Bridget T. McInnes

77 papers B 2Misc 11Journal 38Unranked 26
YearRankTypeTitle / Venue / Authors
2025 — conf
NLP@VCU at BioASQ2025: Information Extraction on the GutBrainIE dataset.
CLEF (Working Notes)
Scott Taylor, Charlie Dil, Aaron Shah, Jannat, Cyd Oldham, Ayush Upadhyay, Joanne Varughese, Nicole Yazbeck, Bridget T. McInnes
2025 J jnl
Predicting implicit concept embeddings for singular relationship discovery replication of closed literature-based discovery.
Frontiers Res. Metrics Anal.
Clint Cuffy, Bridget T. McInnes
2024 J jnl
BioBERT-based Deep Learning and Merged ChemProt-DrugProt for Enhanced Biomedical Relation Extraction.
CoRR
Bridget T. McInnes, Jiawei Tang, Darshini Mahendran, Mai H. Nguyen
2024 J jnl
CACER: Clinical Concept Annotations for Cancer Events and Relations.
CoRR
Yujuan Fu, Giridhar Kaushik Ramachandran, Ahmad Halwani, Bridget T. McInnes, Fei Xia, Kevin Lybarger, Meliha Yetisgen, Özlem Uzuner
2024 J jnl
CACER: Clinical concept Annotations for Cancer Events and Relations.
J. Am. Medical Informatics Assoc.
Yujuan Fu, Giridhar Kaushik Ramachandran, Ahmad Halwani, Bridget T. McInnes, Fei Xia, Kevin Lybarger, Meliha Yetisgen, Özlem Uzuner
2024 J jnl
Semantics-enabled biomedical literature analytics.
J. Biomed. Informatics
Halil Kilicoglu, Faezeh Ensan, Bridget T. McInnes, Lucy Lu Wang
2023 J jnl
An overview of biomedical entity linking throughout the years.
J. Biomed. Informatics
Evan French, Bridget T. McInnes
2023 J jnl
Exploring a deep learning neural architecture for closed Literature-based discovery.
J. Biomed. Informatics
Clint Cuffy, Bridget T. McInnes
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
Effects of data and entity ablation on multitask learning models for biomedical entity recognition.
J. Biomed. Informatics
Nicholas E. Rodriguez, Mai H. Nguyen, Bridget T. McInnes
2022 — conf
Exploring Representations for Singular and Multi-Concept Relations for Biomedical Named Entity Normalization.
WWW (Companion Volume)
Clint Cuffy, Evan French, Sophia Fehrmann, Bridget T. McInnes
2022 — conf
Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.
CLEF (Working Notes)
Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Kojiro Machi, Masaharu Yoshioka, Youngrok Jang, Hosung Song, Junho Lee, Gyeonghun Kim, Yireun Kim, Stanley Jungkyu Choi, Honglak Lee, Kyunghoon Bae, Darshini Mahendran, Christina Tang, Bridget T. McInnes, Timothy Baldwin, Karin Verspoor
2022 J jnl
Extracting experimental parameter entities from scientific articles.
J. Biomed. Informatics
Steele Farnsworth, Gabrielle Gurdin, Jorge Vargas, Andriy Mulyar, Nastassja Lewinski, Bridget T. McInnes
2022 J jnl
Forensic investigation of instant messaging services on linux OS: Discord and Slack as case studies.
Digit. Investig.
Megan Davis, Bridget T. McInnes, Irfan Ahmed
2022 — conf
Graph Convolutional Networks for Chemical Relation Extraction.
WWW (Companion Volume)
Darshini Mahendran, Christina Tang, Bridget T. McInnes
2022 — conf
NLPatVCU: CLEF 2022 ChEMU Shared Task System Description.
CLEF (Working Notes)
Darshini Mahendran, Christina Tang, Bridget T. McInnes
2022 J jnl
Temporal disambiguation of relative temporal expressions in clinical texts.
Frontiers Res. Metrics Anal.
