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Picture for Yifan Peng

Yifan Peng

for the AREDS2 Deep Learning Research Group

Cross-Modal Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop


Apr 11, 2021
Yan Han, Chongyan Chen, Ahmed Tewfik, Benjamin Glicksberg, Ying Ding, Yifan Peng, Zhangyang Wang

* Preprint 

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Pneumonia Detection on Chest X-ray using Radiomic Features and Contrastive Learning


Jan 12, 2021
Yan Han, Chongyan Chen, Ahmed H Tewfik, Ying Ding, Yifan Peng

* Accepted for ISBI 2021 

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Using Radiomics as Prior Knowledge for Abnormality Classification and Localization in Chest X-rays


Nov 25, 2020
Yan Han, Chongyan Chen, Liyan Tang, Mingquan Lin, Ajay Jaiswal, Ying Ding, Yifan Peng

* Under Review 

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Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration


Nov 11, 2020
Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agr贸n, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu

* 5 figures and 4 tables, To appear in Journal of the American Medical Informatics Association 

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Efficient Long-Range Convolutions for Point Clouds


Oct 11, 2020
Yifan Peng, Lin Lin, Lexing Ying, Leonardo Zepeda-N煤帽ez


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Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view


Sep 11, 2020
Lana Yeganova, Rezarta Islamaj, Qingyu Chen, Robert Leaman, Alexis Allot, Chin-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu

* KDD 2020 Health Day: AI for COVID, August 23-27, 2020, Virtual Conference, CA, US 
* 10 pages, 8 Figures, Submitted to KDD 2020 Health Day 

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Predicting risk of late age-related macular degeneration using deep learning


Jul 19, 2020
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agr贸n, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu

* Accepted by npj Digital Medicine 

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COVID-19-CT-CXR: a freely accessible and weakly labeled chest X-ray and CT image collection on COVID-19 from biomedical literature


Jun 11, 2020
Yifan Peng, Yu-Xing Tang, Sungwon Lee, Yingying Zhu, Ronald M. Summers, Zhiyong Lu


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An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining


May 06, 2020
Yifan Peng, Qingyu Chen, Zhiyong Lu

* Accepted by BioNLP 2020 

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MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation


Aug 12, 2019
Ke Yan, Youbao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers

* MICCAI 2019, including appendix. code: https://github.com/rsummers11/CADLab/tree/master/MULAN_universal_lesion_analysis 

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Deep Optics for Single-shot High-dynamic-range Imaging


Aug 01, 2019
Christopher A. Metzler, Hayato Ikoma, Yifan Peng, Gordon Wetzstein


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Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets


Jun 18, 2019
Yifan Peng, Shankai Yan, Zhiyong Lu

* Accepted by BioNLP 2019 

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A deep learning approach for automated detection of geographic atrophy from color fundus photographs


Jun 07, 2019
Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agr贸n, Wai T. Wong, Zhiyong Lu, Emily Y. Chew

* Accepted for publication in Ophthalmology 

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A self-attention based deep learning method for lesion attribute detection from CT reports


Apr 30, 2019
Yifan Peng, Ke Yan, Veit Sandfort, Ronald M. Summers, Zhiyong Lu

* 5 pages, 2 figures, accepted by 2019 IEEE International Conference on Healthcare Informatics (ICHI 2019) 

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Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning from Radiology Reports and Label Ontology


Apr 27, 2019
Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers

* CVPR 2019 oral, main paper + supplementary material 

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Fine-grained lesion annotation in CT images with knowledge mined from radiology reports


Mar 26, 2019
Ke Yan, Yifan Peng, Zhiyong Lu, Ronald M. Summers

* 4 pages, IEEE International Symposium on Biomedical Imaging (ISBI) 2019, oral presentation 

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A multi-task deep learning model for the classification of Age-related Macular Degeneration


Dec 02, 2018
Qingyu Chen, Yifan Peng, Tiarnan Keenan, Shazia Dharssi, Elvira Agron, Wai T. Wong, Emily Y. Chew, Zhiyong Lu

* 10 pages, 5 figures, and 5 tables To appear in the Proceeding of AMIA Informatics 2019 

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DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs


Nov 19, 2018
Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agr贸n, Wai T. Wong, Emily Y. Chew, Zhiyong Lu

* Accepted for publication in Ophthalmology 

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ML-Net: multi-label classification of biomedical texts with deep neural networks


Nov 15, 2018
Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu


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BioSentVec: creating sentence embeddings for biomedical texts


Oct 26, 2018
Qingyu Chen, Yifan Peng, Zhiyong Lu

* 4 pages, 1 table 

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Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models


Feb 05, 2018
Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu

* Accepted in Proceedings of the BioCreative VI Workshop 

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TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-rays


Jan 12, 2018
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers

* v1: Main paper + supplementary material 

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NegBio: a high-performance tool for negation and uncertainty detection in radiology reports


Dec 27, 2017
Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald Summers, Zhiyong Lu

* Final version. Accepted for publication in AMIA 2018 Informatics Summit. 9 pages, 2 figures, 4 tables 

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ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases


Dec 14, 2017
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers

* CVPR 2017 spotlight;V1: CVPR submission+supplementary; V2: Statistics and benchmark results on published ChestX-ray14 dataset are updated in Appendix B V3: Minor correction V4: new data download link upated: https://nihcc.app.box.com/v/ChestXray-NIHCC V5: Update benchmark results on the published data split in the appendix 

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Deep learning for extracting protein-protein interactions from biomedical literature


Jun 07, 2017
Yifan Peng, Zhiyong Lu

* Accepted for publication in Proceedings of the 2017 Workshop on Biomedical Natural Language Processing, 10 pages, 2 figures, 6 tables 

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