Publications

Yan K, Peng Y, Sandfort V, Bagheri M, Lu Z, Summers RM.  0.  Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). :8523-8532.

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.

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.

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K.  2013.  Enhancing the interoperability of iSimp by using the BioC format. Proceedings of the BioCreative IV Workshop. :5-9.

Comeau DC, Batista-Navarro RTheresa, Dai H-J, Doğan RIslamaj, Yepes AJimeno, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M et al..  2014.  BioC interoperability track overview. Database (Oxford). 2014

Peng Y, Torii M, Wu CH, Vijay-Shanker K.  2014.  A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC Bioinformatics. 15:285.

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, Arighi C, Wu CH,.Vijay-Shanker K.  2015.  Extended dependency graph for BioC-compatible protein-protein interaction (PPI) passage detection in full-text articles. Proceedings of the BioCreative V Workshop. :30-35.

Peng Y, Gupta S, Wu C, Shanker V.  2015.  An extended dependency graph for relation extraction in biomedical texts. Proceedings of BioNLP 15. :21–30.

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.

Wei C-H, Peng Y, Leaman R, Davis APeter, Mattingly CJ, Li J, Wiegers TC, Lu Z.  2015.  Overview of the Biocreative V chemical disease relation (CDR) task. Proceedings of the BioCreative V Workshop. :154-166.

Wei C-H, Peng Y, Leaman R, Davis APeter, Mattingly CJ, Li J, Wiegers TC, Lu Z.  2016.  Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database (Oxford). 2016

Peng Y, Arighi C, Wu CH, Vijay-Shanker K.  2016.  BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Peng Y, Wei C-H, Lu Z.  2016.  Improving chemical disease relation extraction with rich features and weakly labeled data. J Cheminform. 8:53.

Doğan RIslamaj, Chatr-aryamontri A, Kim S, Wei C-H, Peng Y, Comeau D, Lu Z.  2017.  BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017. :171–175.

Peng Y, Rios A, Kavuluru R, Lu Z.  2017.  Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models. Proceedings of the BioCreative VI Workshop. :148-151.

Wang X, Peng Y, Lu L, Lu Z, Bagheri M, Summers RM.  2017.  ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). :2097-2106.

Peng Y, Lu Z.  2017.  Deep learning for extracting protein-protein interactions from biomedical literature. BioNLP 2017. :29–38.

Peng Y, Rios A, Kavuluru R, Lu Z.  2018.  Extracting chemical-protein relations with ensembles of SVM and deep learning models. Database (Oxford). 2018

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.

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 .

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.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM et al..  2018.  Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 15(141)