Halil Kilicoglu

Orcid: 0000-0003-3987-9393

According to our database1, Halil Kilicoglu authored at least 81 papers between 2003 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Links

On csauthors.net:

Bibliography

2024
Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition.
J. Am. Medical Informatics Assoc., January, 2024

Enhancing the coverage of SemRep using a relation classification approach.
J. Biomed. Informatics, 2024

Automatic categorization of self-acknowledged limitations in randomized controlled trial publications.
J. Biomed. Informatics, 2024

Semantics-enabled biomedical literature analytics.
J. Biomed. Informatics, 2024

BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine.
CoRR, 2024

2023
Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.
J. Biomed. Informatics, April, 2023

Examining the Causal Effect of First Names on Language Models: The Case of Social Commonsense Reasoning.
CoRR, 2023

Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation.
CoRR, 2023

Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature.
Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

2022
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature.
J. Biomed. Informatics, 2022

Call for papers: Semantics-enabled biomedical literature analytics.
J. Biomed. Informatics, 2022

Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions.
CoRR, 2022

The International Workshop on Semantics-enabled Biomedical Literature Analytics (SeBiLAn).
Proceedings of the Companion of The Web Conference 2022, Virtual Event / Lyon, France, April 25, 2022

CIHLex: Complementary and Integrative Health Lexicon.
Proceedings of the AMIA 2022, 2022

Methodological information extraction from randomized controlled trial publications: a pilot study.
Proceedings of the AMIA 2022, 2022

2021
Toward assessing clinical trial publications for reporting transparency.
J. Biomed. Informatics, 2021

Drug repurposing for COVID-19 via knowledge graph completion.
J. Biomed. Informatics, 2021

Attention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels.
ACM Trans. Comput. Heal., 2021

Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature.
CoRR, 2021

UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions.
Proceedings of the 15th International Workshop on Semantic Evaluation, 2021

2020
Broad-coverage biomedical relation extraction with SemRep.
BMC Bioinform., 2020

Identifying Sample Size Characteristics in Randomized Controlled Trial Publications.
Proceedings of the AMIA 2020, 2020

2019
Towards a characterization of apparent contradictions in the biomedical literature using context analysis.
J. Biomed. Informatics, 2019

Confirm or refute?: A comparative study on citation sentiment classification in clinical research publications.
J. Biomed. Informatics, 2019

Expanding vocabularies for complementary and alternative medicine therapies.
Int. J. Medical Informatics, 2019

Attention-Gated Graph Convolution for Extracting Drugs and Their Interactions from Drug Labels.
CoRR, 2019

SemMedDB-neo4j: A Graph Database of Biomedical Semantic Relations.
Proceedings of the AMIA 2019, 2019

Non-Negative Matrix Factorization for Drug Repositioning: Experiments with the repoDB Dataset.
Proceedings of the AMIA 2019, 2019

2018
Automatic recognition of self-acknowledged limitations in clinical research literature.
J. Am. Medical Informatics Assoc., 2018

Semantic annotation of consumer health questions.
BMC Bioinform., 2018

Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing.
J. Biomed. Semant., 2018

Biomedical text mining for research rigor and integrity: tasks, challenges, directions.
Briefings Bioinform., 2018

A Multi-Task Learning Framework for Extracting Drugs and Their Interactions from Drug Labels.
Proceedings of the 2018 Text Analysis Conference, 2018

Linking Section Labels with Biomedical Relations in SemMedDB.
Proceedings of the AMIA 2018, 2018

Enhancing Identification of Relation Arguments in SemRep.
Proceedings of the AMIA 2018, 2018

Methods and Tools to Enhance Rigor and Reproducibility of Biomedical Research.
Proceedings of the AMIA 2018, 2018

2017
A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources.
J. Assoc. Inf. Sci. Technol., 2017

TextFlow: A Text Similarity Measure based on Continuous Sequences.
Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, 2017

2016
Sortal anaphora resolution to enhance relation extraction from biomedical literature.
BMC Bioinform., 2016

Annotating Named Entities in Consumer Health Questions.
Proceedings of the Tenth International Conference on Language Resources and Evaluation LREC 2016, 2016

Unsupervised Ranking of Knowledge Bases for Named Entity Recognition.
Proceedings of the ECAI 2016 - 22nd European Conference on Artificial Intelligence, 29 August-2 September 2016, The Hague, The Netherlands, 2016

