Tristan Naumann

Principal Researcher

Publications

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- LLaVA-Rad MIMIC-CXR Annotations
  
  Juan Manuel Zambrano Chaves (juanza), Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Akshay Chaudhari, Serena Yeung, Curtis Langlotz, Sheng Wang, Hoifung Poon
  
  January 2025
  
  Publication
- Attribute Structuring Improves LLM-Based Evaluation of Clinical Text Summaries
  
  Zelalem Gero, Chandan Singh, Yiqing Xie, Sheng Zhang, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  NeurIPS 2024 | December 2024
  
  DOI Publication Publication
- BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once
  
  Theodore Zhao, Yu Gu, Jianwei Yang, Naoto Usuyama, Ho Hin Lee, Tristan Naumann, Jianfeng Gao, Angela Crabtree, B. Piening, Carlo Bifulco, Mu-Hsin Wei, Hoifung Poon, Sheng Wang
  
  June 2024
  
  DOI Video
- A whole-slide foundation model for digital pathology from real-world data
  
  Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zelalem Gero, Javier González, Yu Gu, Yanbo Xu, Mu-Hsin Wei, Wenhui Wang, Shuming Ma, Furu Wei, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Jaylen Rosemon, Tucker Bower, Soohee Lee, R. Weerasinghe, Bill Wright, Ari Robicsek, Brian Piening, Carlo Bifulco, Sheng Wang, Hoifung Poon
  
  Nature | May 2024
  
  Publication DOI Publication
- Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation
  
  Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Hassan Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Serena Yeung-Levy, Curtis P. Langlotz, Sheng Wang, Hoifung Poon
  
  March 2024
  
  Publication
- BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Hanwen Xu, Jaspreet Bagga, Rob Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Andrea Tupini, Yu Wang, Matt Mazzola, Swadheen Shukla, Lars Liden, Jianfeng Gao, Matthew P Lungren, Tristan Naumann, Sheng Wang, Hoifung Poon
  
  January 2024
  
  Publication
- TRIALSCOPE: A Unifying Causal Framework for Scaling Real-World Evidence Generation with Biomedical Language Models
  
  Javier González, Cliff Wong, Zelalem Gero, Jaspreet Bagga, Risa Ueno, Isabel Chien, Eduard Orakvin, Emre Kiciman, Aditya Nori, R. Weerasinghe, R. Leidner, B. Piening, Tristan Naumann, C. Bifulco, Hoifung Poon
  
  ArXiv | November 2023, Vol abs/2311.01301
  
  DOI Publication Publication
- Scaling Clinical Trial Matching Using Large Language Models: A Case Study in Oncology
  
  Cliff Wong, Sheng Zhang, Yu Gu, Christine Moung, Jacob Abel, Naoto Usuyama, Roshanthi Weerasinghe, Brian Piening, Tristan Naumann, Carlo Bifulco, Hoifung Poon
  
  August 2023
  
  Publication
- Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events
  
  Yu Gu, Sheng Zhang, Naoto Usuyama, Yonas Woldesenbet, Cliff Wong, Praneeth Sanapathi, Mu Wei, Naveen Valluri, Erika Strandberg, Tristan Naumann, Hoifung Poon
  
  July 2023
  
  Publication
- What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization
  
  Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
  
  ACL 2023 | July 2023
  
  Publication
- Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
  
  Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
  
  ACL 2023 | May 2023
  
  Publication
- Self-Verification Improves Few-Shot Clinical Information Extraction
  
  Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
  
  May 2023
  
  Publication
- Diagnosing Transformers: Illuminating Feature Spaces for Clinical Decision-Making
  
  Aliyah R. Hsu, Yeshwanth Cherapanamjeri, Briton Park, Tristan Naumann, A. Odisho, Bin Yu
  
  ICLR 2024 | May 2023
  
  Publication
- Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Matthew P Lungren, Tristan Naumann, Hoifung Poon
  
  March 2023
  
  Publication
- Making the Most of Text Semantics to Improve Biomedical Vision-Language Processing
  
  Benedikt Boecking, Naoto Usuyama, Shruthi Bannur, Daniel Coelho de Castro, Anton Schwaighofer, Stephanie Hyland, Maria Teodora Wetscherek, Tristan Naumann, Aditya Nori, Javier Alvarez-Valle, Hoifung Poon, Ozan Oktay
  
