Peng, Yifan

Publications

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selected publications

A neural-symbolic AI agent system for biomedical concept mapping. NPJ digital medicine. 2026 Academic Article GET IT
A critical evaluation of generative query expansion on biomedical literature retrieval. Journal of the American Medical Informatics Association : JAMIA. 2026 Academic Article GET IT
CPGPrompt: translating clinical guidelines into large language model-executable decision support. Journal of the American Medical Informatics Association : JAMIA. 2026 Academic Article GET IT
Biomedical multimodal large language models: From model-centric development to clinically grounded evaluation and integration. Journal of biomedical informatics. 2026 Editorial Article GET IT
A Disease-Aware Dual-Stage Framework for Chest X-ray Report Generation. Proceedings of the ... AAAI Conference on Artificial Intelligence. AAAI Conference on Artificial Intelligence. 2026 Academic Article GET IT
The evolving landscape of large language models and non-large language models in health care. npj health systems. 2026 Academic Article GET IT
A cancer-type-aware framework for robust multimodal survival prediction under missing modalities. Briefings in bioinformatics. 2026 Academic Article GET IT
Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow. Scientific data. 2026 Academic Article GET IT
Deep Neural Network With a Smooth Monotonic Output Layer for Dynamic Risk Prediction. Statistics in medicine. 2026 Academic Article GET IT
AMD-Mamba: A Phenotype-Aware Multi-modal Framework for Robust AMD Prognosis. Machine learning in medical imaging. MLMI (Workshop). 2026 Academic Article GET IT
Times cited: 1
SDoH-GPT: using large language models to extract social determinants of health. Journal of the American Medical Informatics Association : JAMIA. 2026 Academic Article GET IT
Times cited: 5
Benchmarking Foundation Models with Multimodal Public Electronic Health Records. IEEE journal of biomedical and health informatics. 2025 Academic Article GET IT
Times cited: 1
Exploring the feasibility of using artificial intelligence to simulate the placebo arm of randomized clinical trials. Postgraduate medical journal. 2025 Academic Article GET IT
Scalable scientific interest profiling using large language models. Journal of biomedical informatics. 2025 Academic Article GET IT
Times cited: 1
A multi-stage large language model framework for extracting suicide-related social determinants of health. Communications medicine. 2025 Academic Article GET IT
Times cited: 1
A foundation model for human-AI collaboration in medical literature mining. Nature communications. 2025 Academic Article GET IT
Times cited: 7
Development and validation of natural language processing algorithms in the national ENACT network. Journal of clinical and translational science. 2025 Academic Article GET IT
Times cited: 1
Extracting post-acute sequelae of SARS-CoV-2 infection symptoms from clinical notes via hybrid natural language processing. npj health systems. 2025 Academic Article GET IT
Scalable Scientific Interest Profiling Using Large Language Models. ArXiv. 2025 Article GET IT
Seeing Far and Clearly: Mitigating Hallucinations in MLLMs with Attention Causal Decoding. Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. 2025 Academic Article GET IT
Times cited: 8
A Pilot Meta-Research on Evolving Evidence Behind Genetic Variant (Re)Classification. Studies in health technology and informatics. 2025 Academic Article GET IT
EvidenceOutcomes: A Dataset of Clinical Trial Publications with Clinically Meaningful Outcomes. Studies in health technology and informatics. 2025 Academic Article GET IT
AMD-Mamba: A Phenotype-Aware Multi-Modal Framework for Robust AMD Prognosis. ArXiv. 2025 Article GET IT
CLEAR: A vision to support clinical evidence lifecycle with continuous learning. Journal of biomedical informatics. 2025 Academic Article GET IT
Times cited: 2
CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. Medical image analysis. 2025 Academic Article GET IT
Times cited: 2
A Pilot Meta-research on Evolving Evidence Behind Genetic Variant (Re)Classification. medRxiv : the preprint server for health sciences. 2025 Article GET IT
Natural Language Processing in Support of Evidence-based Medicine: A Scoping Review. Findings of ACL. ACL. 2025 Academic Article GET IT
Times cited: 1
The Evolution of Radiology Image Annotation in the Era of Large Language Models. Radiology. Artificial intelligence. 2025 Information Resource GET IT
Times cited: 4
DIRI: Adversarial Patient Reidentification with Large Language Models for Evaluating Clinical Text Anonymization. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2025 Academic Article GET IT
Enhancing Disease Detection in Radiology Reports Through Fine-tuning Lightweight LLM on Weak Labels. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2025 Academic Article GET IT
CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. ArXiv. 2025 Article GET IT
Machine learning applications related to suicide in military and Veterans: A scoping literature review. Journal of biomedical informatics. 2025 Information Resource GET IT
Leveraging long context in retrieval augmented language models for medical question answering. NPJ digital medicine. 2025 Academic Article GET IT
Times cited: 36
Generative Large Language Models Trained for Detecting Errors in Radiology Reports. Radiology. 2025 Academic Article GET IT
Times cited: 8
Deciphering genomic codes using advanced natural language processing techniques: a scoping review. Journal of the American Medical Informatics Association : JAMIA. 2025 Information Resource GET IT
Times cited: 6
Semi-supervised learning from small annotated data and large unlabeled data for fine-grained Participants, Intervention, Comparison, and Outcomes entity recognition. Journal of the American Medical Informatics Association : JAMIA. 2025 Academic Article GET IT
Times cited: 5
An empirical study of using radiology reports and images to improve intensive care unit mortality prediction. JAMIA open. 2025 Academic Article GET IT
Times cited: 2
DeepSeek is open-access and the next AI disrupter for radiology. Radiology advances. 2025 Academic Article GET IT
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare. Journal of biomedical informatics. 2025 Editorial Article GET IT
