Publications

Islamaj R, Leaman R, Kim S, Kwon D, Wei C-H, Comeau DC, Peng Y, Cissel D, Coss C, Fisher C et al..  2021.  NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature.. Sci Data. 8(1):91.

Wangyan T, Sun Q, Grizzard P, Liu J, Peng Y.  2023.  A new deep learning framework to process Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) data of Tissue Microarrays (TMAs).. AMIA Jt Summits Transl Sci Proc. 2023:554-561.

Peng Y, Wang X, Lu L, Bagheri M, Summers R, Lu Z.  2018.  NegBio: a high-performance tool for negation and uncertainty detection in radiology reports. AMIA Jt Summits Transl Sci Proc. 2017:188-196.

Yeganova L, Islamaj R, Chen Q, Leaman R, Allot A, Wei C-H, Comeau DC, Kim W, Peng Y, W. Wilbur J et al..  2020.  Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. KDD AI for COVID.

Ghahramani G, Brendel M, Lin M, Chen Q, Keenan T, Chen K, Chew E, Lu Z, Peng Y, Wang F.  2021.  Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.. AMIA Annu Symp Proc. 2021:506-515.

Chen Q, Peng Y, Keenan T, Dharssi S, N EAgro, Wong WT, Chew EY, Lu Z.  2019.  A multi-task deep learning model for the classification of Age-related Macular Degeneration. AMIA Jt Summits Transl Sci Proc. 2019:505-514.

Lin M, Liu L, Gorden M, Kass M, Van Tassel S, Wang F, Peng Y.  2022.  Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction.. Mach Learn Med Imaging. 13583:436-445.

Chen Q, Keenan TDL, Allot A, Peng Y, Agrón E, Domalpally A, Klaver CCW, Luttikhuizen DT, Colyer MH, Cukras CA et al..  2021.  Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration.. J Am Med Inform Assoc.

Yan K, Tang Y, Peng Y, Sandfort V, Bagheri M, Lu Z, Summers RM.  2019.  MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. Medical Image Computing and Computer Assisted Intervention – MICCAI. 11769:194-202.

Du J, Chen Q, Peng Y, Xiang Y, Tao C, Lu Z.  2019.  ML-Net: multi-label classification of biomedical texts with deep neural networks. J Am Med Inform Assoc. 26(11):1279-1285.

Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.  2015.  miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput Biol. 11(9):e1004391.

Johnson AEW, Pollard TJ, Greenbaum NR, Lungren MP, Deng C-ying, Peng Y, Lu Z, Mark RG, Berkowitz SJ, Horng S.  0.  MIMIC-CXR-JPG, a large publicly available database of labeled chest radiographs.

Wang X, Peng Y, Lu L, Lu Z, Summers RM.  2018.  Method and system of building hospital-scale chest x-ray database for entity extraction and weakly-supervised classification and localization of common thorax diseases .

Mathai TSudharshan, Lee S, Elton DC, Shen TC, Peng Y, Lu Z, Summers RM.  2022.  Lymph node detection in T2 MRI with transformers. SPIE Medical Imaging. :120333B.

Holste G, Wang S, Jiang Z, Shen TC, Shih G, Summers RM, Peng Y, Wang Z.  2022.  Long-Tailed Classification of Thorax Diseases on Chest X-Ray: A New Benchmark Study.. Data Augment Label Imperfections (2022). 13567:22-32.

Allot A, Peng Y, Wei C-H, Lee K, Phan L, Lu Z.  2018.  LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic Acids Res. 46(W1):W530-W536.

Lee HGi, Scholle E, Al'Aref S, Beecy A, Peng Y.  2021.  Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality. NAACL.

Tang L, Peng Y, Wang Y, Ding Y, Durrett G, Rousseau JF.  2023.  Less Likely Brainstorming: Using Language Models to Generate Alternative Hypotheses.. Proc Conf Assoc Comput Linguist Meet. 2023:12532-12555.

Paul A, Shen TC, Peng Y, Lu Z, Summers RM.  2021.  Learning few-shot chest X-ray diagnosis using images from the published scientific literature. IEEE International Symposium on Biomedical Imaging (ISBI).

Han Y, Chen C, Tewfik A, Glicksberg B, Ding Y, Peng Y, Wang Z.  2022.  Knowledge-Augmented Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop.. IEEE Winter Conf Appl Comput Vis. 2022:1789-1798.

Wang S, Lin M, Ghosal T, Ding Y, Peng Y.  2022.  Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review.. Health Data Sci. 2022

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K.  2014.  iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database (Oxford). 2014

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K..  2012.  iSimp: A sentence simplification system for biomedicail text. IEEE International Conference on Bioinformatics and Biomedicine. :211-216.

Lin M, Li T, Yang Y, Holste G, Ding Y, Van Tassel SH, Kovacs K, Shih G, Wang Z, Lu Z et al..  2023.  Improving model fairness in image-based computer-aided diagnosis.. Nat Commun. 14(1):6261.

Ji Z, Shaikh MAbuzar, Moukheiber D, Srihari SN, Peng Y, Gao M.  2021.  Improving Joint Learning of Chest X-Ray and Radiology Report by Word Region Alignment. International Workshop on Machine Learning in Medical Imaging.