Directory

Halil Kilicoglu's directory photo.

Halil Kilicoglu

Associate Professor

Primary Affiliation

Cognition, Lifespan Engagement, Aging, and Resilience

Affiliations

Status Affiliate Faculty

Home Information Sciences

Phone

Email halil@illinois.edu

Address

  • Biography

    Halil KIlicoglu is an associate professor in the School of Information Sciences (iSchool). Prior to joining the iSchool faculty in 2019, he worked as a research scientist at the U.S. National Library of Medicine, National Institutes of Health (NIH), where he led the Semantic Knowledge Representation project. His affiliations are: NCSA, Center for Health Informatics, Division of Nutritional Sciences, and Personalized Nutrition Initiative.


    Education

    • PhD., computer science, Concordia University, 2012

  • Honors
    • 2007: Distinguished/best paper awards at the American Medical Informatics Association (AMIA) Annual Symposium

    • 2016: Distinguished/best paper awards at the American Medical Informatics Association (AMIA) Annual Symposium

    • 2017: Best NLP papers in International Medical Informatics Association (IMIA) Yearbook of Medical Informatics

    • 2020: Best NLP papers in International Medical Informatics Association (IMIA) Yearbook of Medical Informatics

    • 2021: International Workshop on Semantic Evaluations (SemEval)

    • 2023: Trustworthy Natural Language Processing (TrustNLP) workshop

    • 2024: Top ranked system at the biomedical lay summarization shared task competition (BioLaySumm) (2024)

    • 2020-2024: Top ranked system at the biomedical lay summarization shared task competition (BioLaySumm) (2024), List of Teachers Ranked Excellent by their Students

  • Research

    Research Areas:

    • Knowledge discovery

    • Scholarly communication

    • Evidence synthesis

    • Scientific reproducibility

    Research Interests:

    • Natural language processing

    • Machine learning

    • Biomedical informatics

    ScienceNLP 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. Current projects include development of NLP/ML methods for assessing reporting quality and transparency of biomedical publications, for verifying accuracy of citations, and creating a trustworthy evidence base for complementary medicine approaches from the literature, and for repurposing drugs. Their work has been supported by NIH, Agency for Health Research Quality (AHRQ), and HHS Office of Research Integrity.

  • 2024

    • 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
    • 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
    • Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics. Sarah Mullin, Robert McDougal, Kei-Hoi Cheung, Halil Kilicoglu, Amanda Beck, and Caroline J Zeiss. Journal of Biomedical Semantics, Jul 2024
    • Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition. Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg Marc Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, and Rui Zhang. Journal of the American Medical Informatics Association, Feb 2024
    • Enhancing the coverage of SemRep using a relation classification approach. Shufan Ming, Rui Zhang, and Halil Kilicoglu. Journal of Biomedical Informatics, May 2024
    • 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
    • NLP Applications—Biomedical Literature Rui Zhang, Andrej Kastrin, Dimitar Hristovski, Marcelo Fiszman, and Halil Kilicoglu. Jun 2024
    • Publication of Results of Registered Trials With Published Study Protocols, 2011-2022. Colby J Vorland, Andrew W Brown, Halil Kilicoglu, Xiangji Ying, and Evan Mayo-Wilson. JAMA Network Open, Jan 2024
    • Repurposing non-pharmacological interventions for Alzheimer’s disease through link prediction on biomedical literature. Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Li Zhou, Halil Kilicoglu, You Chen, Chang Su, Hua Xu, William G Mantyh, and Rui Zhang Scientific Reports, Apr 2024
    • Semantics-enabled biomedical literature analytics Halil Kilicoglu, Faezeh Ensan, Bridget McInnes, and Lucy Lu Wang. Journal of Biomedical Informatics, Feb 2024
    • 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

    2023

    • A comment-driven evidence appraisal approach to promoting research findings into practice when only uncertain evidence is available Shuang Wang, Halil Kilicoglu, and Jian Du Health Research Policy and Systems, Mar 2023
    • Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation Yiren Liu, and Halil Kilicoglu In AAAI’23 Workshop on Knowledge Augmented Methods for NLP, Feb 2023
    • Developing a knowledge graph for pharmacokinetic natural product-drug interactions Sanya B Taneja, Tiffany J Callahan, Mary F Paine, Sandra L Kane-Gill, Halil Kilicoglu, Marcin P Joachimiak, and Richard D Boyce Journal of Biomedical Informatics, Apr 2023
    • Examining the Causal Impact of First Names on Language Models: The Case of Social Commonsense ReasoningSullam Jeoung, Jana . Diesner, and Halil Kilicoglu. In Proceedings of the 3rd Workshop on Trustworthy Natural Language Processing (TrustNLP 2023), Jul 2023
    • Methodology reporting improved over time in 176,469 randomized controlled trials. Halil Kilicoglu, Lan Jiang, Linh Hoang, Evan Mayo-Wilson, Christiaan H Vinkers, and Willem M Otte Journal of Clinical Epidemiology, Oct 2023
    • Repurposing Drugs for Alzheimer’s Diseases through Link Prediction on Biomedical Literature Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G Mantyh, and Rui Zhang. In 2023 IEEE 11th International Conference on Healthcare Informatics (ICHI), Jun 2023

