Yanshan Wang, PhD, FAMIA

Research Interests

My research interests include, but not limited to:

• Clinical Natural Language Processing

• Artificial Intelligence (Machine/Deep Learning) Applications in Healthcare

Publications (pdf)

1. David Oniani, Yanshan Wang. A Qualitative Evaluation of Language Models on Automatic Question-Answering for COVID-19. ACM-BCB 2020.

2. Sam Henry, Yanshan Wang, Feichen Shen, and Ozlem Uzuner. "The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records." Journal of the American Medical Informatics Association (2020).

3. Fu S, Chen D, He H, Liu S, Moon S, Peterson KJ, Shen F, Wang L, Wang Y, Wen A, Zhao Y. Clinical Concept Extraction: a Methodology Review. Journal of Biomedical Informatics. 2020 Aug 6:103526.

4. Nathan D Seligson, Jeremy L Warner, William S Dalton, David Martin, Robert S Miller, Debra Patt, Kenneth L Kehl, Matvey B Palchuk, Gil Alterovitz, Laura K Wiley, Ming Huang, Feichen Shen, Yanshan Wang, Khoa A Nguyen, Anthony F Wong, Funda Meric-Bernstam, Elmer V Bernstam, James L Chen, Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity, Journal of the American Medical Informatics Association, , ocaa159, https://doi.org/10.1093/jamia/ocaa159

5. Fu S, Carlson LA, Peterson KJ, Wang N, Zhou X, Peng S, Jiang J, Wang Y, Sauver JS, Liu H. Natural Language Processing for the Evaluation of Methodological Standards and Best Practices of EHR-based Clinical Research. AMIA Jt Summits Transl Sci Proc. 2020; 2020:171-180.

6. Yanshan Wang, Yiqing Zhao, Terry M. Therneau, Elizabeth J. Atkinson, Ahmad P. Tafti, Nan Zhang, Shreyasee Amin, Andrew H. Limper, Sundeep Khosla, and Hongfang Liu. "Unsupervised Machine Learning for the Discovery of Latent Disease Clusters and Patient Subgroups Using Electronic Health Records." Journal of Biomedical Informatics. 2020. (pdf)

7. Andrew Wen, Liwei Wang, Huan He, Sijia Liu, Sunyang Fu, Sunghwan Sohn, Jacob A Kugel, Vinod C Kaggal, Ming Huang, Yanshan Wang, Feichen Shen, Jungwei Fan, Hongfang Liu. An Aberration Detection-Based Approach for Sentinel Syndromic Surveillance of COVID-19 and Other Novel Influenza-Like Illnesses. under review.

8. Andrew Wen, Yanshan Wang, Vinod C. Kaggal, Sijia Liu, Hongfang Liu, and Jungwei Fan. "Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices." In 2019 IEEE International Conference on Big Data (Big Data), pp. 2800-2807. IEEE, 2019.

9. Sunyang Fu, David Chen, Sijia Liu, Sungrim Moon, Kevin J Peterson, Feichen Shen, Yanshan Wang, Liwei Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu. A Review of the End-to-End Methodologies for Clinical Concept Extraction. arXiv preprint arXiv:1910.11377. 2019. (pdf)

10. Yanshan Wang, Hua Xu, and Ozlem Uzuner. "The second international workshop on health natural language processing (HealthNLP 2019)." (2019): 1-3.

11. Tafti AP, Wang Y, Shen F, Sagheb E, Kingsbury P, Liu H. Integrating word embedding neural networks with PubMed abstracts to extract keyword proximity of chronic diseases. 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). 2019.

12. Liwei Wang, Lei Luo, Yanshan Wang, Jason Wampfler, Ping Yang, and Hongfang Liu. "Natural language processing for populating lung cancer clinical research data." BMC Medical Informatics and Decision Making 19, no. 5 (2019): 239.