Times cited: 93
A foundation model for human-AI collaboration in medical literature mining. ArXiv. 2025 Article GET IT
Development and Validation of Natural Language Processing Algorithms in the ENACT National Electronic Health Record Research Network. medRxiv : the preprint server for health sciences. 2025 Article GET IT
Environment scan of generative AI infrastructure for clinical and translational science. npj health systems. 2025 Academic Article GET IT
Times cited: 8
An Interpretable Complex Knowledge Multi-Hop Reasoning Model for Predicting Synthetic Lethality in Human Cancers. IEEE transactions on computational biology and bioinformatics. 2025 Academic Article GET IT
Times cited: 1
Suicide Risk Assessment on Social Media with Semi-Supervised Learning. Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data. 2024 Academic Article GET IT
A multimodal approach for few-shot biomedical named entity recognition in low-resource languages. Journal of biomedical informatics. 2024 Academic Article GET IT
Times cited: 6
Deciphering genomic codes using advanced NLP techniques: a scoping review. ArXiv. 2024 Article GET IT
Demystifying Large Language Models for Medicine: A Primer. ArXiv. 2024 Article GET IT
Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension. Journal of biomedical informatics. 2024 Academic Article GET IT
Times cited: 4
Development and Implementation of a Multicenter Registry for Resuscitation-Focused Transesophageal Echocardiography. Annals of emergency medicine. 2024 Academic Article GET IT
Times cited: 9
A natural language processing approach to detect inconsistencies in death investigation notes attributing suicide circumstances. Communications medicine. 2024 Academic Article GET IT
Times cited: 2
A framework for human evaluation of large language models in healthcare derived from literature review. NPJ digital medicine. 2024 Academic Article GET IT
Times cited: 176
Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. ArXiv. 2024 Article GET IT
Author Correction: Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. NPJ digital medicine. 2024 Article GET IT
Closing the gap between open source and commercial large language models for medical evidence summarization. NPJ digital medicine. 2024 Academic Article GET IT
Times cited: 47
Improving Fairness of Automated Chest Radiograph Diagnosis by Contrastive Learning. Radiology. Artificial intelligence. 2024 Academic Article GET IT
Times cited: 6
Large language models in biomedicine and health: current research landscape and future directions. Journal of the American Medical Informatics Association : JAMIA. 2024 Editorial Article GET IT
Times cited: 53
Hidden Flaws Behind Expert-Level Accuracy of Multimodal GPT-4 Vision in Medicine. ArXiv. 2024 Article GET IT
Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups. Proceedings. IEEE International Conference on Healthcare Informatics. 2024 Academic Article GET IT
Times cited: 1
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. NPJ digital medicine. 2024 Academic Article GET IT
Times cited: 18
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. ArXiv. 2024 Article GET IT
Closing the gap between open-source and commercial large language models for medical evidence summarization. ArXiv. 2024 Article GET IT
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ digital medicine. 2024 Academic Article GET IT
Times cited: 72
Deep learning with noisy labels in medical prediction problems: a scoping review. Journal of the American Medical Informatics Association : JAMIA. 2024 Information Resource GET IT
Times cited: 19
Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis. JAMA psychiatry. 2024 Academic Article GET IT
Times cited: 39
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. Medical image analysis. 2024 Academic Article GET IT
Times cited: 30
Erratum for: Evaluating GPT-4V (GPT-4 with Vision) on Detection of Radiologic Findings on Chest Radiographs. Radiology. 2024 Article GET IT
Evaluating GPT-V4 (GPT-4 with Vision) on Detection of Radiologic Findings on Chest Radiographs. Radiology. 2024 Academic Article GET IT
Times cited: 56
A survey of recent methods for addressing AI fairness and bias in biomedicine. Journal of biomedical informatics. 2024 Information Resource GET IT
Times cited: 61
A span-based model for extracting overlapping PICO entities from randomized controlled trial publications. Journal of the American Medical Informatics Association : JAMIA. 2024 Academic Article GET IT
Times cited: 15
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
Times cited: 21
Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. Journal of biomedical informatics. 2024 Academic Article GET IT
Times cited: 32
Confidence score: a data-driven measure for inclusive systematic reviews considering unpublished preprints. Journal of the American Medical Informatics Association : JAMIA. 2024 Academic Article GET IT
Times cited: 3
High-performance Data Management for Whole Slide Image Analysis in Digital Pathology. Proceedings of SPIE--the International Society for Optical Engineering. 2024 Academic Article GET IT
Leveraging Generative AI for Clinical Evidence Synthesis Needs to Ensure Trustworthiness. ArXiv. 2024 Article GET IT
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. ArXiv. 2024 Article GET IT
Retrieval augmented scientific claim verification. JAMIA open. 2024 Academic Article GET IT
Times cited: 10
A survey of recent methods for addressing AI fairness and bias in biomedicine. ArXiv. 2024 Article GET IT
Deep learning models to predict primary open-angle glaucoma. Stat (International Statistical Institute). 2024 Academic Article GET IT
Times cited: 3
Identification of Offensive Language in Social Media Using Prompt Learning. Proceedings. IEEE International Conference on Healthcare Informatics. 2023 Academic Article GET IT
Times cited: 1
Faithful AI in Medicine: A Systematic Review with Large Language Models and Beyond. Research square. 2023 Article GET IT
Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare. NPJ digital medicine. 2023 Information Resource GET IT
Times cited: 93
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
Times cited: 6
A scoping review on multimodal deep learning in biomedical images and texts. ArXiv. 2023 Article GET IT
Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports. ArXiv. 2023 Article GET IT
Improving model fairness in image-based computer-aided diagnosis. Nature communications. 2023 Academic Article GET IT
Times cited: 27
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
Times cited: 11
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
Times cited: 23
A scoping review on multimodal deep learning in biomedical images and texts. Journal of biomedical informatics. 2023 Information Resource GET IT
Times cited: 39
Evaluating large language models on medical evidence summarization. NPJ digital medicine. 2023 Academic Article GET IT
Times cited: 327
How Does Pruning Impact Long-Tailed Multi-Label Medical Image Classifiers?. ArXiv. 2023 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
Times cited: 20
AI-generated text may have a role in evidence-based medicine. Nature medicine. 2023 Article GET IT
Times cited: 57
Faithful AI in Medicine: A Systematic Review with Large Language Models and Beyond. medRxiv : the preprint server for health sciences. 2023 Article 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
Times cited: 7
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
Times cited: 131
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: 7
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
Times cited: 14
How Good Is ChatGPT for Medication Evidence Synthesis?. Studies in health technology and informatics. 2023 Academic Article GET IT
Times cited: 8
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
Times cited: 6
Editorial: Pattern recognition for healthcare analytics. Frontiers in digital health. 2023 Editorial Article GET IT
Times cited: 1
Representing and utilizing clinical textual data for real world studies: An OHDSI approach. Journal of biomedical informatics. 2023 Academic Article GET IT
Times cited: 12
Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays. IEEE transactions on medical imaging. 2023 Academic Article GET IT
Times cited: 23
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
Times cited: 4
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: 8
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
Times cited: 17
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: 6
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: 16
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: 4
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: 9
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: 6
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: 39
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: 6
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: 43
Radiology Text Analysis System (RadText): Architecture and Evaluation. Proceedings. IEEE International Conference on Healthcare Informatics. 2022 Academic Article GET IT
Times cited: 11
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: 37
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: 7
Primary Open-Angle Glaucoma Diagnosis from Optic Disc Photographs Using a Siamese Network. Ophthalmology science. 2022 Academic Article GET IT
Times cited: 8
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: 7
Trustworthy assertion classification through prompting. Journal of biomedical informatics. 2022 Academic Article GET IT
Times cited: 11
Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review. Health data science. 2022 Information Resource GET IT
Times cited: 12
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: 30
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: 6
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: 10
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: 12
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: 27
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
Times cited: 14
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: 13
An empirical study of using radiology reports and images to improve ICU-mortality prediction. Proceedings. IEEE International Conference on Healthcare Informatics. 2021 Academic Article GET IT
Times cited: 12
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: 45
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: 13
A reference-free approach for cell type classification with scRNA-seq. iScience. 2021 Academic Article GET IT
Times cited: 45
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: 38
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
Times cited: 6
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: 42
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: 5
NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature. Scientific data. 2021 Academic Article GET IT
Times cited: 58
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: 70
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
Predicting risk of late age-related macular degeneration using deep learning. NPJ digital medicine. 2020 Academic Article GET IT
Times cited: 62
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: 38
Automated abnormality classification of chest radiographs using deep convolutional neural networks. NPJ digital medicine. 2020 Academic Article GET IT
Times cited: 225
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: 129
A Deep Learning Approach for Automated Detection of Geographic Atrophy from Color Fundus Photographs. Ophthalmology. 2019 Academic Article GET IT
Times cited: 72
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: 300
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic acids research. 2018 Academic Article GET IT
Times cited: 107
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 Information Resource GET IT
Times cited: 1770
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: 80
Improving chemical disease relation extraction with rich features and weakly labeled data. Journal of cheminformatics. 2016 Academic Article GET IT
Times cited: 74
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: 25
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: 175
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS computational biology. 2015 Academic Article GET IT
Times cited: 44
A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC bioinformatics. 2014 Academic Article GET IT
Times cited: 22
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: 134

