Publications

Journal Articles

* Note that JAMIA and JBI are leading health informatics journals with impact factor 7.942 and 8.000

• Kang, T., Sun, Y.(Co-first author), Kim, J.H., Ta, C., Perotte, A., Schiffer, K., Wu, M., Zhao, Y., Moustafa-Fahmy, N., Peng, Y. and Weng, C., 2023. EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension. Journal of the American Medical Informatics Association, p.ocad036.

• Lee, J., Liu, C., Kim, J., Chen, Z., Sun, Y., Rogers, J.R., Chung, W.K. and Weng, C., 2022. Deep learning for rare disease: A scoping review. Journal of Biomedical Informatics(JBI), p.104227.

• Fang, Y., Idnay, B., Sun, Y., Chen, Z., Marder, K., Xu, H., Schnall, R., and Weng, C.,”Combining Human and Machine Intelligence for Clinical Trial Eligibility Querying”. Journal of the American Medical Informatics Association(JAMIA), 2022.

• Kim, J., Butler, A., Ta, C., Sun, Y., Maurer, M. and Weng, C., “The Potential Role of EHR data in optimizing eligibility criteria definition for cardiovascular outcome trials”. International Journal of Medical Informatics, 2021. pdf

• Sun, Y., Butler, A., Diallo, I., Kim, J., Ta, C., Rogers, J., Liu, H. and Weng, C., “A Framework for Systematic Assessment of Clinical Trial Population Representativeness Using Electronic Health Records Data”. Applied Clinical Informatics Journal , 2021. pdf

• Sun, Y., Butler, A., Stewart, S.A., Liu, H., Yuan, C., Southard, C.T., Kim, J. and Weng, C., “Building An OMOP Common Data Model-Compliant Annotated Corpus for COVID-19 Clinical Trials”. Journal of Biomedical Informatics(JBI), 2021. code

• Sun, Y., Butler, A., Lin, F., Liu, H., Stewart, A.S., Kim J., Idnay, S.B., Ge, Q., Wei, X., Liu, C., Yuan, C. and Weng, C., “The COVID-19 Trial Finder”. Journal of the American Medical Informatics Association(JAMIA), 2020. pdf code website video

• Sun, Y., Guo, F., Kaffashi, F., Jacono, F.J., DeGeorgia, M. and Loparo, K.A., “INSMA: An integrated system for multimodal data acquisition and analysis in the intensive care unit”. Journal of Biomedical Informatics(JBI), p.103434, 2020.pdf code

• Sun, Y., Kolacinski, R. and Loparo, K., “Transitive Topic Modeling with Conversational Structure Context: Discovering Topics that are Most Popular in Online Discussions”. International Journal of Semantic Computing, 14(02), pp.273-293, 2020. pdf

• Liu, H., Yuan, C., Butler, A., Sun, Y. and Weng, C., “A Knowledge Base of Clinical Trial Eligibility Criteria”. Journal of Biomedical Informatics(JBI), p.103771, 2021. pdf website video

• Kury, F., Butler, A., Yuan, C., Fu, L.H., Sun, Y., Liu, H., Sim, I., Carini, S. and Weng, C., “Chia, a large annotated corpus of clinical trial eligibility criteria”. Scientific data, 7(1), pp.1-11, 2020. pdf code data

• Li, Q., Sun, Y. and Xue, B., “Complex query recognition based on dynamic learning mechanism”. In Journal of Computational Information Systems (Vol. 8, pp. 8333-8340). Springer, 2012. pdf

• Li, Q., Zou, Y. and Sun, Y., “User Personalization Mechanism in Agent-based Meta Search Engine. In Journal of Computational Information Systems (Vol. 8, pp. 1-8). Springer, 2012. pdf

Conference Proceedings

• Idnay, B., Fang, Y., Sun, Y., Liu, H., Chen, Z., Schnall R. and Weng, C., “Criteria2Query: Combining Machine Efficiency and Human Intelligence to Define More Accurate and Feasible Clinical Research Cohorts” International Conference on Artificial Intelligence in Medicine(AIME 2022), 2022

• Sun, Y., Tang, J., Butler, A., Liu, C., Fang, Y. and Weng, C., “Interactive Similarity-Based Search of Clinical Trials”, 290, pp.309-313. In International Medical Informatics Conference 2021 (MEDINFO 2021), 2021. pdf

• Fang, Y., Kim, J., Idnay, B., Garcia, B., Castillo, C., Sun, Y., Liu, H., Liu, C., Yuan, C., Weng C., “Participatory Design of a Clinical Trial Eligibility Criteria Simplification Method” In 31st Medical Informatics Europe Conference (MIE 2021), 2021

• Li, X., Liu, H., Kury, F., Yuan, C., Butler, A., Sun, Y., Ostropolets,A., Xu, H., Weng C., “Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model” In American Medical Informatics Association 2020 Annual Symposium (AMIA) Virtual Summit, 2021

