iSimp: A sentence simplification system for biomedicail text. - Yifan Peng 002; Catalina O. Tudor; Manabu Torii; Cathy H. Wu; K. Vijay-Shanker (BIBM, 2012)

BioC: a minimalist approach to interoperability for biomedical text processing. - Donald C. Comeau; Rezarta Islamaj Dogan; Paolo Ciccarese; Kevin Bretonnel Cohen; Martin Krallinger; Florian Leitner; Zhiyong Lu; Yifan Peng 002; Fabio Rinaldi 001; Manabu Torii; Alfonso Valencia; Karin Verspoor; et al. (Database J. Biol. Databases Curation, 2013)

BioC interoperability track overview. - Donald C. Comeau; Riza Theresa Batista-Navarro; Hong-Jie Dai; Rezarta Islamaj Dogan; Antonio Jimeno-Yepes; Ritu Khare; Zhiyong Lu; Hernani Marques; Carolyn J. Mattingly; Mariana L. Neves; Yifan Peng 002; Rafal Rak; et al. (Database J. Biol. Databases Curation, 2014)

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. - Yifan Peng 002; Catalina O. Tudor; Manabu Torii; Cathy H. Wu; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2014)

A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. - Yifan Peng 002; Manabu Torii; Cathy H. Wu; K. Vijay-Shanker (BMC Bioinform., 2014)

An extended dependency graph for relation extraction in biomedical texts. - Yifan Peng 002; Samir Gupta; Cathy H. Wu; K. Vijay-Shanker (BioNLP@IJCNLP, 2015)

miRTex: A Text Mining System for miRNA-Gene Relation Extraction. - Gang Li 021; Karen E. Ross; Cecilia N. Arighi; Yifan Peng 002; Cathy H. Wu; K. Vijay-Shanker (PLoS Comput. Biol., 2015)

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - Sun Kim; Rezarta Islamaj Dogan; Andrew Chatr-aryamontri; Christie S. Chang; Rose Oughtred; Jennifer M. Rust; Riza Batista-Navarro; Jacob Carter; Sophia Ananiadou; Sérgio Matos; André Santos; David Campos 001; et al. (Database J. Biol. Databases Curation, 2016)

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. - Yifan Peng 002; Cecilia N. Arighi; Cathy H. Wu; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2016)

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. - Chih-Hsuan Wei; Yifan Peng 002; Robert Leaman; Allan Peter Davis; Carolyn J. Mattingly; Jiao Li 001; Thomas C. Wiegers; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

Improving chemical disease relation extraction with rich features and weakly labeled data. - Yifan Peng 002; Chih-Hsuan Wei; Zhiyong Lu (J. Cheminformatics, 2016)

Text Mining Radiology Reports for Deep Learning Radiology Images. - Yifan Peng 002; Xiaosong Wang 001; Le Lu 001; Mohammadhadi Bagheri; Ronald M. Summers; Zhiyong Lu (AMIA, 2017)

BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. - Rezarta Islamaj Dogan; Andrew Chatr-aryamontri; Sun Kim; Chih-Hsuan Wei; Yifan Peng 002; Donald C. Comeau; Zhiyong Lu (BioNLP, 2017)

Deep learning for extracting protein-protein interactions from biomedical literature. - Yifan Peng 002; Zhiyong Lu (BioNLP, 2017)

ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases. - Xiaosong Wang 001; Yifan Peng 002; Le Lu 001; Zhiyong Lu; Mohammadhadi Bagheri; Ronald M. Summers (CVPR, 2017)

NegBio: a high-performance tool for negation and uncertainty detection in radiology reports. - Yifan Peng 002; Xiaosong Wang 001; Le Lu 001; Mohammadhadi Bagheri; Ronald M. Summers; Zhiyong Lu (CoRR, 2017)

TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays. - Xiaosong Wang 001; Yifan Peng 002; Le Lu 001; Zhiyong Lu; Ronald M. Summers (CVPR, 2018)

Extracting chemical-protein relations with ensembles of SVM and deep learning models. - Yifan Peng 002; Anthony Rios; Ramakanth Kavuluru; Zhiyong Lu (Database J. Biol. Databases Curation, 2018)

Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models. - Yifan Peng 002; Anthony Rios; Ramakanth Kavuluru; Zhiyong Lu (CoRR, 2018)

DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs. - Yifan Peng 002; Shazia Dharssi; Qingyu Chen 001; Tiarnan D. Keenan; Elvira Agrón; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (CoRR, 2018)

A multi-task deep learning model for the classification of Age-related Macular Degeneration. - Qingyu Chen 001; Yifan Peng 002; Tiarnan D. Keenan; Shazia Dharssi; Elvira Agrón; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (CoRR, 2018)

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. - Alexis Allot; Yifan Peng 002; Chih-Hsuan Wei; Kyubum Lee; Lon Phan; Zhiyong Lu (Nucleic Acids Res., 2018)

ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on Weakly Supervised Classification and Localization of Common Thorax Diseases. - Xiaosong Wang 001; Yifan Peng 002; Le Lu 001; Zhiyong Lu; Mohammadhadi Bagheri; Ronald M. Summers (Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, 2019)

Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs. - Xiaosong Wang 001; Yifan Peng 002; Le Lu 001; Zhiyong Lu; Ronald M. Summers (Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, 2019)

