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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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
Learning to Exploit Temporal Structure for Biomedical Vision-Language Processing
Shruthi Bannur, Stephanie Hyland, Flora Liu, Fernando Pérez-García, Maximilian Ilse, Daniel Coelho de Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Teodora Wetscherek, Matthew Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
The IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) | June 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
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
-
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
-
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
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.
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
-
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
-
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
-
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
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
The SIGNLL Conference on Computational Natural Language Learning
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
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
Learning to Exploit Temporal Structure for Biomedical Vision-Language Processing
Shruthi Bannur, Stephanie Hyland, Flora Liu, Fernando Pérez-García, Maximilian Ilse, Daniel Coelho de Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Teodora Wetscherek, Matthew Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
The IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) | June 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
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
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
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.
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
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
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
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
Learning to Exploit Temporal Structure for Biomedical Vision-Language Processing
Shruthi Bannur, Stephanie Hyland, Flora Liu, Fernando Pérez-García, Maximilian Ilse, Daniel Coelho de Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Teodora Wetscherek, Matthew Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
The IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) | June 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
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
EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation
Maxim Grechkin, Hoifung Poon, Bill Howe
July 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
-
Learning to Exploit Temporal Structure for Biomedical Vision-Language Processing
Shruthi Bannur, Stephanie Hyland, Flora Liu, Fernando Pérez-García, Maximilian Ilse, Daniel Coelho de Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Teodora Wetscherek, Matthew Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
The IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) | June 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
-
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
The SIGNLL Conference on Computational Natural Language Learning
Grounded Semantic Parsing for Complex Knowledge Extraction
Ankur P. Parikh, Hoifung Poon, Kristina Toutanova
NAACL HLT 2015 | June 2015
-
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
-
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
-
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
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
Learning to Exploit Temporal Structure for Biomedical Vision-Language Processing
Shruthi Bannur, Stephanie Hyland, Flora Liu, Fernando Pérez-García, Maximilian Ilse, Daniel Coelho de Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Teodora Wetscherek, Matthew Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
The IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) | June 2023
Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon
ACL 2023 | 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
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
Self-supervised self-supervision by combining deep learning and probabilistic logic
Hunter Lang, Hoifung Poon
AAAI-21 | February 2021
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
The SIGNLL Conference on Computational Natural Language Learning
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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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
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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)
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
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
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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.