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
Real-world Evidence
Advancing health at the speed of AI
Publications
Publications by Year
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From Medprompt to o1: Exploration of Run-Time Strategies for Medical Challenge Problems and Beyond
Harsha Nori, Naoto Usuyama, Nicholas King, S. McKinney, Xavier Fernandes, Sheng Zhang, Eric Horvitz
November 2024
MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging
Noel Codella, Yu Gu, Shrey Jain, Ho Hin Lee, Asma Ben Abacha, Alberto Santamaria-Pang, Will Guyman, Natieek Sangani, Sheng Zhang, Hoifung Poon, Stephanie Hyland, Shruthi Bannur, Javier Alvarez-Valle, Xue Li, John Garett, Alan McMillan, Gaurav Rajguru, Madhu Maddi, Nilesh Vijayrania, Reehan Bhimai, Nick Mecklenburg, Rupal Jain, Daniel Holstein, Naveen Gaur, Vijay Aski, Jenq-Neng Hwang, Thomas Lin, Ivan Tarapov, Matthew P Lungren, Mu Wei
October 2024
Does Reasoning Emerge? Examining the Probabilities of Causation in Large Language Models
NeurIPS 2024 | August 2024
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
MedFuzz: Exploring the Robustness of Large Language Models in Medical Question Answering
Robert Osazuwa Ness, Hayden Helm, Katie Matton, Sheng Zhang, Junaid Bajwa, Carey E. Priebe, Eric Horvitz
June 2024
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
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
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
Widespread Adoption of Precision Anticancer Therapies After Implementation of Pathologist-Directed Comprehensive Genomic Profiling Across a Large US Health System
A. Dowdell, R. Meng, A. Vita, B. Bapat, D. Hanes, Shu-Ching Chang, L. Harold, Cliff Wong, Hoifung Poon, Brock Schroeder, R. Weerasinghe, R. Leidner, W.J. Urba, Carlo Bifulco, B. Piening
JCO Oncology Practice | January 2024, Vol 20: pp. 1523-1532
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When an Image is Worth 1,024 x 1,024 Words: A Case Study in Computational Pathology
Wenhui Wang, Shuming Ma, Hanwen Xu, Naoto Usuyama, Jiayu Ding, Hoifung Poon, Furu Wei
December 2023
Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
November 2023
Exploring the Boundaries of GPT-4 in Radiology
Qianchu Liu, Stephanie Hyland, Shruthi Bannur, Kenza Bouzid, Daniel Coelho de Castro, Maria Teodora Wetscherek, Robert Tinn, Harshita Sharma, Fernando Pérez-García, Anton Schwaighofer, Pranav Rajpurkar, Sameer Tajdin Khanna, Hoifung Poon, Naoto Usuyama, Anja Thieme, Aditya Nori, Matthew P Lungren, Ozan Oktay, Javier Alvarez-Valle
EMNLP 2023 | October 2023
BiomedJourney: Counterfactual Biomedical Image Generation by Instruction-Learning from Multimodal Patient Journeys
Yu Gu, Jianwei Yang, Naoto Usuyama, Chunyuan Li, Sheng Zhang, Matthew P Lungren, Jianfeng Gao, Hoifung Poon
October 2023
UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition
Wenxuan Zhou, Sheng Zhang, Yu Gu, Muhao Chen, Hoifung Poon
ICLR 2024 | September 2023
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
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
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
Fine-tuning large neural language models for biomedical natural language processing
Rob Tinn, Hao Cheng, Yu Gu, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
Patterns | June 2023, Vol 4(4)
LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day
Chunyuan Li, Cliff Wong, Sheng Zhang, Naoto Usuyama, Haotian Liu, Jianwei Yang, Tristan Naumann, Hoifung Poon, Jianfeng Gao
June 2023
Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
ACL 2023 | May 2023
Self-Verification Improves Few-Shot Clinical Information Extraction
Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
May 2023
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
Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision
Sam Preston, Mu Wei, Rajesh Rao, Rob Tinn, Naoto Usuyama, Michael Lucas, Yu Gu, Roshanthi Weerasinghe, Soohee Lee, Brian Piening, Paul Tittel, Naveen Valluri, Tristan Naumann, Carlo Bifulco, Hoifung Poon
Patterns | April 2023, Vol 4(4)
Compositional Zero-Shot Domain Transfer with Text-to-Text Models
Fangyu Liu, Qianchu Liu, Shruthi Bannur, Fernando Pérez-García, Naoto Usuyama, Sheng Zhang, Tristan Naumann, Aditya Nori, Hoifung Poon, Javier Alvarez-Valle, Ozan Oktay, Stephanie Hyland
TACL 2023 | March 2023
Context-faithful Prompting for Large Language Models
Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen
March 2023
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
Multilingual translation for zero-shot biomedical classification using BioTranslator
Hanwen Xu, Addie Woicik, Hoifung Poon, Russ B. Altman, Sheng Wang
Nature Communications | February 2023, Vol 14
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BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining
Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, Tie-Yan Liu
Briefings in Bioinformatics | November 2022, Vol 23(6)
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
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
Predicting the impact of treatments over time with uncertainty aware neural differential equations
