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 Siebel School of Computing and Data Science, Beckman Institute, National Center for Supercomputing Applications, Center for Health Informatics, Division of Nutritional Sciences, Personalized Nutrition Initiative, and the Interdisciplinary Health Sciences Institute.

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

Jul 02, 2026	Congratulations to Mengfei Lan for oral presentation at ACL 2026, Sylvey Lin for oral presentation at the co-located BioNLP 2026, and Yikun Han for poster presentation at BioNLP 2026!
Jun 03, 2026	Congratulations to Shufan Ming for presenting her paper “Robust Biomedical Publication Type and Study Design Classification with Knowledge-Guided Perturbations” at IEEE ICHI 2026 and to Shiwei Liu and Evan Guerra for presenting their work on reporting transparency and scientific rigor assessment at the WCRI 2026!
Apr 15, 2026	Congratulations to Lan Jiang for successfully defending her PhD thesis ‘‘Effective and Fair Writing Assessment with Large Language Models’’. We wish her every success as she begins her postdoctoral position at Yale University!
Feb 01, 2026	Our review paper ‘‘A Narrative Review of Knowledge Resources for Complementary and Integrative Health” led by Robin Austin, Marcelo Fiszman, and Evan Guerra has been published in The Journal of Nutrition!
Nov 15, 2025	Congratulations to Janina Sarol for successfully defending her PhD thesis ‘‘Cross-document Citation Content Analysis’’. We wish her every success as she begins her postdoctoral position at the University of Minnesota!

selected publications

Journal Article

Goals and strategies for the indexing of publication types and study designs

Neil R Smalheiser, Joe D Menke, Arthur W Holt, Halil Kilicoglu, and Jodi Schneider

Database, Jul 2026

Bib HTML

@article{smalheiser2026goals,
  title = {Goals and strategies for the indexing of publication types and study designs},
  author = {Smalheiser, Neil R and Menke, Joe D and Holt, Arthur W and Kilicoglu, Halil and Schneider, Jodi},
  journal = {Database},
  volume = {2026},
  month = jul,
  pages = {baag039},
  doi = {10.1093/database/baag039},
  url = {https://doi.org/10.1093/database/baag039},
  year = {2026},
  publisher = {Oxford University Press},
}

Workshop Paper

When Evidence Conflicts: Uncertainty and Order Effects in Retrieval-Augmented Biomedical Question Answering

Yikun Han, Mengfei Lan, and Halil Kilicoglu

In BioNLP 2026, Jul 2026

Bib HTML

@inproceedings{han-etal-2026-evidence,
  title = {When Evidence Conflicts: Uncertainty and Order Effects in Retrieval-Augmented Biomedical Question Answering},
  author = {Han, Yikun and Lan, Mengfei and Kilicoglu, Halil},
  booktitle = {{B}io{NLP} 2026},
  month = jul,
  year = {2026},
  address = {San Diego, CA},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2026.bionlp-1.50/},
  doi = {10.18653/v1/2026.bionlp-1.50},
  pages = {630--643},
}

Workshop Paper

Divide-Prompt-Refine: a Training-Free, Structure-Aware Framework for Biomedical Abstract Generation

Sylvey Lin, Joseph Menke, Shufan Ming, Dongin Nam, Neil Smalheiser, and Halil Kilicoglu

In BioNLP 2026, Jul 2026

Bib HTML

@inproceedings{lin-etal-2026-divide,
  title = {Divide-Prompt-Refine: a Training-Free, Structure-Aware Framework for Biomedical Abstract Generation},
  author = {Lin, Sylvey and Menke, Joseph and Ming, Shufan and Nam, Dongin and Smalheiser, Neil and Kilicoglu, Halil},
  booktitle = {{B}io{NLP} 2026},
  month = jul,
  year = {2026},
  address = {San Diego, CA},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2026.bionlp-1.64/},
  doi = {10.18653/v1/2026.bionlp-1.64},
  pages = {770--790},
}

Conference Paper

BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labels

Mengfei Lan, Lecheng Zheng, and Halil Kilicoglu

In Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers), Jul 2026

Bib HTML

@inproceedings{lan-etal-2026-biohicl,
  title = {{B}io{H}i{CL}: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with {M}e{SH} Labels},
  author = {Lan, Mengfei and Zheng, Lecheng and Kilicoglu, Halil},
  booktitle = {Proceedings of the 64th Annual Meeting of the {A}ssociation for {C}omputational {L}inguistics (Volume 2: Short Papers)},
  month = jul,
  year = {2026},
  address = {San Diego, CA},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2026.acl-short.62/},
  doi = {10.18653/v1/2026.acl-short.62},
  pages = {759--769},
}

Conference Paper

Robust biomedical publication type and study design classification with knowledge-guided perturbations

Shufan Ming, Joe D Menke, Neil R Smalheiser, and Halil Kilicoglu

In Proceedings of the IEEE International Conference on Healthcare Informatics (ICHI), Jun 2026

Bib HTML

@inproceedings{ming2026robust,
  title = {{Robust biomedical publication type and study design classification with knowledge-guided perturbations}},
  author = {Ming, Shufan and Menke, Joe D and Smalheiser, Neil R and Kilicoglu, Halil},
  booktitle = {Proceedings of the IEEE International Conference on Healthcare Informatics (ICHI)},
  year = {2026},
  month = jun,
  pages = {1--10},
  publisher = {Wiley Online Library},
  doi = {10.48550/arXiv.2605.11502},
  url = {https://arxiv.org/abs/2605.11502},
}

Journal Article

Advancing Whole-Person Health through Informatics: A Narrative Review of Knowledge Resources for Complementary and Integrative Health.

Robin R Austin, Marcelo Fiszman, Evan Guerra, Rui Zhang, and Halil Kilicoglu

The Journal of Nutrition, May 2026

Bib HTML

@article{austin2026advancing,
  title = {Advancing Whole-Person Health through Informatics: A Narrative Review of Knowledge Resources for Complementary and Integrative Health.},
  author = {Austin, Robin R and Fiszman, Marcelo and Guerra, Evan and Zhang, Rui and Kilicoglu, Halil},
  journal = {The Journal of Nutrition},
  volume = {156},
  number = {5},
  pages = {101461--101461},
  year = {2026},
  month = may,
  publisher = {Elsevier},
  doi = {10.1016/j.tjnut.2026.101461},
  url = {https://doi.org/10.1016/j.tjnut.2026.101461},
}

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},
}