  The European Conference on Computer Vision (ECCV) | October 2022
  
  Preprint Video Download Download Project
- Knowledge-Rich Self-Supervision for Biomedical Entity Linking
  
  Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  EMNLP 2022 | May 2022
  
  Publication
- Modular Self-Supervision for Document-Level Relation Extraction
  
  Sheng Zhang, Cliff Wong, Naoto Usuyama, Sarthak Jain, Tristan Naumann, Hoifung Poon
  
  2021 Empirical Methods in Natural Language Processing | September 2021
  
  Publication PDF
- Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature
  
  Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Rob Tinn, Cliff Wong, Naoto Usuyama, Rick Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz, Paul Bennett, Jianfeng Gao, Hoifung Poon
  
  KDD 2021 | August 2021
  
  Publication Publication Project
- Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing
  
  Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  August 2020
  
  PDF Video Download
- Leveraging text representations for clinical predictive tasks
  
  Tristan Naumann
  
  June 2018
  
  PhD Thesis: Massachusetts Institute of Technology | June 2018
  
  PDF
- Natural Language Processing for EHR-Based Computational Phenotyping
  
  Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo
  
  Computation and Language | June 2018
  
  Publication
- Opportunities in Machine Learning for Healthcare
  
  Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
  
  June 2018
  
  Publication
- Visualizing Patient Timelines in the Intensive Care Unit
  
  Dina Levy-Lambert, Jen J. Gong, Tristan Naumann, Tom J. Pollard, John V. Guttag
  
  June 2018
  
  Publication
- CliNER 2.0: Accessible and Accurate Clinical Concept Extraction
  
  Willie Boag, Elena Sergeeva, Saurabh Kulshreshtha, Peter Szolovits, Anna Rumshisky, Tristan Naumann
  
  March 2018
  
  Publication
- Towards the Creation of a Large Corpus of Synthetically-Identified Clinical Notes
  
  Willie Boag, Tristan Naumann, Peter Szolovits
  
  March 2018
  
  Publication

- LLaVA-Rad MIMIC-CXR Annotations
  
  Juan Manuel Zambrano Chaves (juanza), Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Akshay Chaudhari, Serena Yeung, Curtis Langlotz, Sheng Wang, Hoifung Poon
  
  January 2025
  
  Publication
- Attribute Structuring Improves LLM-Based Evaluation of Clinical Text Summaries
  
  Zelalem Gero, Chandan Singh, Yiqing Xie, Sheng Zhang, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  NeurIPS 2024 | December 2024
  
  DOI Publication Publication
- A whole-slide foundation model for digital pathology from real-world data
  
  Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zelalem Gero, Javier González, Yu Gu, Yanbo Xu, Mu-Hsin Wei, Wenhui Wang, Shuming Ma, Furu Wei, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Jaylen Rosemon, Tucker Bower, Soohee Lee, R. Weerasinghe, Bill Wright, Ari Robicsek, Brian Piening, Carlo Bifulco, Sheng Wang, Hoifung Poon
  
  Nature | May 2024
  
  Publication DOI Publication
- Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation
  
  Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Hassan Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Serena Yeung-Levy, Curtis P. Langlotz, Sheng Wang, Hoifung Poon
  
  March 2024
  
  Publication
- TRIALSCOPE: A Unifying Causal Framework for Scaling Real-World Evidence Generation with Biomedical Language Models
  
  Javier González, Cliff Wong, Zelalem Gero, Jaspreet Bagga, Risa Ueno, Isabel Chien, Eduard Orakvin, Emre Kiciman, Aditya Nori, R. Weerasinghe, R. Leidner, B. Piening, Tristan Naumann, C. Bifulco, Hoifung Poon
  
  ArXiv | November 2023, Vol abs/2311.01301
  
  DOI Publication Publication
- Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events
  
  Yu Gu, Sheng Zhang, Naoto Usuyama, Yonas Woldesenbet, Cliff Wong, Praneeth Sanapathi, Mu Wei, Naveen Valluri, Erika Strandberg, Tristan Naumann, Hoifung Poon
  
  July 2023
  
  Publication
- Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
  
  Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
  
  ACL 2023 | May 2023
  
  Publication
- Self-Verification Improves Few-Shot Clinical Information Extraction
  
  Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
  
  May 2023
  
  Publication
- Diagnosing Transformers: Illuminating Feature Spaces for Clinical Decision-Making
  
  Aliyah R. Hsu, Yeshwanth Cherapanamjeri, Briton Park, Tristan Naumann, A. Odisho, Bin Yu
  
  ICLR 2024 | May 2023
  
  Publication
- Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Matthew P Lungren, Tristan Naumann, Hoifung Poon
  
  March 2023
  
  Publication
- Making the Most of Text Semantics to Improve Biomedical Vision-Language Processing
  
  Benedikt Boecking, Naoto Usuyama, Shruthi Bannur, Daniel Coelho de Castro, Anton Schwaighofer, Stephanie Hyland, Maria Teodora Wetscherek, Tristan Naumann, Aditya Nori, Javier Alvarez-Valle, Hoifung Poon, Ozan Oktay
  
  The European Conference on Computer Vision (ECCV) | October 2022
  
  Preprint Video Download Download Project
- Knowledge-Rich Self-Supervision for Biomedical Entity Linking
  
  Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  EMNLP 2022 | May 2022
  
  Publication
- Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature
  
  Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Rob Tinn, Cliff Wong, Naoto Usuyama, Rick Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz, Paul Bennett, Jianfeng Gao, Hoifung Poon
  
  KDD 2021 | August 2021
  
  Publication Publication Project
- Leveraging text representations for clinical predictive tasks
  
  Tristan Naumann
  
  June 2018
  
  PhD Thesis: Massachusetts Institute of Technology | June 2018
  
  PDF
- Visualizing Patient Timelines in the Intensive Care Unit
  
  Dina Levy-Lambert, Jen J. Gong, Tristan Naumann, Tom J. Pollard, John V. Guttag
  
  June 2018
  
  Publication
- Opportunities in Machine Learning for Healthcare
  
  Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
  
  June 2018
  
  Publication
- Natural Language Processing for EHR-Based Computational Phenotyping
  
  Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo
  
  Computation and Language | June 2018
  
  Publication
- CliNER 2.0: Accessible and Accurate Clinical Concept Extraction
  
  Willie Boag, Elena Sergeeva, Saurabh Kulshreshtha, Peter Szolovits, Anna Rumshisky, Tristan Naumann
  
  March 2018
  
  Publication
- Towards the Creation of a Large Corpus of Synthetically-Identified Clinical Notes
  
  Willie Boag, Tristan Naumann, Peter Szolovits
  
  March 2018
  
  Publication
- LLaVA-Rad MIMIC-CXR Annotations
  
  Juan Manuel Zambrano Chaves (juanza), Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Akshay Chaudhari, Serena Yeung, Curtis Langlotz, Sheng Wang, Hoifung Poon
  
  January 2025
  
  Publication
- BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once
  
  Theodore Zhao, Yu Gu, Jianwei Yang, Naoto Usuyama, Ho Hin Lee, Tristan Naumann, Jianfeng Gao, Angela Crabtree, B. Piening, Carlo Bifulco, Mu-Hsin Wei, Hoifung Poon, Sheng Wang
  
  June 2024
  
  DOI Video
- Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation
  
  Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Hassan Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Serena Yeung-Levy, Curtis P. Langlotz, Sheng Wang, Hoifung Poon
  
  March 2024
  
  Publication
- BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Hanwen Xu, Jaspreet Bagga, Rob Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Andrea Tupini, Yu Wang, Matt Mazzola, Swadheen Shukla, Lars Liden, Jianfeng Gao, Matthew P Lungren, Tristan Naumann, Sheng Wang, Hoifung Poon
  
  January 2024
  
  Publication
- Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Matthew P Lungren, Tristan Naumann, Hoifung Poon
  
  March 2023
  
  Publication
- Making the Most of Text Semantics to Improve Biomedical Vision-Language Processing
  
  Benedikt Boecking, Naoto Usuyama, Shruthi Bannur, Daniel Coelho de Castro, Anton Schwaighofer, Stephanie Hyland, Maria Teodora Wetscherek, Tristan Naumann, Aditya Nori, Javier Alvarez-Valle, Hoifung Poon, Ozan Oktay
  
  The European Conference on Computer Vision (ECCV) | October 2022
  
  Preprint Video Download Download Project
- LLaVA-Rad MIMIC-CXR Annotations
  
  Juan Manuel Zambrano Chaves (juanza), Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Akshay Chaudhari, Serena Yeung, Curtis Langlotz, Sheng Wang, Hoifung Poon
  
