The Duluth Word Alignment System. - Bridget T. McInnes; Ted Pedersen (ParallelTexts@NAACL-HLT, 2003)

Using UMLS Concept Unique Identifiers (CUIs) for Word Sense Disambiguation in the Biomedical Domain. - Bridget T. McInnes; Ted Pedersen; John Carlis (AMIA, 2007)

Determining the Syntactic Structure of Medical Terms in Clinical Notes. - Bridget T. McInnes; Ted Pedersen; Serguei Pakhomov (BioNLP@ACL, 2007)

An Unsupervised Vector Approach to Biomedical Term Disambiguation: Integrating UMLS and Medline. - Bridget T. McInnes (ACL (Student Research Workshop), 2008)

UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. - Bridget T. McInnes; Ted Pedersen; Serguei V. S. Pakhomov (AMIA, 2009)

Automated Identification of Synonyms in Biomedical Acronym Sense Inventories. - Genevieve B. Melton; Sungrim Moon; Bridget T. McInnes; Serguei Pakhomov (Louhi@NAACL-HLT, 2010)

Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation. - Bridget T. McInnes; Ted Pedersen; Ying Liu 042; Serguei V. S. Pakhomov; Genevieve B. Melton (CoNLL, 2011)

The Ngram Statistics Package (Text: : NSP) : A Flexible Tool for Identifying Ngrams, Collocations, and Word Associations. - Ted Pedersen; Satanjeev Banerjee; Bridget T. McInnes; Saiyam Kohli; Mahesh Joshi; Ying Liu 042 (MWE@ACL, 2011)

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. - Antonio José Jimeno-Yepes; Bridget T. McInnes; Alan R. Aronson (BMC Bioinform., 2011)

Collocation analysis for UMLS knowledge-based word sense disambiguation. - Antonio Jimeno-Yepes; Bridget T. McInnes; Alan R. Aronson (BMC Bioinform., 2011)

Towards a framework for developing semantic relatedness reference standards. - Serguei V. S. Pakhomov; Ted Pedersen; Bridget T. McInnes; Genevieve B. Melton; Alexander Ruggieri; Christopher G. Chute (J. Biomed. Informatics, 2011)

Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries. - Robert Bill; Ying Liu 042; Bridget T. McInnes; Genevieve B. Melton; Ted Pedersen; Serguei V. S. Pakhomov (AMIA, 2012)

Semantic relatedness study using second order co-occurrence vectors computed from biomedical corpora, UMLS and WordNet. - Ying Liu 042; Bridget T. McInnes; Ted Pedersen; Genevieve Melton-Meaux; Serguei V. S. Pakhomov (IHI, 2012)

Measuring the similarity and relatedness of concepts in the medical domain: IHI 2012 tutorial overview. - Ted Pedersen; Serguei V. S. Pakhomov; Bridget T. McInnes; Ying Liu 042 (IHI, 2012)

Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. - Sergey V. Pakhomov; Bridget T. McInnes; J. Lamba; Y. Liu; Genevieve B. Melton; Yogita Ghodke; N. Bhise; V. Lamba; Angela K. Birnbaum (J. Biomed. Informatics, 2012)

UMLS: : Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts. - Bridget T. McInnes; Ted Pedersen; Serguei V. S. Pakhomov; Ying Liu 042; Genevieve Melton-Meaux (HLT-NAACL, 2013)

Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. - Bridget T. McInnes; Ted Pedersen (J. Biomed. Informatics, 2013)

U-path: An undirected path-based measure of semantic similarity. - Bridget T. McInnes; Ted Pedersen; Ying Liu 042; Genevieve B. Melton; Serguei V. S. Pakhomov (AMIA, 2014)

Determining the difficulty of Word Sense Disambiguation. - Bridget T. McInnes; Mark Stevenson (J. Biomed. Informatics, 2014)

Evaluating semantic similarity and relatedness over the semantic grouping of clinical term pairs. - Bridget T. McInnes; Ted Pedersen (J. Biomed. Informatics, 2015)

Nanomedicine Entity Extraction. - Bridget T. McInnes; Ryan Murphy; Gabrielle N. Jones; Marley Hodson; Tanin Izadi; Ivan Jimenez; Nastassja Lewinski (AMIA, 2016)

VCU-TSA at Semeval-2016 Task 4: Sentiment Analysis in Twitter. - Gerard Briones; Kasun Amarasinghe; Bridget T. McInnes (SemEval@NAACL-HLT, 2016)

VCU at Semeval-2016 Task 14: Evaluating definitional-based similarity measure for semantic taxonomy enrichment. - Bridget T. McInnes (SemEval@NAACL-HLT, 2016)

Improving Correlation with Human Judgments by Embedding Second Order Vectors with Semantic Similarity. - Bridget T. McInnes; Ted Pedersen (CoRR, 2016)

Semantic Association for Literature Based Discovery. - Sam Henry 001; Bridget T. McInnes (AMIA, 2017)

