Halil Kilicoglu

96 papers A 1B 2Misc 19Journal 54Unranked 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
Issues regarding the Indexing of Publication Types and Study Designs.
CoRR
Neil R. Smalheiser, Joe D. Menke, Arthur W. Holt, Halil Kilicoglu, Jodi Schneider
2025 J jnl
BiomedRAG: A retrieval augmented large language model for biomedicine.
J. Biomed. Informatics
Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang
2025 J jnl
DiMB-RE: mining the scientific literature for diet-microbiome associations.
J. Am. Medical Informatics Assoc.
Gibong Hong, Veronica Hindle, Nadine M. Veasley, Hannah D. Holscher, Halil Kilicoglu
2025 J jnl
Use as Directed? A Comparison of Software Tools Intended to Check Rigor and Transparency of Published Work.
CoRR
Peter Eckmann, Adrian Barnett, Alexandra Bannach-Brown, Elisa Pilar Bascunan Atria, Guillaume Cabanac, Louise Delwen Owen Franzen, Malgorzata Anna Gazda, Kaitlyn Hair, James Howison, Halil Kilicoglu, Cyril Labbé, Sarah McCann, Vladislav Nachev, Martijn Roelandse, Maia Salholz-Hillel, Robert Schulz, Gerben ter Riet, Colby Vorland, Anita E. Bandrowski, Tracey L. Weissgerber
2024 J jnl
Assessing citation integrity in biomedical publications: corpus annotation and NLP models.
Bioinform.
Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna, Jodi Schneider, Halil Kilicoglu
2024 J jnl
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications.
J. Biomed. Informatics
Mengfei Lan, Mandy Cheng, Linh K. Hoang, Gerben ter Riet, Halil Kilicoglu
2024 J jnl
BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine.
CoRR
Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang
2024 J jnl
Chemical entity normalization for successful translational development of Alzheimer's disease and dementia therapeutics.
J. Biomed. Semant.
Sarah Mullin, Robert A. McDougal, Kei-Hoi Cheung, Halil Kilicoglu, Amanda Beck, Caroline J. Zeiss
2024 J jnl
Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition.
J. Am. Medical Informatics Assoc.
Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang
2024 J jnl
DiMB-RE: Mining the Scientific Literature for Diet-Microbiome Associations.
CoRR
Gibong Hong, Veronica Hindle, Nadine M. Veasley, Hannah D. Holscher, Halil Kilicoglu
2024 J jnl
Enhancing the coverage of SemRep using a relation classification approach.
J. Biomed. Informatics
Shufan Ming, Rui Zhang, Halil Kilicoglu
2024 J jnl
Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach.
Database J. Biol. Databases Curation
M. Janina Sarol, Gibong Hong, Evan Guerra, Halil Kilicoglu
2024 — conf
Multi-label Sequential Sentence Classification via Large Language Model.
EMNLP (Findings)
Mengfei Lan, Lecheng Zheng, Shufan Ming, Halil Kilicoglu
2024 J jnl
Multi-label Sequential Sentence Classification via Large Language Model.
CoRR
Mengfei Lan, Lecheng Zheng, Shufan Ming, Halil Kilicoglu
2024 J jnl
Semantics-enabled biomedical literature analytics.
J. Biomed. Informatics
Halil Kilicoglu, Faezeh Ensan, Bridget T. McInnes, Lucy Lu Wang
2024 — conf
UIUC_BioNLP at BioLaySumm: An Extract-then-Summarize Approach Augmented with Wikipedia Knowledge for Biomedical Lay Summarization.
BioNLP@ACL
Zhiwen You, Shruthan Radhakrishna, Shufan Ming, Halil Kilicoglu
2023 J jnl
Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation.
CoRR
Yiren Liu, Halil Kilicoglu
2023 J jnl
Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.
J. Biomed. Informatics
Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
2023 J jnl
Examining the Causal Effect of First Names on Language Models: The Case of Social Commonsense Reasoning.
CoRR
Sullam Jeoung, Jana Diesner, Halil Kilicoglu
2023 — conf
Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature.
ICHI
Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G. Mantyh, Rui Zhang
2022 Misc conf
CIHLex: Complementary and Integrative Health Lexicon.
