Halil Kilicoglu

614 E Daniel Street #5109

Champaign, IL, 61821

I am an associate professor at the School of Information Sciences (iSchool) at the University of Illinois Urbana-Champaign. I am also affiliated with the National Center for Supercomputing Applications, Center for Health Informatics, Division of Nutritional Sciences, and Personalized Nutrition Initiative. I specialize in natural language processing and machine learning with a particular focus on biomedical text. I use a combination of data-driven analytical techniques and knowledge-based semantic approaches to extract and organize knowledge buried in textual artifacts, with benefits for biomedical discovery and scholarship, and healthcare outcomes.

Prior to joining the iSchool in 2019, I was a research scientist at the U.S. National Library of Medicine, National Institutes of Health, where I led the Semantic Knowledge Representation project. I earned my PhD in Computer Science from Concordia University.

CV: pdf

news

Jun 19, 2024	Our paper “Assessing citation integrity in biomedical publications: corpus annotation and NLP models” led by Janina Sarol has been accepted to Bioinformatics!
Jun 12, 2024	I co-authored a chapter on NLP applications for biomedical literature in the textbook Natural Language Processing in Biomedicine: A Practical Guide published by Springer (editors: Hua Xu, Dina Demner-Fushman)!
May 07, 2024	Our team (UIUC_BioNLP) took the first place (overall) in the BioLaySumm 2024 shared task on the lay summarization of biomedical research articles. Congratulations to Jerome You, Shruthan Radhakrishna, and Shufan Ming!

selected publications

Journal Article

Assessing citation integrity in biomedical publications: corpus annotation and NLP models

Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna, Jodi Schneider, and Halil Kilicoglu

Bioinformatics, Jun 2024

Bib HTML

@article{10.1093/bioinformatics/btae420,
  author = {Sarol, Maria Janina and Ming, Shufan and Radhakrishna, Shruthan and Schneider, Jodi and Kilicoglu, Halil},
  title = {{Assessing citation integrity in biomedical publications: corpus annotation and NLP models}},
  journal = {Bioinformatics},
  volume = {40},
  number = {7},
  pages = {btae420},
  year = {2024},
  month = jun,
  doi = {10.1093/bioinformatics/btae420},
  url = {https://doi.org/10.1093/bioinformatics/btae420},
}

Journal Article

Enhancing the coverage of SemRep using a relation classification approach

Shufan Ming, Rui Zhang, and Halil Kilicoglu

Journal of Biomedical Informatics, May 2024

Bib HTML

@article{ming2024enhancing,
  title = {{Enhancing the coverage of SemRep using a relation classification approach}},
  author = {Ming, Shufan and Zhang, Rui and Kilicoglu, Halil},
  journal = {Journal of Biomedical Informatics},
  volume = {155},
  pages = {104658},
  year = {2024},
  month = may,
  issn = {1532-0464},
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2024.104658},
  url = {https://doi.org/10.1016/j.jbi.2024.104658},
}

Journal Article

Automatic categorization of self-acknowledged limitations in randomized controlled trial publications

Mengfei Lan, Mandy Cheng, Linh Hoang, Gerben Ter Riet, and Halil Kilicoglu

Journal of Biomedical Informatics, Apr 2024

Bib HTML

@article{lan2024automatic,
  title = {Automatic categorization of self-acknowledged limitations in randomized controlled trial publications},
  author = {Lan, Mengfei and Cheng, Mandy and Hoang, Linh and Ter Riet, Gerben and Kilicoglu, Halil},
  journal = {Journal of Biomedical Informatics},
  volume = {152},
  pages = {104628},
  year = {2024},
  month = apr,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2024.104628},
  url = {https://doi.org/10.1016/j.jbi.2024.104628},
}