  January 2025
  
  Publication
- Attribute Structuring Improves LLM-Based Evaluation of Clinical Text Summaries
  
  Zelalem Gero, Chandan Singh, Yiqing Xie, Sheng Zhang, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  NeurIPS 2024 | December 2024
  
  DOI Publication Publication
- A whole-slide foundation model for digital pathology from real-world data
  
  Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zelalem Gero, Javier González, Yu Gu, Yanbo Xu, Mu-Hsin Wei, Wenhui Wang, Shuming Ma, Furu Wei, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Jaylen Rosemon, Tucker Bower, Soohee Lee, R. Weerasinghe, Bill Wright, Ari Robicsek, Brian Piening, Carlo Bifulco, Sheng Wang, Hoifung Poon
  
  Nature | May 2024
  
  Publication DOI Publication
- Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation
  
  Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Hassan Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Serena Yeung-Levy, Curtis P. Langlotz, Sheng Wang, Hoifung Poon
  
  March 2024
  
  Publication
- TRIALSCOPE: A Unifying Causal Framework for Scaling Real-World Evidence Generation with Biomedical Language Models
  
  Javier González, Cliff Wong, Zelalem Gero, Jaspreet Bagga, Risa Ueno, Isabel Chien, Eduard Orakvin, Emre Kiciman, Aditya Nori, R. Weerasinghe, R. Leidner, B. Piening, Tristan Naumann, C. Bifulco, Hoifung Poon
  
  ArXiv | November 2023, Vol abs/2311.01301
  
  DOI Publication Publication
- Scaling Clinical Trial Matching Using Large Language Models: A Case Study in Oncology
  
  Cliff Wong, Sheng Zhang, Yu Gu, Christine Moung, Jacob Abel, Naoto Usuyama, Roshanthi Weerasinghe, Brian Piening, Tristan Naumann, Carlo Bifulco, Hoifung Poon
  
  August 2023
  
  Publication
- Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events
  
  Yu Gu, Sheng Zhang, Naoto Usuyama, Yonas Woldesenbet, Cliff Wong, Praneeth Sanapathi, Mu Wei, Naveen Valluri, Erika Strandberg, Tristan Naumann, Hoifung Poon
  
  July 2023
  
  Publication
- What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization
  
  Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
  
  ACL 2023 | July 2023
  
  Publication
- Self-Verification Improves Few-Shot Clinical Information Extraction
  
  Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
  
  May 2023
  
  Publication
- Diagnosing Transformers: Illuminating Feature Spaces for Clinical Decision-Making
  
  Aliyah R. Hsu, Yeshwanth Cherapanamjeri, Briton Park, Tristan Naumann, A. Odisho, Bin Yu
  
  ICLR 2024 | May 2023
  
  Publication
- Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Matthew P Lungren, Tristan Naumann, Hoifung Poon
  
  March 2023
  
  Publication
- Making the Most of Text Semantics to Improve Biomedical Vision-Language Processing
  
  Benedikt Boecking, Naoto Usuyama, Shruthi Bannur, Daniel Coelho de Castro, Anton Schwaighofer, Stephanie Hyland, Maria Teodora Wetscherek, Tristan Naumann, Aditya Nori, Javier Alvarez-Valle, Hoifung Poon, Ozan Oktay
  
  The European Conference on Computer Vision (ECCV) | October 2022
  
  Preprint Video Download Download Project
- Modular Self-Supervision for Document-Level Relation Extraction
  
  Sheng Zhang, Cliff Wong, Naoto Usuyama, Sarthak Jain, Tristan Naumann, Hoifung Poon
  
  2021 Empirical Methods in Natural Language Processing | September 2021
  
  Publication PDF
- Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature
  
  Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Rob Tinn, Cliff Wong, Naoto Usuyama, Rick Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz, Paul Bennett, Jianfeng Gao, Hoifung Poon
  
  KDD 2021 | August 2021
  
  Publication Publication Project
- Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing
  
  Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  August 2020
  
  PDF Video Download
- Leveraging text representations for clinical predictive tasks
  