• Fang, Y., Sun, Y., Liu, H., Chen Z. and Weng, C., “Criteria2Query 2.0: An Editable User Interface for Human-Machine Collaboration in Cohort Definition”. In Observational Health Data Sciences & Informatics (OHDSI) Software Showcase. 2021, August. pdf video

• Sun, Y., Kolacinski, R. and Loparo, K., “Eliminating search intent bias in learning to rank”. In IEEE 14th International Conference on Semantic Computing (ICSC) (pp. 108-115). IEEE, 2020, February. (Best Paper Candidate)

• Sun, Y., Loparo, K. and Kolacinski, R., “Conversational structure aware and context sensitive topic model for online discussions”. In IEEE 14th International Conference on Semantic Computing (ICSC) (pp. 85-92). IEEE, 2020, February. (Best Paper Candidate)

• Liu, H., Yuan, C., Butler, A., Sun, Y. and Weng, C., “Potential Role of Clinical Trial Eligibility Criteria in Electronic Phenotyping”. In American Medical Informatics Association 2020 Annual Symposium (AMIA). 2020, December. video

• Sun, Y. and Loparo, K., “Opinion Spam Detection Based on Heterogeneous Information Network”. In IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI) (pp. 1156-1163). IEEE. 2019, November.

• Sun, Y., Cai, X. and Loparo, K., “Learning - based Adaptation Framework for Elastic Software Systems”. In IEEE 31st International Conference on Software Engineering and Knowledge Engineering (SEKE) (Vol. 1, pp. 281-286). IEEE. 2019, July.

• Sun, Y. and Loparo, K., “Topic Shift Detection in Online Discussions using Structural Context”. In IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC) (Vol. 1, pp. 948-949). IEEE. 2019, July.

• Sun, Y. and Loparo, K., “Information Extraction from Free Text in Clinical Trials with Knowledge-Based Distant Supervision”. In IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC) (Vol. 1, pp. 954-955). IEEE. 2019, July.

• Sun, Y. and Loparo, K., “A Clicked-URL Feature for Transactional Query Identification”. In IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC) (Vol. 1, pp. 950-951). IEEE. 2019, July.

• Sun, Y. and Loparo, K., “Context Aware Image Annotation in Active Learning with Batch Mode”. In IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC) (Vol. 1, pp. 952-953). IEEE. 2019, July.

• Sun, Y. and Loparo, K., “A Common Gene Expression Signature Analysis Method for Multiple Types of Cancer”. In 19th Industrial Conference on Data Mining. (Vol. 1, pp. 200-211). Springer. 2019, July.

• Sun, Y. and Loparo, K., “Knowledge-guided Text Structuring in Clinical Trials”. In 19th Industrial Conference on Data Mining. (Vol. 1, pp. 211-219). Springer. 2019, July.

• Sun, Y. and Loparo, K., “Context Aware Image Annotation in Active Learning”. In 19th Industrial Conference on Data Mining. (Vol. 1, pp. 251-262). Springer. 2019, July.

• Sun, Y. and Li, Q., “The research situation and prospect analysis of meta-search engines”. In 2nd International Conference on Uncertainty Reasoning and Knowledge Engineering (pp. 224-229). IEEE. 2012, August.

• Li, Q. and Sun, Y., “An agent based intelligent meta search engine”. In 2012 4th International Conference on Web Information Systems and Mining (WISM) (pp. 572-579). Springer. 2012, October.

• Li, Q., Zou, Y. and Sun, Y., “Ontology based user personalization mechanism in meta search engine”. In 2nd International Conference on Uncertainty Reasoning and Knowledge Engineering (pp. 230-234). IEEE. 2012, August.

Papers in Submission

• Sun, Y., Tian, K., Perotte, A., Kim, J., Liu, H., Turfah, A. and Weng, C., “EvidenceBase: A Natural Language Search Engine for Medical Evidence Curation”. Journal of the American Medical Informatics Association(JAMIA), 2021. (in submission)

Patents

• Li, Q., Sun, Y., Zou, Y., Xu, J., Xi, B. “Agent Based Intelligent Meta Search Engines System”, CN Patent No. 102902800 A. 2012.
• Li, Q., Zou, Y., Sun, Y., Xu, J., Xi, B.,”A Personalized Method of Agent Based Meta Search Engines”, CN Patent No.103593413 A. 2013.

Thesis

• Sun, Y., “Topic Modeling and Spam Detection for Short Text Segments in Web Forums”, 2020 (Doctoral dissertation, Case Western Reserve University).
• Sun, Y., “Research and Implementation of Personalization of Agent-based Intelligent Meta Search Engine”, 2013 (Master dissertation, Xidian University).

You can also find my articles on my Google Scholar profile.