Halil Kilicoglu

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 49

Top Topics

Named Entity Recognition

Medical Literature

Causal Relations

Relation Extraction

Top Venues

J. Biomed. Informatics

Publications

Sarah Mullin, Robert A. McDougal, Kei-Hoi Cheung, Halil Kilicoglu, Amanda Beck, Caroline J. Zeiss
Chemical entity normalization for successful translational development of Alzheimer's disease and dementia therapeutics. J. Biomed. Semant. 15 (1) (2024)
Halil Kilicoglu, Faezeh Ensan, Bridget T. McInnes, Lucy Lu Wang
Semantics-enabled biomedical literature analytics. J. Biomed. Informatics 150 (2024)
Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang
Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition. J. Am. Medical Informatics Assoc. 31 (2) (2024)
Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang
BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine. CoRR (2024)
Mengfei Lan, Mandy Cheng, Linh K. Hoang, Gerben ter Riet, Halil Kilicoglu
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications. J. Biomed. Informatics 152 (2024)
Shufan Ming, Rui Zhang, Halil Kilicoglu
Enhancing the coverage of SemRep using a relation classification approach. J. Biomed. Informatics 155 (2024)
Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang
Complementary and Integrative Health Lexicon (CIHLex) and Entity Recognition in the Literature. CoRR (2023)
Yiren Liu, Halil Kilicoglu
Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation. CoRR (2023)
Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G. Mantyh, Rui Zhang
Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature. ICHI (2023)
Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions. J. Biomed. Informatics 140 (2023)
Sullam Jeoung, Jana Diesner, Halil Kilicoglu
Examining the Causal Effect of First Names on Language Models: The Case of Social Commonsense Reasoning. CoRR (2023)
Halil Kilicoglu, Faezeh Ensan, Bridget Mcinnes, Lucy Lu Wang
Call for papers: Semantics-enabled biomedical literature analytics. J. Biomed. Informatics 132 (2022)
Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions. CoRR (2022)
Linh K. Hoang, Yingjun Guan, Halil Kilicoglu
Methodological information extraction from randomized controlled trial publications: a pilot study. AMIA (2022)
Faezeh Ensan, Halil Kilicoglu, Bridget Mcinnes, Lucy Lu Wang
The International Workshop on Semantics-enabled Biomedical Literature Analytics (SeBiLAn). WWW (Companion Volume) (2022)
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. J. Biomed. Informatics 131 (2022)
Huixue Zhou, Robin Austin, Halil Kilicoglu, Sheng-Chieh Lu, Rui Zhang
CIHLex: Complementary and Integrative Health Lexicon. AMIA (2022)
Halil Kilicoglu, Graciela Rosemblat, Linh K. Hoang, Sahil Wadhwa, Zeshan Peng, Mario Malicki, Jodi Schneider, Gerben ter Riet
Toward assessing clinical trial publications for reporting transparency. J. Biomed. Informatics 116 (2021)
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
Drug repurposing for COVID-19 via knowledge graph completion. J. Biomed. Informatics 115 (2021)
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
Attention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels. ACM Trans. Comput. Heal. 2 (2) (2021)
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature. CoRR (2021)
Haoyang Liu, Maria Janina Sarol, Halil Kilicoglu
UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions. SemEval@ACL/IJCNLP (2021)
Haoyang Liu, Maria Janina Sarol, Halil Kilicoglu
UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions. CoRR (2021)
Halil Kilicoglu, Linh K. Hoang, Sahil Wadhwa
Identifying Sample Size Characteristics in Randomized Controlled Trial Publications. AMIA (2020)
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin
Broad-coverage biomedical relation extraction with SemRep. BMC Bioinform. 21 (1) (2020)
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
Drug Repurposing for COVID-19 via Knowledge Graph Completion. CoRR (2020)
Halil Kilicoglu, Zeshan Peng, Shabnam Tafreshi, Tung Tran, Graciela Rosemblat, Jodi Schneider
Confirm or refute?: A comparative study on citation sentiment classification in clinical research publications. J. Biomed. Informatics 91 (2019)
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
A Multi-Task Learning Framework for Extracting Drugs and Their Interactions from Drug Labels. CoRR (2019)
Lou Ann Scarton, Liqin Wang, Halil Kilicoglu, Margaret Jahries, Guilherme Del Fiol
Expanding vocabularies for complementary and alternative medicine therapies. Int. J. Medical Informatics 121 (2019)
Mehmet G. Bakal, Halil Kilicoglu, Ramakanth Kavuluru