13. Xin Zhou, Yanshan Wang*, Sunghwan Sohn, Terry M. Therneau, Hongfang Liu, and David S. Knopman. "Automatic extraction and assessment of lifestyle exposures for Alzheimer’s disease using natural language processing." International journal of medical informatics 130 (2019): 103943. [*Corresponding Author]

14. Yanshan Wang, Krishna B. Soundararajan, Sunyang Fu, Luke A. Carlson, Rebecca A. Smith, David S. Knopman, and Hongfang Liu. "How Good is Artificial Intelligence at Automatically Answering Consumer Questions Related to Alzheimer's Disease?." arXiv preprint arXiv:1908.10678 (2019).

15. Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, and Hongfang Liu. "HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology." Journal of biomedical informatics 96 (2019): 103246.

16. Cody C. Wyles, Meagan E. Tibbo, Sunyang Fu, Yanshan Wang, Sunghwan Sohn, Walter K. Kremers, Daniel J. Berry, David G. Lewallen, and Hilal Maradit-Kremers. "Use of Natural Language Processing Algorithms to Identify Common Data Elements in Operative Notes for Total Hip Arthroplasty." JBJS (2019).

17. Liwei Wang, Lei Luo, Yanshan Wang, Jason A. Wampfler, Ping Yang, and Hongfang Liu. "Information Extraction for Populating Lung Cancer Clinical Research Data." In 2019 IEEE International Conference on Healthcare Informatics (ICHI), pp. 1-2. IEEE, 2019.

18. Yanshan Wang, Andrew Wen, Sijia Liu, William Hersh, Steven Bedrick, and Hongfang Liu. Test collections for electronic health record-based clinical information retrieval. JAMIA Open. 2019.

19. Yanshan Wang, Ahmad Tafti, Sunghwan Sohn, and Rui Zhang. Applications of Natural Language Processing in Clinical Research and Practice. In Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Tutorials, pp. 22-25. 2019.

20. Yanshan Wang, Saeed Mehrabi, Sunghwan Sohn, Elizabeth J Atkinson, Shreyasee Amin, Hongfang Liu. Natural Language Processing of Radiology Reports for Identification of Skeletal Site-Specific Fractures. BMC Medical Informatics and Decision Making. 2019.

21. Sunyang Fu, Lester Y. Leung, Yanshan Wang, Anne-Olivia Raulli, David F. Kallmes, Kristin A. Kinsman, Kristoff B. Nelson et al. Natural Language Processing for the Identification of Silent Brain Infarcts From Neuroimaging Reports. JMIR medical informatics 7, no. 2. 2019.

22. Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William Hersh, and Hongfang Liu. CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. arXiv preprint arXiv:1901.07601. 2019. (pdf)

23. Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database. 2019.

24. Sungrim Moon, Sijia Liu, David Chen, Yanshan Wang, Douglas L Wood, Rajeev Chaudhry, Hongfang Liu, Paul Kingsbury. Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients. Journal of Healthcare Informatics Research. 2019.

25. Feichen Shen, Yiqing Zhao, Liwei Wang, Majid Rastegar Mojarad, Yanshan Wang, Sijia Liu, Hongfang Liu. Rare Disease Knowledge Enrichment through a Data-Driven Approach. BMC Medical Informatics and Decision Making. 2019.

26. Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J Atkinson, Shreyasee Amin, Hongfang Liu. A Clinical Text Classification Paradigm based on Deep Representation and Weak Supervision. BMC Medical Informatics and Decision Making. 2018. (pdf)

27. Majid Rastegar-Mojarad, Sijia Liu, Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu. BioCreative/OHNLP Challenge 2018. Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2018.

28. Yanshan Wang, Naveed Afzal, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu. Overview of the BioCreative/OHNLP Challenge 2018 Task 2: Clinical Semantic Textual Similarity. Proceedings of the BioCreative/OHNLP Challenge. 2018. (pdf)

29. Yiqing Zhao, Yanshan Wang, Henry Wang, Benjamin Yan, Feichen Shen, Kevin J Peterson, Walter A Rocca, Jennifer St Sauver, Hongfang Liu. Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2018.

