| 2022 | WWW | Exploring Representations for Singular and Multi-Concept Relations for Biomedical Named Entity Normalization. | Clint Cuffy, Evan French, Sophia Fehrmann, Bridget T. McInnes |
| 2022 | WWW | The International Workshop on Semantics-enabled Biomedical Literature Analytics (SeBiLAn). | Faezeh Ensan, Halil Kilicoglu, Bridget T. McInnes, Lucy Lu Wang |
| 2022 | WWW | Graph Convolutional Networks for Chemical Relation Extraction. | Darshini Mahendran, Christina Tang, Bridget T. McInnes |
| 2020 | AMIA | Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context. | Paul Barry, Sam Henry, Meliha Yetisgen, Bridget T. McInnes, zlem Uzuner |
| 2019 | AMIA | Improving Accuracy of Patient Speech Transcription Using Dialect-Specific Automatic Speech Recognition Models. | Rachel Dorn, Scott Vrana, Bridget T. McInnes |
| 2019 | AMIA | Untapped Potential of Clinical Text for Opioid Surveillance. | Amy L. Olex, Tams Gl, 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 |
| 2019 | NAACL | NLP Whack-A-Mole: Challenges in Cross-Domain Temporal Expression Extraction. | Amy L. Olex, Luke Maffey, Bridget T. McInnes |
| 2017 | AMIA | Semantic Association for Literature Based Discovery. | Sam Henry, Bridget T. McInnes |
| 2017 | AMIA | Parsing MetaMap Files in Hadoop. | Amy L. Olex, Alberto Cano, Bridget T. McInnes |
| 2017 | HAIS | Sentiment Classification from Multi-class Imbalanced Twitter Data Using Binarization. | Bartosz Krawczyk, Bridget T. McInnes, Alberto Cano |
| 2017 | IM | DroidVisor: An Android secure application recommendation system. | Pulkit Rustgi, Carol J. Fung, Bahman Rashidi, Bridget T. McInnes |
| 2016 | AMIA | Nanomedicine Entity Extraction. | Bridget T. McInnes, Ryan Murphy, Gabrielle N. Jones, Marley Hodson, Tanin Izadi, Ivan Jimenez, Nastassja Lewinski |
| 2014 | AMIA | U-path: An undirected path-based measure of semantic similarity. | Bridget T. McInnes, Ted Pedersen, Ying Liu, Genevieve B. Melton, Serguei V. S. Pakhomov |
| 2013 | NAACL | UMLS: : Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts. | Bridget T. McInnes, Ted Pedersen, Serguei V. S. Pakhomov, Ying Liu, Genevieve Melton-Meaux |
| 2012 | AMIA | Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries. | Robert Bill, Ying Liu, Bridget T. McInnes, Genevieve B. Melton, Ted Pedersen, Serguei V. S. Pakhomov |
| 2011 | CoNLL | Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation. | Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei V. S. Pakhomov, Genevieve B. Melton |
| 2009 | AMIA | UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. | Bridget T. McInnes, Ted Pedersen, Serguei V. S. Pakhomov |
| 2008 | ACL | An Unsupervised Vector Approach to Biomedical Term Disambiguation: Integrating UMLS and Medline. | Bridget T. McInnes |
| 2007 | AMIA | Using UMLS Concept Unique Identifiers (CUIs) for Word Sense Disambiguation in the Biomedical Domain. | Bridget T. McInnes, Ted Pedersen, John Carlis |
| 2003 | NAACL | The Duluth Word Alignment System. | Bridget T. McInnes, Ted Pedersen |