Non-Negative Matrix Factorization for Drug Repositioning: Experiments with the repoDB Dataset. AMIA (2019)
Dimitar Hristovski, Andrej Kastrin, Halil Kilicoglu
SemMedDB-neo4j: A Graph Database of Biomedical Semantic Relations. AMIA (2019)
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
Attention-Gated Graph Convolution for Extracting Drugs and Their Interactions from Drug Labels. CoRR (2019)
Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin, Halil Kilicoglu
Towards a characterization of apparent contradictions in the biomedical literature using context analysis. J. Biomed. Informatics 98 (2019)
Halil Kilicoglu, Aurélie Névéol, Timothy Clark, Hua Xu, Neil R. Smalheiser
Methods and Tools to Enhance Rigor and Reproducibility of Biomedical Research. AMIA (2018)
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
A Multi-Task Learning Framework for Extracting Drugs and Their Interactions from Drug Labels. TAC (2018)
Halil Kilicoglu, Graciela Rosemblat, Mario Malicki, Gerben ter Riet
Automatic recognition of self-acknowledged limitations in clinical research literature. J. Am. Medical Informatics Assoc. 25 (7) (2018)
Halil Kilicoglu
Biomedical text mining for research rigor and integrity: tasks, challenges, directions. Briefings Bioinform. 19 (6) (2018)
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton, Dina Demner-Fushman
Semantic annotation of consumer health questions. BMC Bioinform. 19 (1) (2018)
Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu
Enhancing Identification of Relation Arguments in SemRep. AMIA (2018)
Dongwook Shin, Halil Kilicoglu
Linking Section Labels with Biomedical Relations in SemMedDB. AMIA (2018)
Thomas C. Rindflesch, Catherine Blake, Michael J. Cairelli, Marcelo Fiszman, Caroline J. Zeiss, Halil Kilicoglu
Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing. J. Biomed. Semant. 9 (1) (2018)
Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman
TextFlow: A Text Similarity Measure based on Continuous Sequences. ACL (1) (2017)
Ariel Deardorff, Kate Masterton, Kirk Roberts, Halil Kilicoglu, Dina Demner-Fushman
A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources. J. Assoc. Inf. Sci. Technol. 68 (7) (2017)
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch
Sortal anaphora resolution to enhance relation extraction from biomedical literature. BMC Bioinform. 17 (2016)
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Kirk Roberts, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman
Annotating Named Entities in Consumer Health Questions. LREC (2016)
Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman
Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. ECAI (2016)
Yassine Mrabet, Pavlos Vougiouklis, Halil Kilicoglu, Claire Gardent, Dina Demner-Fushman, Jonathon S. Hare, Elena Simperl
Aligning Texts and Knowledge Bases with Semantic Sentence Simplification. WebNLG (2016)
Halil Kilicoglu
Inferring Implicit Causal Relationships in Biomedical Literature. BioNLP@ACL (2016)
Yassine Mrabet, Halil Kilicoglu, Kirk Roberts, Dina Demner-Fushman
Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. AMIA (2016)
Kirk Roberts, Sonya E. Shooshan, Laritza Rodriguez, Swapna Abhyankar, Halil Kilicoglu, Dina Demner-Fushman
The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs. J. Biomed. Informatics 58 (2015)
Halil Kilicoglu, Marcelo Fiszman, Kirk Roberts, Dina Demner-Fushman
An Ensemble Method for Spelling Correction in Consumer Health Questions. AMIA (2015)
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
Decomposing Consumer Health Questions. BioNLP@ACL (2014)
Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch
Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference. PLoS Comput. Biol. 10 (6) (2014)
Kirk Roberts, Kate Masterton, Marcelo Fiszman, Halil Kilicoglu, Dina Demner-Fushman
Annotating Question Decomposition on Complex Medical Questions. LREC (2014)
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
Automatically Classifying Question Types for Consumer Health Questions. AMIA (2014)
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Graciela Rosemblat, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. S. Pakhomov, Genevieve B. Melton
Using semantic predications to uncover drug-drug interactions in clinical data. J. Biomed. Informatics 49 (2014)
Halil Kilicoglu, Dina Demner-Fushman
Coreference Resolution for Structured Drug Product Labels. BioNLP@ACL (2014)
Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu, Charles Sneiderman, Thomas C. Rindflesch
A methodology for extending domain coverage in SemRep. J. Biomed. Informatics 46 (6) (2013)
