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


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. 

Office hours

Thursday 10:00 a.m.-noon or by appointment, please contact professor

Publications & Papers

Kilicoglu H, Rosemblat G, Fiszman M, Shin D. "Broad-coverage biomedical relation extraction with SemRep." BMC Bioinformatics. 2020;21:1-28. https://doi.org/10.1186/s12859-020-3517-7.

Zeiss CJ, Shin D, Vander Wyk B, Beck AP, Zatz N, Sneiderman CA, Kilicoglu H. "Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research." PLoS ONE. 2019;14(12):e0226176. https://doi.org/10.1371/journal.pone.0226176

Keserlioglu K, Kilicoglu H, Ter Riet G. "Impact of peer review on discussion of study limitations and strength of claims in randomized trial reports: a before and after study." Research integrity and peer review. 2019;4(1):19. https://doi.org/10.1186/s41073-019-0078-2

Rosemblat G, Fiszman M, Shin D, Kilicoglu H. "Towards a characterization of apparent contradictions in the biomedical literature using context analysis." Journal of biomedical informatics. 2019;98:103275. https://doi.org/10.1016/j.jbi.2019.103275

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

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 


University of Kentucky Institute for Biomedical Informatics, Lexington, KY.  Promoting Transparency in Biomedical Publications using Natural Language Processing (2020).

Conference on "Meta-research for transforming clinical research" at Académie Nationale de Médecine in Paris, France.  Natural language processing  to promote transparency  of clinical publications (2019).

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.

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.

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