A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. - Yifan Peng 002; Tiarnan D. Keenan; Qingyu Chen 001; Elvira Agrón; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (AMIA, 2019)

Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. - Yifan Peng 002; Shankai Yan; Zhiyong Lu (BioNLP@ACL, 2019)

Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology. - Ke Yan 006; Yifan Peng 002; Veit Sandfort; Mohammadhadi Bagheri; Zhiyong Lu; Ronald M. Summers (CVPR, 2019)

BioSentVec: creating sentence embeddings for biomedical texts. - Qingyu Chen 001; Yifan Peng 002; Zhiyong Lu (ICHI, 2019)

A self-attention based deep learning method for lesion attribute detection from CT reports. - Yifan Peng 002; Ke Yan 006; Veit Sandfort; Ronald M. Summers; Zhiyong Lu (ICHI, 2019)

Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports. - Ke Yan 006; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (ISBI, 2019)

MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. - Ke Yan 006; Youbao Tang; Yifan Peng 002; Veit Sandfort; Mohammadhadi Bagheri; Zhiyong Lu; Ronald M. Summers (MICCAI (6), 2019)

A deep learning approach for automated detection of geographic atrophy from color fundus photographs. - Tiarnan D. Keenan; Shazia Dharssi; Yifan Peng 002; Qingyu Chen 001; Elvira Agrón; Wai T. Wong; Zhiyong Lu; Emily Y. Chew (CoRR, 2019)

ML-Net: multi-label classification of biomedical texts with deep neural networks. - Jingcheng Du; Qingyu Chen 001; Yifan Peng 002; Yang Xiang 003; Cui Tao; Zhiyong Lu (J. Am. Medical Informatics Assoc., 2019)

Automatic recognition of abdominal lymph nodes from clinical text. - Yifan Peng 002; Sungwon Lee 003; Daniel C. Elton; Thomas C. Shen; Yuxing Tang; Qingyu Chen 001; Shuai Wang; Yingying Zhu 003; Ronald M. Summers; Zhiyong Lu (ClinicalNLP@EMNLP, 2020)

Detection of reticular pseudodrusen using deep learning. - Qingyu Chen 001; Tiarnan D. Keenan; Yifan Peng 002; Elvira Agrón; Christopher Hwang; Alisa T. Thavikulwat; Debora Lee; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (AMIA, 2020)

An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. - Yifan Peng 002; Qingyu Chen 001; Zhiyong Lu (BioNLP, 2020)

COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized Zero-Shot Diagnosis of Chest Radiographs. - Angshuman Paul; Thomas C. Shen; Niranjan Balachandar; Yuxing Tang; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (iMIMIC/MIL3ID/LABELS@MICCAI, 2020)

When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? - Xing He 003; Rui Zhang 028; Jordan Alpert; Sicheng Zhou; Terrence J. Adam; Aantaki Raisa; Yifan Peng 002; Hansi Zhang; Jiang Bian 001 (CoRR, 2020)

Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. - Lana Yeganova; Rezarta Islamaj Dogan; Qingyu Chen 001; Robert Leaman; Alexis Allot; Chih-Hsuan Wei; Donald C. Comeau; Won Kim 003; Yifan Peng 002; W. John Wilbur; Zhiyong Lu (CoRR, 2020)

Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration. - Qingyu Chen 001; Tiarnan D. L. Keenan; Alexis Allot; Yifan Peng 002; Elvira Agrón; Amitha Domalpally; Caroline C. W. Klaver; Daniel T. Luttikhuizen; Marcus H. Colyer; Catherine A. Cukras; Henry E. Wiley; M. Teresa Magone; et al. (CoRR, 2020)

Using Radiomics as Prior Knowledge for Abnormality Classification and Localization in Chest X-rays. - Yan Han 001; Chongyan Chen; Liyan Tang; Mingquan Lin; Ajay Jaiswal; Ying Ding 001; Yifan Peng 002 (CoRR, 2020)

Predicting risk of late age-related macular degeneration using deep learning. - Yifan Peng 002; Tiarnan D. Keenan; Qingyu Chen 001; Elvira Agrón; Alexis Allot; Wai T. Wong; Emily Y. Chew; Zhiyong Lu (npj Digit. Medicine, 2020)

Automated abnormality classification of chest radiographs using deep convolutional neural networks. - Yuxing Tang; Youbao Tang; Yifan Peng 002; Ke Yan 006; Mohammadhadi Bagheri; Bernadette A. Redd; Catherine J. Brandon; Zhiyong Lu; Mei Han; Jing Xiao 006; Ronald M. Summers (npj Digit. Medicine, 2020)

Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. - Gregory C. Ghahramani; Matthew Brendel; Mingquan Lin; Qingyu Chen 001; Tiarnan D. Keenan; Kun Chen 002; Emily Y. Chew; Zhiyong Lu; Yifan Peng 002; Fei Wang 001 (AMIA, 2021)

Using Radiomics as Prior Knowledge for Thorax Disease Classification and Localization in Chest X-rays. - Yan Han 001; Chongyan Chen; Liyan Tang; Mingquan Lin; Ajay Jaiswal; Song Wang 026; Ahmed H. Tewfik; George Shih; Ying Ding 001; Yifan Peng 002 (AMIA, 2021)