30. Sijia Liu, Majid Rastegar Mojarad, Yanshan Wang, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu. Overview of the BioCreative/OHNLP 2018 Family History Extraction Task. Proceedings of the BioCreative/OHNLP Challenge. 2018. (pdf)

31. Yanshan Wang, Naveed Afzal, Sunyang Fu, Liwei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu. MedSTS: a resource for clinical semantic textual similarity. Language Resources and Evaluation. 2018. (pdf)

32. Feichen Shen, Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Hongfang Liu. Utilization of Electronic Medical Records and Biomedical Literature to Support the Diagnosis of Rare Diseases Using Data Fusion and Collaborative Filtering Approaches. JMIR medical informatics. 2018.

33. Yanshan Wang, Saeed Mehrabi, Sunghwan Sohn, Elizabeth Atkinson, Shreyasee Amin, Hongfang Liu. Automatic Extraction of Major Osteoporotic Fractures from Radiology Reports using Natural Language Processing. IEEE International Conference on Healthcare Informatics Workshop. 2018.

34. Xin Zhou, Hongfang Liu, Yanshan Wang. A Comparison of Lifestyle Interventions for Alzheimer's Disease Extracted from Clinical Notes and Literature. IEEE International Conference on Healthcare Informatics Workshop. 2018.

35. Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew H Limper, Hongfang Liu. Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. IEEE International Conference on Healthcare Informatics Workshop. 2018.

36. Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu. Predicting Practice Setting Using Topic Modeling. IEEE International Conference on Healthcare Informatics Workshop. 2018.

37. Liwei Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Yanshan Wang, Hongfang Liu. Identification of Genetic Causality Statements in Medline Abstracts Leveraging Distant Supervision. IEEE International Conference on Healthcare Informatics Workshop. 2018.

38. Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Hongfang Liu. A Comparison of Word Embeddings for the Biomedical Natural Language Processing. Journal of Biomedical Informatics. 2018. (pdf)

39. Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur-Elayavilli, Hongfang Liu. Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. Database. 2017. (pdf)

40. Stephen Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu. Aligned-Layer Text Search in Clinical Notes. Studies in health technology and informatics 245. 2017.

41. Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sungrim Moon, Feichen Shen, Naveed Afzal, Sijia Liu, Yuqun Zeng, Saeed Mehrabi, Sunghwan Sohn, Hongfang Liu. Clinical Information Extraction Applications: A Literature Review. Journal of Biomedical Informatics 77. 2017. (pdf) [Most downloaded articles from JBI!!!]

42. Sunghwan Sohn, Yanshan Wang, Chung-Il Wi, Elizabeth A Krusemark, Euijung Ryu, Mir H Ali, Young J Juhn, Hongfang Liu; Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions, Journal of the American Medical Informatics Association, ocx138, https://doi.org/10.1093/jamia/ocx138

43. Zeng, Yuqun, Xusheng Liu, Yanshan Wang, Feichen Shen, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, and Hongfang Liu. "Recommending Education Materials for Diabetic Questions Using Information Retrieval Approaches." Journal of medical Internet research 19, no. 10. 2017.

44. Stephen Wu, Sijia Liu, Yanshan Wang, T Timmons, H Uppili, S Bedrick, W Hersh, and H Liu. Intra-institutional EHR Collections for Patient-Level Information Retrieval. Journal of the American Society for Information Science and Technology. 2017.

45. Susan McRoy, Majid Rastegar-Mojarad, Yanshan Wang, Kathryn Ruddy, Tufia Haddad, Hongfang Liu. Content-based Analysis of Health Forum Text to Assess Potential the Unmet Needs of Breast Cancer Survivors. Individualizing Medicine Conference, Rochester, MN USA, 2017.

46. Sijia Liu, Feichen Shen, Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Vipin Chaudhary, Hongfang Liu. Attention-based Neural Networks for Chemical Protein Relation Extraction. Proceedings of BioCreative VI challenge, Bethesda, Maryland USA, 2017.