  Tristan Naumann
  
  June 2018
  
  PhD Thesis: Massachusetts Institute of Technology | June 2018
  
  PDF
- Visualizing Patient Timelines in the Intensive Care Unit
  
  Dina Levy-Lambert, Jen J. Gong, Tristan Naumann, Tom J. Pollard, John V. Guttag
  
  June 2018
  
  Publication
- Opportunities in Machine Learning for Healthcare
  
  Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
  
  June 2018
  
  Publication
- Natural Language Processing for EHR-Based Computational Phenotyping
  
  Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo
  
  Computation and Language | June 2018
  
  Publication
- CliNER 2.0: Accessible and Accurate Clinical Concept Extraction
  
  Willie Boag, Elena Sergeeva, Saurabh Kulshreshtha, Peter Szolovits, Anna Rumshisky, Tristan Naumann
  
  March 2018
  
  Publication
- Towards the Creation of a Large Corpus of Synthetically-Identified Clinical Notes
  
  Willie Boag, Tristan Naumann, Peter Szolovits
  
  March 2018
  
  Publication
- What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization
  
  Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
  
  ACL 2023 | July 2023
  
  Publication
- Knowledge-Rich Self-Supervision for Biomedical Entity Linking
  
  Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  EMNLP 2022 | May 2022
  
  Publication
- Modular Self-Supervision for Document-Level Relation Extraction
  
  Sheng Zhang, Cliff Wong, Naoto Usuyama, Sarthak Jain, Tristan Naumann, Hoifung Poon
  
  2021 Empirical Methods in Natural Language Processing | September 2021
  
  Publication PDF
- Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature
  
  Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Rob Tinn, Cliff Wong, Naoto Usuyama, Rick Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz, Paul Bennett, Jianfeng Gao, Hoifung Poon
  
  KDD 2021 | August 2021
  
  Publication Publication Project
- Natural Language Processing for EHR-Based Computational Phenotyping
  
  Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo
  
  Computation and Language | June 2018
  
  Publication
- Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature
  
  Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Rob Tinn, Cliff Wong, Naoto Usuyama, Rick Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz, Paul Bennett, Jianfeng Gao, Hoifung Poon
  
  KDD 2021 | August 2021
  
  Publication Publication Project

- LLaVA-Rad MIMIC-CXR Annotations
  
  Juan Manuel Zambrano Chaves (juanza), Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Akshay Chaudhari, Serena Yeung, Curtis Langlotz, Sheng Wang, Hoifung Poon
  
  January 2025
  
  Publication
- Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation
  
  Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama (naotous), Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Hassan Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu-Hsin Wei, Tristan Naumann, Muhao Chen, Matthew P Lungren, Serena Yeung-Levy, Curtis P. Langlotz, Sheng Wang, Hoifung Poon
  
  March 2024
  
  Publication
- BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Hanwen Xu, Jaspreet Bagga, Rob Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Andrea Tupini, Yu Wang, Matt Mazzola, Swadheen Shukla, Lars Liden, Jianfeng Gao, Matthew P Lungren, Tristan Naumann, Sheng Wang, Hoifung Poon
  
  January 2024
  
  Publication
- Self-Verification Improves Few-Shot Clinical Information Extraction
  
  Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
  
  May 2023
  
  Publication
- Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing
  
  Sheng Zhang, Yanbo Xu, Naoto Usuyama, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Matthew P Lungren, Tristan Naumann, Hoifung Poon
  
  March 2023
  
  Publication
- Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing
  
  Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  August 2020
  
  PDF Video Download
- Visualizing Patient Timelines in the Intensive Care Unit
  
  Dina Levy-Lambert, Jen J. Gong, Tristan Naumann, Tom J. Pollard, John V. Guttag
  
  June 2018
  
  Publication
- Opportunities in Machine Learning for Healthcare
  
  Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
  
  June 2018
  
  Publication
- CliNER 2.0: Accessible and Accurate Clinical Concept Extraction
  
  Willie Boag, Elena Sergeeva, Saurabh Kulshreshtha, Peter Szolovits, Anna Rumshisky, Tristan Naumann
  
  March 2018
  
  Publication
- Towards the Creation of a Large Corpus of Synthetically-Identified Clinical Notes
  
  Willie Boag, Tristan Naumann, Peter Szolovits
  
  March 2018
  
  Publication
- A whole-slide foundation model for digital pathology from real-world data
  
  Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zelalem Gero, Javier González, Yu Gu, Yanbo Xu, Mu-Hsin Wei, Wenhui Wang, Shuming Ma, Furu Wei, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Jaylen Rosemon, Tucker Bower, Soohee Lee, R. Weerasinghe, Bill Wright, Ari Robicsek, Brian Piening, Carlo Bifulco, Sheng Wang, Hoifung Poon
  
  Nature | May 2024
  
  Publication DOI Publication
- TRIALSCOPE: A Unifying Causal Framework for Scaling Real-World Evidence Generation with Biomedical Language Models
  
  Javier González, Cliff Wong, Zelalem Gero, Jaspreet Bagga, Risa Ueno, Isabel Chien, Eduard Orakvin, Emre Kiciman, Aditya Nori, R. Weerasinghe, R. Leidner, B. Piening, Tristan Naumann, C. Bifulco, Hoifung Poon
  
  ArXiv | November 2023, Vol abs/2311.01301
  
  DOI Publication Publication
- Natural Language Processing for EHR-Based Computational Phenotyping
  
  Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo
  
  Computation and Language | June 2018
  
  Publication
- Attribute Structuring Improves LLM-Based Evaluation of Clinical Text Summaries
  
  Zelalem Gero, Chandan Singh, Yiqing Xie, Sheng Zhang, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  NeurIPS 2024 | December 2024
  
  DOI Publication Publication
- What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization
  
  Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
  
  ACL 2023 | July 2023
  
  Publication
- Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
  
  Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
  
  ACL 2023 | May 2023
  
  Publication
- Diagnosing Transformers: Illuminating Feature Spaces for Clinical Decision-Making
  
  Aliyah R. Hsu, Yeshwanth Cherapanamjeri, Briton Park, Tristan Naumann, A. Odisho, Bin Yu
  
  ICLR 2024 | May 2023
  
  Publication
- Making the Most of Text Semantics to Improve Biomedical Vision-Language Processing
  
  Benedikt Boecking, Naoto Usuyama, Shruthi Bannur, Daniel Coelho de Castro, Anton Schwaighofer, Stephanie Hyland, Maria Teodora Wetscherek, Tristan Naumann, Aditya Nori, Javier Alvarez-Valle, Hoifung Poon, Ozan Oktay
  
  The European Conference on Computer Vision (ECCV) | October 2022
  
  Preprint Video Download Download Project
- Knowledge-Rich Self-Supervision for Biomedical Entity Linking
  
  Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
  
  EMNLP 2022 | May 2022
  
  Publication
- Modular Self-Supervision for Document-Level Relation Extraction
  
  Sheng Zhang, Cliff Wong, Naoto Usuyama, Sarthak Jain, Tristan Naumann, Hoifung Poon
  
  2021 Empirical Methods in Natural Language Processing | September 2021
  
  Publication PDF
- Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature
  
  Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Rob Tinn, Cliff Wong, Naoto Usuyama, Rick Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz, Paul Bennett, Jianfeng Gao, Hoifung Poon
  
  KDD 2021 | August 2021
  
  Publication Publication Project
- BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once
  
  Theodore Zhao, Yu Gu, Jianwei Yang, Naoto Usuyama, Ho Hin Lee, Tristan Naumann, Jianfeng Gao, Angela Crabtree, B. Piening, Carlo Bifulco, Mu-Hsin Wei, Hoifung Poon, Sheng Wang
  
  June 2024
  
  DOI Video
- Scaling Clinical Trial Matching Using Large Language Models: A Case Study in Oncology
  
  Cliff Wong, Sheng Zhang, Yu Gu, Christine Moung, Jacob Abel, Naoto Usuyama, Roshanthi Weerasinghe, Brian Piening, Tristan Naumann, Carlo Bifulco, Hoifung Poon
  
  August 2023
  
  Publication
- Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events
  
  Yu Gu, Sheng Zhang, Naoto Usuyama, Yonas Woldesenbet, Cliff Wong, Praneeth Sanapathi, Mu Wei, Naveen Valluri, Erika Strandberg, Tristan Naumann, Hoifung Poon
  
  July 2023
  
  Publication
- Leveraging text representations for clinical predictive tasks
  
  Tristan Naumann
  
  June 2018
  
  PhD Thesis: Massachusetts Institute of Technology | June 2018
  
  PDF