Amy L. Olex, Bridget T. McInnes
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
2022 J jnl
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4.
Database J. Biol. Databases Curation
Amy L. Olex, Evan French, Peter Burdette, Srilakshmi Sagiraju, Thomas Neumann, Tamas S. Gal, Bridget T. McInnes
2021 J jnl
Extracting Adverse Drug Events from Clinical Notes.
CoRR
Darshini Mahendran, Bridget T. McInnes
2021 J jnl
Identifying Chemical Reactions and Their Associated Attributes in Patents.
Frontiers Res. Metrics Anal.
Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes
2021 J jnl
Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context.
CoRR
Paul Barry, Sam Henry, Meliha Yetisgen, Bridget T. McInnes, Özlem Uzuner
2021 J jnl
MT-clinical BERT: scaling clinical information extraction with multitask learning.
J. Am. Medical Informatics Assoc.
Andriy Mulyar, Özlem Uzuner, Bridget T. McInnes
2021 J jnl
Review of Temporal Reasoning in the Clinical Domain for Timeline Extraction: Where we are and where we need to be.
J. Biomed. Informatics
Amy L. Olex, Bridget T. McInnes
2021 J jnl
Review: Privacy-Preservation in the Context of Natural Language Processing.
IEEE Access
Darshini Mahendran, Changqing Luo, Bridget T. McInnes
2021 J jnl
Transferability of Neural Network-based De-identification Systems.
CoRR
Kahyun Lee, Nicholas J. Dobbins, Bridget T. McInnes, Meliha Yetisgen, Özlem Uzuner
2021 J jnl
Transferability of neural network clinical deidentification systems.
J. Am. Medical Informatics Assoc.
Kahyun Lee, Nicholas J. Dobbins, Bridget T. McInnes, Meliha Yetisgen, Özlem Uzuner
2021 J jnl
Using Literature Based Discovery to Gain Insights Into the Metabolomic Processes of Cardiac Arrest.
Frontiers Res. Metrics Anal.
Sam Henry, D. Shanaka Wijesinghe, Aidan Myers, Bridget T. McInnes
2020 J jnl
Adverse drug event detection using reason assignments in FDA drug labels.
J. Biomed. Informatics
Corey Sutphin, Kahyun Lee, Antonio Jimeno-Yepes, Özlem Uzuner, Bridget T. McInnes
2020 — conf
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents.
CLEF (Working Notes)
Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M. Couto, Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro, Daniel M. Lowe, John Mayfield, Abdullatif Köksal, Hilal Dönmez, Elif Özkirimli, Arzucan Özgür, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes, C. S. Malarkodi, Pattabhi R. K. Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor
2020 Misc conf
Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context.
AMIA
Paul Barry, Sam Henry, Meliha Yetisgen, Bridget T. McInnes, Özlem Uzuner
2020 J jnl
MT-Clinical BERT: Scaling Clinical Information Extraction with Multitask Learning.
CoRR
Andriy Mulyar, Bridget T. McInnes
2020 J jnl
Measuring the quality of patient-physician communication.
J. Biomed. Informatics
Clint Cuffy, Nao Hagiwara, Scott Vrana, Bridget T. McInnes
2020 — conf
NLP@VCU: Identifying Adverse Effects in English Tweets for Unbalanced Data.
SMM4H@COLING
Darshini Mahendran, Cora Lewis, Bridget T. McInnes
2020 — conf
NLPatVCU CLEF 2020 ChEMU Shared Task System Description.
CLEF (Working Notes)
Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes
2019 J jnl
Association measures for estimating semantic similarity and relatedness between biomedical concepts.
Artif. Intell. Medicine
Sam Henry, Alex McQuilkin, Bridget T. McInnes
2019 — conf
Evaluating ontology coverage and internal structure to better align patients with clinical trials.
ASIST
Jooho Lee, Catherine Blake, Bridget T. McInnes
2019 Misc conf
Improving Accuracy of Patient Speech Transcription Using Dialect-Specific Automatic Speech Recognition Models.
