Halil Kilicoglu

Halil Kilicoglu

Associate Professor

PhD, Computer Science, Concordia University

Research focus

Biomedical informatics, natural language processing, computational semantics, literature-based knowledge discovery, scholarly communication, science of science, and scientific reproducibility.

Honors and Awards

  • IMIA Yearbook of Medical Informatics, Best Paper Selection (Natural Language Processing) for the paper titled "Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text," 2017
  • AMIA Annual Symposium Distinguished Paper Award for the paper titled "Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions," 2016
  • AMIA Annual Symposium Distinguished Paper Award for the paper titled "Using the Literature-Based Discovery Paradigm to Investigate Drug Mechanisms," 2007
     

Biography

Halil Kilicoglu is an associate professor in the School of Information Sciences at the University of Illinois at Urbana-Champaign. His research is primarily concerned with natural language understanding, with a particular focus on biomedical text. He uses a combination of data-driven analytical techniques and knowledge-based semantic approaches to extract and organize knowledge buried in textual artifacts, with potential benefits for biomedical discovery and scholarship, and healthcare outcomes. 
Kilicoglu earned his PhD in computer science from Concordia University in 2012. Prior to joining the iSchool faculty, he worked as a staff scientist at the U.S. National Library of Medicine, National Institutes of Health, where he led the Semantic Knowledge Representation project. 

Courses currently teaching

Office hours

By appointment

Publications & Papers

Halil Kilicoglu, Zeshan Peng, Shabnam Tafreshi, Tung Tran, Graciela Rosemblat, and Jodi Schneider. "Confirm or Refute?: A Comparative Study on Citation Sentiment Classification in Clinical Research Publications." Journal of Biomedical Informatics 2019; 91:103123. https://doi.org/10.1016/j.jbi.2019.103123

Thomas C. Rindflesch, Catherine L. Blake, Michael J. Cairelli, Marcelo Fiszman, Caroline J. Zeiss, and Halil Kilicoglu. "Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing." Journal of Biomedical Semantics 2018; 9:25. https://doi.org/10.1186/s13326-018-0192-y

Halil Kilicoglu. "Biomedical text mining for research rigor and integrity: tasks, challenges, directions." Briefings in Bioinformatics 2018; 19(6):1400-1414. https://doi.org/10.1093/bib/bbx057

Halil Kilicoglu, Graciela Rosemblat, Mario Malički, and Gerben ter Riet. "Automatic recognition of self-acknowledged limitations in clinical research literature." JAMIA, 2018; 25(7): 855-861. https://doi.org/10.1093/jamia/ocy038

Halil Kilicoglu, Graciela Rosemblat, and Thomas C. Rindflesch. "Assigning factuality values to semantic relations extracted from biomedical research literature." PLoS ONE, 12(7): e0179926. https://doi.org/10.1371/journal.pone.0179926

Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, and Thomas C. Rindflesch. "Sortal anaphora resolution to enhance relation extraction from biomedical literature." BMC Bioinformatics, 17(1): 163. https://doi.org/10.1186/s12859-016-1009-6

Halil Kilicoglu and Dina Demner-Fushman. "Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text." PLoS ONE, 11(3): e0148538. https://doi.org/10.1371/journal.pone.0148538

Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, and Thomas C. Rindflesch. "Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference." PLoS Computational Biology, 10(6): e1003666.  https://doi.org/10.1371/journal.pcbi.1003666 

Halil Kilicoglu, Dongwook Shin, Marcelo Fiszman, Graciela Rosemblat, and Thomas C. Rindflesch. "SemMedDB: a PubMed-scale repository of biomedical semantic predications." Bioinformatics, 28(23): 3158-3160. https://doi.org/10.1093/bioinformatics/bts591 

Thomas C. Rindflesch, Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, and Dongwook Shin. "Semantic MEDLINE: An advanced information management application for biomedicine." Information Services & Use. 31(1-2): 15-21. https://doi.org/10.3233/ISU-2011-0627 

Presentations

University of California San Francisco, Bakar Computational Health Sciences Institute. San Francisco, CA. Enhancing Rigor and Integrity of Biomedical Research using Language Technology. 2018.

University of Illinois at Urbana-Champaign, School of Information Sciences. Champaign, IL. Enhancing Rigor and Integrity of Biomedical Research using Language Technology. 2018.

University of Arizona, Department of Management Information Systems. Tucson, AZ. Enhancing Rigor and Integrity of Biomedical Research using Natural Language Processing. 2018.

GeoSemantics Symposium. Bethesda, MD. Semantic MEDLINE: Knowledge Discovery and Hypothesis Generation from Biomedical Research Literature. 2018.

George Washington University Biomedical Informatics Center. Washington, DC. Knowledge Discovery and Hypothesis Generation through Semantic Processing of Biomedical Research Literature. 2017.

University of Illinois at Urbana-Champaign, School of Information Sciences, Center for Informatics Research in Science and Scholarship (CIRSS). Champaign, IL. Can Natural Language Processing Help in Fostering Responsible Research Practices? 2016.

University of Illinois at Urbana-Champaign, School of Information Sciences, Conceptual Foundations Research Group Seminar. Champaign, IL. Advances in Deep Semantic Representation and Parsing. 2016.

Virginia Commonwealth University, Department of Computer Science. Richmond, VA. Towards Biomedical Text Understanding: A Linguistic Perspective. 2014.