Improving BERT Model Using Contrastive Learning for Biomedical Relation Extraction. - Peng Su; Yifan Peng 002; K. Vijay-Shanker (BioNLP@NAACL-HLT, 2021)

SCALP - Supervised Contrastive Learning for Cardiopulmonary Disease Classification and Localization in Chest X-rays using Patient Metadata. - Ajay Jaiswal; Tianhao Li; Cyprian Zander; Yan Han 001; Justin F. Rousseau; Yifan Peng 002; Ying Ding 001 (ICDM, 2021)

An empirical study of using radiology reports and images to improve ICU-mortality prediction. - Mingquan Lin; Song Wang 026; Ying Ding 001; Lihui Zhao; Fei Wang 001; Yifan Peng 002 (ICHI, 2021)

Pneumonia Detection On Chest X-Ray Using Radiomic Features And Contrastive Learning. - Yan Han 001; Chongyan Chen; Ahmed H. Tewfik; Ying Ding 001; Yifan Peng 002 (ISBI, 2021)

Learning Few-Shot Chest X-Ray Diagnosis Using Images From The Published Scientific Literature. - Angshuman Paul; Thomas C. Shen; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (ISBI, 2021)

Improving Joint Learning of Chest X-Ray and Radiology Report by Word Region Alignment. - Zhanghexuan Ji; Mohammad Abuzar Shaikh; Dana Moukheiber; Sargur N. Srihari; Yifan Peng 002; Mingchen Gao (MLMI@MICCAI, 2021)

Detection of Lymph Nodes in T2 MRI Using Neural Network Ensembles. - Tejas Sudharshan Mathai; Sungwon Lee 003; Daniel C. Elton; Thomas C. Shen; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (MLMI@MICCAI, 2021)

RadBERT-CL: Factually-Aware Contrastive Learning For Radiology Report Classification. - Ajay Jaiswal; Liyan Tang; Meheli Ghosh; Justin F. Rousseau; Yifan Peng 002; Ying Ding 001 (ML4H@NeurIPS, 2021)

Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality. - Hyun Gi Lee; Evan Sholle; Ashley Beecy; Subhi J. Al'Aref; Yifan Peng 002 (NAACL-HLT, 2021)

Cross-Modal Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop. - Yan Han 001; Chongyan Chen; Ahmed H. Tewfik; Benjamin S. Glicksberg; Ying Ding 001; Yifan Peng 002; Zhangyang Wang (CoRR, 2021)

CU-UD: text-mining drug and chemical-protein interactions with ensembles of BERT-based models. - Mehmet Efruz Karabulut; K. Vijay-Shanker; Yifan Peng 002 (CoRR, 2021)

Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration. - Qingyu Chen 001; Tiarnan D. L. Keenan; Alexis Allot; Yifan Peng 002; Elvira Agrón; Amitha Domalpally; Caroline C. W. Klaver; Daniel T. Luttikhuizen; Marcus H. Colyer; Catherine A. Cukras; Henry E. Wiley; M. Teresa Magone; et al. (J. Am. Medical Informatics Assoc., 2021)

COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature. - Yifan Peng 002; Yuxing Tang; Sungwon Lee 003; Yingying Zhu 003; Ronald M. Summers; Zhiyong Lu (IEEE Trans. Big Data, 2021)

Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View Semantic Embedding With Self-Training. - Angshuman Paul; Thomas C. Shen; Sungwon Lee 003; Niranjan Balachandar; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (IEEE Trans. Medical Imaging, 2021)

Prompt-based Learning for Assertion Classification in Clinical Notes. - Song Wang 026; Liyan Tang; Akash Majety; Justin F. Rousseau; George Shih; Ying Ding 001; Yifan Peng 002 (AMIA, 2022)

Supervised pretraining through contrastive categorical positive samplings to improve COVID-19 mortality prediction. - Tingyi Wanyan; Mingquan Lin; Eyal Klang; Kartikeya M. Menon; Faris F. Gulamali; Ariful Azad; Yiye Zhang; Ying Ding 001; Zhangyang Wang; Fei Wang 001; Benjamin S. Glicksberg; Yifan Peng 002 (BCB, 2022)

EchoGen: Generating Conclusions from Echocardiogram Notes. - Liyan Tang; Shravan Kooragayalu; Yanshan Wang; Ying Ding 001; Greg Durrett; Justin F. Rousseau; Yifan Peng 002 (BioNLP@ACL, 2022)

Classifying Cyber-Risky Clinical Notes by Employing Natural Language Processing. - Suzanna Schmeelk; Martins Samuel Dogo; Braja Gopal Patra; Yifan Peng 002 (HICSS, 2022)

RoS-KD: A Robust Stochastic Knowledge Distillation Approach for Noisy Medical Imaging. - Ajay Jaiswal; Kumar Ashutosh; Justin F. Rousseau; Yifan Peng 002; Zhangyang Wang; Ying Ding 001 (ICDM, 2022)

Radiology Text Analysis System (RadText): Architecture and Evaluation. - Song Wang 026; Mingquan Lin; Ying Ding 001; George Shih; Zhiyong Lu; Yifan Peng 002 (ICHI, 2022)

