Real-world Evidence

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

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

Preprint Download Project

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)

Publication Publication

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

Publication Project

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

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)

Publication Publication

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

Publication Project

Context-faithful Prompting for Large Language Models

Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen

March 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

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

Publication

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)

DOI Publication Github

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

Self-supervised self-supervision by combining deep learning and probabilistic logic

Hunter Lang, Hoifung Poon

AAAI-21 | February 2021

PDF

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.

PDF 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

Adversarial Training for Large Neural Language Models

Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao

April 2020

Publication Github Project

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

PDF

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

Publication Publication

Document-Level N-ary Relation Extraction with Multiscale Representation Learning

Robin Jia, Cliff Wong, Hoifung Poon

NAACL 2019 | June 2019

Publication Download

Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision

Hai Wang, Hoifung Poon

EMNLP 2018 | August 2018

Publication Github

EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation

Maxim Grechkin, Hoifung Poon, Bill Howe

July 2018

PDF

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

PDF PDF PDF Publication Publication

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

Publication

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

Publication Github Project

Distant Supervision For Relation Extraction Beyond The Sentence Boundary

Chris Quirk, Hoifung Poon

Fifteenth Conference of the European Association for Computational Linguistics (EACL), 2017 | September 2016

Publication Project

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

Publication Publication Download

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

Publication

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

Publication

Grounded Semantic Parsing for Complex Knowledge Extraction

Ankur P. Parikh, Hoifung Poon, Kristina Toutanova

NAACL HLT 2015 | June 2015

Publication Publication

Distant Supervision for Cancer Pathway Extraction from Text

Hoifung Poon, Kristina Toutanova, Chris Quirk

Pacific Symposium on Biocomputing, 2015 | January 2015

Publication Project

Literome: PubMed-scale Genomic Knowledge Base in the Cloud

Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman

Bioinformatics 2014 | May 2014

Publication Publication Project

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

Preprint Download Project

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)

Publication Publication

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

Publication Project

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

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)

Publication Publication

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

Publication Project

Context-faithful Prompting for Large Language Models

Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen

March 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

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)

DOI Publication Github

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

Self-supervised self-supervision by combining deep learning and probabilistic logic

Hunter Lang, Hoifung Poon

AAAI-21 | February 2021

PDF

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.

PDF Publication

Adversarial Training for Large Neural Language Models

Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao

April 2020

Publication Github Project

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

PDF

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

Publication Publication

Document-Level N-ary Relation Extraction with Multiscale Representation Learning

Robin Jia, Cliff Wong, Hoifung Poon

NAACL 2019 | June 2019

Publication Download

Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision

Hai Wang, Hoifung Poon

EMNLP 2018 | August 2018

Publication Github

EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation

Maxim Grechkin, Hoifung Poon, Bill Howe

July 2018

PDF

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

PDF PDF PDF Publication Publication

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

Publication Publication Download

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

Publication

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

Preprint Download Project

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

Publication Project

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

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

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

Preprint Download Project

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)

Publication Publication

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

Publication Project

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

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)

Publication Publication

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

Publication Project

Context-faithful Prompting for Large Language Models

Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen

March 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

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

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

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

PDF

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

Publication Publication

Document-Level N-ary Relation Extraction with Multiscale Representation Learning

Robin Jia, Cliff Wong, Hoifung Poon

NAACL 2019 | June 2019

Publication Download

EZLearn: Exploiting Organic Supervision in Large-Scale Data Annotation

Maxim Grechkin, Hoifung Poon, Bill Howe

July 2018

PDF

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

PDF PDF PDF Publication Publication

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

Publication

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

Publication Github Project

Distant Supervision For Relation Extraction Beyond The Sentence Boundary

Chris Quirk, Hoifung Poon

Fifteenth Conference of the European Association for Computational Linguistics (EACL), 2017 | September 2016

Publication Project

Distant Supervision for Cancer Pathway Extraction from Text

Hoifung Poon, Kristina Toutanova, Chris Quirk

Pacific Symposium on Biocomputing, 2015 | January 2015

Publication Project

Literome: PubMed-scale Genomic Knowledge Base in the Cloud

Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman

Bioinformatics 2014 | May 2014

Publication Publication Project

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

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)

DOI Publication Github

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

Adversarial Training for Large Neural Language Models

Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao

April 2020

Publication Github Project

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

Publication

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

Publication

Grounded Semantic Parsing for Complex Knowledge Extraction

Ankur P. Parikh, Hoifung Poon, Kristina Toutanova

NAACL HLT 2015 | June 2015

Publication 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

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.

PDF Publication

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

PDF PDF PDF Publication Publication

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

Publication

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

Publication Project

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

Context-faithful Prompting for Large Language Models

Wenxuan Zhou, Sheng Zhang, Hoifung Poon, Muhao Chen

March 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

Adversarial Training for Large Neural Language Models

Xiaodong Liu, Hao Cheng, Pengcheng He, Weizhu Chen, Yu Wang, Hoifung Poon, Jianfeng Gao

April 2020

Publication Github Project

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)

Publication Publication

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)

Publication Publication

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

Publication

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)

DOI Publication Github

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

Publication Publication

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

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

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

Preprint Download Project

Continual Contrastive Finetuning Improves Low-Resource Relation Extraction

Wenxuan Zhou, Sheng Zhang, Tristan Naumann, Muhao Chen, Hoifung Poon

ACL 2023 | May 2023

Publication

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

Publication Project

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

Self-supervised self-supervision by combining deep learning and probabilistic logic

Hunter Lang, Hoifung Poon

AAAI-21 | February 2021

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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

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Document-Level N-ary Relation Extraction with Multiscale Representation Learning

Robin Jia, Cliff Wong, Hoifung Poon

NAACL 2019 | June 2019

Publication Download

Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision

Hai Wang, Hoifung Poon

EMNLP 2018 | August 2018

Publication Github

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

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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

Publication Github Project

Distant Supervision For Relation Extraction Beyond The Sentence Boundary

Chris Quirk, Hoifung Poon

Fifteenth Conference of the European Association for Computational Linguistics (EACL), 2017 | September 2016

Publication Project

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

Publication Publication Download

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

Publication

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

Publication

Grounded Semantic Parsing for Complex Knowledge Extraction

Ankur P. Parikh, Hoifung Poon, Kristina Toutanova

NAACL HLT 2015 | June 2015

Publication Publication

Distant Supervision for Cancer Pathway Extraction from Text

Hoifung Poon, Kristina Toutanova, Chris Quirk

Pacific Symposium on Biocomputing, 2015 | January 2015

Publication Project

Literome: PubMed-scale Genomic Knowledge Base in the Cloud

Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman

Bioinformatics 2014 | May 2014

Publication Publication Project

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.

PDF Publication