Edward De Brouwer, Javier González, Stephanie Hyland
International Conference on Artificial Intelligence and Statistics (AISTATS 2022) | February 2022
Learning Inconsistent Preferences with Gaussian Processes
Siu Lun Chau, Javier González, Dino Sejdinovic
International Conference on Artificial Intelligence and Statistics (AISTATS 2022) | January 2022
-
BayesIMP: Uncertainty Quantification for Causal Data Fusion
Siu Lun Chau, Jean-Francois Ton, Javier González, Yee The, Dino Sejdinovic
Neural Information Processing Systems (NeurIPS 2021) | December 2021
Dynamic Causal Bayesian Optimization
Virginia Aglietti, Neil Dhir, Javier González, Theodoros Damoulas
Neural Information Processing Systems (NeurIPS 2021) | November 2021
GIBBON: General-purpose Information-Based Bayesian Optimisation
Henry B. Moss, David S. Leslie, Javier González, Paul Rayson
Journal of Machine Learning Research | October 2021, Vol 22(235): pp. 1-49
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
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
Targeted Adversarial Training for Natural Language Understanding
Lis Pereira, Xiaodong Liu, Hao Cheng, Hoifung Poon, Jianfeng Gao, Ichiro Kobayashi
NAACL | June 2021
Self-supervised self-supervision by combining deep learning and probabilistic logic
Hunter Lang, Hoifung Poon
AAAI-21 | February 2021
-
CMT in TREC-COVID Round 2: Mitigating the Generalization Gaps from Web to Special Domain Search
Chenyan Xiong, Zhenghao Liu, Si Sun, Zhuyun Dai, Kaitao Zhang, Shi Yu, Zhiyuan Liu, Hoifung Poon, Jianfeng Gao, Paul Bennett
MSR-TR-2020-49 | November 2020
Published by Microsoft
The participation report of our top non-manual entry in TREC COVID Round 2.
Multi-task Causal Learning with Gaussian Processes
Virgina Aglietti, Theodoros Damoulas, Mauricio A. Álvarez, Javier González
Neural Information Processing Systems (NeurIPS 2020) | October 2020
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
BOSS: Bayesian Optimization over String Spaces
Henry B. Moss, Daniel Beck, Javier González, David S. Leslie, Paul Rayson
Neural Information Processing Systems (NeurIPS 2020) | August 2020
BINOCULARS for Efficient, Nonmyopic Sequential Experimental Design
Roman Garnett, Henry Chai, Javier González, Shali Jiang
International Conference on Machine Learning (ICML 2020) | June 2020
ePillID Dataset: A Low-Shot Fine-Grained Benchmark for Pill Identification
Naoto Usuyama, Natalia Larios Delgado, Amanda K. Hall, Jessica Lundin
CVPR 2020 | June 2020
Adversarial Training for Large Neural Language Models
Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao
April 2020
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DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain.
Yichong Xu, Xiaodong Liu, Chunyuan Li, Hoifung Poon, Jianfeng Gao
BioNLP 2019 | August 2019
Augmenting subnetwork inference with information extracted from the scientific literature
Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven
PLOS Computational Biology | June 2019
Document-Level N-ary Relation Extraction with Multiscale Representation Learning
Robin Jia, Cliff Wong, Hoifung Poon
NAACL 2019 | June 2019
Fast and accurate medication identification
Natalia Larios Delgado, Naoto Usuyama, Amanda K. Hall, Rebecca J. Hazen, Max Ma, Siva Sahu , Jessica Lundin
Nature Digital Medicine | February 2019
-
Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision
Hai Wang, Hoifung Poon
EMNLP 2018 | August 2018
EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation
Maxim Grechkin, Hoifung Poon, Bill Howe
July 2018
Opportunities in Machine Learning for Healthcare
Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
June 2018
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Estimating Accuracy from Unlabeled Data: A Probabilistic Logic Approach
Emmanouil Antonios Platanios, Hoifung Poon, Tom M. Mitchell, Eric Horvitz
Neural Information Processing Systems | December 2017
Molecularly-targeted drug combinations demonstrate selective effectiveness for myeloid and lymphoid-derived hematologic malignancies
Ravi Pandya, Bill Bolosky, Hoifung Poon, Brian Druker, OHSU, Jeffrey Tyner, OHSU
Proceedings of the National Academy of Sciences | August 2017
Cross-Sentence N-ary Relation Extraction with Graph LSTMs
Nanyun Peng, Hoifung Poon, Chris Quirk, Kristina Toutanova, Scott Yih
Transactions of the Association for Computational Linguistics (TACL), 2017 | June 2017
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Distant Supervision For Relation Extraction Beyond The Sentence Boundary
Fifteenth Conference of the European Association for Computational Linguistics (EACL), 2017 | September 2016
Compositional Learning of Embeddings for Relation Paths in Knowledge Bases and Text
Kristina Toutanova, Xi Victoria Lin, Scott Wen-tau Yih, Hoifung Poon, Chris Quirk
ACL | June 2016
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Representing Text for Joint Embedding of Text and Knowledge Bases
Kristina Toutanova, Danqi Chen, Patrick Pantel, Hoifung Poon, Pallavi Choudhury, Michael Gamon
Empirical Methods in Natural Language Processing (EMNLP) | September 2015