Lymph node detection in T2 MRI with transformers. - Tejas Sudharshan Mathai; Sungwon Lee 003; Daniel C. Elton; Thomas C. Shen; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (Computer-Aided Diagnosis, 2022)

Long-Tailed Classification of Thorax Diseases on Chest X-Ray: A New Benchmark Study. - Gregory Holste; Song Wang 026; Ziyu Jiang; Thomas C. Shen; George Shih; Ronald M. Summers; Yifan Peng 002; Zhangyang Wang (DALI@MICCAI, 2022)

Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. - Junghwan Lee; Tingyi Wanyan; Qingyu Chen 001; Tiarnan D. L. Keenan; Benjamin S. Glicksberg; Emily Y. Chew; Zhiyong Lu; Fei Wang 001; Yifan Peng 002 (MLMI@MICCAI, 2022)

Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction. - Mingquan Lin; Lei Liu; Mae Gorden; Michael Kass; Sarah Van Tassel; Fei Wang 001; Yifan Peng 002 (MLMI@MICCAI, 2022)

Few-Shot Learning Geometric Ensemble for Multi-label Classification of Chest X-Rays. - Dana Moukheiber; Saurabh Mahindre; Lama Moukheiber; Mira Moukheiber; Song Wang 026; Chunwei Ma; George Shih; Yifan Peng 002; Mingchen Gao (DALI@MICCAI, 2022)

Knowledge-Augmented Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop. - Yan Han 001; Chongyan Chen; Ahmed H. Tewfik; Benjamin S. Glicksberg; Ying Ding 001; Yifan Peng 002; Zhangyang Wang (WACV, 2022)

Prior Knowledge Enhances Radiology Report Generation. - Song Wang 026; Liyan Tang; Mingquan Lin; George Shih; Ying Ding 001; Yifan Peng 002 (CoRR, 2022)

SODA: A Natural Language Processing Package to Extract Social Determinants of Health for Cancer Studies. - Zehao Yu 001; Xi Yang 015; Chong Dang; Prakash Adekkanattu; Braja Gopal Patra; Yifan Peng 002; Jyotishman Pathak; Debbie L. Wilson; Ching-Yuan Chang; Wei-Hsuan Lo-Ciganic; Thomas J. George; William R. Hogan; et al. (CoRR, 2022)

Design and validation of a FHIR-based EHR-driven phenotyping toolbox. - Pascal S. Brandt; Jennifer A. Pacheco; Prakash Adekkanattu; Evan Sholle; Sajjad Abedian; Daniel J. Stone; David Knaack; Jie Xu 012; Zhenxing Xu; Yifan Peng 002; Natalie C. Benda; Fei Wang 001; et al. (J. Am. Medical Informatics Assoc., 2022)

Trustworthy assertion classification through prompting. - Song Wang 026; Liyan Tang; Akash Majety; Justin F. Rousseau; George Shih; Ying Ding 001; Yifan Peng 002 (J. Biomed. Informatics, 2022)

Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images. - Shuai Wang; Yingying Zhu 003; Sungwon Lee 003; Daniel C. Elton; Thomas C. Shen; Youbao Tang; Yifan Peng 002; Zhiyong Lu; Ronald M. Summers (Medical Image Anal., 2022)

Robust convolutional neural networks against adversarial attacks on medical images. - Xiaoshuang Shi; Yifan Peng 002; Qingyu Chen 001; Tiarnan D. Keenan; Alisa T. Thavikulwat; Sungwon Lee 003; Yuxing Tang; Emily Y. Chew; Ronald M. Summers; Zhiyong Lu (Pattern Recognit., 2022)

Less Likely Brainstorming: Using Language Models to Generate Alternative Hypotheses. - Liyan Tang; Yifan Peng 002; Yanshan Wang; Ying Ding 001; Greg Durrett; Justin F. Rousseau (ACL (Findings), 2023)

Identification of Offensive Language in Social Media Using Prompt Learning. - Leilei Su; Zezheng Wang; Yifan Peng 002; Cong Sun 004 (ICHI, 2023)

Optimizing Embedding Space with Sub-categorical Supervised Pre-training: A Theoretical Approach Towards Improving Sepsis Prediction. - Tingyi Wanyan; Mingquan Lin; Ying Ding 001; Benjamin S. Glicksberg; Fei Wang 001; Yifan Peng 002 (ICHI, 2023)

How Does Pruning Impact Long-Tailed Multi-label Medical Image Classifiers? - Gregory Holste; Ziyu Jiang; Ajay Jaiswal; Maria Hanna; Shlomo Minkowitz; Alan C. Legasto; Joanna G. Escalon; Sharon Steinberger; Mark Bittman; Thomas C. Shen; Ying Ding 001; Ronald M. Summers; et al. (MICCAI (5), 2023)

Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports. - Qingqing Zhu; Tejas Sudharshan Mathai; Pritam Mukherjee; Yifan Peng 002; Ronald M. Summers; Zhiyong Lu (MICCAI (5), 2023)

How Good Is ChatGPT for Medication Evidence Synthesis? - Hao Liu 054; Yifan Peng 002; Chunhua Weng (MIE, 2023)

Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances. - Ajay Jaiswal; Tianlong Chen 001; Justin F. Rousseau; Yifan Peng 002; Ying Ding 001; Zhangyang Wang (WACV, 2023)

Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served patient populations. - Mingquan Lin; Yuyun Xiao; Bo-Jian Hou; Tingyi Wanyan; Mohit Manoj Sharma; Zhangyang Wang; Fei Wang 001; Sarah Van Tassel; Yifan Peng 002 (CoRR, 2023)

FactReranker: Fact-guided Reranker for Faithful Radiology Report Summarization. - Qianqian Xie; Jiayu Zhou; Yifan Peng 002; Fei Wang 001 (CoRR, 2023)

High-performance Data Management for Whole Slide Image Analysis in Digital Pathology. - Haoju Leng; Ruining Deng; Shunxing Bao; Dazheng Fang; Bryan A. Millis; Yucheng Tang; Haichun Yang; Xiao Wang 004; Yifan Peng 002; Lipeng Wan; Yuankai Huo (CoRR, 2023)

Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. - Gregory Holste; Yiliang Zhou; Song Wang 013; Ajay Jaiswal; Mingquan Lin; Sherry Zhuge; Yuzhe Yang 003; Dongkyun Kim; Trong-Hieu Nguyen Mau; Minh-Triet Tran; Jaehyup Jeong; Wongi Park; et al. (CoRR, 2023)

Leveraging Generative AI for Clinical Evidence Summarization Needs to Achieve Trustworthiness. - Gongbo Zhang; Qiao Jin 001; Denis Jered McInerney; Yong Chen 016; Fei Wang 001; Curtis L. Cole; Qian Yang 004; Yanshan Wang; Bradley A. Malin; Mor Peleg; Byron C. Wallace; Zhiyong Lu; et al. (CoRR, 2023)

EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension. - Tian Kang; Yingcheng Sun; Jae Hyun Kim; Casey N. Ta; Adler J. Perotte; Kayla Schiffer; Mutong Wu; Yang Zhao; Nour Moustafa-Fahmy; Yifan Peng 002; Chunhua Weng (J. Am. Medical Informatics Assoc., 2023)

Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare. - David Oniani; Jordan Hilsman; Yifan Peng 002; Ronald K. Poropatich; Jeremy C. Pamplin; Gary L. Legault; Yanshan Wang (npj Digit. Medicine, 2023)

Evaluating large language models on medical evidence summarization. - Liyan Tang; Zhaoyi Sun; Betina Ross S. Idnay; Jordan G. Nestor; Ali Soroush; Pierre A. Elias; Ziyang Xu; Ying Ding 001; Greg Durrett; Justin F. Rousseau; Chunhua Weng; Yifan Peng 002 (npj Digit. Medicine, 2023)

Editorial: Pattern recognition for healthcare analytics. - Inci M. Baytas; Yifan Peng 002; Arzucan Özgür (Frontiers Digit. Health, 2023)

Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays. - Yan Han 001; Gregory Holste; Ying Ding 001; Ahmed H. Tewfik; Yifan Peng 002; Zhangyang Wang (IEEE Trans. Medical Imaging, 2023)

Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access. - Mingquan Lin; Bo-Jian Hou; Swati Mishra 006; Tianyuan Yao; Yuankai Huo; Qian Yang 004; Fei Wang 001; George Shih; Yifan Peng 002 (Comput. Biol. Medicine, 2023)

Representing and utilizing clinical textual data for real world studies: An OHDSI approach. - Vipina Kuttichi Keloth; Juan M. Banda; Michael J. Gurley; Paul M. Heider; Georgina Kennedy; Hongfang Liu; Feifan Liu; Timothy Miller 002; Karthik Natarajan; Olga V. Patterson; Yifan Peng 002; Kalpana Raja; et al. (J. Biomed. Informatics, 2023)

An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives. - Song Wang 026; Yifang Dang; Zhaoyi Sun; Ying Ding 001; Jyotishman Pathak; Cui Tao; Yunyu Xiao; Yifan Peng 002 (J. Am. Medical Informatics Assoc., 2023)

A scoping review on multimodal deep learning in biomedical images and texts. - Zhaoyi Sun; Mingquan Lin; Qingqing Zhu; Qianqian Xie; Fei Wang 001; Zhiyong Lu; Yifan Peng 002 (J. Biomed. Informatics, 2023)

Suicide Risk Assessment on Social Media with Semi-Supervised Learning. - Max Lovitt; Haotian Ma; Song Wang 026; Yifan Peng 002 (IEEE Big Data, 2024)

Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups. - Richard Li Xu; Song Wang 026; Zewei Wang; Yuhan Zhang; Yunyu Xiao; Jyotishman Pathak; David Hodge; Yan Leng; S. Craig Watkins; Ying Ding 001; Yifan Peng 002 (ICHI, 2024)

A Span-based Model for Extracting Overlapping PICO Entities from RCT Publications. - Gongbo Zhang; Yiliang Zhou; Yan Hu; Hua Xu 001; Chunhua Weng; Yifan Peng 002 (CoRR, 2024)

