Peng, Yifan

Publications

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selected publications

Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias. Journal of biomedical informatics. 2024 Academic Article GET IT
Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. Journal of biomedical informatics. 2024 Academic Article GET IT
Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis. JAMA psychiatry. 2024 Academic Article GET IT
A span-based model for extracting overlapping PICO entities from RCT publications. Journal of the American Medical Informatics Association : JAMIA. 2024 Academic Article GET IT
Retrieval augmented scientific claim verification. JAMIA open. 2024 Academic Article GET IT
A survey of recent methods for addressing AI fairness and bias in biomedicine. 2024 GET IT
Hidden Flaws Behind Expert-Level Accuracy of GPT-4 Vision in Medicine. 2024 GET IT
Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints. Journal of the American Medical Informatics Association : JAMIA. 2023 Academic Article GET IT
Faithful AI in Medicine: A Systematic Review with Large Language Models and Beyond. 2023 GET IT
Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare. NPJ digital medicine. 2023 Review GET IT
Automated classification of lay health articles using natural language processing: a case study on pregnancy health and postpartum depression. Frontiers in psychiatry. 2023 Academic Article GET IT
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. 2023 GET IT
Improving model fairness in image-based computer-aided diagnosis. Nature communications. 2023 Academic Article GET IT
How Does Pruning Impact Long-Tailed Multi-label Medical Image Classifiers?. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2023 Academic Article GET IT
Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2023 Academic Article GET IT
A scoping review on multimodal deep learning in biomedical images and texts. Journal of biomedical informatics. 2023 Review GET IT
Evaluating large language models on medical evidence summarization. NPJ digital medicine. 2023 Academic Article GET IT
How Does Pruning Impact Long-Tailed Multi-Label Medical Image Classifiers? 2023 GET IT
Less Likely Brainstorming: Using Language Models to Generate Alternative Hypotheses. Proceedings of the conference. Association for Computational Linguistics. Meeting. 2023 Academic Article GET IT
A new deep learning framework to process Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) data of Tissue Microarrays (TMAs). AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2023 Academic Article GET IT
Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served populations. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2023 Academic Article GET IT
Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports. 2023 GET IT
Evaluating GPT4 on Impressions Generation in Radiology Reports. Radiology. 2023 Academic Article GET IT
AI-generated text may have a role in evidence-based medicine. Nature medicine. 2023 Letter GET IT
Times cited: 11
Comparing the effects of four common drug classes on the progression of mild cognitive impairment to dementia using electronic health records. Scientific reports. 2023 Academic Article GET IT
Times cited: 3
How Good Is ChatGPT for Medication Evidence Synthesis?. Studies in health technology and informatics. 2023 Academic Article GET IT
Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access. Computers in biology and medicine. 2023 Academic Article GET IT
An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives. Journal of the American Medical Informatics Association : JAMIA. 2023 Academic Article GET IT
Editorial: Pattern recognition for healthcare analytics. Frontiers in digital health. 2023 Editorial Article GET IT
Representing and Utilizing Clinical Textual Data for Real World Studies: An OHDSI Approach. Journal of biomedical informatics. 2023 Academic Article GET IT
EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension. Journal of the American Medical Informatics Association : JAMIA. 2023 Academic Article GET IT
Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances. IEEE Winter Conference on Applications of Computer Vision. IEEE Winter Conference on Applications of Computer Vision. 2023 Academic Article GET IT
RoS-KD: A Robust Stochastic Knowledge Distillation Approach for Noisy Medical Imaging. Proceedings. IEEE International Conference on Data Mining. 2023 Academic Article GET IT
Times cited: 1
Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction. BMC medical research methodology. 2023 Academic Article GET IT
Improving Cancer Care Communication: Identifying Sociodemographic Differences in Patient Portal Secure Messages Not Authored by the Patient. Applied clinical informatics. 2023 Academic Article GET IT
Times cited: 1
Prediction of left ventricular ejection fraction changes in heart failure patients using machine learning and electronic health records: a multi-site study. Scientific reports. 2023 Academic Article GET IT
Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction. Machine learning in medical imaging. MLMI (Workshop). 2022 Academic Article GET IT
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. Machine learning in medical imaging. MLMI (Workshop). 2022 Academic Article GET IT
Identifying Nonpatient Authors of Patient Portal Secure Messages in Oncology: A Proof-of-Concept Demonstration of Natural Language Processing Methods. JCO clinical cancer informatics. 2022 Academic Article GET IT
Times cited: 3
Topical and emotional expressions regarding extreme weather disasters on social media: a comparison of posts from official media and the public. Humanities & social sciences communications. 2022 Academic Article GET IT
Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays. IEEE transactions on medical imaging. 2022 Academic Article GET IT
Radiology Text Analysis System (RadText): Architecture and Evaluation. IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics. 2022 Academic Article GET IT
Automated diagnosing primary open-angle glaucoma from fundus image by simulating human's grading with deep learning. Scientific reports. 2022 Academic Article GET IT
Primary Open-Angle Glaucoma Diagnosis from Optic Disc Photographs Using a Siamese Network. Ophthalmology science. 2022 Academic Article GET IT