Rashmi Mishra, Guilherme Del Fiol, Halil Kilicoglu, Siddhartha Jonnalagadda, Marcelo Fiszman
Automatically Extracting Clinically Useful Sentences from UpToDate to Support Clinicians' Information Needs. AMIA (2013)
Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis. BioNLP@ACL (2013)
Halil Kilicoglu, Dongwook Shin, Marcelo Fiszman, Graciela Rosemblat, Thomas C. Rindflesch
SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinform. 28 (23) (2012)
Sabine Rosenberg, Halil Kilicoglu, Sabine Bergler
CLaC Labs: Processing Modality and Negation. Working Notes for QA4MRE Pilot Task at CLEF 2012. CLEF (Online Working Notes/Labs/Workshop) (2012)
Halil Kilicoglu, Sabine Bergler
Biological event composition. BMC Bioinform. 13 (S-11) (2012)
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch
Constructing a semantic predication gold standard from the biomedical literature. BMC Bioinform. 12 (2011)
Halil Kilicoglu, Sabine Bergler
Effective Bio-Event Extraction Using Trigger Words and Syntactic Dependencies. Comput. Intell. 27 (4) (2011)
Thomas C. Rindflesch, Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, Dongwook Shin
Semantic MEDLINE: An advanced information management application for biomedicine. Inf. Serv. Use 31 (1-2) (2011)
Halil Kilicoglu, Sabine Bergler
Adapting a General Semantic Interpretation Approach to Biological Event Extraction. BioNLP@ACL (Shared Task) (2011)
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
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12 (2011)
Alla Keselman, Graciela Rosemblat, Halil Kilicoglu, Marcelo Fiszman, Honglan Jin, Dongwook Shin, Thomas C. Rindflesch
Adapting semantic natural language processing technology to address information overload in influenza epidemic management. J. Assoc. Inf. Sci. Technol. 61 (12) (2010)
Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, Sean Marimpietri, Thomas C. Rindflesch
Arguments of Nominals in Semantic Interpretation of Biomedical Text. BioNLP@ACL (2010)
Halil Kilicoglu, Sabine Bergler
A High-Precision Approach to Detecting Hedges and their Scopes. CoNLL Shared Task (2010)
Marcelo Fiszman, Bruce E. Bray, Dongwook Shin, Halil Kilicoglu, Glen C. Bennett, Olivier Bodenreider, Thomas C. Rindflesch
Combining Relevance Assignment with Quality of the Evidence to Support Guideline Development. MedInfo (2010)
Marcelo Fiszman, Dina Demner-Fushman, Halil Kilicoglu, Thomas C. Rindflesch
Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation. J. Biomed. Informatics 42 (5) (2009)
Halil Kilicoglu, Sabine Bergler
Syntactic Dependency Based Heuristics for Biological Event Extraction. BioNLP@HLT-NAACL (Shared Task) (2009)
Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes
Viewpoint Paper: Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence. J. Am. Medical Informatics Assoc. 16 (1) (2009)
Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes
Toward Automatic Recognition of High Quality Clinical Evidence. AMIA (2008)
Halil Kilicoglu, Sabine Bergler
Recognizing Speculative Language in Biomedical Research Articles: A Linguistically Motivated Perspective. BioNLP (2008)
Halil Kilicoglu, Sabine Bergler
Recognizing speculative language in biomedical research articles: a linguistically motivated perspective. BMC Bioinform. 9 (S-11) (2008)
Caroline B. Ahlers, Dimitar Hristovski, Halil Kilicoglu, Thomas C. Rindflesch
Using the Literature-Based Discovery Paradigm to Investigate Drug Mechanisms. AMIA (2007)
Susanne M. Humphrey, Willie J. Rogers, Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch
Word sense disambiguation by selecting the best semantic type based on Journal Descriptor Indexing: Preliminary experiment. J. Assoc. Inf. Sci. Technol. 57 (1) (2006)
Marco Masseroli, Halil Kilicoglu, François-Michel Lang, Thomas C. Rindflesch
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. BMC Bioinform. 7 (2006)
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
Summarizing Drug Information in Medline Citations. AMIA (2006)
Thomas C. Rindflesch, Serguei Pakhomov, Marcelo Fiszman, Halil Kilicoglu, Vincent R. Sánchez
Medical Facts to Support Inferencing in Natural Language Processing. AMIA (2005)
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
Summarization of an Online Medical Encyclopedia. MedInfo (2004)
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts. AMIA (2003)
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
Interpreting Hypernymic Propositions in an Online Medical Encyclopedia. AMIA (2003)
Thomas C. Rindflesch, Bisharah Libbus, Dimitar Hristovski, Alan R. Aronson, Halil Kilicoglu
Semantic Relations Asserting the Etiology of Genetic Diseases. AMIA (2003)