Yanshan Wang's Homepage

An informatician in need is an informatician indeed.

Yanshan Wang

Research Associate,

Department of Health Sciences Research,

Mayo Clinic.

Address: 200 1st ST SW, Rochester, MN 55901

Email: Wang dot Yanshan at mayo dot edu


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Research

My research interests include, but not limited to:

  • Biomedical Informatics
  • Clinical/Medical Natural Language Processing
  • Information Retrieval
  • Machine Learning Applications

Publications (pdf)

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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)
  6. 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.
  7. 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)
  8. 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)
  9. 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)
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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)
  17. 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)
  18. 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.
  19. 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) (One of the most downloaded articles from JBI!)
  20. 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
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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).
  30. 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.
  31. Yanshan Wang, In-Chan Choi, and Hongfang Liu. "Generalized Ensemble Model for Document Ranking in Information Retrieval." Computer Science & Information Systems 14.1 (2017).
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. Yanshan Wang, Stephen Wu, and Hongfang Liu. MayoNLPTeam at the 2016 CLEF eHealth Information Retrieval Task., CLEF eHealth 2016.
  39. Sijia Liu, Yanshan Wang, Saeed Mehrabi, Dingcheng Li, Hongfang Liu. MayoBMI at ImageCLEF 2016 Handwritten Document Retrieval Task, CLEF eHealth 2016.
  40. 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)
  41. 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)
  42. 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]
  43. 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
  44. 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]
  45. 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.
  46. 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.
  47. 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.
  48. Yanshan Wang, Dingcheng Li, Stephen Wu, Hongfang Liu. Improving Clinical Information Retrieval by Incorporating Part-Of-Speech Tagging. Delivery Science Summit, 2015.
  49. 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.]
  50. 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%.)
  51. 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.
  52. Yanshan Wang. A novel soft keyboard for touchscreen phones: QWERT. International Journal of Human Factors and Ergonomics (IJHFE), 2(4), 246-261, 2013.

Research Activities

  • Editorial: Biomedical Informatics Insights, Frontiers in AI, MedInfo 2017
  • Journal Reviewer: Knowledge-Based Systems, Journal of Biomedical Informatics, Journal of American Medical Informatics Association, Journal of Medical Internet Research, International Journal of Medical Informatics, 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.

Research Projects

  • 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: Investigator.
  • NIH-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: Investigator
  • NIH-R21 Enhanced Ascertainment of Asthma Status Via Natural Language Processing.
    • The major goal of this project is to enhance asthma care and research through application of (NLP) Natural Language Processing, to electronic health records.
    • Role: Investigator.