47. Yanshan Wang, Feichen Shen, Ravikumar Komandur Elayavilli, Sijia Liu, Majid Rastegar-Mojarad, Hongfang Liu. Entity-enhanced Hierarchical Attention Neural Networks for Mining Protein Interactions from Biomedical Texts. Proceedings of BioCreative VI challenge, Bethesda, Maryland USA, 2017.

48. Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Yanshan Wang, Sijia Liu, Feichen Shen, Hongfang Liu. Semantic Information Retrieval: Exploring dependency and word embedding features in biomedical Information Retrieval. Proceedings of BioCreative VI challenge, Bethesda, Maryland USA, 2017.

49. Sijia Liu, Yanshan Wang, Na Hong, Feichen Shen, Stephen Wu, William Hersh, and Hongfang Liu. On Mapping Textual Queries to a Common Data Model. In Proceedings of 2017 IEEE International Conference on Healthcare Informatics (ICHI), Park City, Utah, 2017.

50. Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, H Melissa, P Robinson, and H Liu. Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA Annual Symposium Proceedings 2017.

51. Yanshan Wang, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Fei Liu, and Hongfang Liu. Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Texts. In Proceedings of ACM BCB conference, Boston, MA USA, August 2017 (ACM-BCB’ 17).

52. Yanshan Wang, Liwei Wang, Sijia Liu, Feichen Shen, and Hongfang Liu. Systematic Analysis of Free-Text Family History in Electronic Health Record. AMIA Summits on Translational Science Proceedings, 2017.

53. Yanshan Wang, In-Chan Choi, and Hongfang Liu. "Generalized Ensemble Model for Document Ranking in Information Retrieval." Computer Science & Information Systems 14.1 (2017).

54. Zeng, Yuqun, Xusheng Liu, Liwei Wang, Hongfang Liu, and Yanshan Wang. "Answering diabetic patients' questions using expert-vetted online resources: A case study." In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on, pp. 525-528. IEEE, 2016.

55. Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur-Elayavilli, Sijia Liu and Hongfang Liu. MayoNLPTeam at TREC 2016 Clinical Decision Support Track: An Ensemble Approach of Clinical Information Extraction and Retrieval, Proceedings of the Text REtrieval Conference (TREC), 2016.

56. Dingcheng Li, Sijia Liu, Majid Mojarad Rastegar, Yanshan Wang, Xiaodi Li, Vipin Chaudhary, Terry Therneau, Hongfang Liu. A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text, AMIA Annual Symposium, 2016.

57. Yuqun Zeng, Liwei Wang, Hongfang Liu, Xusheng Liu, Yanshan Wang. Answering Diabetic Patients’ Questions Using Expert-ventted Online Resources: A Case Study. IEEE International Conference on Bioinformation and biomedicine (BIBM), 2016.

58. Stephen Wu, Yanshan Wang, Sunghwan Sohn, Chung-Il Wi, Elizabeth Krusemark, Hongfang Liu, Young Juhn. Probabilistic Population-level Modeling of Disease Event Timelines, AMIA Annual Symposium, 2016.

59. Yanshan Wang, Stephen Wu, Dingcheng Li, Saeed Mehrabi, Hongfang Liu. A Part-Of-Speech term weighting scheme for biomedical information retrieval. Journal of Biomedical Informatics 63 (2016): 379-389.

60. Yanshan Wang, Stephen Wu, and Hongfang Liu. MayoNLPTeam at the 2016 CLEF eHealth Information Retrieval Task., CLEF eHealth 2016.

61. Sijia Liu, Yanshan Wang, Saeed Mehrabi, Dingcheng Li, Hongfang Liu. MayoBMI at ImageCLEF 2016 Handwritten Document Retrieval Task, CLEF eHealth 2016.