Inferring Implicit Causal Relationships in Biomedical Literature.
Proceedings of the 15th Workshop on Biomedical Natural Language Processing, 2016

Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions.
Proceedings of the AMIA 2016, 2016

Aligning Texts and Knowledge Bases with Semantic Sentence Simplification.
Proceedings of the 2nd International Workshop on Natural Language Generation and the Semantic Web, 2016

2015
The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs.
J. Biomed. Informatics, 2015

An Ensemble Method for Spelling Correction in Consumer Health Questions.
Proceedings of the AMIA 2015, 2015

2014
Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference.
PLoS Comput. Biol., 2014

Using semantic predications to uncover drug-drug interactions in clinical data.
J. Biomed. Informatics, 2014

Annotating Question Decomposition on Complex Medical Questions.
Proceedings of the Ninth International Conference on Language Resources and Evaluation, 2014

Decomposing Consumer Health Questions.
Proceedings of BioNLP, Baltimore, Maryland, USA, 2014

Coreference Resolution for Structured Drug Product Labels.
Proceedings of BioNLP, Baltimore, Maryland, USA, 2014

Automatically Classifying Question Types for Consumer Health Questions.
Proceedings of the AMIA 2014, 2014

2013
A methodology for extending domain coverage in SemRep.
J. Biomed. Informatics, 2013

Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis.
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing, 2013

Automatically Extracting Clinically Useful Sentences from UpToDate to Support Clinicians' Information Needs.
Proceedings of the AMIA 2013, 2013

2012
Biological event composition.
BMC Bioinform., 2012

SemMedDB: a PubMed-scale repository of biomedical semantic predications.
Bioinform., 2012

CLaC Labs: Processing Modality and Negation. Working Notes for QA4MRE Pilot Task at CLEF 2012.
Proceedings of the CLEF 2012 Evaluation Labs and Workshop, 2012

2011
Semantic MEDLINE: An advanced information management application for biomedicine.
Inf. Serv. Use, 2011

Effective Bio-Event Extraction Using Trigger Words and Syntactic Dependencies.
Comput. Intell., 2011

Constructing a semantic predication gold standard from the biomedical literature.
BMC Bioinform., 2011

U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC Bioinform., 2011

Adapting a General Semantic Interpretation Approach to Biological Event Extraction.
Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon, USA, June 24, 2011, 2011

2010
Adapting semantic natural language processing technology to address information overload in influenza epidemic management.
J. Assoc. Inf. Sci. Technol., 2010

Combining Relevance Assignment with Quality of the Evidence to Support Guideline Development.
Proceedings of the MEDINFO 2010, 2010

A High-Precision Approach to Detecting Hedges and their Scopes.
Proceedings of the Fourteenth Conference on Computational Natural Language Learning: Shared Task, 2010

Arguments of Nominals in Semantic Interpretation of Biomedical Text.
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, 2010

2009
Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation.
J. Biomed. Informatics, 2009

Viewpoint Paper: Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence.
J. Am. Medical Informatics Assoc., 2009

Syntactic Dependency Based Heuristics for Biological Event Extraction.
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, BioNLP@HLT-NAACL 2009, 2009

2008
Recognizing speculative language in biomedical research articles: a linguistically motivated perspective.
BMC Bioinform., 2008

Toward Automatic Recognition of High Quality Clinical Evidence.
Proceedings of the AMIA 2008, 2008

2007
Using the Literature-Based Discovery Paradigm to Investigate Drug Mechanisms.
Proceedings of the AMIA 2007, 2007

2006
Word sense disambiguation by selecting the best semantic type based on Journal Descriptor Indexing: Preliminary experiment.
J. Assoc. Inf. Sci. Technol., 2006

Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease.
BMC Bioinform., 2006

Summarizing Drug Information in Medline Citations.
Proceedings of the AMIA 2006, 2006

2005
Medical Facts to Support Inferencing in Natural Language Processing.
Proceedings of the AMIA 2005, 2005

2004
Summarization of an Online Medical Encyclopedia.
Proceedings of the MEDINFO 2004, 2004

2003
Semantic Relations Asserting the Etiology of Genetic Diseases.
Proceedings of the AMIA 2003, 2003

Interpreting Hypernymic Propositions in an Online Medical Encyclopedia.
Proceedings of the AMIA 2003, 2003

Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts.
Proceedings of the AMIA 2003, 2003


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