Parsing MetaMap Files in Hadoop. - Amy L. Olex; Alberto Cano 001; Bridget T. McInnes (AMIA, 2017)

Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation. - Sam Henry 001; Clint Cuffy; Bridget T. McInnes (BioNLP, 2017)

Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second-Order Vectors. - Bridget T. McInnes; Ted Pedersen (BioNLP, 2017)

Sentiment Classification from Multi-class Imbalanced Twitter Data Using Binarization. - Bartosz Krawczyk; Bridget T. McInnes; Alberto Cano 001 (HAIS, 2017)

DroidVisor: An Android secure application recommendation system. - Pulkit Rustgi; Carol J. Fung; Bahman Rashidi; Bridget T. McInnes (IM, 2017)

Literature Based Discovery: Models, methods, and trends. - Sam Henry 001; Bridget T. McInnes (J. Biomed. Informatics, 2017)

SciREL at SemEval-2018 Task 7: A System for Semantic Relation Extraction and Classification. - Darshini Mahendran; Chathurika Brahmana; Bridget T. McInnes (SemEval@NAACL-HLT, 2018)

Chrono at SemEval-2018 Task 6: A System for Normalizing Temporal Expressions. - Amy L. Olex; Luke Maffey; Nicholas Morgan; Bridget T. McInnes (SemEval@NAACL-HLT, 2018)

TAC SRIE 2018: Extracting Systematic Review Information with MedaCy. - Andriy Mulyar; Darshini Mahendran; Luke Maffey; Amy L. Olex; Grant Matteo; Neha Dill; Nastassja Lewinski; Bridget T. McInnes (TAC, 2018)

Vector representations of multi-word terms for semantic relatedness. - Sam Henry 001; Clint Cuffy; Bridget T. McInnes (J. Biomed. Informatics, 2018)

Local ensemble learning from imbalanced and noisy data for word sense disambiguation. - Bartosz Krawczyk; Bridget T. McInnes (Pattern Recognit., 2018)

Improving Accuracy of Patient Speech Transcription Using Dialect-Specific Automatic Speech Recognition Models. - Rachel Dorn; Scott Vrana; Bridget T. McInnes (AMIA, 2019)

Untapped Potential of Clinical Text for Opioid Surveillance. - 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; et al. (AMIA, 2019)

Evaluating ontology coverage and internal structure to better align patients with clinical trials. - Jooho Lee 005; Catherine Blake; Bridget T. McInnes (ASIST, 2019)

NLP Whack-A-Mole: Challenges in Cross-Domain Temporal Expression Extraction. - Amy L. Olex; Luke Maffey; Bridget T. McInnes (NAACL-HLT (1), 2019)

Association measures for estimating semantic similarity and relatedness between biomedical concepts. - Sam Henry 001; Alex McQuilkin; Bridget T. McInnes (Artif. Intell. Medicine, 2019)

Indirect association and ranking hypotheses for literature based discovery. - Sam Henry 001; Bridget T. McInnes (BMC Bioinform., 2019)

Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context. - Paul Barry; Sam Henry 001; Meliha Yetisgen; Bridget T. McInnes; Özlem Uzuner (AMIA, 2020)

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. - Jiayuan He 002; Dat Quoc Nguyen; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Ralph Hoessel; Zubair Afzal; Zenan Zhai; Biaoyan Fang; Hiyori Yoshikawa; Ameer Albahem; Jingqi Wang; et al. (CLEF (Working Notes), 2020)

NLPatVCU CLEF 2020 ChEMU Shared Task System Description. - Darshini Mahendran; Gabrielle Gurdin; Nastassja Lewinski; Christina Tang; Bridget T. McInnes (CLEF (Working Notes), 2020)

NLP@VCU: Identifying Adverse Effects in English Tweets for Unbalanced Data. - Darshini Mahendran; Cora Lewis; Bridget T. McInnes (SMM4H@COLING, 2020)

MT-Clinical BERT: Scaling Clinical Information Extraction with Multitask Learning. - Andriy Mulyar; Bridget T. McInnes (CoRR, 2020)

Measuring the quality of patient-physician communication. - Clint Cuffy; Nao Hagiwara; Scott Vrana; Bridget T. McInnes (J. Biomed. Informatics, 2020)

Adverse drug event detection using reason assignments in FDA drug labels. - Corey Sutphin; Kahyun Lee; Antonio Jimeno-Yepes; Özlem Uzuner; Bridget T. McInnes (J. Biomed. Informatics, 2020)

Review: Privacy-Preservation in the Context of Natural Language Processing. - Darshini Mahendran; Changqing Luo; Bridget T. McInnes (IEEE Access, 2021)

Transferability of Neural Network-based De-identification Systems. - Kahyun Lee; Nicholas J. Dobbins; Bridget T. McInnes; Meliha Yetisgen; Özlem Uzuner (CoRR, 2021)