    2022

    • Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. Dalton Schutte, Jake Vasilakes, Anu Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R Bishop, Terrence Adam, and Rui Zhang Journal of Biomedical Informatics, Jul 2022
    • Investigating the impact of weakly supervised data on text mining models of publication transparency: a case study on randomized controlled trials Linh Hoang, Lan Jiang, and Halil Kilicoglu In AMIA Summits on Translational Science Proceedings, Mar 2022
    • Is the future of peer review automated? Robert Schulz, Adrian Barnett, René Bernard, Nicholas JL Brown, Jennifer A Byrne, Peter Eckmann, Malgorzata A Gazda, Halil Kilicoglu, Eric M Prager, Maia Salholz-Hillel, Gerben Riet, Timothy Vines, Colby J Vorland, Han Zhuang, Anita Bandrowski, and Tracey L Weissgerber BMC Research Notes, Jun 2022
    • Methodological information extraction from randomized controlled trial publications: a pilot study Linh Hoang, Yingjun Guan, and Halil Kilicoglu In AMIA Annual Symposium Proceedings, Nov 2022

    2021

    • Attention-gated graph convolutions for extracting drug interaction information from drug labels Tung Tran, Ramakanth Kavuluru, and Halil Kilicoglu ACM Transactions on Computing for Healthcare, Jan 2021
    • Automated screening of COVID-19 preprints: can we help authors to improve transparency and reproducibility? Tracey Weissgerber, Nico Riedel, Halil Kilicoglu, Cyril Labbé, Peter Eckmann, Gerben Ter Riet, Jennifer Byrne, Guillaume Cabanac, Amanda Capes-Davis, Bertrand Favier, Shyam Saladi, Peer Grabitz, Alexandra Bannach-Brown, Robert Schulz, Sarah McCann, Rene Bernard, and Anita Bandrowski. Nature Medicine, Jan 2021
    • Drug repurposing for COVID-19 via knowledge graph completion Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, and Halil Kilicoglu Journal of Biomedical Informatics, Mar 2021
    • UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions. Haoyang Liu, M. Janina Sarol, and Halil Kilicoglu. In Proceedings of the 15th International Workshop on Semantic Evaluation (SemEval-2021), Aug 2021

    2020

    • Broad-coverage biomedical relation extraction with SemRep. Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, and Dongwook Shin. BMC Bioinformatics, May 2020

    2019

    • Confirm or refute?: A comparative study on citation sentiment classification in clinical research publications. Halil Kilicoglu, Zeshan Peng, Shabnam Tafreshi, Tung Tran, Graciela Rosemblat, and Jodi Schneider Journal of Biomedical Informatics, Mar 2019
    • Expanding vocabularies for complementary and alternative medicine therapies. Lou Ann Scarton, Liqin Wang, Halil Kilicoglu, Margaret Jahries, and Guilherme Del Fiol International Journal of Medical Informatics, Jan 2019
    • Impact of peer review on discussion of study limitations and strength of claims in randomized trial reports: a before and after study Kerem Keserlioglu, Halil Kilicoglu, and Gerben Ter Riet. Research Integrity and Peer Review, Sep 2019
    • Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research Caroline J Zeiss, Dongwook Shin, Brent Vander Wyk, Amanda P Beck, Natalie Zatz, Charles A Sneiderman, and Halil Kilicoglu. PLoS ONE, Dec 2019
    • Towards a characterization of apparent contradictions in the biomedical literature using context analysis. Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin, and Halil Kilicoglu. Journal of Biomedical Informatics, Oct 2019

    2018

    • A multi-task learning framework for extracting drugs and their interactions from drug labels Tung Tran, Ramakanth Kavuluru, and Halil Kilicoglu In Text Analysis Conference (TAC 2018) Proceedings, Nov 2018
    • Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing Thomas C Rindflesch, Catherine L Blake, Michael J Cairelli, Marcelo Fiszman, Caroline J Zeiss, and Halil Kilicoglu. Journal of Biomedical Semantics, Dec 2018
    • Semantic annotation of consumer health questions. Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E Shooshan, Laritza Rodriguez, Kate Masterton, and Dina Demner-Fushman. BMC Bioinformatics, Feb 2018