Supervised Pretraining through Contrastive Categorical Positive Samplings to Improve COVID-19 Mortality Prediction. ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2022 Academic Article GET IT
Design and validation of a FHIR-based EHR-driven phenotyping toolbox. Journal of the American Medical Informatics Association : JAMIA. 2022 Academic Article GET IT
Trustworthy assertion classification through prompting. Journal of biomedical informatics. 2022 Academic Article GET IT
Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review. Health data science. 2022 Academic Article GET IT
Prior Knowledge Enhances Radiology Report Generation. AMIA ... Annual Symposium proceedings. AMIA Symposium. 2022 Academic Article GET IT
EchoGen: A New Benchmark Study on Generating Conclusions from Echocardiogram Notes. Proceedings of the conference. Association for Computational Linguistics. Meeting. 2022 Academic Article GET IT
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. AMIA ... Annual Symposium proceedings. AMIA Symposium. 2022 Academic Article GET IT
Using Radiomics as Prior Knowledge for Thorax Disease Classification and Localization in Chest X-rays. AMIA ... Annual Symposium proceedings. AMIA Symposium. 2022 Academic Article GET IT
Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images. Medical image analysis. 2022 Academic Article GET IT
Classifying Cyber-Risky Clinical Notes by Employing Natural Language Processing. Proceedings of the ... Annual Hawaii International Conference on System Sciences. Annual Hawaii International Conference on System Sciences. 2022 Academic Article GET IT
Primary Open-Angle Glaucoma Diagnosis From Optic Disc Photographs Using a Siamese Network. Ophthalmology Science. 2022 Academic Article GET IT
Robust convolutional neural networks against adversarial attacks on medical images. Pattern Recognition. 2022 Academic Article GET IT
Benchmarking Effectiveness and Efficiency of Deep Learning Models for Semantic Textual Similarity in the Clinical Domain: Validation Study. JMIR medical informatics. 2021 Academic Article GET IT
RadBERT-CL: Factually-Aware Contrastive Learning For Radiology Report Classification. Proceedings of machine learning research. 2021 Academic Article GET IT
A reference-free approach for cell type classification with scRNA-seq. iScience. 2021 Academic Article GET IT
Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration. Journal of the American Medical Informatics Association : JAMIA. 2021 Academic Article GET IT
Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality. Proceedings of the conference. Association for Computational Linguistics. North American Chapter. Meeting. 2021 Academic Article GET IT
When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information?. JAMIA open. 2021 Academic Article GET IT
NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature. Scientific data. 2021 Academic Article GET IT
Times cited: 26
Generalized Zero-shot Chest X-ray Diagnosis through Trait-Guided Multi-view Semantic Embedding with Self-training. IEEE transactions on medical imaging. 2021 Academic Article GET IT
Times cited: 1
Detection of lymph nodes in T2 MRI using neural network ensembles. 2021 Conference Paper GET IT
COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature. IEEE transactions on big data. 2020 Academic Article GET IT
Times cited: 47
Predicting risk of late age-related macular degeneration using deep learning. NPJ digital medicine. 2020 Academic Article GET IT
Deep Learning Automated Detection of Reticular Pseudodrusen from Fundus Autofluorescence Images or Color Fundus Photographs in AREDS2. Ophthalmology. 2020 Academic Article GET IT
Times cited: 4
Automated abnormality classification of chest radiographs using deep convolutional neural networks. NPJ digital medicine. 2020 Academic Article GET IT
Times cited: 140
ML-Net: multi-label classification of biomedical texts with deep neural networks. Journal of the American Medical Informatics Association : JAMIA. 2019 Academic Article GET IT
Times cited: 93
A Deep Learning Approach for Automated Detection of Geographic Atrophy from Color Fundus Photographs. Ophthalmology. 2019 Academic Article GET IT
Times cited: 50
A multi-task deep learning model for the classification of Age-related Macular Degeneration. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2019 Academic Article GET IT
DeepSeeNet: A Deep Learning Model for Automated Classification of Patient-based Age-related Macular Degeneration Severity from Color Fundus Photographs. Ophthalmology. 2018 Academic Article GET IT
Times cited: 207
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic acids research. 2018 Academic Article GET IT
Times cited: 86
NegBio: a high-performance tool for negation and uncertainty detection in radiology reports. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2018 Academic Article GET IT
Extracting chemical-protein relations with ensembles of SVM and deep learning models. Database : the journal of biological databases and curation. 2018 Academic Article GET IT
Times cited: 64
Improving chemical disease relation extraction with rich features and weakly labeled data. Journal of cheminformatics. 2016 Academic Article GET IT
Times cited: 67
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database : the journal of biological databases and curation. 2016 Academic Article GET IT
Times cited: 22
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database : the journal of biological databases and curation. 2016 Academic Article GET IT
Times cited: 5
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database : the journal of biological databases and curation. 2016 Academic Article GET IT
Times cited: 132
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS computational biology. 2015 Academic Article GET IT
Times cited: 37
A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC bioinformatics. 2014 Academic Article GET IT
Times cited: 21
BioC interoperability track overview. Database : the journal of biological databases and curation. 2014 Information Resource GET IT
Times cited: 13
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database : the journal of biological databases and curation. 2014 Academic Article GET IT
Times cited: 9
BioC: a minimalist approach to interoperability for biomedical text processing. Database : the journal of biological databases and curation. 2013 Academic Article GET IT
Times cited: 118

