Peng, Yifan

Publications

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selected publications

Faithful AI in Medicine: A Systematic Review with Large Language Models and Beyond. medRxiv : the preprint server for health sciences. 2023 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
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
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
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
How Good Is ChatGPT for Medication Evidence Synthesis?. Studies in health technology and informatics. 2023 Academic Article GET IT
Evaluating Large Language Models on Medical Evidence Summarization. medRxiv : the preprint server for health sciences. 2023 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
Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays. IEEE transactions on medical imaging. 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: 1578
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
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
Times cited: 1
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
Times cited: 1685
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
Times cited: 23
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: 1
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
Times cited: 44
Few-Shot Learning Geometric Ensemble for Multi-label Classification of Chest X-Rays. Data augmentation, labelling, and imperfections : second MICCAI workshop, DALI 2022, held in conjunction with MICCAI 2022, Singapore, September 22, 2022, proceedings. DALI (Workshop) (2nd : 2022 : Singapore). 2022 Academic Article GET IT
Times cited: 2
Long-Tailed Classification of Thorax Diseases on Chest X-Ray: A New Benchmark Study. Data augmentation, labelling, and imperfections : second MICCAI workshop, DALI 2022, held in conjunction with MICCAI 2022, Singapore, September 22, 2022, proceedings. DALI (Workshop) (2nd : 2022 : Singapore). 2022 Academic Article GET IT
Times cited: 11
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
Times cited: 177
Automated diagnosing primary open-angle glaucoma from fundus image by simulating human's grading with deep learning. Scientific reports. 2022 Academic Article GET IT
Times cited: 3
Design and validation of a FHIR-based EHR-driven phenotyping toolbox. Journal of the American Medical Informatics Association : JAMIA. 2022 Academic Article GET IT
Times cited: 2
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
Times cited: 33
Trustworthy assertion classification through prompting. Journal of biomedical informatics. 2022 Academic Article GET IT
Times cited: 1
Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review. Health data science. 2022 Academic Article GET IT
Times cited: 3
Prior Knowledge Enhances Radiology Report Generation. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2022 Academic Article GET IT
Times cited: 1
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
Times cited: 3
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
Times cited: 4
Knowledge-Augmented Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop. IEEE Winter Conference on Applications of Computer Vision. IEEE Winter Conference on Applications of Computer Vision. 2022 Academic Article GET IT
Times cited: 3
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
Times cited: 7
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
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
Times cited: 4
RadBERT-CL: Factually-Aware Contrastive Learning For Radiology Report Classification. Proceedings of machine learning research. 2021 Academic Article GET IT
SCALP - Supervised Contrastive Learning for Cardiopulmonary Disease Classification and Localization in Chest X-rays using Patient Metadata. Proceedings. IEEE International Conference on Data Mining. 2021 Academic Article GET IT
Times cited: 3
An empirical study of using radiology reports and images to improve ICU-mortality prediction. IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics. 2021 Academic Article GET IT
Times cited: 3
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: 11
Improving Joint Learning of Chest X-Ray and Radiology Report by Word Region Alignment. Machine learning in medical imaging. MLMI (Workshop). 2021 Academic Article GET IT
Times cited: 380
A reference-free approach for cell type classification with scRNA-seq. iScience. 2021 Academic Article GET IT
Times cited: 11
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
Times cited: 10
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
PNEUMONIA DETECTION ON CHEST X-RAY USING RADIOMIC FEATURES AND CONTRASTIVE LEARNING. Proceedings. IEEE International Symposium on Biomedical Imaging. 2021 Academic Article GET IT
Times cited: 7
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
Times cited: 2
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: 524
Predicting risk of late age-related macular degeneration using deep learning. NPJ digital medicine. 2020 Academic Article GET IT
Times cited: 1156
COVID-19-CT-CXR: a freely accessible and weakly labeled chest X-ray and CT image collection on COVID-19 from biomedical literature. ArXiv. 2020 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: 16
Automated abnormality classification of chest radiographs using deep convolutional neural networks. NPJ digital medicine. 2020 Academic Article GET IT
Times cited: 14733
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: 74
A Deep Learning Approach for Automated Detection of Geographic Atrophy from Color Fundus Photographs. Ophthalmology. 2019 Academic Article GET IT
Times cited: 39
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: 166
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic acids research. 2018 Academic Article GET IT
Times cited: 69
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
Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 2018 Review GET IT
Times cited: 984
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: 53
Improving chemical disease relation extraction with rich features and weakly labeled data. Journal of cheminformatics. 2016 Academic Article GET IT
Times cited: 2
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: 21
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: 112
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS computational biology. 2015 Academic Article GET IT
Times cited: 35
A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC bioinformatics. 2014 Academic Article GET IT
Times cited: 20
BioC interoperability track overview. Database : the journal of biological databases and curation. 2014 Review 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: 8
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: 111

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Research

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Co-investigator Network

Funding awarded

CAREER: Knowledge-enhanced and interpretable radiology report generation awarded by National Science Foundation Principal Investigator 2022 - 2027
ImageNet in Medicine, a large-scale hierarchical medical image database from PubMed Central awarded by Cornell University Principal Investigator 2022 - 2023
A framework to enhance radiology structured report by invoking NLP and DL: Models and Applications awarded by National Library of Medicine Principal Investigator 2020 - 2023

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Background

education and training

M.S., University of Delaware 2913
Ph.D., University of Delaware 2016
M.Eng, Peking University (China) 2010
B.S.E., Beijing University of Technology (China) 2007

Contact

full name

Yifan Peng

primary email

yip4002@med.cornell.edu

VIVO Weill Cornell Medical College

Yifan Peng Assistant Professor

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email