Publications

Yan K, Peng Y, Lu Z, Summers RM.  2019.  Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports. IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019). :285-288.

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.

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.

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.

Peng Y, Yan K, Sandfort V, Summers RM, Lu Z.  2019.  A self-attention based deep learning method for lesion attribute detection from CT reports. 2019 IEEE International Conference on Healthcare Informatics (ICHI).

Peng Y, Zhang Z, Wang X, Yang L, Lu L.  2019.  Text Mining and Deep Learning for Disease Classification. Handbook of Medical Image Computing and Computer Assisted Intervention. :109-136.

Peng Y, Yan S, Lu Z.  2019.  Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. Proceedings of the 18th BioNLP Workshop and Shared Task. :58–65.

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.

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 .

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.

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)

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)

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)

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)

Wang X, Peng Y, Lu L, Lu Z, Summers RM.  2018.  TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays. IEEE/CVF Conference on Computer Vision and Pattern Recognition. :9049-9058.

Wang X, Peng Y, Lu L, Lu Z, Summers RM.  2018.  TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays. IEEE/CVF Conference on Computer Vision and Pattern Recognition. :9049-9058.

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.

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.