Model Selection for Type-Supervised Learning with application to POS Tagging
Kristina Toutanova, Waleed Ammar, Pallavi Chourdhury, Hoifung Poon, Pallavi Choudhury
The SIGNLL Conference on Computational Natural Language Learning | July 2015
Grounded Semantic Parsing for Complex Knowledge Extraction
Ankur P. Parikh, Hoifung Poon, Kristina Toutanova
NAACL HLT 2015 | June 2015
Distant Supervision for Cancer Pathway Extraction from Text
Hoifung Poon, Kristina Toutanova, Chris Quirk
Pacific Symposium on Biocomputing, 2015 | January 2015
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Literome: PubMed-scale Genomic Knowledge Base in the Cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman
Bioinformatics 2014 | May 2014
Publications by Research Area
-
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
From Medprompt to o1: Exploration of Run-Time Strategies for Medical Challenge Problems and Beyond
Harsha Nori, Naoto Usuyama, Nicholas King, S. McKinney, Xavier Fernandes, Sheng Zhang, Eric Horvitz
November 2024
MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging
Noel Codella, Yu Gu, Shrey Jain, Ho Hin Lee, Asma Ben Abacha, Alberto Santamaria-Pang, Will Guyman, Natieek Sangani, Sheng Zhang, Hoifung Poon, Stephanie Hyland, Shruthi Bannur, Javier Alvarez-Valle, Xue Li, John Garett, Alan McMillan, Gaurav Rajguru, Madhu Maddi, Nilesh Vijayrania, Reehan Bhimai, Nick Mecklenburg, Rupal Jain, Daniel Holstein, Naveen Gaur, Vijay Aski, Jenq-Neng Hwang, Thomas Lin, Ivan Tarapov, Matthew P Lungren, Mu Wei
October 2024
Does Reasoning Emerge? Examining the Probabilities of Causation in Large Language Models
NeurIPS 2024 | August 2024
MedFuzz: Exploring the Robustness of Large Language Models in Medical Question Answering
Robert Osazuwa Ness, Hayden Helm, Katie Matton, Sheng Zhang, Junaid Bajwa, Carey E. Priebe, Eric Horvitz
June 2024
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
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
Widespread Adoption of Precision Anticancer Therapies After Implementation of Pathologist-Directed Comprehensive Genomic Profiling Across a Large US Health System
A. Dowdell, R. Meng, A. Vita, B. Bapat, D. Hanes, Shu-Ching Chang, L. Harold, Cliff Wong, Hoifung Poon, Brock Schroeder, R. Weerasinghe, R. Leidner, W.J. Urba, Carlo Bifulco, B. Piening
JCO Oncology Practice | January 2024, Vol 20: pp. 1523-1532
When an Image is Worth 1,024 x 1,024 Words: A Case Study in Computational Pathology
Wenhui Wang, Shuming Ma, Hanwen Xu, Naoto Usuyama, Jiayu Ding, Hoifung Poon, Furu Wei
December 2023
Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
November 2023
Exploring the Boundaries of GPT-4 in Radiology
Qianchu Liu, Stephanie Hyland, Shruthi Bannur, Kenza Bouzid, Daniel Coelho de Castro, Maria Teodora Wetscherek, Robert Tinn, Harshita Sharma, Fernando Pérez-García, Anton Schwaighofer, Pranav Rajpurkar, Sameer Tajdin Khanna, Hoifung Poon, Naoto Usuyama, Anja Thieme, Aditya Nori, Matthew P Lungren, Ozan Oktay, Javier Alvarez-Valle
EMNLP 2023 | October 2023
UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition
Wenxuan Zhou, Sheng Zhang, Yu Gu, Muhao Chen, Hoifung Poon
ICLR 2024 | September 2023
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
Fine-tuning large neural language models for biomedical natural language processing
Rob Tinn, Hao Cheng, Yu Gu, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
Patterns | June 2023, Vol 4(4)
LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day
Chunyuan Li, Cliff Wong, Sheng Zhang, Naoto Usuyama, Haotian Liu, Jianwei Yang, Tristan Naumann, Hoifung Poon, Jianfeng Gao
June 2023
Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
ACL 2023 | May 2023
Self-Verification Improves Few-Shot Clinical Information Extraction
Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
May 2023
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
Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision
Sam Preston, Mu Wei, Rajesh Rao, Rob Tinn, Naoto Usuyama, Michael Lucas, Yu Gu, Roshanthi Weerasinghe, Soohee Lee, Brian Piening, Paul Tittel, Naveen Valluri, Tristan Naumann, Carlo Bifulco, Hoifung Poon
Patterns | April 2023, Vol 4(4)
Compositional Zero-Shot Domain Transfer with Text-to-Text Models
Fangyu Liu, Qianchu Liu, Shruthi Bannur, Fernando Pérez-García, Naoto Usuyama, Sheng Zhang, Tristan Naumann, Aditya Nori, Hoifung Poon, Javier Alvarez-Valle, Ozan Oktay, Stephanie Hyland
TACL 2023 | March 2023
Context-faithful Prompting for Large Language Models
Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen
March 2023
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
BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining
Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, Tie-Yan Liu
Briefings in Bioinformatics | November 2022, Vol 23(6)
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
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
Predicting the impact of treatments over time with uncertainty aware neural differential equations
Edward De Brouwer, Javier González, Stephanie Hyland
International Conference on Artificial Intelligence and Statistics (AISTATS 2022) | February 2022