62. Vinod C. Kaggal, Ravikumar Komandur Elayavilli, Saeed Mehrabi, Joshua J. Pankratz, Sunghwan Sohn, Yanshan Wang, Dingcheng Li, Majid Mojarad Rastegar, Sean P. Murphy, Jason L. Ross, Rajeev Chaudhry, James D. Buntrock, Hongfang Liu. Towards Learning Healthcare System -- Knowledge Delivery at the Point of Care Empowered by Big Data and NLP. Journal of Biomedical Informatics Insights, 2016. (Our paper is mentioned in Wikipedia: https://en.m.wikipedia.org/wiki/Health_care_analytics)

63. Naveed Afzal*, Yanshan Wang*, Hongfang Liu. MayoNLP at SemEval-2016 Task 1: Semantic Textual Similarity based on Lexical Semantic Net and Deep Learning Semantic Model. Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016). Association for Computational Linguistics, 2016. (*co-first authors)

64. Yanshan Wang, Stephen Wu, Dingcheng Li, Hongfang Liu. Influence of Part-of-Speech on the Clinical Information Retrieval, AMIA iHealth Clinical Informatics Conference, 2016. [Poster]

65. Saeed Mehrabi, Yanshan Wang, Donna Ihrke, Hongfang Liu. ``Exploring Gaps of Family History Documentation in EHR for Precision Medicine - A Case Study of Familial Hypercholesterolemia Ascertainment.'' AMIA 2016 Joint Summits on Translational Science, 2016

66. Yanshan Wang, Stephen Wu, Dingcheng Li, Hongfang Liu. POS-MRF: A Part-Of-Speech Weighted Markov Random Field Model for Clinical Information Retrieval, AMIA 2016 Joint Summits on Translational Science, 2016. [Poster]

67. Yanshan Wang, Saeed Mehrabi, Majid Rastegar-Mojarad, Dingcheng Li, Hongfang Liu. Retrieval of Semantically Similar Healthcare Questions in Healthcare Forums. IEEE International Conference on Healthcare Informatics (ICHI), 2015.

68. Dingcheng Li, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Yanshan Wang, Yue Yu, Saeed Mehrabi, Naveed Afzal, Sunghwan Sohn, Yanpeng Li, Hongfang Liu. A Frequency-filtering Strategy of Obtaining PHI-free sentences from clinical data repository. The 6th ACM conference of Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), 2015.

69. Dingcheng Li, Naveed Afzal, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Sijia Liu, Yanshan Wang, Feichen Shen, Hongfang Liu. Resolution of Chemical Disease Relations with Diverse Features and Rules. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 2015.

70. Yanshan Wang, Dingcheng Li, Stephen Wu, Hongfang Liu. Improving Clinical Information Retrieval by Incorporating Part-Of-Speech Tagging. Delivery Science Summit, 2015.

71. Yanshan Wang, In-Chan Choi, Jae-Sung Lee. Indexing by Latent Dirichlet Allocation and Ensemble Model. Journal of the American Society for Information Science and Technology (ASIS&T), 2015. [ASIS&T is the No.1 journal in information science research.]

72. Yanshan Wang, In-Chan Choi. A Text Classification Method Based on Latent Topics. Proceedings of the 1st International Conference on Operations Research and Enterprise Systems, 212-214, 2012. (The acceptance ratio for ICORES 2012 was 14%.)

73. Yanshan Wang. Stock price direction prediction by directly using prices data: an empirical study on the KOSPI and HSI. International Journal of BUsiness Intelligence and Data Mining, 9(2), 145-160, 2014.

74. Yanshan Wang. A novel soft keyboard for touchscreen phones: QWERT. International Journal of Human Factors and Ergonomics (IJHFE), 2(4), 246-261, 2013.

Awards

• Amazon AWS Diagnostics Development Initiative Award

• Fellow of AMIA (FAMIA)

Research Datasets

• MedSTS Dataset

  • The first accessible dataset for the semantic textual similarity (STS) task from the real-world clinical texts.

