Bridget T. McInnes

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 49

Top Topics

Human Judgments

Multitask Learning

Semantic Similarity

Information Extraction

Top Venues

J. Biomed. Informatics

SemEval@NAACL-HLT

Publications

Evan French, Bridget T. McInnes
An overview of biomedical entity linking throughout the years. J. Biomed. Informatics 137 (2023)
Clint Cuffy, Bridget T. McInnes
Exploring a deep learning neural architecture for closed Literature-based discovery. J. Biomed. Informatics 143 (2023)
Darshini Mahendran, Christina Tang, Bridget T. McInnes
NLPatVCU: CLEF 2022 ChEMU Shared Task System Description. CLEF (Working Notes) (2022)
Steele Farnsworth, Gabrielle Gurdin, Jorge Vargas, Andriy Mulyar, Nastassja Lewinski, Bridget T. McInnes
Extracting experimental parameter entities from scientific articles. J. Biomed. Informatics 126 (2022)
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
Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. CLEF (Working Notes) (2022)
Megan Davis, Bridget T. McInnes, Irfan Ahmed
Forensic investigation of instant messaging services on linux OS: Discord and Slack as case studies. Digit. Investig. 42 (Supplement) (2022)
Amy L. Olex, Evan French, Peter Burdette, Srilakshmi Sagiraju, Thomas Neumann, Tamas S. Gal, Bridget T. McInnes
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4. Database J. Biol. Databases Curation 2022 (2022) (2022)
Clint Cuffy, Evan French, Sophia Fehrmann, Bridget T. McInnes
Exploring Representations for Singular and Multi-Concept Relations for Biomedical Named Entity Normalization. WWW (Companion Volume) (2022)
Darshini Mahendran, Christina Tang, Bridget T. McInnes
Graph Convolutional Networks for Chemical Relation Extraction. WWW (Companion Volume) (2022)
Nicholas E. Rodriguez, Mai H. Nguyen, Bridget T. McInnes
Effects of data and entity ablation on multitask learning models for biomedical entity recognition. J. Biomed. Informatics 130 (2022)
Amy L. Olex, Bridget T. McInnes
Temporal disambiguation of relative temporal expressions in clinical texts. Frontiers Res. Metrics Anal. 7 (2022)
Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes
Identifying Chemical Reactions and Their Associated Attributes in Patents. Frontiers Res. Metrics Anal. 6 (2021)
Andriy Mulyar, Özlem Uzuner, Bridget T. McInnes
MT-clinical BERT: scaling clinical information extraction with multitask learning. J. Am. Medical Informatics Assoc. 28 (10) (2021)
Kahyun Lee, Nicholas J. Dobbins, Bridget T. McInnes, Meliha Yetisgen, Özlem Uzuner
Transferability of neural network clinical deidentification systems. J. Am. Medical Informatics Assoc. 28 (12) (2021)
Darshini Mahendran, Changqing Luo, Bridget T. McInnes
Review: Privacy-Preservation in the Context of Natural Language Processing. IEEE Access 9 (2021)
Kahyun Lee, Nicholas J. Dobbins, Bridget T. McInnes, Meliha Yetisgen, Özlem Uzuner
Transferability of Neural Network-based De-identification Systems. CoRR (2021)
Sam Henry, D. Shanaka Wijesinghe, Aidan Myers, Bridget T. McInnes
Using Literature Based Discovery to Gain Insights Into the Metabolomic Processes of Cardiac Arrest. Frontiers Res. Metrics Anal. 6 (2021)
Amy L. Olex, Bridget T. McInnes
Review of Temporal Reasoning in the Clinical Domain for Timeline Extraction: Where we are and where we need to be. J. Biomed. Informatics 118 (2021)
Darshini Mahendran, Bridget T. McInnes
Extracting Adverse Drug Events from Clinical Notes. CoRR (2021)
Paul Barry, Sam Henry, Meliha Yetisgen, Bridget T. McInnes, Özlem Uzuner
Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context. CoRR (2021)
Paul Barry, Sam Henry, Meliha Yetisgen, Bridget T. McInnes, Özlem Uzuner
Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context. AMIA (2020)
Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes
NLPatVCU CLEF 2020 ChEMU Shared Task System Description. CLEF (Working Notes) (2020)
Andriy Mulyar, Bridget T. McInnes
MT-Clinical BERT: Scaling Clinical Information Extraction with Multitask Learning. CoRR (2020)
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 Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) (2020)
Corey Sutphin, Kahyun Lee, Antonio Jimeno-Yepes, Özlem Uzuner, Bridget T. McInnes
Adverse drug event detection using reason assignments in FDA drug labels. J. Biomed. Informatics 110 (2020)
Clint Cuffy, Nao Hagiwara, Scott Vrana, Bridget T. McInnes
Measuring the quality of patient-physician communication. J. Biomed. Informatics 112 (2020)
Sam Henry, Bridget T. McInnes
Indirect association and ranking hypotheses for literature based discovery. BMC Bioinform. 20 (1) (2019)
Sam Henry, Alex McQuilkin, Bridget T. McInnes
Association measures for estimating semantic similarity and relatedness between biomedical concepts. Artif. Intell. Medicine 93 (2019)
Amy L. Olex, Luke Maffey, Bridget T. McInnes
NLP Whack-A-Mole: Challenges in Cross-Domain Temporal Expression Extraction. NAACL-HLT (1) (2019)
Rachel Dorn, Scott Vrana, Bridget T. McInnes
Improving Accuracy of Patient Speech Transcription Using Dialect-Specific Automatic Speech Recognition Models. AMIA (2019)
Jooho Lee, Catherine Blake, Bridget T. McInnes
Evaluating ontology coverage and internal structure to better align patients with clinical trials. ASIST (2019)
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
Untapped Potential of Clinical Text for Opioid Surveillance. AMIA (2019)
Bartosz Krawczyk, Bridget T. McInnes
Local ensemble learning from imbalanced and noisy data for word sense disambiguation. Pattern Recognit. 78 (2018)
Sam Henry, Clint Cuffy, Bridget T. McInnes
Vector representations of multi-word terms for semantic relatedness. J. Biomed. Informatics 77 (2018)
Darshini Mahendran, Chathurika Brahmana, Bridget T. McInnes
SciREL at SemEval-2018 Task 7: A System for Semantic Relation Extraction and Classification. SemEval@NAACL-HLT (2018)
Andriy Mulyar, Darshini Mahendran, Luke Maffey, Amy L. Olex, Grant Matteo, Neha Dill, Nastassja Lewinski, Bridget T. McInnes
TAC SRIE 2018: Extracting Systematic Review Information with MedaCy. TAC (2018)
Amy L. Olex, Luke Maffey, Nicholas Morgan, Bridget T. McInnes
Chrono at SemEval-2018 Task 6: A System for Normalizing Temporal Expressions. SemEval@NAACL-HLT (2018)
Sam Henry, Bridget T. McInnes
Literature Based Discovery: Models, methods, and trends. J. Biomed. Informatics 74 (2017)
Amy L. Olex, Alberto Cano, Bridget T. McInnes
Parsing MetaMap Files in Hadoop. AMIA (2017)
Bartosz Krawczyk, Bridget T. McInnes, Alberto Cano
Sentiment Classification from Multi-class Imbalanced Twitter Data Using Binarization. HAIS (2017)
Pulkit Rustgi, Carol J. Fung, Bahman Rashidi, Bridget T. McInnes
DroidVisor: An Android secure application recommendation system. IM (2017)
Bridget T. McInnes, Ted Pedersen
Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second-Order Vectors. BioNLP (2017)
Sam Henry, Bridget T. McInnes
Semantic Association for Literature Based Discovery. AMIA (2017)
Sam Henry, Clint Cuffy, Bridget T. McInnes
Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation. BioNLP (2017)
Gerard Briones, Kasun Amarasinghe, Bridget T. McInnes
VCU-TSA at Semeval-2016 Task 4: Sentiment Analysis in Twitter. SemEval@NAACL-HLT (2016)
Bridget T. McInnes, Ted Pedersen
Improving Correlation with Human Judgments by Embedding Second Order Vectors with Semantic Similarity. CoRR (2016)
