healthcare.
Kun-Hsing Yu, Andrew L. Beam, Isaac S. Kohane.
Nature Biomedical Engineering. 2018 Oct;2(10):719-731. [PubMed]
- Predicting Non-Small Cell Lung Cancer Prognosis by Fully Automated Microscopic Pathology Image Features.
Kun-Hsing Yu, Ce Zhang, Gerald J. Berry, Russ B. Altman, Christopher Ré, Daniel L. Rubin, Michael Snyder.
Nature Communications. 2016 Aug 16;7:12474. [PubMed] [Source Codes] [Dataset of Image Features]
- Quantitative Pathology Analysis and Diagnosis using Neural Networks.
Kun-Hsing Yu.
U.S. Patent 10,832,406. Patent assigned to Harvard University.
Integrative Pathology and Multi-Omics Analyses
- Histopathology Images Predicted Multi-Omics Aberrations and Prognoses in Colorectal Cancer Patients.
Pei-Chen Tsai, Tsung-Hua Lee, Kun-Chi Kuo, Fang-Yi Su, Tsung-Lu Michael Lee, Eliana Marostica, Tomotaka Ugai, Melissa Zhao, Mai Chan Lau, Juha P. Väyrynen, Marios Giannakis, Yasutoshi Takashima, Seyed Mousavi Kahaki, Kana Wu, Mingyang Song, Jeffrey A. Meyerhardt, Andrew T. Chan, Jung-Hsien Chiang, Jonathan Nowak, Shuji Ogino, Kun-Hsing Yu.
Nature Communications. 2023 Apr 13;14(1):2102. [Pubmed] [Codes]
- Development of a Histopathology Informatics Pipeline for Classification and Prediction of Clinical Outcome in Subtypes of Renal Cell Carcinoma.
Eliana Marostica, Rebecca Barber, Thomas Denize, Isaac S. Kohane, Sabina Signoretti, Jeffrey A Golden, Kun-Hsing Yu.
Clinical Cancer Research. 2021 May 15;27(10):2868-2878. [Pubmed] [Codes]
- Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction.
Kun-Hsing Yu, Michael R. Fitzpatrick, Luke Pappas, Warren Chan, Jessica Kung, Michael Snyder.
Bioinformatics. 2018 Jan 15;34(2):319-320. [PubMed] [Codes] [Running Server]
- Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.
Kun-Hsing Yu, Gerald J. Berry, Daniel L. Rubin, Christopher Ré, Russ B. Altman, Michael Snyder.
Cell Systems. 2017 Dec 27;5(6):620-627.e3. [PubMed]
- Deep Proteogenomic Characterization of Human Ovarian Cancer.
Hui Zhang, Tao Liu, Zhen Zhang, Samuel H Payne, Jason E McDermott, Jian-Ying Zhou, Vladislav A Petyuk, Lily Chen, Debjit Ray, Shisheng Sun, Feng Yang, Bai Zhang, Jing Wang, Seong Won Cha, Lijun Chen, Sunghee Woo, Punit Shah, Paul Aiyetan, Yuan Tian, Caitlin Choi, Marina A Gritsenko, Ronald J Moore, Matthew E Monroe, Kun-Hsing Yu, David Tabb, David Fenyo, Vineet Bafna, Joseph Wang, Ie-Ming Shih, Akhilesh Pandey, Bing Zhang, Michael Snyder, Doug Levine, Richard D Smith, Daniel W Chan, Karin D Rodland and the TCGA investigators.
Cell. 2016 Jul 28;166(3):755-65. [PubMed]
- Transcriptomic Analysis of Inter and Intra Patient Variation in hiPSC-Cardiomyocytes is Predictive of Patient-Specific Cardiotoxicity.
Elena Matsa, Paul W. Burridge, Kun-Hsing Yu, John H. Ahrens, Haodi Wu, Praveen Shukla, Jared M. Churko, Joseph D. Gold, Michael P. Snyder, Joseph C. Wu.
Cell Stem Cell. 2016 Sep 1;19(3):311-25. [PubMed]
Big Data in Medicine
- Medical Artificial Intelligence and Human Values.
Kun-Hsing Yu, Elizabeth Healey, Tze-Yun Leong, Isaac S. Kohane, Arjun K. Manrai.
New England Journal of Medicine. 2024 May 30;390(20):1895-1904. [Pubmed]
- Association of Race and Socioeconomic Disadvantage With Missed Telemedicine Visits for Pediatric Patients During the COVID-19 Pandemic.
Evan Brociner, Kun-Hsing Yu, Isaac S. Kohane, McGreggor Crowley.
JAMA Pediatrics. 2022 Sep 1;176(9):933-935. [PubMed]
- Real-World Data Analyses Unveiled the Immune-Related Adverse Effects of Immune Checkpoint Inhibitors Across Cancer Types.
Feicheng Wang, Shihao Yang, Nathan Palmer, Kathe Fox, Isaac S. Kohane, Katherine P. Liao, Kun-Hsing Yu*, S. C. Kou*.
npj Precision Oncology. 2021 Sep 10;5(1):82. [PubMed]
- Suicide Rates Among Adolescents and Young Adults in the United States, 2000-2017.
Oren Miron, Kun-Hsing Yu, Rachel Wilf-Miron, Isaac S. Kohane.
JAMA. 2019 Jun 18;321(23):2362-2364. [PubMed]
- Data-Driven Analyses Revealed the Comorbidity Landscape of Tuberous Sclerosis Complex.
Kun-Hsing Yu, Oren Miron, Nathan Palmer, Dario Lemos, Kathe Fox, S. C. Kou, Mustafa Sahin, Isaac S. Kohane.
Neurology. 2018 Nov 20;91(21):974-976. [PubMed]
A complete publication list could be found here.