Hidden Flaws Behind Expert-Level Accuracy of GPT-4 Vision in Medicine. - Qiao Jin 001; Fangyuan Chen; Yiliang Zhou; Ziyang Xu; Justin M. Cheung; Robert Chen; Ronald M. Summers; Justin F. Rousseau; Peiyun Ni; Marc J. Landsman; Sally L. Baxter; Subhi J. Al'Aref; et al. (CoRR, 2024)

Improving Fairness of Automated Chest X-ray Diagnosis by Contrastive Learning. - Mingquan Lin; Tianhao Li; Zhaoyi Sun; Gregory Holste; Ying Ding 001; Fei Wang 001; George Shih; Yifan Peng 002 (CoRR, 2024)

Evaluating GPT-4 with Vision on Detection of Radiological Findings on Chest Radiographs. - Yiliang Zhou; Hanley Ong; Patrick Kennedy; Carol C. Wu; Jacob Kazam; Keith Hentel; Adam E. Flanders; George Shih; Yifan Peng 002 (CoRR, 2024)

Uncovering Misattributed Suicide Causes through Annotation Inconsistency Detection in Death Investigation Notes. - Song Wang 026; Yiliang Zhou; Ziqiang Han; Cui Tao; Yunyu Xiao; Ying Ding 001; Joydeep Ghosh; Yifan Peng 002 (CoRR, 2024)

A Literature Review and Framework for Human Evaluation of Generative Large Language Models in Healthcare. - Thomas Yu Chow Tam; Sonish Sivarajkumar; Sumit Kapoor; Alisa V. Stolyar; Katelyn Polanska; Karleigh R. McCarthy; Hunter Osterhoudt; Xizhi Wu; Shyam Visweswaran; Sunyang Fu; Piyush Mathur; Giovanni E. Cacciamani; et al. (CoRR, 2024)

SDoH-GPT: Using Large Language Models to Extract Social Determinants of Health (SDoH). - Bernardo Consoli; Xizhi Wu; Song Wang 026; Xinyu Zhao; Yanshan Wang; Justin F. Rousseau; Tom Hartvigsen; Li Shen 001; Huanmei Wu; Yifan Peng 002; Qi Long; Tianlong Chen 001; et al. (CoRR, 2024)

Enhancing disease detection in radiology reports through fine-tuning lightweight LLM on weak labels. - Yishu Wei; Xindi Wang; Hanley Ong; Yiliang Zhou; Adam E. Flanders; George Shih; Yifan Peng 002 (CoRR, 2024)

Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. - Betina Idnay; Zihan Xu; William G. Adams; Mohammad Adibuzzaman; Nicholas R. Anderson 001; Neil Bahroos; Douglas S. Bell; Cody Bumgardner; Thomas R. Campion Jr.; Victor M. Castro; James J. Cimino; I. Glenn Cohen; et al. (CoRR, 2024)

DIRI: Adversarial Patient Reidentification with Large Language Models for Evaluating Clinical Text Anonymization. - John X. Morris; Thomas R. Campion Jr.; Sri Laasya Nutheti; Yifan Peng 002; Akhil Raj; Ramin Zabih; Curtis L. Cole (CoRR, 2024)

Demystifying Large Language Models for Medicine: A Primer. - Qiao Jin 001; Nicholas Wan; Robert Leaman; Shubo Tian; Zhizheng Wang; Yifan Yang 006; Zifeng Wang 008; Guangzhi Xiong; Po-Ting Lai; Qingqing Zhu; Benjamin Hou; Maame Sarfo-Gyamfi; et al. (CoRR, 2024)

Deciphering genomic codes using advanced NLP techniques: a scoping review. - Shuyan Cheng; Yishu Wei; Yiliang Zhou; Zihan Xu; Drew N. Wright; Jinze Liu; Yifan Peng 002 (CoRR, 2024)

A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models. - Gongbo Zhang; Zihan Xu; Qiao Jin 001; Fangyi Chen; Yilu Fang; Yi Liu 059; Justin F. Rousseau; Ziyang Xu; Zhiyong Lu; Chunhua Weng; Yifan Peng 002 (CoRR, 2024)

Semi-Supervised Learning from Small Annotated Data and Large Unlabeled Data for Fine-grained PICO Entity Recognition. - Fangyi Chen; Gongbo Zhang; Yilu Fang; Yifan Peng 002; Chunhua Weng (CoRR, 2024)

Large language models in biomedicine and health: current research landscape and future directions. - Zhiyong Lu; Yifan Peng 002; Trevor Cohen; Marzyeh Ghassemi; Chunhua Weng; Shubo Tian (J. Am. Medical Informatics Assoc., 2024)

Confidence score: a data-driven measure for inclusive systematic reviews considering unpublished preprints. - Jiayi Tong; Chongliang Luo; Yifei Sun; Rui Duan 004; M. Elle Saine; Lifeng Lin; Yifan Peng 002; Yiwen Lu; Anchita Batra; Anni Pan; Olivia Wang; Ruowang Li; et al. (J. Am. Medical Informatics Assoc., 2024)

Deep learning with noisy labels in medical prediction problems: a scoping review. - Yishu Wei; Yu Deng; Cong Sun 004; Mingquan Lin; Hongmei Jiang; Yifan Peng 002 (J. Am. Medical Informatics Assoc., 2024)