  • Related Shared Tasks:

    • 2018 BioCreative/OHNLP Challenge Task 2: ClinicalSTS

    • 2019 n2c2/OHNLP Shared Task Track 1: ClinicalSTS

Lectures/Tutorials

• Methods and Applications of Natural Language Processing in Medicine. International Conference on Artificial Intelligence in Medicine (AIME), Minneapolis, MN (Virtual due to COVID), August 25, 2020. (Slides)

• A Simple Introduction to Natural Language Processing and Its Clinical Applications in the Era of Artificial Intelligence. South Dakota State University Data Science Symposium, February, 2020. (Abstract)

• Applications of Natural Language Processing in Clinical Research and Practice. The 2019 Conference of the North American Chapter of the Association for Computational Linguistics (NAACL), Minneapolis, MN, 2019. (Slides)

• RNN / LSTM Architectures and their applications in clinical note analytics, OSCT Annual Meeting: Deep Learning Foundation and Application with a Special Focus on Medical Informatics, Milwaukee, WI, May 6, 2019. (Video)

Research Activities

• Editorial: Biomedical Informatics Insights, Frontiers in AI, MedInfo

• Journal Reviewer: Journal of Biomedical Informatics, Journal of American Medical Informatics Association, Journal of Medical Internet Research, International Journal of Medical Informatics, Knowledge-Based Systems, Neurocomputing, Plos One, Applied Clinical Informatics, Journal of Medical Internet Research, Journal of Healthcare Informatics Research, IEEE Transactions on Neural Networks and Learning Systems, Pharmaceutical Medicine, Nucleic Acids Research.

• Conference Reviewer: COLING, EMNLP, ACL, ACM-BCB, IEEE-BIBM, IEEE-ICHI, AMIA, AMIA-CRI, AMIA Joint Summits on Translational Science, AMIA Annual Symposium, HEALTHINFO, BIOTECHNO, SEPDA, ICIBM.

• PC member: ICHI, BIOTECHNO, NAACL, NLPCC, IHKDM, KDTBI, BIOTECHNO, LREC.

• Chair: HealthNLP Workshop 2018, 2019.

• Organizer: BioCreative/OHNLP 2018 Challenge (send me an email if you are interested in the ClinicalSTS dataset), 2019 n2c2/OHNLP Challenge

Funded Projects

• CHECE Research Award Developing Artificial Intelligence Models to Automatically Identify Social Determinants of Health Among Minority Populations from the Electronic Health Records and to Provide Implications for Health Equity

  • This study attempts to automatically infer the presence of social determinants of health status of minority populations based on their EHRs, and provide implications for health equity.

  • Role: Principal Investigator.

• NIH NLM-R01 Semi-structured Information Retrieval in Clinical Text for Cohort Identification

  • The goal is to make full use of clinical text in retrieving patients from the EMR. A layered language model for searching clinical text is introduced, addressing the need for both fine-grained information and big-picture contextual information.

  • Role: Co-Investigator.

• NIH NCATS-UL1 Supplement Investigation of Chronic Pain Management Based on Electronic Health Records

  • The long-term goal is to leverage the REP data and advanced informatics and analytics approaches to derive data-driven insights on chronic disease managements and build decision support tools for precision healthcare delivery.

  • Role: Co-Investigator.

• NIH NMH-R01 Leveraging EHR-linked biobanks for deep phenotyping, polygenic risk score modeling, and outcomes analysis in psychiatric disorders

  • This proposal will apply big data techniques for development of polygenic risk scores and their association to clinical outcomes and social determinants using large-scale integrated phenotype-genotype data.

  • Role: Co-Investigator .

• NIH NINDS-R01 Enabling Comparative Effectiveness Research in Silent Brain Infarction Through Natural Language Processing and Big Data

  • The goal of this project is to improve the evidence base for the prevention of stroke in patients with silent brain infarct, i.e., a stroke on neuroimaging (head CT or MRI) but no clinical evidence of a stroke, using natural language processing that can accurately identify cases of silent brain infarction among a large population of adults.

  • Role: Co-Investigator.