Comparing Variation in Tokenizer Outputs Using a Series of Problematic and Challenging Biomedical Sentences

Abstract: Background & Objective: Biomedical text data are increasingly available for research. Tokenization is an initial step in many biomedical text mining pipelines. Tokenization is the process of parsing an input biomedical sentence (represented as a digital character sequence) into a discrete set of word/token symbols, which convey focused semantic/syntactic meaning. The objective of this study is to explore variation in tokenizer outputs when applied across a series of challenging biomedical sentences. Method: Diaz [2015] introduce 24 challenging example biomedical sentences for comparing tokenizer performance. In this study, we descriptively explore variation in outputs of eight tokenizers applied to each example biomedical sentence. The tokenizers compared in this study are the NLTK white space tokenizer, the NLTK Penn Tree Bank tokenizer, Spacy and SciSpacy tokenizers, Stanza/Stanza-Craft tokenizers, the UDPipe tokenizer, and R-tokenizers. Results: For many examples, tokenizers performed similarly effectively; however, for certain examples, there were meaningful variation in returned outputs. The white space tokenizer often performed differently than other tokenizers. We observed performance similarities for tokenizers implementing rule-based systems (e.g. pattern matching and regular expressions) and tokenizers implementing neural architectures for token classification. Oftentimes, the challenging tokens resulting in the greatest variation in outputs, are those words which convey substantive and focused biomedical/clinical meaning (e.g. x-ray, IL-10, TCR/CD3, CD4+ CD8+, and (Ca2+)-regulated). Conclusion: When state-of-the-art, open-source tokenizers from Python and R were applied to a series of challenging biomedical example sentences, we observed subtle variation in the returned outputs.