Learning Inconsistent Preferences with Gaussian Processes
Siu Lun Chau, Javier González, Dino Sejdinovic
International Conference on Artificial Intelligence and Statistics (AISTATS 2022) | January 2022
BayesIMP: Uncertainty Quantification for Causal Data Fusion
Siu Lun Chau, Jean-Francois Ton, Javier González, Yee The, Dino Sejdinovic
Neural Information Processing Systems (NeurIPS 2021) | December 2021
Dynamic Causal Bayesian Optimization
Virginia Aglietti, Neil Dhir, Javier González, Theodoros Damoulas
Neural Information Processing Systems (NeurIPS 2021) | November 2021
GIBBON: General-purpose Information-Based Bayesian Optimisation
Henry B. Moss, David S. Leslie, Javier González, Paul Rayson
Journal of Machine Learning Research | October 2021, Vol 22(235): pp. 1-49
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
Targeted Adversarial Training for Natural Language Understanding
Lis Pereira, Xiaodong Liu, Hao Cheng, Hoifung Poon, Jianfeng Gao, Ichiro Kobayashi
NAACL | June 2021
Self-supervised self-supervision by combining deep learning and probabilistic logic
Hunter Lang, Hoifung Poon
AAAI-21 | February 2021
CMT in TREC-COVID Round 2: Mitigating the Generalization Gaps from Web to Special Domain Search
Chenyan Xiong, Zhenghao Liu, Si Sun, Zhuyun Dai, Kaitao Zhang, Shi Yu, Zhiyuan Liu, Hoifung Poon, Jianfeng Gao, Paul Bennett
MSR-TR-2020-49 | November 2020
Published by Microsoft
The participation report of our top non-manual entry in TREC COVID Round 2.
Multi-task Causal Learning with Gaussian Processes
Virgina Aglietti, Theodoros Damoulas, Mauricio A. Álvarez, Javier González
Neural Information Processing Systems (NeurIPS 2020) | October 2020
BOSS: Bayesian Optimization over String Spaces
Henry B. Moss, Daniel Beck, Javier González, David S. Leslie, Paul Rayson
Neural Information Processing Systems (NeurIPS 2020) | August 2020
BINOCULARS for Efficient, Nonmyopic Sequential Experimental Design
Roman Garnett, Henry Chai, Javier González, Shali Jiang
International Conference on Machine Learning (ICML 2020) | June 2020
Adversarial Training for Large Neural Language Models
Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao
April 2020
DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain.
Yichong Xu, Xiaodong Liu, Chunyuan Li, Hoifung Poon, Jianfeng Gao
BioNLP 2019 | August 2019
Augmenting subnetwork inference with information extracted from the scientific literature
Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven
PLOS Computational Biology | June 2019
Document-Level N-ary Relation Extraction with Multiscale Representation Learning
Robin Jia, Cliff Wong, Hoifung Poon
NAACL 2019 | June 2019
Fast and accurate medication identification
Natalia Larios Delgado, Naoto Usuyama, Amanda K. Hall, Rebecca J. Hazen, Max Ma, Siva Sahu , Jessica Lundin
Nature Digital Medicine | February 2019
Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision
Hai Wang, Hoifung Poon
EMNLP 2018 | August 2018
EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation
Maxim Grechkin, Hoifung Poon, Bill Howe
July 2018
Opportunities in Machine Learning for Healthcare
Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
June 2018
Estimating Accuracy from Unlabeled Data: A Probabilistic Logic Approach
Emmanouil Antonios Platanios, Hoifung Poon, Tom M. Mitchell, Eric Horvitz
Neural Information Processing Systems | December 2017
Compositional Learning of Embeddings for Relation Paths in Knowledge Bases and Text
Kristina Toutanova, Xi Victoria Lin, Scott Wen-tau Yih, Hoifung Poon, Chris Quirk
ACL | June 2016
Representing Text for Joint Embedding of Text and Knowledge Bases
Kristina Toutanova, Danqi Chen, Patrick Pantel, Hoifung Poon, Pallavi Choudhury, Michael Gamon
Empirical Methods in Natural Language Processing (EMNLP) | September 2015
-
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
From Medprompt to o1: Exploration of Run-Time Strategies for Medical Challenge Problems and Beyond
Harsha Nori, Naoto Usuyama, Nicholas King, S. McKinney, Xavier Fernandes, Sheng Zhang, Eric Horvitz
November 2024
MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging
Noel Codella, Yu Gu, Shrey Jain, Ho Hin Lee, Asma Ben Abacha, Alberto Santamaria-Pang, Will Guyman, Natieek Sangani, Sheng Zhang, Hoifung Poon, Stephanie Hyland, Shruthi Bannur, Javier Alvarez-Valle, Xue Li, John Garett, Alan McMillan, Gaurav Rajguru, Madhu Maddi, Nilesh Vijayrania, Reehan Bhimai, Nick Mecklenburg, Rupal Jain, Daniel Holstein, Naveen Gaur, Vijay Aski, Jenq-Neng Hwang, Thomas Lin, Ivan Tarapov, Matthew P Lungren, Mu Wei
October 2024
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
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
Widespread Adoption of Precision Anticancer Therapies After Implementation of Pathologist-Directed Comprehensive Genomic Profiling Across a Large US Health System
A. Dowdell, R. Meng, A. Vita, B. Bapat, D. Hanes, Shu-Ching Chang, L. Harold, Cliff Wong, Hoifung Poon, Brock Schroeder, R. Weerasinghe, R. Leidner, W.J. Urba, Carlo Bifulco, B. Piening
JCO Oncology Practice | January 2024, Vol 20: pp. 1523-1532
When an Image is Worth 1,024 x 1,024 Words: A Case Study in Computational Pathology