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Research

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Funding awarded

Extraction and summarization of evidence-based medicine awarded by National Library of Medicine Principal Investigator 2024 - 2028
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 - 2026
AIM-AHEAD OT2OD032581 Principal Investigator 2023 - 2025
Amazon Research Award Principal Investigator 2022 - 2023
Multi-Investigator Seed Grant Principal Investigator

Development of An Integrated Pipeline for Early PD Prediction and Disease Modifying Drug Repurposing awarded by National Institute of Neurological Disorders & Stroke Co-Investigator 2026 - 2031
Progression Subtyping and Drug Target Identification for Parkinson''s Disease with Integrative Machine Learning awarded by National Institute of Neurological Disorders & Stroke Co-Investigator 2024 - 2029
Disparities of Alzheimer''s disease progression in sexual and gender minorities awarded by National Institute on Aging Co-Investigator 2023 - 2028
PASC EHR/ORWD Phase II Proposal (RECOVER) Year 3 awarded by National Heart, Lung, & Blood Institute Co-Investigator 2023 - 2025

ClinEX - Clinical Evidence Extraction, Representation, and Appraisal Co-Principal Investigator 2023 - 2028

Clinical and Translational Science Center- Institutional CTSC Internal Funding UL1 awarded by CTSC Cost Share Key Personnel 2022 - 2027
PASC EHR/ORWD Phase II Proposal (RECOVER) Year 5 awarded by National Heart, Lung, & Blood Institute Key Personnel 2025 - 2026

Transfer learning NLP to improve adoption of clinical text analytics in multi-site studies awarded by National Institute on Aging Principal Investigator Subaward 2025 - 2029
Multimodal AI Fusion Model for Early Detection for Pancreatic Cancer awarded by Patient-Centered Outcomes Research Institute Principal Investigator Subaward 2024 - 2029
ClinEX - Clinical Evidence Extraction, Representation, and Appraisal awarded by National Institute on Minority Health & Health Disparities Principal Investigator Subaward 2023 - 2028
Methods Supplement to Support Innovative Research on AI and Large Language Models in Patient-Centered CER awarded by Health Resources & Services Administration Principal Investigator Subaward 2024 - 2027
SCH: Interpretable survival analysis of complex longitudinal data awarded by National Institute on Aging Principal Investigator Subaward 2023 - 2027

other research activities

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

Sun, Cong, 2023 -

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 Associate Professor of Population Health Sciences

Publications

selected publications

Research

Funding awarded

Teaching

teaching activities

Background

education and training

advisee of

Contact

full name

primary email

webpage

phone