AMIA
Rachel Dorn, Scott Vrana, Bridget T. McInnes
2019 J jnl
Indirect association and ranking hypotheses for literature based discovery.
BMC Bioinform.
Sam Henry, Bridget T. McInnes
2019 — conf
NLP Whack-A-Mole: Challenges in Cross-Domain Temporal Expression Extraction.
NAACL-HLT (1)
Amy L. Olex, Luke Maffey, Bridget T. McInnes
2019 Misc conf
Untapped Potential of Clinical Text for Opioid Surveillance.
AMIA
Amy L. Olex, Tamás Gál, Majid Afshar, Dmitriy Dligach, Niranjan S. Karnik, Travis Oakes, Brihat Sharma, Meng Xie, Bridget T. McInnes, Julian Solway, Abel N. Kho, William Cramer, F. G. Moeller
2018 — conf
Chrono at SemEval-2018 Task 6: A System for Normalizing Temporal Expressions.
SemEval@NAACL-HLT
Amy L. Olex, Luke Maffey, Nicholas Morgan, Bridget T. McInnes
2018 J jnl
Local ensemble learning from imbalanced and noisy data for word sense disambiguation.
Pattern Recognit.
Bartosz Krawczyk, Bridget T. McInnes
2018 — conf
SciREL at SemEval-2018 Task 7: A System for Semantic Relation Extraction and Classification.
SemEval@NAACL-HLT
Darshini Mahendran, Chathurika Brahmana, Bridget T. McInnes
2018 — conf
TAC SRIE 2018: Extracting Systematic Review Information with MedaCy.
TAC
Andriy Mulyar, Darshini Mahendran, Luke Maffey, Amy L. Olex, Grant Matteo, Neha Dill, Nastassja Lewinski, Bridget T. McInnes
2018 J jnl
Vector representations of multi-word terms for semantic relatedness.
J. Biomed. Informatics
Sam Henry, Clint Cuffy, Bridget T. McInnes
2017 B conf
DroidVisor: An Android secure application recommendation system.
IM
Pulkit Rustgi, Carol J. Fung, Bahman Rashidi, Bridget T. McInnes
2017 — conf
Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation.
BioNLP
Sam Henry, Clint Cuffy, Bridget T. McInnes
2017 — conf
Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second-Order Vectors.
BioNLP
Bridget T. McInnes, Ted Pedersen
2017 J jnl
Literature Based Discovery: Models, methods, and trends.
J. Biomed. Informatics
Sam Henry, Bridget T. McInnes
2017 Misc conf
Parsing MetaMap Files in Hadoop.
AMIA
Amy L. Olex, Alberto Cano, Bridget T. McInnes
2017 Misc conf
Semantic Association for Literature Based Discovery.
AMIA
Sam Henry, Bridget T. McInnes
2017 Misc conf
Sentiment Classification from Multi-class Imbalanced Twitter Data Using Binarization.
HAIS
Bartosz Krawczyk, Bridget T. McInnes, Alberto Cano
2016 J jnl
Improving Correlation with Human Judgments by Embedding Second Order Vectors with Semantic Similarity.
CoRR
Bridget T. McInnes, Ted Pedersen
2016 Misc conf
Nanomedicine Entity Extraction.
AMIA
Bridget T. McInnes, Ryan Murphy, Gabrielle N. Jones, Marley Hodson, Tanin Izadi, Ivan Jimenez, Nastassja Lewinski
2016 — conf
VCU at Semeval-2016 Task 14: Evaluating definitional-based similarity measure for semantic taxonomy enrichment.
SemEval@NAACL-HLT
Bridget T. McInnes
2016 — conf
VCU-TSA at Semeval-2016 Task 4: Sentiment Analysis in Twitter.
SemEval@NAACL-HLT
Gerard Briones, Kasun Amarasinghe, Bridget T. McInnes
2015 J jnl
Evaluating semantic similarity and relatedness over the semantic grouping of clinical term pairs.
