Halil Kilicoglu

614 E Daniel Street #5109

Champaign, IL, 61820

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, Personalized Nutrition Initiative, Beckman Institute and the Interdisciplinary Health Sciences Institute.

My lab specializes in natural language processing and machine learning with a particular focus on biomedical text. We 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

May 04, 2025	Congratulations to Shufan Ming for presenting her paper “Towards Knowledge-Guided Biomedical Lay Summarization using Large Language Models” at CL4Health workshop @ NAACL 2025!
Mar 27, 2025	Our paper ‘‘DiMB-RE: mining the scientific literature for diet-microbiome associations” led by Gibong Hong has been published in JAMIA!
Feb 28, 2025	Our paper ‘‘SPIRIT-CONSORT-TM: a corpus for assessing transparency of clinical trial protocol and results publications” led by Lan Jiang, Colby J Vorland, and Xiangji Ying has been published in Scientific Data!

selected publications

Workshop Paper

Towards Knowledge-Guided Biomedical Lay Summarization using Large Language Models

Shufan Ming, Yue Guo, and Halil Kilicoglu

In Proceedings of the Second Workshop on Patient-Oriented Language Processing (CL4Health), May 2025

Bib HTML

@inproceedings{ming2025towards,
  title = {Towards Knowledge-Guided Biomedical Lay Summarization using Large Language Models},
  author = {Ming, Shufan and Guo, Yue and Kilicoglu, Halil},
  booktitle = {Proceedings of the Second Workshop on Patient-Oriented Language Processing (CL4Health)},
  pages = {285--297},
  year = {2025},
  month = may,
  address = {Albuquerque,NM},
  publisher = {Association for Computational Linguistics},
  doi = {10.18653/v1/2025.cl4health-1.24},
  url = {https://doi.org/10.18653/v1/2025.cl4health-1.24},
}

Journal Article

DiMB-RE: mining the scientific literature for diet-microbiome associations

Gibong Hong, Veronica Hindle, Nadine M Veasley, Hannah D Holscher, and Halil Kilicoglu

Journal of the American Medical Informatics Association, Mar 2025

Bib HTML

@article{hong2025dimbre,
  title = {{DiMB-RE: mining the scientific literature for diet-microbiome associations}},
  author = {Hong, Gibong and Hindle, Veronica and Veasley, Nadine M and Holscher, Hannah D and Kilicoglu, Halil},
  journal = {Journal of the American Medical Informatics Association},
  volume = {32},
  number = {6},
  pages = {998--1006},
  year = {2025},
  month = mar,
  publisher = {Oxford University Press},
  doi = {10.1093/jamia/ocaf054},
  url = {https://doi.org/10.1093/jamia/ocaf054},
}

Journal Article

SPIRIT-CONSORT-TM: a corpus for assessing transparency of clinical trial protocol and results publications

Lan Jiang, Colby J Vorland, Xiangji Ying, Andrew W Brown, Joe D Menke, Gibong Hong, Mengfei Lan, Evan Mayo-Wilson, and Halil Kilicoglu

Scientific Data, Feb 2025

Bib HTML

@article{jiang2025spirit,
  title = {{SPIRIT-CONSORT-TM: a corpus for assessing transparency of clinical trial protocol and results publications}},
  author = {Jiang, Lan and Vorland, Colby J and Ying, Xiangji and Brown, Andrew W and Menke, Joe D and Hong, Gibong and Lan, Mengfei and Mayo-Wilson, Evan and Kilicoglu, Halil},
  journal = {Scientific Data},
  volume = {12},
  number = {1},
  pages = {355},
  year = {2025},
  publisher = {Nature Publishing Group UK London},
  month = feb,
  doi = {10.1038/s41597-025-04629-1},
  url = {https://doi.org/10.1038/s41597-025-04629-1},
}

Journal Article

BiomedRAG: A retrieval augmented large language model for biomedicine

Mingchen Li, Halil Kilicoglu, Hua Xu, and Rui Zhang

Journal of Biomedical Informatics, Feb 2025

Bib HTML

@article{li2025biomedrag,
  title = {BiomedRAG: A retrieval augmented large language model for biomedicine},
  author = {Li, Mingchen and Kilicoglu, Halil and Xu, Hua and Zhang, Rui},
  journal = {Journal of Biomedical Informatics},
  volume = {162},
  pages = {104769},
  year = {2025},
  publisher = {Elsevier},
  month = feb,
  doi = {10.1016/j.jbi.2024.104769},
  url = {https://doi.org/10.1016/j.jbi.2024.104769},
}

Conference Paper

Multi-label Sequential Sentence Classification via Large Language Model

Mengfei Lan, Lecheng Zheng, Shufan Ming, and Halil Kilicoglu

In Findings of the Association for Computational Linguistics: EMNLP 2024, Nov 2024

Bib HTML

@inproceedings{lan2024multi,
  title = {Multi-label Sequential Sentence Classification via Large Language Model},
  author = {Lan, Mengfei and Zheng, Lecheng and Ming, Shufan and Kilicoglu, Halil},
  booktitle = {Findings of the Association for Computational Linguistics: EMNLP 2024},
  pages = {16086--16104},
  year = {2024},
  month = nov,
  address = {Miami, FL},
  publisher = {Association for Computational Linguistics},
  doi = {10.18653/v1/2024.findings-emnlp.944},
  url = {https://doi.org/10.18653/v1/2024.findings-emnlp.944},
}

Conference Paper

Publication Type Tagging using Transformer Models and Multi-Label Classification

Joe D Menke, Halil Kilicoglu, and Neil R Smalheiser

In AMIA Annual Symposium Proceedings, Nov 2024

Bib HTML

@inproceedings{menke2024publication,
  title = {Publication Type Tagging using Transformer Models and Multi-Label Classification},
  author = {Menke, Joe D and Kilicoglu, Halil and Smalheiser, Neil R},
  booktitle = {AMIA Annual Symposium Proceedings},
  volume = {2024},
  pages = {818--827},
  year = {2024},
  month = nov,
  organization = {American Medical Informatics Association},
  url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC12099436/},
}