AMIA
Huixue Zhou, Robin Austin, Halil Kilicoglu, Sheng-Chieh Lu, Rui Zhang
2022 J jnl
Call for papers: Semantics-enabled biomedical literature analytics.
J. Biomed. Informatics
Halil Kilicoglu, Faezeh Ensan, Bridget T. McInnes, Lucy Lu Wang
2022 J jnl
Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions.
CoRR
Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
2022 J jnl
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature.
J. Biomed. Informatics
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
2022 Misc conf
Methodological information extraction from randomized controlled trial publications: a pilot study.
AMIA
Linh K. Hoang, Yingjun Guan, Halil Kilicoglu
2022 — conf
The International Workshop on Semantics-enabled Biomedical Literature Analytics (SeBiLAn).
WWW (Companion Volume)
Faezeh Ensan, Halil Kilicoglu, Bridget T. McInnes, Lucy Lu Wang
2021 J jnl
Attention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels.
ACM Trans. Comput. Heal.
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2021 J jnl
Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature.
CoRR
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
2021 J jnl
Drug repurposing for COVID-19 via knowledge graph completion.
J. Biomed. Informatics
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
2021 J jnl
Toward assessing clinical trial publications for reporting transparency.
J. Biomed. Informatics
Halil Kilicoglu, Graciela Rosemblat, Linh K. Hoang, Sahil Wadhwa, Zeshan Peng, Mario Malicki, Jodi Schneider, Gerben ter Riet
2021 — conf
UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions.
SemEval@ACL/IJCNLP
Haoyang Liu, Maria Janina Sarol, Halil Kilicoglu
2021 J jnl
UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions.
CoRR
Haoyang Liu, Maria Janina Sarol, Halil Kilicoglu
2020 J jnl
Broad-coverage biomedical relation extraction with SemRep.
BMC Bioinform.
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin
2020 J jnl
Drug Repurposing for COVID-19 via Knowledge Graph Completion.
CoRR
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
2020 Misc conf
Identifying Sample Size Characteristics in Randomized Controlled Trial Publications.
AMIA
Halil Kilicoglu, Linh K. Hoang, Sahil Wadhwa
2019 J jnl
A Multi-Task Learning Framework for Extracting Drugs and Their Interactions from Drug Labels.
CoRR
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2019 J jnl
Attention-Gated Graph Convolution for Extracting Drugs and Their Interactions from Drug Labels.
CoRR
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2019 J jnl
Confirm or refute?: A comparative study on citation sentiment classification in clinical research publications.
J. Biomed. Informatics
Halil Kilicoglu, Zeshan Peng, Shabnam Tafreshi, Tung Tran, Graciela Rosemblat, Jodi Schneider
2019 J jnl
Expanding vocabularies for complementary and alternative medicine therapies.
Int. J. Medical Informatics
Lou Ann Scarton, Liqin Wang, Halil Kilicoglu, Margaret Jahries, Guilherme Del Fiol
2019 Misc conf
Non-Negative Matrix Factorization for Drug Repositioning: Experiments with the repoDB Dataset.
AMIA
Mehmet G. Bakal, Halil Kilicoglu, Ramakanth Kavuluru
2019 Misc conf
SemMedDB-neo4j: A Graph Database of Biomedical Semantic Relations.
AMIA
Dimitar Hristovski, Andrej Kastrin, Halil Kilicoglu
2019 J jnl
Towards a characterization of apparent contradictions in the biomedical literature using context analysis.
J. Biomed. Informatics
Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin, Halil Kilicoglu
2018 — conf
A Multi-Task Learning Framework for Extracting Drugs and Their Interactions from Drug Labels.
TAC
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2018 J jnl
Automatic recognition of self-acknowledged limitations in clinical research literature.
J. Am. Medical Informatics Assoc.
Halil Kilicoglu, Graciela Rosemblat, Mario Malicki, Gerben ter Riet
2018 J jnl
Biomedical text mining for research rigor and integrity: tasks, challenges, directions.
Briefings Bioinform.
Halil Kilicoglu
2018 Misc conf
Enhancing Identification of Relation Arguments in SemRep.
AMIA
Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu
2018 J jnl
Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing.
