Publications

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)

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, Lee S, Elton DC, Shen T, Tang Y-xing, Chen Q, Wang S, Zhu Y, Summers R, Lu Z.  2020.  Automatic recognition of abdominal lymph nodes from clinical text. Proceedings of the 3rd Clinical Natural Language Processing Workshop.

Peng Y, Tang Y, Lee S, Zhu Y, Summers RM, Lu Z.  2021.  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. 7(1):3-12.

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.

Jaiswal A, Li T, Zander C, Han Y, Rousseau JF, Peng Y, Ding Y.  2021.  SCALP - Supervised Contrastive Learning for Cardiopulmonary Disease Classification and Localization in Chest X-rays using Patient Metadata. The IEEE International Conference on Data Mining (ICDM).

He X, Zhang R, Alpert J, Zhou S, Adam TJ, Raisa A, Peng Y, Zhang H, Guo Y, Bian J.  2021.  When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? JAMIA Open. 4(1):ooab026.

He X, Zhang R, Alpert J, Zhou S, Adam TJ, Raisa A, Peng Y, Zhang H, Guo Y, Bian J.  2021.  When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? JAMIA Open. 4(1):ooab026.

He X, Zhang R, Alpert J, Zhou S, Adam TJ, Raisa A, Peng Y, Zhang H, Guo Y, Bian J.  2021.  When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? JAMIA Open. 4(1):ooab026.

Wang S, Zhu Y, Lee S, Elton DC, Shen TC, Tang Y, Peng Y, Lu Z, Summers RM.  2022.  Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images.. Med Image Anal. 77:102345.

Wanyan T, Lin M, Klang E, Menon KM, Gulamali FF, Azad A, Zhang Y, Ding Y, Wang Z, Wang F et al..  2022.  Supervised Pretraining through Contrastive Categorical Positive Samplings to Improve COVID-19 Mortality Prediction.. ACM BCB. 2022

Patra BGopal, Sun Z, Cheng Z, Kumar PKasi Reddy, Altammami A, Liu Y, Joly R, Jedlicka C, Delgado D, Pathak J et al..  2023.  Automated classification of lay health articles using natural language processing: a case study on pregnancy health and postpartum depression.. Front Psychiatry. 14:1258887.

Xu J, Wang F, Zang C, Zhang H, Niotis K, Liberman AL, Stonnington CM, Ishii M, Adekkanattu P, Luo Y et al..  2023.  Comparing the effects of four common drug classes on the progression of mild cognitive impairment to dementia using electronic health records.. Sci Rep. 13(1):8102.

Xu J, Wang F, Zang C, Zhang H, Niotis K, Liberman AL, Stonnington CM, Ishii M, Adekkanattu P, Luo Y et al..  2023.  Comparing the effects of four common drug classes on the progression of mild cognitive impairment to dementia using electronic health records.. Sci Rep. 13(1):8102.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Tong J, Luo C, Sun Y, Duan R, Saine E, Lin L, Peng Y, Lu Y, Batra A, Pan A et al..  2023.  Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints.. J Am Med Inform Assoc.

Kang T, Sun Y, Kim JHyun, Ta C, Perotte A, Schiffer K, Wu M, Zhao Y, Moustafa-Fahmy N, Peng Y et al..  2023.  EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension.. J Am Med Inform Assoc.

Keloth VK, Banda JM, Gurley M, Heider PM, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, Patterson OV et al..  2023.  Representing and Utilizing Clinical Textual Data for Real World Studies: An OHDSI Approach.. J Biomed Inform. :104343.

Sun Z, Lin M, Zhu Q, Xie Q, Wang F, Lu Z, Peng Y.  2023.  A scoping review on multimodal deep learning in biomedical images and texts.. J Biomed Inform. 146:104482.

Xu RLi, Wang S, Wang Z, Zhang Y, Xiao Y, Pathak J, Hodge D, Leng Y, S Watkins C, Ding Y et al..  2024.  Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups.. Proc (IEEE Int Conf Healthc Inform). 2024:189-199.

Zhang G, Jin Q, Zhou Y, Wang S, Idnay B, Luo Y, Park E, Nestor JG, Spotnitz ME, Soroush A et al..  2024.  Closing the gap between open source and commercial large language models for medical evidence summarization.. NPJ Digit Med. 7(1):239.

Zhang G, Jin Q, Zhou Y, Wang S, Idnay B, Luo Y, Park E, Nestor JG, Spotnitz ME, Soroush A et al..  2024.  Closing the gap between open source and commercial large language models for medical evidence summarization.. NPJ Digit Med. 7(1):239.