NATURAL LANGUAGE PROCESSING LAB

• NLP@VCU: Identifying adverse effects in English tweets for unbalanced data. Mahendran, Darshini, Cora Lewis, and Bridget McInnes. In Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task, pp. 158-160. 2020.
• Measuring the quality of patient-physician communication. Cuffy, Clint, Nao Hagiwara, Scott Vrana, and Bridget T. McInnes. Journal of biomedical informatics 112 (2020): 103589.
• NLPatVCU CLEF 2020 ChEMU Shared Task System Description. Mahendran, Darshini, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, and Bridget T. McInnes. In the Conference and Labs of the Evaluation Forum (CLEF) 2020 Working Notes.
• Analysis of Inter-Domain and Cross-Domain Drug Review Polarity Classification. Gurdin, Gabrielle, Jorge A. Vargas, Luke G. Maffey, Amy L. Olex, Nastassja A. Lewinski, and Bridget T. McInnes. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2020 (2020): 201-210.
• Local Topic Mining for Reflective Medical Writing. Olex, Amy L., Deborah DiazGranados, Bridget T. McInnes, and Stephanie Goldberg. AMIA Summits on Translational Science Proceedings 2020 (2020): 459.
• Adverse drug event detection using reason assignments in FDA drug labels. Corey Sutphin, Kahyun Lee, Antonio Jimeno Yepes, Özlem Uzuner, and Bridget T. McInnes. Journal of Biomedical Informatics 110 (2020): 103552.

2019

• Indirect association and ranking hypotheses for literature based discovery. Sam Henry and Bridget T. McInnes. BMC bioinformatics 20 (1), 425, 2019.
• NLP Whack-A-Mole: Challenges in Cross-Domain Temporal Expression Extraction. Amy Olex, Luke Maffey, and Bridget T. McInnes. In Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics, pp. 3682-3692, 2019.
• Evaluating ontology coverage and internal structure to better align patients with clinical trials. Jooho Lee, Cathy Blake, Bridget T McInnes. In Proceedings of the Association for Information Science and Technology 56(1), 157, 2019.
• A Literature Based Discovery Visualization System with Hierarchical Clustering and Linking Set Associations. Sam Henry, Ali Panahi, Dayanjan S. Wijesinghe and Bridget T. McInnes. In Proceedings of the AMIA Summits on Translational Science, pp. 582, 2019.
• Association measures for estimating semantic similarity and relatedness between biomedical concepts. Sam Henry, Alex McQuilkin and Bridget T. McInnes. Artificial intelligence in medicine 93, 1-10, 2019.
• Dialect-Specific Models for Automatic Speech Recognition of African American Vernacular English. Rachel Dorn. In Proceedings of the Student Research Workshop associated with The 12th International Conference on Recent Advances in Natural Language Processing, pp. 16-20, 2019.
• Quantifying the Sentiment of Online Drug Reviews. Gabrielle Gurdin, Jorge Vargas, Nastassja A. Lewinski and Bridget T. McInnes. Grace Hopper Celebration, 2019. (poster presentation).
• Unsupervised Text Similarity. Clint Cuffy, Sam Henry and Bridget T. McInnes. The 2019 n2c2/OHNLP Shared-Task and Workshop, Washington, D.C.
• Untapped Potential of Clinical Text for Opioid Surveillance. Amy L. Olex, Tamas Gal, Majid Afshar, Dmitriy Dligach, Niranjan Karnik, Travis Oakes, Brihat Sharma, Meng Xie, Bridget McInnes, Julian Solway, Abel N. Kho, William Cramer, and F. G. Moeller. In Proceedings of the American Medical Informatics Annual Symposium, 2019. (poster).

2018

• Vector representations of multi-word terms for semantic relatedness. Sam Henry, Clint Cuffy and Bridget McInnes. Journal of Biomedical Informatics (JBI), Volume 77, pages 111-119, January 2018.
• Local Ensemble Learning from Imbalanced and Noisy Data for Word Sense Disambiguation. Bartosz Krawczyk and Bridget T. McInnes. Pattern Recognition, 2018.
• SciREL at SemEval-2018 Task 7: A System for Semantic Relation Extraction and Classification. Darshini Mahendran, Chathurika S. Wickramasinghe and Bridget T. McInnces. Proceedings of The 12th International Workshop on Semantic Evaluation, pages 853-857, June 2018.
• Chrono at SemEval-2018 Task 6: A System for Normalizing Temporal Expressions. Amy Olex, Luke Maffey, Nicholas Morgan, and B T. McInnes. Proceedings of The 12th International Workshop on Semantic Evaluation. pages 97-101, June 2018.