J. Biomed. Semant.
Thomas C. Rindflesch, Catherine Blake, Michael J. Cairelli, Marcelo Fiszman, Caroline J. Zeiss, Halil Kilicoglu
2018 Misc conf
Linking Section Labels with Biomedical Relations in SemMedDB.
AMIA
Dongwook Shin, Halil Kilicoglu
2018 Misc conf
Methods and Tools to Enhance Rigor and Reproducibility of Biomedical Research.
AMIA
Halil Kilicoglu, Aurélie Névéol, Timothy Clark, Hua Xu, Neil R. Smalheiser
2018 J jnl
Semantic annotation of consumer health questions.
BMC Bioinform.
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton, Dina Demner-Fushman
2017 J jnl
A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources.
J. Assoc. Inf. Sci. Technol.
Ariel Deardorff, Kate Masterton, Kirk Roberts, Halil Kilicoglu, Dina Demner-Fushman
2017 — conf
TextFlow: A Text Similarity Measure based on Continuous Sequences.
ACL (1)
Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman
2016 — conf
Aligning Texts and Knowledge Bases with Semantic Sentence Simplification.
WebNLG
Yassine Mrabet, Pavlos Vougiouklis, Halil Kilicoglu, Claire Gardent, Dina Demner-Fushman, Jonathon S. Hare, Elena Simperl
2016 B conf
Annotating Named Entities in Consumer Health Questions.
LREC
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Kirk Roberts, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman
2016 Misc conf
Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions.
AMIA
Yassine Mrabet, Halil Kilicoglu, Kirk Roberts, Dina Demner-Fushman
2016 — conf
Inferring Implicit Causal Relationships in Biomedical Literature.
BioNLP@ACL
Halil Kilicoglu
2016 J jnl
Sortal anaphora resolution to enhance relation extraction from biomedical literature.
BMC Bioinform.
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch
2016 A conf
Unsupervised Ranking of Knowledge Bases for Named Entity Recognition.
ECAI
Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman
2015 Misc conf
An Ensemble Method for Spelling Correction in Consumer Health Questions.
AMIA
Halil Kilicoglu, Marcelo Fiszman, Kirk Roberts, Dina Demner-Fushman
2015 J jnl
The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs.
J. Biomed. Informatics
Kirk Roberts, Sonya E. Shooshan, Laritza Rodriguez, Swapna Abhyankar, Halil Kilicoglu, Dina Demner-Fushman
2014 B conf
Annotating Question Decomposition on Complex Medical Questions.
LREC
Kirk Roberts, Kate Masterton, Marcelo Fiszman, Halil Kilicoglu, Dina Demner-Fushman
2014 J jnl
Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference.
PLoS Comput. Biol.
Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch
2014 Misc conf
Automatically Classifying Question Types for Consumer Health Questions.
AMIA
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
2014 — conf
Coreference Resolution for Structured Drug Product Labels.
BioNLP@ACL
Halil Kilicoglu, Dina Demner-Fushman
2014 — conf
Decomposing Consumer Health Questions.
BioNLP@ACL
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
2014 J jnl
Using semantic predications to uncover drug-drug interactions in clinical data.
J. Biomed. Informatics
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Graciela Rosemblat, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. S. Pakhomov, Genevieve B. Melton
2013 J jnl
A methodology for extending domain coverage in SemRep.
J. Biomed. Informatics
Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu, Charles Sneiderman, Thomas C. Rindflesch
2013 Misc conf
Automatically Extracting Clinically Useful Sentences from UpToDate to Support Clinicians' Information Needs.
AMIA
Rashmi Mishra, Guilherme Del Fiol, Halil Kilicoglu, Siddhartha Jonnalagadda, Marcelo Fiszman
2013 — conf
Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis.
BioNLP@ACL
Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
2012 J jnl
Biological event composition.
BMC Bioinform.
Halil Kilicoglu, Sabine Bergler
2012 — conf
CLaC Labs: Processing Modality and Negation. Working Notes for QA4MRE Pilot Task at CLEF 2012.
CLEF (Online Working Notes/Labs/Workshop)
Sabine Rosenberg, Halil Kilicoglu, Sabine Bergler
2012 J jnl
SemMedDB: a PubMed-scale repository of biomedical semantic predications.
Bioinform.