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Research

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Co-investigator Network

Funding awarded

Closing the loop with an automatic referral population and summarization system awarded by National Library of Medicine Principal Investigator 2023 - 2028
CAREER: Knowledge-enhanced and interpretable radiology report generation awarded by National Science Foundation Principal Investigator 2022 - 2027
Achieving Model Fairness on Automatic Primary Open-angle Glaucoma Screening awarded by National Eye Institute/NIH/DHHS Principal Investigator 2023 - 2025
Amazon Research Award Principal Investigator 2022 - 2023
missing activity Principal Investigator 2022 - 2023
Multi-Investigator Seed Grant Principal Investigator

Disparities of Alzheimer''s disease progression in sexual and gender minorities awarded by National Cancer Institute Co-Investigator 2023 - 2028
PASC EHR/ORWD Phase II Proposal (RECOVER) awarded by National Heart, Lung, & Blood Institute Co-Investigator 2023 - 2024
PASC EHR/ORWD Phase II Proposal (RECOVER) awarded by National Heart, Lung, & Blood Institute Co-Investigator 2022 - 2024

Clinical and Translational Science Center- Institutional CTSC Internal Funding UL1 awarded by CTSC Cost Share Key Personnel 2022 - 2027

ClinEX - Clinical Evidence Extraction, Representation, and Appraisal awarded by National Institute of Environmental Health Sciences Principal Investigator Subaward 2023 - 2028
SCH: Interpretable survival analysis of complex longitudinal data awarded by National Institute on Aging Principal Investigator Subaward 2023 - 2027
Use AI/ML to Address the Crisis of Black Youth Suicide awarded by Dynavax Technologies Principal Investigator Subaward 2023 - 2024

other research activities

missing activity co-I
AWS Diagnostic Development Initiative Credit 2022 - 2022

Teaching

teaching activities

HINF 5016 Natural Language Processing in Health Instructor 2021 -

Background

education and training

Ph.D., University of Delaware 2016
M.S., University of Delaware 2013
M.Eng, Peking University (China) 2010
B.S.E., Beijing University of Technology (China) 2007

advisee of

postdoc or fellow advising relationship

Lin, Mingquan (Postdoc) advising Peng, Yifan

Wanyan, Tingyi (Postdoc) advising Peng, Yifan

Contact

full name

Yifan Peng

primary email

yip4002@med.cornell.edu

webpage

Peng Lab

phone

+1 646-962-9227

other research activities

postdoc or fellow advising relationship

VIVO Weill Cornell Medical College

Yifan Peng Assistant Professor

Publications

selected publications

Research

Funding awarded

Teaching

teaching activities

Background

education and training

advisee of

Contact

full name

primary email

webpage

phone