2017

• Literature Based Discovery: models, methods and trends. Sam Henry and Bridget McInnes. Journal of Biomedical Informatics (JBI), Volume 74, pages 20-32, October 2017.
• An annotated corpus with nanomedicine and pharmacokinetic parameters. Nastassja Lewinski, Ivan Jimenez and Bridget McInnes. Journal of Nanomedicine. 2017; 12: 7519–7527.
• Semantic association for literature based discovery. Sam Henry and Bridget McInnes. In Proceedings of the American Medical Informatics Association. November 2017. (poster)
• Linking Term Association: ranking implicit terms in literature-based discovery. Sam Henry. In Proceedings of the American Medical Informatics Association Graduate Student NLP-WG Workshop. November 2017. (poster)
• Parsing MetaMap Files in Hadoop. Amy Olex, Albert Cano and Bridget McInnes. In Proceedings of the American Medical Informatics Association. November 2017. (poster)
• Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation. Sam Henry, Clint Cuffy and Bridget McInnes. In Proceedings of the 16th Workshop on Biomedical Natural Language Processing (BioNLP) at the Association of Computational Linguistics, 2017.
• Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second--Order Vectors. Bridget McInnes and Ted Pedersen. In Proceedings of the 16th Workshop on Biomedical Natural Language Processing (BioNLP) at the Association of Computational Linguistics, 2017.
• DroidVisor: An Android Secure Application Recommendation System. Pulkit Rustgi, Carol Fung, Bahman Rashidi, and Bridget McInnes. In Proceedings of the 3rd IEEE/IFIP Workshop on Security for Emerging Distributed Network Technologies (DISSECT), 2017.
• Sentiment Classification from Multi-Class Imbalanced Twitter Data using Binarization. Bartosz Krawczyk, Bridget McInnes and Alberto Cano. In Proceedings of the 12th International Conference on Hybrid Artificial Intelligent Systems (HAIS), 2017.

2016

• Nanomedicine Entity Extraction. Bridget McInnes, Ryan Murphy, Gabrielle Jones, Marley Hodson, Tanin Izadi, Ivan Jimenez, and Nastassja Lewinski. Appears in the American Medical Informatics Symposium (AMIA), November 2016. (poster)
• END, an Annotated Nanomedicine Corpus. Nastassja Lewinski, Marley Hodson, Tanin Izadi, Ivan Jimenez, Ryan Murphy, Gabrielle Jones and Bridget McInnes. Appears in the International Nanotoxicology Congress (nanoTOX), June 2016. (poster)
• VCU at Semeval-2016 Task 14: Evaluating Similarity Measures for Semantic Taxonomy Enrichment. Bridget T. McInnes. Appears in the Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval), June 2016.
• VCU-TSA at Semeval-2016 Task 4: Sentiment Analysis in Twitter. Gerard Briones, Kasun Amarasinghe and Bridget T. McInnes. Appears in the Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval), June 2016.
• Automated Linguistic Analysis of Patients with Dementia and Mild Cognitive Impairment. Ellen Korcovelos, Serguei Pakhomov, and Bridget T. McInnes. Appears in the Proceedings of the Alzheimer’s Association International Conference (AAIC), July 2016. (poster)

2015

• Using natural language processing techniques to inform research on nanotechnology. Nastassja A. Lewinski and Bridget T. McInnes. Beilstein J. Nanotechnol. 2015, 6, 1439-1449
• Evaluating Semantic Similarity and Relatedness over the Semantic Grouping of Clinical Term Pairs. Bridget T. McInnes and Ted Pedersen. Journal of Biomedical Informatics. 2015 Apr; 54:329-336. (data: UMNSRS MayoSRS MiniMayoSRS; code: UMLS-Similarity)
• Challenges and Practical Approaches with Word Sense Disambiguation of Acronyms and Abbreviations in the Clinical Domain. Sungrim Moon, Bridget T. McInnes, and Genevieve B Melton. Healthcare informatics research, 2015, 21 (1), 35-42.