A span-based model for extracting overlapping PICO entities from randomized controlled trial publications. - Gongbo Zhang; Yiliang Zhou; Yan Hu; Hua Xu 001; Chunhua Weng; Yifan Peng 002 (J. Am. Medical Informatics Assoc., 2024)

Call for papers: Special issue on biomedical multimodal large language models - novel approaches and applications. - Jiang Bian 001; Yifan Peng 002; Eneida A. Mendonça; Imon Banerjee; Hua Xu 001; Hong Sun; Ye Ye; Casey Overby Taylor; Anália Maria Garcia Lourenço; Alejandro Rodríguez González; Elena Tutubalina (J. Biomed. Informatics, 2024)

Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension. - Leilei Su; Jian Chen; Yifan Peng 002; Cong Sun 004 (J. Biomed. Informatics, 2024)

A survey of recent methods for addressing AI fairness and bias in biomedicine. - Yifan Yang 006; Mingquan Lin; Han Zhao 002; Yifan Peng 002; Furong Huang; Zhiyong Lu (J. Biomed. Informatics, 2024)

Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias. - Zehao Yu 001; Cheng Peng 009; Xi Yang 015; Chong Dang; Prakash Adekkanattu; Braja Gopal Patra; Yifan Peng 002; Jyotishman Pathak; Debbie L. Wilson; Ching-Yuan Chang; Wei-Hsuan Lo-Ciganic; Thomas J. George; et al. (J. Biomed. Informatics, 2024)

Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. - Gongbo Zhang; Qiao Jin 001; Denis Jered McInerney; Yong Chen 016; Fei Wang 001; Curtis L. Cole; Qian Yang 004; Yanshan Wang; Bradley A. Malin; Mor Peleg; Byron C. Wallace; Zhiyong Lu; et al. (J. Biomed. Informatics, 2024)

Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. - Gregory Holste; Yiliang Zhou; Song Wang 026; Ajay Jaiswal; Mingquan Lin; Sherry Zhuge; Yuzhe Yang 003; Dongkyun Kim; Trong-Hieu Nguyen Mau; Minh-Triet Tran; Jaehyup Jeong; Wongi Park; et al. (Medical Image Anal., 2024)

Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. - Gregory Holste; Mingquan Lin; Ruiwen Zhou; Fei Wang 001; Lei Liu; Qi Yan 008; Sarah Van Tassel; Kyle Kovacs; Emily Y. Chew; Zhiyong Lu; Zhangyang Wang; Yifan Peng 002 (npj Digit. Medicine, 2024)

Author Correction: Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. - Gregory Holste; Mingquan Lin; Ruiwen Zhou; Fei Wang 001; Lei Liu; Qi Yan 008; Sarah Van Tassel; Kyle Kovacs; Emily Y. Chew; Zhiyong Lu; Zhangyang Wang; Yifan Peng 002 (npj Digit. Medicine, 2024)

Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. - Qiao Jin 001; Fangyuan Chen; Yiliang Zhou; Ziyang Xu; Justin M. Cheung; Robert Chen; Ronald M. Summers; Justin F. Rousseau; Peiyun Ni; Marc J. Landsman; Sally L. Baxter; Subhi J. Al'Aref; et al. (npj Digit. Medicine, 2024)

A framework for human evaluation of large language models in healthcare derived from literature review. - Thomas Yu Chow Tam; Sonish Sivarajkumar; Sumit Kapoor; Alisa V. Stolyar; Katelyn Polanska; Karleigh R. McCarthy; Hunter Osterhoudt; Xizhi Wu; Shyam Visweswaran; Sunyang Fu; Piyush Mathur; Giovanni E. Cacciamani; et al. (npj Digit. Medicine, 2024)

Closing the gap between open source and commercial large language models for medical evidence summarization. - Gongbo Zhang; Qiao Jin 001; Yiliang Zhou; Song Wang 026; Betina Idnay; Yiming Luo; Elizabeth Park; Jordan G. Nestor; Matthew E. Spotnitz; Ali Soroush; Thomas Campion; Zhiyong Lu; et al. (npj Digit. Medicine, 2024)

Natural Language Processing in Support of Evidence-based Medicine: A Scoping Review. - Zihan Xu; Haotian Ma; Yihao Ding; Gongbo Zhang; Chunhua Weng; Yifan Peng 002 (ACL (Findings), 2025)

Seeing Far and Clearly: Mitigating Hallucinations in MLLMs with Attention Causal Decoding. - Feilong Tang; Chengzhi Liu; Zhongxing Xu; Ming Hu; Zile Huang; Haochen Xue; Ziyang Chen 003; Zelin Peng; Zhiwei Yang; Sijin Zhou; Wenxue Li; Yulong Li; et al. (CVPR, 2025)

Semi-supervised learning from small annotated data and large unlabeled data for fine-grained Participants, Intervention, Comparison, and Outcomes entity recognition. - Fangyi Chen; Gongbo Zhang; Yilu Fang; Yifan Peng 002; Chunhua Weng (J. Am. Medical Informatics Assoc., 2025)

Deciphering genomic codes using advanced natural language processing techniques: a scoping review. - Shuyan Cheng; Yishu Wei; Yiliang Zhou; Zihan Xu; Drew N. Wright; Jinze Liu; Yifan Peng 002 (J. Am. Medical Informatics Assoc., 2025)