Bridget T. McInnes, Ryan Murphy, Gabrielle N. Jones, Marley Hodson, Tanin Izadi, Ivan Jimenez, Nastassja Lewinski
Nanomedicine Entity Extraction. AMIA (2016)
Bridget T. McInnes
VCU at Semeval-2016 Task 14: Evaluating definitional-based similarity measure for semantic taxonomy enrichment. SemEval@NAACL-HLT (2016)
Bridget T. McInnes, Ted Pedersen
Evaluating semantic similarity and relatedness over the semantic grouping of clinical term pairs. J. Biomed. Informatics 54 (2015)
Bridget T. McInnes, Mark Stevenson
Determining the difficulty of Word Sense Disambiguation. J. Biomed. Informatics 47 (2014)
Bridget T. McInnes, Ted Pedersen, Ying Liu, Genevieve B. Melton, Serguei V. S. Pakhomov
U-path: An undirected path-based measure of semantic similarity. AMIA (2014)
Bridget T. McInnes, Ted Pedersen
Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. J. Biomed. Informatics 46 (6) (2013)
Bridget T. McInnes, Ted Pedersen, Serguei V. S. Pakhomov, Ying Liu, Genevieve Melton-Meaux
UMLS: : Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts. HLT-NAACL (2013)
Sergey V. Pakhomov, Bridget T. McInnes, J. Lamba, Y. Liu, Genevieve B. Melton, Yogita Ghodke, N. Bhise, V. Lamba, Angela K. Birnbaum
Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. J. Biomed. Informatics 45 (5) (2012)
Robert Bill, Ying Liu, Bridget T. McInnes, Genevieve B. Melton, Ted Pedersen, Serguei V. S. Pakhomov
Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries. AMIA (2012)
Ying Liu, Bridget T. McInnes, Ted Pedersen, Genevieve Melton-Meaux, Serguei V. S. Pakhomov
Semantic relatedness study using second order co-occurrence vectors computed from biomedical corpora, UMLS and WordNet. IHI (2012)
Ted Pedersen, Serguei V. S. Pakhomov, Bridget T. McInnes, Ying Liu
Measuring the similarity and relatedness of concepts in the medical domain: IHI 2012 tutorial overview. IHI (2012)
Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei V. S. Pakhomov, Genevieve B. Melton
Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation. CoNLL (2011)
Ted Pedersen, Satanjeev Banerjee, Bridget T. McInnes, Saiyam Kohli, Mahesh Joshi, Ying Liu
The Ngram Statistics Package (Text: : NSP) : A Flexible Tool for Identifying Ngrams, Collocations, and Word Associations. MWE@ACL (2011)
Antonio José Jimeno-Yepes, Bridget T. McInnes, Alan R. Aronson
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. BMC Bioinform. 12 (2011)
Antonio Jimeno-Yepes, Bridget T. McInnes, Alan R. Aronson
Collocation analysis for UMLS knowledge-based word sense disambiguation. BMC Bioinform. 12 (S-3) (2011)
Serguei V. S. Pakhomov, Ted Pedersen, Bridget T. McInnes, Genevieve B. Melton, Alexander Ruggieri, Christopher G. Chute
Towards a framework for developing semantic relatedness reference standards. J. Biomed. Informatics 44 (2) (2011)
Genevieve B. Melton, Sungrim Moon, Bridget T. McInnes, Serguei Pakhomov
Automated Identification of Synonyms in Biomedical Acronym Sense Inventories. Louhi@NAACL-HLT (2010)
Bridget T. McInnes, Ted Pedersen, Serguei V. S. Pakhomov
UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. AMIA (2009)
Bridget T. McInnes
An Unsupervised Vector Approach to Biomedical Term Disambiguation: Integrating UMLS and Medline. ACL (Student Research Workshop) (2008)
Bridget T. McInnes, Ted Pedersen, John Carlis
Using UMLS Concept Unique Identifiers (CUIs) for Word Sense Disambiguation in the Biomedical Domain. AMIA (2007)
Bridget T. McInnes, Ted Pedersen, Serguei Pakhomov
Determining the Syntactic Structure of Medical Terms in Clinical Notes. BioNLP@ACL (2007)
Bridget T. McInnes, Ted Pedersen
The Duluth Word Alignment System. ParallelTexts@NAACL-HLT (2003)