Wenhui Wang, Shuming Ma, Hanwen Xu, Naoto Usuyama, Jiayu Ding, Hoifung Poon, Furu Wei
December 2023
Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
November 2023
Exploring the Boundaries of GPT-4 in Radiology
Qianchu Liu, Stephanie Hyland, Shruthi Bannur, Kenza Bouzid, Daniel Coelho de Castro, Maria Teodora Wetscherek, Robert Tinn, Harshita Sharma, Fernando Pérez-García, Anton Schwaighofer, Pranav Rajpurkar, Sameer Tajdin Khanna, Hoifung Poon, Naoto Usuyama, Anja Thieme, Aditya Nori, Matthew P Lungren, Ozan Oktay, Javier Alvarez-Valle
EMNLP 2023 | October 2023
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
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
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
Fine-tuning large neural language models for biomedical natural language processing
Rob Tinn, Hao Cheng, Yu Gu, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
Patterns | June 2023, Vol 4(4)
LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day
Chunyuan Li, Cliff Wong, Sheng Zhang, Naoto Usuyama, Haotian Liu, Jianwei Yang, Tristan Naumann, Hoifung Poon, Jianfeng Gao
June 2023
Self-Verification Improves Few-Shot Clinical Information Extraction
Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
May 2023
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
Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision
Sam Preston, Mu Wei, Rajesh Rao, Rob Tinn, Naoto Usuyama, Michael Lucas, Yu Gu, Roshanthi Weerasinghe, Soohee Lee, Brian Piening, Paul Tittel, Naveen Valluri, Tristan Naumann, Carlo Bifulco, Hoifung Poon
Patterns | April 2023, Vol 4(4)
Compositional Zero-Shot Domain Transfer with Text-to-Text Models
Fangyu Liu, Qianchu Liu, Shruthi Bannur, Fernando Pérez-García, Naoto Usuyama, Sheng Zhang, Tristan Naumann, Aditya Nori, Hoifung Poon, Javier Alvarez-Valle, Ozan Oktay, Stephanie Hyland
TACL 2023 | March 2023
Context-faithful Prompting for Large Language Models
Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen
March 2023
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
Multilingual translation for zero-shot biomedical classification using BioTranslator
Hanwen Xu, Addie Woicik, Hoifung Poon, Russ B. Altman, Sheng Wang
Nature Communications | February 2023, Vol 14
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
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
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
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
DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain.
Yichong Xu, Xiaodong Liu, Chunyuan Li, Hoifung Poon, Jianfeng Gao
BioNLP 2019 | August 2019
Augmenting subnetwork inference with information extracted from the scientific literature
Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven
PLOS Computational Biology | June 2019
Document-Level N-ary Relation Extraction with Multiscale Representation Learning
Robin Jia, Cliff Wong, Hoifung Poon
NAACL 2019 | June 2019
Fast and accurate medication identification
Natalia Larios Delgado, Naoto Usuyama, Amanda K. Hall, Rebecca J. Hazen, Max Ma, Siva Sahu , Jessica Lundin
Nature Digital Medicine | February 2019
EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation
Maxim Grechkin, Hoifung Poon, Bill Howe
July 2018
Opportunities in Machine Learning for Healthcare
Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
June 2018
Estimating Accuracy from Unlabeled Data: A Probabilistic Logic Approach
Emmanouil Antonios Platanios, Hoifung Poon, Tom M. Mitchell, Eric Horvitz
Neural Information Processing Systems | December 2017
Molecularly-targeted drug combinations demonstrate selective effectiveness for myeloid and lymphoid-derived hematologic malignancies
Ravi Pandya, Bill Bolosky, Hoifung Poon, Brian Druker, OHSU, Jeffrey Tyner, OHSU
Proceedings of the National Academy of Sciences | August 2017
Cross-Sentence N-ary Relation Extraction with Graph LSTMs
Nanyun Peng, Hoifung Poon, Chris Quirk, Kristina Toutanova, Scott Yih
Transactions of the Association for Computational Linguistics (TACL), 2017 | June 2017
Distant Supervision For Relation Extraction Beyond The Sentence Boundary
Fifteenth Conference of the European Association for Computational Linguistics (EACL), 2017 | September 2016
Distant Supervision for Cancer Pathway Extraction from Text
Hoifung Poon, Kristina Toutanova, Chris Quirk
Pacific Symposium on Biocomputing, 2015 | January 2015
Literome: PubMed-scale Genomic Knowledge Base in the Cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman
Bioinformatics 2014 | May 2014
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MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging
Noel Codella, Yu Gu, Shrey Jain, Ho Hin Lee, Asma Ben Abacha, Alberto Santamaria-Pang, Will Guyman, Natieek Sangani, Sheng Zhang, Hoifung Poon, Stephanie Hyland, Shruthi Bannur, Javier Alvarez-Valle, Xue Li, John Garett, Alan McMillan, Gaurav Rajguru, Madhu Maddi, Nilesh Vijayrania, Reehan Bhimai, Nick Mecklenburg, Rupal Jain, Daniel Holstein, Naveen Gaur, Vijay Aski, Jenq-Neng Hwang, Thomas Lin, Ivan Tarapov, Matthew P Lungren, Mu Wei
October 2024
