Halil Kilicoglu

• Faculty Affiliate, NCSA
• Faculty Affiliate, Division of Nutritional Sciences
• Faculty Affiliate, Personalized Nutrition Initiative
• Faculty Affiliate, Center for Health Informatics

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

• Workshop on Trustworthy Natural Language Processing (TrustNLP 2023) Best Paper Award for the paper titled “Examining the Causal Effect of First Names on Language Models: The Case of Social Commonsense Reasoning”, 2023
• International Workshop on Semantic Evaluation (SemEval 2021) Best System Paper Award for the paper titled “A Cascade of Neural Models for Structuring Scholarly NLP Contributions”, 2021
• IMIA Yearbook of Medical Informatics, Best Paper Selection (Natural Language Processing) for the paper titled "Towards a characterization of apparent contradictions in the biomedical literature using context analysis," 2020
• 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. 

• Spring 2025 - Independent Study - IS389HK
• Spring 2025 - Text Mining - IS567AC
• Spring 2025 - Independent Study - IS589HHK
• Summer 2025 - Independent Study - IS589HHK

Monday: 10 a.m. – noon

Sarol MJ, Ming S, Radhakrishna S, Schneider J, Kilicoglu H. Assessing citation integrity in biomedical publications: corpus annotation and NLP models. Bioinformatics. 2024;40(7).  https://doi.org/10.1093/bioinformatics/btae420

Kilicoglu H, Jiang L, Hoang L, Mayo-Wilson E, Vinkers CH, Otte WM. Methodology reporting improved over time in 176,469 randomized controlled trials. Journal of Clinical Epidemiology. 2023 Oct 1;162:19-28. https://doi.org/10.1016/j.jclinepi.2023.08.004

Kilicoglu H, Rosemblat G, Hoang L, Wadhwa S, Peng Z, Malički M, Schneider J, Ter Riet G. Toward assessing clinical trial publications for reporting transparency. Journal of Biomedical Informatics. 2021;116:103717. https://doi.org/10.1016/j.jbi.2021.103717

Weissgerber T, Riedel N, Kilicoglu H, Labbé C, Eckmann P, Ter Riet G, Byrne J, Cabanac G, Capes-Davis A, Favier B, Saladi S, et al. Automated screening of COVID-19 preprints: can we help authors to improve transparency and reproducibility?. Nature Medicine. 2021;27(1):6-7. https://doi.org/10.1038/s41591-020-01203-7

Zhang R, Hristovski D, Schutte D, Kastrin A, Fiszman M, Kilicoglu H. Drug repurposing for COVID-19 via knowledge graph completion. Journal of Biomedical Informatics. 2021;115:103696. https://doi.org/10.1016/j.jbi.2021.103696

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

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

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, 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.

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.