Extracting Adverse Drug Events from Clinical Notes. - Darshini Mahendran; Bridget T. McInnes (CoRR, 2021)

Using Literature Based Discovery to Gain Insights Into the Metabolomic Processes of Cardiac Arrest. - Sam Henry 001; D. Shanaka Wijesinghe; Aidan Myers; Bridget T. McInnes (Frontiers Res. Metrics Anal., 2021)

Identifying Chemical Reactions and Their Associated Attributes in Patents. - Darshini Mahendran; Gabrielle Gurdin; Nastassja Lewinski; Christina Tang; Bridget T. McInnes (Frontiers Res. Metrics Anal., 2021)

Transferability of neural network clinical deidentification systems. - Kahyun Lee; Nicholas J. Dobbins; Bridget T. McInnes; Meliha Yetisgen; Özlem Uzuner (J. Am. Medical Informatics Assoc., 2021)

MT-clinical BERT: scaling clinical information extraction with multitask learning. - Andriy Mulyar; Özlem Uzuner; Bridget T. McInnes (J. Am. Medical Informatics Assoc., 2021)

Review of Temporal Reasoning in the Clinical Domain for Timeline Extraction: Where we are and where we need to be. - Amy L. Olex; Bridget T. McInnes (J. Biomed. Informatics, 2021)

Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. - Yuan Li 012; Biaoyan Fang; Jiayuan He 002; Hiyori Yoshikawa; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Zubair Afzal; Zenan Zhai; Kojiro Machi; Masaharu Yoshioka; Youngrok Jang; et al. (CLEF (Working Notes), 2022)

NLPatVCU: CLEF 2022 ChEMU Shared Task System Description. - Darshini Mahendran; Christina Tang; Bridget T. McInnes (CLEF (Working Notes), 2022)

Exploring Representations for Singular and Multi-Concept Relations for Biomedical Named Entity Normalization. - Clint Cuffy; Evan French; Sophia Fehrmann; Bridget T. McInnes (WWW (Companion Volume), 2022)

The International Workshop on Semantics-enabled Biomedical Literature Analytics (SeBiLAn). - Faezeh Ensan; Halil Kilicoglu; Bridget T. McInnes; Lucy Lu Wang (WWW (Companion Volume), 2022)

Graph Convolutional Networks for Chemical Relation Extraction. - Darshini Mahendran; Christina Tang; Bridget T. McInnes (WWW (Companion Volume), 2022)

TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4. - Amy L. Olex; Evan French; Peter Burdette; Srilakshmi Sagiraju; Thomas Neumann 012; Tamas S. Gal; Bridget T. McInnes (Database J. Biol. Databases Curation, 2022)

Forensic investigation of instant messaging services on linux OS: Discord and Slack as case studies. - Megan Davis; Bridget T. McInnes; Irfan Ahmed 001 (Digit. Investig., 2022)

Temporal disambiguation of relative temporal expressions in clinical texts. - Amy L. Olex; Bridget T. McInnes (Frontiers Res. Metrics Anal., 2022)

Extracting experimental parameter entities from scientific articles. - Steele Farnsworth; Gabrielle Gurdin; Jorge Vargas; Andriy Mulyar; Nastassja Lewinski; Bridget T. McInnes (J. Biomed. Informatics, 2022)

Call for papers: Semantics-enabled biomedical literature analytics. - Halil Kilicoglu; Faezeh Ensan; Bridget T. McInnes; Lucy Lu Wang (J. Biomed. Informatics, 2022)

Effects of data and entity ablation on multitask learning models for biomedical entity recognition. - Nicholas E. Rodriguez; Mai H. Nguyen; Bridget T. McInnes (J. Biomed. Informatics, 2022)

Exploring a deep learning neural architecture for closed Literature-based discovery. - Clint Cuffy; Bridget T. McInnes (J. Biomed. Informatics, 2023)

An overview of biomedical entity linking throughout the years. - Evan French; Bridget T. McInnes (J. Biomed. Informatics, 2023)

BioBERT-based Deep Learning and Merged ChemProt-DrugProt for Enhanced Biomedical Relation Extraction. - Bridget T. McInnes; Jiawei Tang; Darshini Mahendran; Mai H. Nguyen (CoRR, 2024)

CACER: Clinical concept Annotations for Cancer Events and Relations. - Yujuan Fu; Giridhar Kaushik Ramachandran; Ahmad Halwani; Bridget T. McInnes; Fei Xia 004; Kevin Lybarger; Meliha Yetisgen; Özlem Uzuner (J. Am. Medical Informatics Assoc., 2024)

Semantics-enabled biomedical literature analytics. - Halil Kilicoglu; Faezeh Ensan; Bridget T. McInnes; Lucy Lu Wang (J. Biomed. Informatics, 2024)

Predicting implicit concept embeddings for singular relationship discovery replication of closed literature-based discovery. - Clint Cuffy; Bridget T. McInnes (Frontiers Res. Metrics Anal., 2025)