2014

• U-path: An undirected path-based measure of semantic similarity. Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei Pakhomov, and Genevieve B. Melton. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), November 2014. (data: UMNSRS MayoSRS MiniMayoSRS; code: UMLS-Similarity)
• Determining the Difficulty of Word Sense Disambiguation. Bridget T. McInnes and Mark Stevenson. Journal of Biomedical Informatics. 2014 Feb; 47:83-90. (data: MSH-WSD NLM-WSD Abbrev; code: UMLS-Similarity)

2013

• Evaluating Measures of Semantic Similarity and Relatedness to Disambiguate Terms in Biomedical Text. Bridget T. McInnes and Ted Pedersen. Journal of Biomedical Informatics. 2013 December; 46(6):1116-24. (data: MSH-WSD; code: UMLS-SenseRelate)
• UMLS::Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts. Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei Pakhomov, and Genevieve B. Melton. In the Proceedings of the North American Association of Computational Linguistics Demonstration Systems. June 10-12, 2013, Atlanta, Georgia.
• Understanding European Institutional Policy Discourse on the Council of Europe's Convention on Preventing and Combating Violence Against Women through Automated Topic-based Content Analysis. Karen Vogel and Bridget T. McInnes. In the Proceedings of the Midwest Political Science Association Annual Conference, April 11-14, 2013, Chicago, IL. (presentation: pptx, pdf)

2012

• Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries. Robert W. Bill, Ying Liu, Bridget T. McInnes, Genevieve B. Melton, Ted Pedersen, and Serguei Pakhomov. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), November 2012. (code: UMLS-Similarity)
• Using PharmGKB to Train Text Mining Approaches for Identifying Potential Gene Targets for Pharmacogenomic Studies. Serguei Pakhomov, Bridget T. McInnes, Jatinder Lamba, Ying Liu, Genevieve B. Melton, Yogita Ghodke, Neha Bhise, Vishal Lamba and Angela K. Birnbaum. Journal of Biomedical Informatics. 2012 Oct; 45(5):862-9. (code: CuiTools)
• Understanding the Regional and Constitutional Impact of CEDAW Using Automated Content Analysis of Nation-state Constitutions. Karen Vogel and Bridget T. McInnes. Appears in the Proceedings of the Midwest Political Science Association Annual Conference, April 12-15, 2012, Chicago, IL. (presentation: pptx, pdf)
• Measuring the Similarity and Relatedness of Concepts in the Medical Domain : IHI 2012 Tutorial Overview. Ted Pedersen, Serguei Pakhomov, Bridget T. McInnes, and Ying Liu. Appears in the Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, January 28-30, 2012, Miami, FL. (code: UMLS-Similarity)
• Semantic Relatedness Study Using Second Order Co-occurrence Vectors Computed from Biomedical Corpora, UMLS and WordNet. Ying Liu, Bridget T. McInnes, Ted Pedersen, Serguei Pakhomov and Genevieve B. Melton. Appears in the Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, January 28-30, 2012, Miami, FL. (data: UMNSRS; code: UMLS-Similarity)

2011

• Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity. Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei Pakhomov, and Genevieve B. Melton. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA). Oct. 2011, Washington DC. (data: MSHWSD; code: UMLS-SenseRelate; presentation: pptx, pdf)
• Evaluating Measures of Redundancy in Clinical Texts. Rui Zhang, Serguei Pakhomov, Bridget T. McInnes, and Genevieve B. Melton. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA). Oct. 2011, Washington DC. (code: UMLS-Similarity)
• Exploiting MeSH Indexing in MEDLINE to Generate a Data Set for Word Sense Disambiguation. Antonio Jimen-Yepes, Bridget T. McInnes and Alan R. Aronson. BMC Bioinformatics. 2011 Jun 2;12(1):223. (data: MSHWSD)
• Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation. Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei Pakhomov, and Genevieve B. Melton. Appears in the Proceedings of the Fifteenth Conference on Computational Natural Language Learning (CoNLL 2011), June 23-24, 2011, pp. 145 - 153, Portland, Oregon. (data: Abbrev; code: CuiTools)
• 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, and Ying Liu. Appears in the Proceedings of Multiword Expressions: from Parsing and generation to the Real World (MWE), an ACL HLT 2011 Workshop. June 23, 2011, pp. 131 - 133, Portland, Oregon. (Demonstration System). (code: Text::NSP)
• Collocation Analysis for UMLS Knowledge-based Word Sense Disambiguation. Antonio Jimen-Yepes, Bridget T. McInnes and Alan R. Aronson. BMC Bioinformatics. 2011, 12(Suppl 3):S4.
• Towards a Framework for Developing Semantic Relatedness Reference Standards. Serguei V. Pakhomov, Ted Pedersen, Bridget T. McInnes, Genevieve B. Melton, Alexander Ruggieri, and Christopher G. Chute. Journal of Biomedical Informatics. 2011 44(2), 251-265. (data: MiniMayoSRS; code: UMLS-Interface, UMLS-Similarity)

