| 2026 | ACL | BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labels. | Mengfei Lan, Lecheng Zheng, Halil Kilicoglu |
| 2024 | EMNLP | Multi-label Sequential Sentence Classification via Large Language Model. | Mengfei Lan, Lecheng Zheng, Shufan Ming, Halil Kilicoglu |
| 2022 | AMIA | Methodological information extraction from randomized controlled trial publications: a pilot study. | Linh K. Hoang, Yingjun Guan, Halil Kilicoglu |
| 2022 | AMIA | CIHLex: Complementary and Integrative Health Lexicon. | Huixue Zhou, Robin Austin, Halil Kilicoglu, Sheng-Chieh Lu, Rui Zhang |
| 2022 | WWW | The International Workshop on Semantics-enabled Biomedical Literature Analytics (SeBiLAn). | Faezeh Ensan, Halil Kilicoglu, Bridget T. McInnes, Lucy Lu Wang |
| 2020 | AMIA | Identifying Sample Size Characteristics in Randomized Controlled Trial Publications. | Halil Kilicoglu, Linh K. Hoang, Sahil Wadhwa |
| 2019 | AMIA | Non-Negative Matrix Factorization for Drug Repositioning: Experiments with the repoDB Dataset. | Mehmet G. Bakal, Halil Kilicoglu, Ramakanth Kavuluru |
| 2019 | AMIA | SemMedDB-neo4j: A Graph Database of Biomedical Semantic Relations. | Dimitar Hristovski, Andrej Kastrin, Halil Kilicoglu |
| 2018 | AMIA | Methods and Tools to Enhance Rigor and Reproducibility of Biomedical Research. | Halil Kilicoglu, Aurlie Nvol, Timothy Clark, Hua Xu, Neil R. Smalheiser |
| 2018 | AMIA | Enhancing Identification of Relation Arguments in SemRep. | Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu |
| 2018 | AMIA | Linking Section Labels with Biomedical Relations in SemMedDB. | Dongwook Shin, Halil Kilicoglu |
| 2017 | ACL | TextFlow: A Text Similarity Measure based on Continuous Sequences. | Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman |
| 2016 | AMIA | Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. | Yassine Mrabet, Halil Kilicoglu, Kirk Roberts, Dina Demner-Fushman |
| 2016 | ECAI | Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. | Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman |
| 2016 | LREC | Annotating Named Entities in Consumer Health Questions. | Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Kirk Roberts, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman |
| 2015 | AMIA | An Ensemble Method for Spelling Correction in Consumer Health Questions. | Halil Kilicoglu, Marcelo Fiszman, Kirk Roberts, Dina Demner-Fushman |
| 2014 | AMIA | Automatically Classifying Question Types for Consumer Health Questions. | Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman |
| 2014 | LREC | Annotating Question Decomposition on Complex Medical Questions. | Kirk Roberts, Kate Masterton, Marcelo Fiszman, Halil Kilicoglu, Dina Demner-Fushman |
| 2013 | AMIA | Automatically Extracting Clinically Useful Sentences from UpToDate to Support Clinicians' Information Needs. | Rashmi Mishra, Guilherme Del Fiol, Halil Kilicoglu, Siddhartha Jonnalagadda, Marcelo Fiszman |
| 2010 | CoNLL | A High-Precision Approach to Detecting Hedges and their Scopes. | Halil Kilicoglu, Sabine Bergler |
| 2008 | AMIA | Toward Automatic Recognition of High Quality Clinical Evidence. | Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes |
| 2007 | AMIA | Using the Literature-Based Discovery Paradigm to Investigate Drug Mechanisms. | Caroline B. Ahlers, Dimitar Hristovski, Halil Kilicoglu, Thomas C. Rindflesch |
| 2006 | AMIA | Summarizing Drug Information in Medline Citations. | Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu |
| 2005 | AMIA | Medical Facts to Support Inferencing in Natural Language Processing. | Thomas C. Rindflesch, Serguei Pakhomov, Marcelo Fiszman, Halil Kilicoglu, Vincent R. Snchez |
| 2003 | AMIA | Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts. | Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu |
| 2003 | AMIA | Interpreting Hypernymic Propositions in an Online Medical Encyclopedia. | Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu |
| 2003 | AMIA | Semantic Relations Asserting the Etiology of Genetic Diseases. | Thomas C. Rindflesch, Bisharah Libbus, Dimitar Hristovski, Alan R. Aronson, Halil Kilicoglu |