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
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
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
BiomedJourney: Counterfactual Biomedical Image Generation by Instruction-Learning from Multimodal Patient Journeys
Yu Gu, Jianwei Yang, Naoto Usuyama, Chunyuan Li, Sheng Zhang, Matthew P Lungren, Jianfeng Gao, Hoifung Poon
October 2023
LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day
Chunyuan Li, Cliff Wong, Sheng Zhang, Naoto Usuyama, Haotian Liu, Jianwei Yang, Tristan Naumann, Hoifung Poon, Jianfeng Gao
June 2023
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
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
ePillID Dataset: A Low-Shot Fine-Grained Benchmark for Pill Identification
Naoto Usuyama, Natalia Larios Delgado, Amanda K. Hall, Jessica Lundin
CVPR 2020 | June 2020
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UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition
Wenxuan Zhou, Sheng Zhang, Yu Gu, Muhao Chen, Hoifung Poon
ICLR 2024 | September 2023
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
BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining
Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, Tie-Yan Liu
Briefings in Bioinformatics | November 2022, Vol 23(6)
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
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
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
Adversarial Training for Large Neural Language Models
Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao
April 2020
Representing Text for Joint Embedding of Text and Knowledge Bases
Kristina Toutanova, Danqi Chen, Patrick Pantel, Hoifung Poon, Pallavi Choudhury, Michael Gamon
Empirical Methods in Natural Language Processing (EMNLP) | September 2015
Model Selection for Type-Supervised Learning with application to POS Tagging
Kristina Toutanova, Waleed Ammar, Pallavi Chourdhury, Hoifung Poon, Pallavi Choudhury
The SIGNLL Conference on Computational Natural Language Learning | July 2015
Grounded Semantic Parsing for Complex Knowledge Extraction
Ankur P. Parikh, Hoifung Poon, Kristina Toutanova
NAACL HLT 2015 | June 2015
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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
CMT in TREC-COVID Round 2: Mitigating the Generalization Gaps from Web to Special Domain Search
Chenyan Xiong, Zhenghao Liu, Si Sun, Zhuyun Dai, Kaitao Zhang, Shi Yu, Zhiyuan Liu, Hoifung Poon, Jianfeng Gao, Paul Bennett
MSR-TR-2020-49 | November 2020
Published by Microsoft
The participation report of our top non-manual entry in TREC COVID Round 2.
-
Estimating Accuracy from Unlabeled Data: A Probabilistic Logic Approach
Emmanouil Antonios Platanios, Hoifung Poon, Tom M. Mitchell, Eric Horvitz
Neural Information Processing Systems | December 2017
-
Targeted Adversarial Training for Natural Language Understanding
Lis Pereira, Xiaodong Liu, Hao Cheng, Hoifung Poon, Jianfeng Gao, Ichiro Kobayashi
NAACL | June 2021
-
Molecularly-targeted drug combinations demonstrate selective effectiveness for myeloid and lymphoid-derived hematologic malignancies
Ravi Pandya, Bill Bolosky, Hoifung Poon, Brian Druker, OHSU, Jeffrey Tyner, OHSU
Proceedings of the National Academy of Sciences | August 2017
Publications by Type
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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
Widespread Adoption of Precision Anticancer Therapies After Implementation of Pathologist-Directed Comprehensive Genomic Profiling Across a Large US Health System
A. Dowdell, R. Meng, A. Vita, B. Bapat, D. Hanes, Shu-Ching Chang, L. Harold, Cliff Wong, Hoifung Poon, Brock Schroeder, R. Weerasinghe, R. Leidner, W.J. Urba, Carlo Bifulco, B. Piening
JCO Oncology Practice | January 2024, Vol 20: pp. 1523-1532
Fine-tuning large neural language models for biomedical natural language processing
Rob Tinn, Hao Cheng, Yu Gu, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
Patterns | June 2023, Vol 4(4)
Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision
Sam Preston, Mu Wei, Rajesh Rao, Rob Tinn, Naoto Usuyama, Michael Lucas, Yu Gu, Roshanthi Weerasinghe, Soohee Lee, Brian Piening, Paul Tittel, Naveen Valluri, Tristan Naumann, Carlo Bifulco, Hoifung Poon
Patterns | April 2023, Vol 4(4)
Multilingual translation for zero-shot biomedical classification using BioTranslator
Hanwen Xu, Addie Woicik, Hoifung Poon, Russ B. Altman, Sheng Wang
Nature Communications | February 2023, Vol 14
BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining
Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, Tie-Yan Liu
Briefings in Bioinformatics | November 2022, Vol 23(6)
GIBBON: General-purpose Information-Based Bayesian Optimisation
Henry B. Moss, David S. Leslie, Javier González, Paul Rayson
Journal of Machine Learning Research | October 2021, Vol 22(235): pp. 1-49
Augmenting subnetwork inference with information extracted from the scientific literature
Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven
PLOS Computational Biology | June 2019
Fast and accurate medication identification
