Olivier Bodenreider


Evaluating Biomedical Word Embeddings for Vocabulary Alignment at Scale in the UMLS Metathesaurus Using Siamese Networks
Goonmeet Bajaj | Vinh Nguyen | Thilini Wijesiriwardene | Hong Yung Yip | Vishesh Javangula | Amit Sheth | Srinivasan Parthasarathy | Olivier Bodenreider
Proceedings of the Third Workshop on Insights from Negative Results in NLP

Recent work uses a Siamese Network, initialized with BioWordVec embeddings (distributed word embeddings), for predicting synonymy among biomedical terms to automate a part of the UMLS (Unified Medical Language System) Metathesaurus construction process. We evaluate the use of contextualized word embeddings extracted from nine different biomedical BERT-based models for synonym prediction in the UMLS by replacing BioWordVec embeddings with embeddings extracted from each biomedical BERT model using different feature extraction methods. Finally, we conduct a thorough grid search, which prior work lacks, to find the best set of hyperparameters. Surprisingly, we find that Siamese Networks initialized with BioWordVec embeddings still out perform the Siamese Networks initialized with embedding extracted from biomedical BERT model.


From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches
Alan R. Aronson | Olivier Bodenreider | Dina Demner-Fushman | Kin Wah Fung | Vivian K. Lee | James G. Mork | Aurélie Névéol | Lee Peters | Willie J. Rogers
Biological, translational, and clinical language processing


Exploring Adjectival Modification in Biomedical Discourse Across Two Genres
Olivier Bodenreider | Serguei V. Pakhomov
Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine


Unsupervised,corpus-based method for extending a biomedical terminology
Olivier Bodenreider | Thomas Rindflesch | Anita Burgun
Proceedings of the ACL-02 Workshop on Natural Language Processing in the Biomedical Domain