J. Biomed. Informatics
Bridget T. McInnes, Ted Pedersen
2014 J jnl
Determining the difficulty of Word Sense Disambiguation.
J. Biomed. Informatics
Bridget T. McInnes, Mark Stevenson
2014 Misc conf
U-path: An undirected path-based measure of semantic similarity.
AMIA
Bridget T. McInnes, Ted Pedersen, Ying Liu, Genevieve B. Melton, Serguei V. S. Pakhomov
2013 J jnl
Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text.
J. Biomed. Informatics
Bridget T. McInnes, Ted Pedersen
2013 — conf
UMLS: : Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts.
HLT-NAACL
Bridget T. McInnes, Ted Pedersen, Serguei V. S. Pakhomov, Ying Liu, Genevieve Melton-Meaux
2012 Misc conf
Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries.
AMIA
Robert Bill, Ying Liu, Bridget T. McInnes, Genevieve B. Melton, Ted Pedersen, Serguei V. S. Pakhomov
2012 — conf
Measuring the similarity and relatedness of concepts in the medical domain: IHI 2012 tutorial overview.
IHI
Ted Pedersen, Serguei V. S. Pakhomov, Bridget T. McInnes, Ying Liu
2012 — conf
Semantic relatedness study using second order co-occurrence vectors computed from biomedical corpora, UMLS and WordNet.
IHI
Ying Liu, Bridget T. McInnes, Ted Pedersen, Genevieve Melton-Meaux, Serguei V. S. Pakhomov
2012 J jnl
Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies.
J. Biomed. Informatics
Sergey V. Pakhomov, Bridget T. McInnes, J. Lamba, Y. Liu, Genevieve B. Melton, Yogita Ghodke, N. Bhise, V. Lamba, Angela K. Birnbaum
2011 J jnl
Collocation analysis for UMLS knowledge-based word sense disambiguation.
BMC Bioinform.
Antonio Jimeno-Yepes, Bridget T. McInnes, Alan R. Aronson
2011 J jnl
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation.
BMC Bioinform.
Antonio José Jimeno-Yepes, Bridget T. McInnes, Alan R. Aronson
2011 — conf
The Ngram Statistics Package (Text: : NSP) : A Flexible Tool for Identifying Ngrams, Collocations, and Word Associations.
MWE@ACL
Ted Pedersen, Satanjeev Banerjee, Bridget T. McInnes, Saiyam Kohli, Mahesh Joshi, Ying Liu
2011 J jnl
Towards a framework for developing semantic relatedness reference standards.
J. Biomed. Informatics
Serguei V. S. Pakhomov, Ted Pedersen, Bridget T. McInnes, Genevieve B. Melton, Alexander Ruggieri, Christopher G. Chute
2011 B conf
Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation.
CoNLL
Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei V. S. Pakhomov, Genevieve B. Melton
2010 — conf
Automated Identification of Synonyms in Biomedical Acronym Sense Inventories.
Louhi@NAACL-HLT
Genevieve B. Melton, Sungrim Moon, Bridget T. McInnes, Serguei Pakhomov
2009 Misc conf
UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity.
AMIA
Bridget T. McInnes, Ted Pedersen, Serguei V. S. Pakhomov
2008 — conf
An Unsupervised Vector Approach to Biomedical Term Disambiguation: Integrating UMLS and Medline.
ACL (Student Research Workshop)
Bridget T. McInnes
2007 — conf
Determining the Syntactic Structure of Medical Terms in Clinical Notes.
BioNLP@ACL
Bridget T. McInnes, Ted Pedersen, Serguei Pakhomov
2007 Misc conf
Using UMLS Concept Unique Identifiers (CUIs) for Word Sense Disambiguation in the Biomedical Domain.
AMIA
Bridget T. McInnes, Ted Pedersen, John Carlis
2003 — conf
The Duluth Word Alignment System.
ParallelTexts@NAACL-HLT
Bridget T. McInnes, Ted Pedersen