Natalia Larios Delgado, Naoto Usuyama, Amanda K. Hall, Rebecca J. Hazen, Max Ma, Siva Sahu , Jessica Lundin
Nature Digital Medicine | February 2019
Molecularly-targeted drug combinations demonstrate selective effectiveness for myeloid and lymphoid-derived hematologic malignancies
Ravi Pandya, Bill Bolosky, Hoifung Poon, Brian Druker, OHSU, Jeffrey Tyner, OHSU
Proceedings of the National Academy of Sciences | August 2017
-
From Medprompt to o1: Exploration of Run-Time Strategies for Medical Challenge Problems and Beyond
Harsha Nori, Naoto Usuyama, Nicholas King, S. McKinney, Xavier Fernandes, Sheng Zhang, Eric Horvitz
November 2024
MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging
Noel Codella, Yu Gu, Shrey Jain, Ho Hin Lee, Asma Ben Abacha, Alberto Santamaria-Pang, Will Guyman, Natieek Sangani, Sheng Zhang, Hoifung Poon, Stephanie Hyland, Shruthi Bannur, Javier Alvarez-Valle, Xue Li, John Garett, Alan McMillan, Gaurav Rajguru, Madhu Maddi, Nilesh Vijayrania, Reehan Bhimai, Nick Mecklenburg, Rupal Jain, Daniel Holstein, Naveen Gaur, Vijay Aski, Jenq-Neng Hwang, Thomas Lin, Ivan Tarapov, Matthew P Lungren, Mu Wei
October 2024
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
MedFuzz: Exploring the Robustness of Large Language Models in Medical Question Answering
Robert Osazuwa Ness, Hayden Helm, Katie Matton, Sheng Zhang, Junaid Bajwa, Carey E. Priebe, Eric Horvitz
June 2024
Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine
Harsha Nori, Yin Tat Lee, Sheng Zhang, Dean Carignan, Richard Edgar, Nicolo Fusi, Nicholas King, Jonathan Larson, Yuanzhi Li, Weishung Liu, Renqian Luo, Scott Mayer McKinney, Robert Osazuwa Ness, Hoifung Poon, Tao Qin, Naoto Usuyama, Chris White, Eric Horvitz
November 2023
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
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
-
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
Does Reasoning Emerge? Examining the Probabilities of Causation in Large Language Models
NeurIPS 2024 | August 2024
Exploring the Boundaries of GPT-4 in Radiology
Qianchu Liu, Stephanie Hyland, Shruthi Bannur, Kenza Bouzid, Daniel Coelho de Castro, Maria Teodora Wetscherek, Robert Tinn, Harshita Sharma, Fernando Pérez-García, Anton Schwaighofer, Pranav Rajpurkar, Sameer Tajdin Khanna, Hoifung Poon, Naoto Usuyama, Anja Thieme, Aditya Nori, Matthew P Lungren, Ozan Oktay, Javier Alvarez-Valle
EMNLP 2023 | October 2023
UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition
Wenxuan Zhou, Sheng Zhang, Yu Gu, Muhao Chen, Hoifung Poon
ICLR 2024 | September 2023
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
Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
ACL 2023 | May 2023
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
Compositional Zero-Shot Domain Transfer with Text-to-Text Models
Fangyu Liu, Qianchu Liu, Shruthi Bannur, Fernando Pérez-García, Naoto Usuyama, Sheng Zhang, Tristan Naumann, Aditya Nori, Hoifung Poon, Javier Alvarez-Valle, Ozan Oktay, Stephanie Hyland
TACL 2023 | March 2023
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
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
Predicting the impact of treatments over time with uncertainty aware neural differential equations
Edward De Brouwer, Javier González, Stephanie Hyland
International Conference on Artificial Intelligence and Statistics (AISTATS 2022) | February 2022
Learning Inconsistent Preferences with Gaussian Processes
Siu Lun Chau, Javier González, Dino Sejdinovic
International Conference on Artificial Intelligence and Statistics (AISTATS 2022) | January 2022
BayesIMP: Uncertainty Quantification for Causal Data Fusion
Siu Lun Chau, Jean-Francois Ton, Javier González, Yee The, Dino Sejdinovic
Neural Information Processing Systems (NeurIPS 2021) | December 2021
Dynamic Causal Bayesian Optimization
Virginia Aglietti, Neil Dhir, Javier González, Theodoros Damoulas
Neural Information Processing Systems (NeurIPS 2021) | November 2021
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
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
Targeted Adversarial Training for Natural Language Understanding
Lis Pereira, Xiaodong Liu, Hao Cheng, Hoifung Poon, Jianfeng Gao, Ichiro Kobayashi
NAACL | June 2021
Self-supervised self-supervision by combining deep learning and probabilistic logic
Hunter Lang, Hoifung Poon
AAAI-21 | February 2021
Multi-task Causal Learning with Gaussian Processes
Virgina Aglietti, Theodoros Damoulas, Mauricio A. Álvarez, Javier González
Neural Information Processing Systems (NeurIPS 2020) | October 2020
BOSS: Bayesian Optimization over String Spaces
Henry B. Moss, Daniel Beck, Javier González, David S. Leslie, Paul Rayson
Neural Information Processing Systems (NeurIPS 2020) | August 2020
BINOCULARS for Efficient, Nonmyopic Sequential Experimental Design
Roman Garnett, Henry Chai, Javier González, Shali Jiang
International Conference on Machine Learning (ICML 2020) | June 2020
ePillID Dataset: A Low-Shot Fine-Grained Benchmark for Pill Identification
Naoto Usuyama, Natalia Larios Delgado, Amanda K. Hall, Jessica Lundin
CVPR 2020 | June 2020
DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain.