Halil Kilicoglu, Dongwook Shin, Marcelo Fiszman, Graciela Rosemblat, Thomas C. Rindflesch
2011 — conf
Adapting a General Semantic Interpretation Approach to Biological Event Extraction.
BioNLP@ACL (Shared Task)
Halil Kilicoglu, Sabine Bergler
2011 J jnl
Constructing a semantic predication gold standard from the biomedical literature.
BMC Bioinform.
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch
2011 J jnl
Effective Bio-Event Extraction Using Trigger Words and Syntactic Dependencies.
Comput. Intell.
Halil Kilicoglu, Sabine Bergler
2011 J jnl
Semantic MEDLINE: An advanced information management application for biomedicine.
Inf. Serv. Use
Thomas C. Rindflesch, Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, Dongwook Shin
2011 J jnl
U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC Bioinform.
Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010 — conf
A High-Precision Approach to Detecting Hedges and their Scopes.
CoNLL Shared Task
Halil Kilicoglu, Sabine Bergler
2010 J jnl
Adapting semantic natural language processing technology to address information overload in influenza epidemic management.
J. Assoc. Inf. Sci. Technol.
Alla Keselman, Graciela Rosemblat, Halil Kilicoglu, Marcelo Fiszman, Honglan Jin, Dongwook Shin, Thomas C. Rindflesch
2010 — conf
Arguments of Nominals in Semantic Interpretation of Biomedical Text.
BioNLP@ACL
Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, Sean Marimpietri, Thomas C. Rindflesch
2010 — conf
Combining Relevance Assignment with Quality of the Evidence to Support Guideline Development.
MedInfo
Marcelo Fiszman, Bruce E. Bray, Dongwook Shin, Halil Kilicoglu, Glen C. Bennett, Olivier Bodenreider, Thomas C. Rindflesch
2009 J jnl
Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation.
J. Biomed. Informatics
Marcelo Fiszman, Dina Demner-Fushman, Halil Kilicoglu, Thomas C. Rindflesch
2009 — conf
Syntactic Dependency Based Heuristics for Biological Event Extraction.
BioNLP@HLT-NAACL (Shared Task)
Halil Kilicoglu, Sabine Bergler
2009 J jnl
Viewpoint Paper: Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence.
J. Am. Medical Informatics Assoc.
Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes
2008 — conf
Recognizing Speculative Language in Biomedical Research Articles: A Linguistically Motivated Perspective.
BioNLP
Halil Kilicoglu, Sabine Bergler
2008 J jnl
Recognizing speculative language in biomedical research articles: a linguistically motivated perspective.
BMC Bioinform.
Halil Kilicoglu, Sabine Bergler
2008 Misc conf
Toward Automatic Recognition of High Quality Clinical Evidence.
AMIA
Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes
2007 Misc conf
Using the Literature-Based Discovery Paradigm to Investigate Drug Mechanisms.
AMIA
Caroline B. Ahlers, Dimitar Hristovski, Halil Kilicoglu, Thomas C. Rindflesch
2006 J jnl
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease.
BMC Bioinform.
Marco Masseroli, Halil Kilicoglu, François-Michel Lang, Thomas C. Rindflesch
2006 Misc conf
Summarizing Drug Information in Medline Citations.
AMIA
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2006 J jnl
Word sense disambiguation by selecting the best semantic type based on Journal Descriptor Indexing: Preliminary experiment.
J. Assoc. Inf. Sci. Technol.
Susanne M. Humphrey, Willie J. Rogers, Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch
2005 Misc conf
Medical Facts to Support Inferencing in Natural Language Processing.
AMIA
Thomas C. Rindflesch, Serguei Pakhomov, Marcelo Fiszman, Halil Kilicoglu, Vincent R. Sánchez
2004 — conf
Summarization of an Online Medical Encyclopedia.
MedInfo
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2003 Misc conf
Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts.
AMIA
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2003 Misc conf
Interpreting Hypernymic Propositions in an Online Medical Encyclopedia.
AMIA
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2003 Misc conf
Semantic Relations Asserting the Etiology of Genetic Diseases.
AMIA
Thomas C. Rindflesch, Bisharah Libbus, Dimitar Hristovski, Alan R. Aronson, Halil Kilicoglu