2010

• Semantic Similarity and Relatedness between Clinical Terms: An Experimental Study. Serguei Pakhomov, Bridget T. McInnes, Terrence Adam, Ying Liu, Ted Pedersen and Genevieve B. Melton. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association. Nov 13-17, 2010, Washington, DC. (data: similarity, relatedness)
• Automated Identification of Synonyms in Biomedical Acronym Sense Inventories. Genevieve B. Melton, SungRim Moon, Bridget T. McInnes, and Serguei Pakhomov. Appears in the Proceedings of the Louhi Workshop at the North American Association of Computational Linguistics (NAACL). June 1- 16, 2010, Los Angeles, CA.

2009

• UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. Bridget T. McInnes, Ted Pedersen, and Serguei V. Pakhomov. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, Nov 14-18, 2009, San Francisco, CA. (data: MiniMayoSRS; code: UMLS-Interface, UMLS-Similarity; presentation: pptx, pdf)
• Supervised and Knowledge-based Methods for Disambiguating Terms in Biomedical Text using the UMLS and MetaMap. Bridget T. McInnes, Doctor of Philosophy Dissertation, Department of Computer Science, University of Minnesota, Twin Cities, September, 2009. (code: CuiTools; data: NLM-WSD)

2008

• Using CuiTools to Identify Obesity and its Co-morbidities in Discharge Summaries. Bridget T. McInnes. Appears in the Proceedings of the Second i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data, Nov 7-8, 2008, Washington, DC. (code: CuiTools)
• An Unsupervised Vector Approach to Biomedical Term Disambiguation: Integrating UMLS and Medline. Bridget T. McInnes. Appears in the Proceedings of the Association for Computational Linguistics Student Research Workshop (ACL-SRW) 2008. (code: CuiTools; data: Conflate Data; poster: ppt)

2007

• Using Domain Specific Information for Word Sense Disambiguation. Bridget T. McInnes, Ted Pedersen and John Carlis. Grace Hopper Conference for Women in Computing, October 2007, Orlando, Florida. (code: CuiTools; poster: pdf)
• Using UMLS Concept Unique Identifiers (CUIs) for Word Sense Disambiguation in the Biomedical Domain. Bridget T. McInnes, Ted Pedersen, and John Carlis. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), pages 533-37, Nov. 2007, Chicago, IL. (code: CuiTools; data: NLM-WSD)
• Determining the Syntactic Structure of Medical Terms in Clinical Notes. Bridget T. McInnes, Ted Pedersen, and Serguei V. Pakhomov. Appears in the Proceedings of the BioNLP Workshop at ACL, June 29, 2007, Prague, Czech Republic. (code: NSP)

2006

• TLR at DUC 2006: Approximate tree similarity and a new evaluation regime. F. Shilder and B.T. McInnes. Appears in the Proceedings of the Document Understanding Conference (DUC-2006), New York, NY, USA.
• Word and tree-based similarities for textual entailment. F. Schilder and B.T. McInnes. Appears in the Proceedings of the Second PASCAL Challenges Workshop on Recognising Textual Entailment (RTE-2). 2006.

2005

• TLR at DUC: Tree Similarity. F. Schilder, A. McCulloh, A. Zhou, Thomson Legal and Regulatory, B.T. McInnes, University of Minnesota, Document Understanding Conference (DUC), 2005.
• Resolving Structural Ambiguity of Medical Terms with Statistical Model Fitting. Serguei V. Pakhomov and Bridget T. McInnes, Linguistic Society of America (LSA) Presentation, 2005. (code: NSP)

2004

• Extending the Log-Likelihood Ratio to Improve Collocation Identification. Bridget T. McInnes, Master of Science Thesis, Department of Computer Science, University of Minnesota, Duluth, December, 2004. (code: NSP)
• Incorporating Bigram Statistics to Spelling Correction Tools. Bridget T. McInnes, Serguei V. Pakhomov, Ted Pedersen and Christopher G. Chute. Poster Presentation, MEDINFO 2004. (code: NSP)

2003

• The Duluth Word Alignment System. Bridget T. McInnes and Ted Pedersen. HLT/NAACL 2003, Building and Using Parallel Texts and Beyond Workshop. (code: DWAS)