Yichong Xu, Xiaodong Liu, Chunyuan Li, Hoifung Poon, Jianfeng Gao
BioNLP 2019 | August 2019
Document-Level N-ary Relation Extraction with Multiscale Representation Learning
Robin Jia, Cliff Wong, Hoifung Poon
NAACL 2019 | June 2019
Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision
Hai Wang, Hoifung Poon
EMNLP 2018 | August 2018
Estimating Accuracy from Unlabeled Data: A Probabilistic Logic Approach
Emmanouil Antonios Platanios, Hoifung Poon, Tom M. Mitchell, Eric Horvitz
Neural Information Processing Systems | December 2017
Cross-Sentence N-ary Relation Extraction with Graph LSTMs
Nanyun Peng, Hoifung Poon, Chris Quirk, Kristina Toutanova, Scott Yih
Transactions of the Association for Computational Linguistics (TACL), 2017 | June 2017
Distant Supervision For Relation Extraction Beyond The Sentence Boundary
Fifteenth Conference of the European Association for Computational Linguistics (EACL), 2017 | September 2016
Compositional Learning of Embeddings for Relation Paths in Knowledge Bases and Text
Kristina Toutanova, Xi Victoria Lin, Scott Wen-tau Yih, Hoifung Poon, Chris Quirk
ACL | June 2016
Representing Text for Joint Embedding of Text and Knowledge Bases
Kristina Toutanova, Danqi Chen, Patrick Pantel, Hoifung Poon, Pallavi Choudhury, Michael Gamon
Empirical Methods in Natural Language Processing (EMNLP) | September 2015
Model Selection for Type-Supervised Learning with application to POS Tagging
Kristina Toutanova, Waleed Ammar, Pallavi Chourdhury, Hoifung Poon, Pallavi Choudhury
The SIGNLL Conference on Computational Natural Language Learning | July 2015
Grounded Semantic Parsing for Complex Knowledge Extraction
Ankur P. Parikh, Hoifung Poon, Kristina Toutanova
NAACL HLT 2015 | June 2015
Distant Supervision for Cancer Pathway Extraction from Text
Hoifung Poon, Kristina Toutanova, Chris Quirk
Pacific Symposium on Biocomputing, 2015 | January 2015
Literome: PubMed-scale Genomic Knowledge Base in the Cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman
Bioinformatics 2014 | May 2014
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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
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
When an Image is Worth 1,024 x 1,024 Words: A Case Study in Computational Pathology
Wenhui Wang, Shuming Ma, Hanwen Xu, Naoto Usuyama, Jiayu Ding, Hoifung Poon, Furu Wei
December 2023
BiomedJourney: Counterfactual Biomedical Image Generation by Instruction-Learning from Multimodal Patient Journeys
Yu Gu, Jianwei Yang, Naoto Usuyama, Chunyuan Li, Sheng Zhang, Matthew P Lungren, Jianfeng Gao, Hoifung Poon
October 2023
LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day
Chunyuan Li, Cliff Wong, Sheng Zhang, Naoto Usuyama, Haotian Liu, Jianwei Yang, Tristan Naumann, Hoifung Poon, Jianfeng Gao
June 2023
Self-Verification Improves Few-Shot Clinical Information Extraction
Zelalem Gero, Chandan Singh, Hao Cheng, Tristan Naumann, Michel Galley, Jianfeng Gao, Hoifung Poon
May 2023
Context-faithful Prompting for Large Language Models
Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen
March 2023
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
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
Adversarial Training for Large Neural Language Models
Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao
April 2020
EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation
Maxim Grechkin, Hoifung Poon, Bill Howe
July 2018
Opportunities in Machine Learning for Healthcare
Marzyeh Ghassemi, Tristan Naumann, Peter Schulam, Andrew L. Beam, Rajesh Ranganath
June 2018
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CMT in TREC-COVID Round 2: Mitigating the Generalization Gaps from Web to Special Domain Search
Chenyan Xiong, Zhenghao Liu, Si Sun, Zhuyun Dai, Kaitao Zhang, Shi Yu, Zhiyuan Liu, Hoifung Poon, Jianfeng Gao, Paul Bennett
MSR-TR-2020-49 | November 2020
Published by Microsoft
The participation report of our top non-manual entry in TREC COVID Round 2.