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 and Beckman 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

Sep 30, 2024	Our 5-year R01 project ‘‘Improving Results and Conclusions about Harms in Systematic Reviews of Drugs’’ has been funded by AHRQ!
Sep 17, 2024	Our 5-year U01 project ‘‘COMBINI: connecting Complementary Medicine and Biological kNowledge to support Integrative Health’’ has been funded by NIH/NCCIH!
Sep 17, 2024	Our paper ‘‘Text classification models for assessing the completeness of randomized controlled trial publications based on CONSORT reporting guidelines” led by Lan Jiang has been published in Scientific Reports!

selected publications

Journal Article

Text classification models for assessing the completeness of randomized controlled trial publications based on CONSORT reporting guidelines

Lan Jiang, Mengfei Lan, Joe D Menke, Colby J Vorland, and Halil Kilicoglu

Scientific Reports, Sep 2024

Bib HTML

@article{jiang2024text,
  title = {Text classification models for assessing the completeness of randomized controlled trial publications based on CONSORT reporting guidelines},
  author = {Jiang, Lan and Lan, Mengfei and Menke, Joe D and Vorland, Colby J and Kilicoglu, Halil},
  journal = {Scientific Reports},
  volume = {14},
  number = {1},
  pages = {21721},
  year = {2024},
  month = sep,
  publisher = {Nature Publishing Group UK London},
  doi = {10.1038/s41598-024-72130-7},
  url = {https://doi.org/10.1038/s41598-024-72130-7},
}

Journal Article

Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach

M Janina Sarol, Gibong Hong, Evan Guerra, and Halil Kilicoglu

Database, Aug 2024

Bib HTML

@article{sarol2024integrating,
  title = {{Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach}},
  author = {Sarol, M Janina and Hong, Gibong and Guerra, Evan and Kilicoglu, Halil},
  journal = {Database},
  volume = {2024},
  pages = {baae079},
  year = {2024},
  month = aug,
  publisher = {Oxford University Press UK},
  doi = {10.1093/database/baae079},
  url = {https://doi.org/10.1093/database/baae079},
}

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},
}

Book Chapter

NLP Applications—Biomedical Literature

Rui Zhang, Andrej Kastrin, Dimitar Hristovski, Marcelo Fiszman, and Halil Kilicoglu

Jun 2024

Bib HTML

@inbook{Zhang2024,
  author = {Zhang, Rui and Kastrin, Andrej and Hristovski, Dimitar and Fiszman, Marcelo and Kilicoglu, Halil},
  editor = {Xu, Hua and Demner Fushman, Dina},
  title = {NLP Applications---Biomedical Literature},
  booktitle = {Natural Language Processing in Biomedicine: A Practical Guide},
  year = {2024},
  month = jun,
  publisher = {Springer International Publishing},
  address = {Cham},
  pages = {351--395},
  isbn = {978-3-031-55865-8},
  doi = {10.1007/978-3-031-55865-8_13},
  url = {https://doi.org/10.1007/978-3-031-55865-8_13},
}

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},
}