A multimodal approach for few-shot biomedical named entity recognition in low-resource languages. - Jian Chen; Leilei Su; Yihong Li; Mingquan Lin; Yifan Peng 002; Cong Sun 004 (J. Biomed. Informatics, 2025)

CLEAR: A vision to support clinical evidence lifecycle with continuous learning. - Yilu Fang; Gongbo Zhang; Fangyi Chen; George Hripcsak; Yifan Peng 002; Patrick B. Ryan; Chunhua Weng (J. Biomed. Informatics, 2025)

Machine learning applications related to suicide in military and Veterans: A scoping literature review. - Yuhan Zhang; Yishu Wei; Yanshan Wang; Yunyu Xiao; Ronald K. Poropatich; Gretchen L. Haas; Yiye Zhang; Chunhua Weng; Jinze Liu; Lisa A. Brenner; James M. Bjork; Yifan Peng 002 (J. Biomed. Informatics, 2025)

CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. - Mingquan Lin; Gregory Holste; Song Wang 026; Yiliang Zhou; Yishu Wei; Imon Banerjee; Pengyi Chen; Tianjie Dai; Yuexi Du; Nicha C. Dvornek; Yuyan Ge; Zuwei Guo; et al. (Medical Image Anal., 2025)

Leveraging long context in retrieval augmented language models for medical question answering. - Gongbo Zhang; Zihan Xu; Qiao Jin 001; Fangyi Chen; Yilu Fang; Yi Liu 059; Justin F. Rousseau; Ziyang Xu; Zhiyong Lu; Chunhua Weng; Yifan Peng 002 (npj Digit. Medicine, 2025)

A foundation model for human-AI collaboration in medical literature mining. - Zifeng Wang 008; Lang Cao; Qiao Jin 001; Joey Chan; Nicholas Wan; Behdad Afzali; Hyunjin Cho; Changin Choi; Mehdi Emamverdi; Manjot K. Gill; Sun-Hyung Kim; Yijia Li; et al. (CoRR, 2025)

WatchGuardian: Enabling User-Defined Personalized Just-in-Time Intervention on Smartwatch. - Ying Lei; Yancheng Cao; Will Wang; Yuanzhe Dong; Changchang Yin; Weidan Cao; Ping Zhang 016; Jingzhen Yang; Bingsheng Yao; Yifan Peng 002; Chunhua Weng; Randy Auerbach; et al. (CoRR, 2025)

MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs. - Juncheng Wu; Wenlong Deng; Xingxuan Li; Sheng Liu; Taomian Mi; Yifan Peng 002; Ziyang Xu; Yi Liu 059; Hyunjin Cho; Changin Choi; Yihan Cao; Hui Ren 001; et al. (CoRR, 2025)

Generative Large Language Models Trained for Detecting Errors in Radiology Reports. - Cong Sun 004; Kurt Teichman; Yiliang Zhou; Brian Critelli; David Nauheim; Graham Keir; Xindi Wang; Judy Zhong; Adam E. Flanders; George Shih; Yifan Peng 002 (CoRR, 2025)

Seeing Far and Clearly: Mitigating Hallucinations in MLLMs with Attention Causal Decoding. - Feilong Tang; Chengzhi Liu; Zhongxing Xu; Ming Hu; Zelin Peng; Zhiwei Yang; Jionglong Su; Minquan Lin; Yifan Peng 002; Xuelian Cheng; Imran Razzak; Zongyuan Ge (CoRR, 2025)

EvidenceOutcomes: a Dataset of Clinical Trial Publications with Clinically Meaningful Outcomes. - Yiliang Zhou; Abigail M. Newbury; Gongbo Zhang; Betina Ross S. Idnay; Hao Liu 054; Chunhua Weng; Yifan Peng 002 (CoRR, 2025)

CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. - Mingquan Lin; Gregory Holste; Song Wang 026; Yiliang Zhou; Yishu Wei; Imon Banerjee; Pengyi Chen; Tianjie Dai; Yuexi Du; Nicha C. Dvornek; Yuyan Ge; Zuowei Guo; et al. (CoRR, 2025)

A Multi-Stage Large Language Model Framework for Extracting Suicide-Related Social Determinants of Health. - Song Wang 026; Yishu Wei; Haotian Ma; Max Lovitt; Kelly Deng; Yuan Meng; Zihan Xu; Jingze Zhang; Yunyu Xiao; Ying Ding 001; Xuhai Xu; Joydeep Ghosh; et al. (CoRR, 2025)

Extracting Post-Acute Sequelae of SARS-CoV-2 Infection Symptoms from Clinical Notes via Hybrid Natural Language Processing. - Zilong Bai; Zihan Xu; Cong Sun 004; Chengxi Zang; H. Timothy Bunnell; Catherine Sinfield; Jacqueline R. M. A. Maasch; Aaron Thomas Martinez; L. Charles Bailey; Mark G. Weiner; Thomas R. Campion Jr.; Thomas Carton; et al. (CoRR, 2025)

Scalable Scientific Interest Profiling Using Large Language Models. - Yilun Liang; Gongbo Zhang; Edward Sun; Betina Idnay; Yilu Fang; Fangyi Chen; Casey N. Ta; Yifan Peng 002; Chunhua Weng (CoRR, 2025)