MARIE: A context-aware term mapping with string matching and embedding vectors

Abstract

With growing interest in machine learning, text standardization is becoming an increasingly important aspect of data pre-processing within biomedical communities. As performances of machine learning algorithms are affected by both the amount and the quality of their training data, effective data standardization is needed to guarantee consistent data integrity. Furthermore, biomedical organizations, depending on their geographical locations or affiliations, rely on different sets of text standardization in practice. To facilitate easier machine learning-related collaborations between these organizations, an effective yet practical text data standardization method is needed. In this paper, we introduce MARIE (a context-aware term mapping method with string matching and embedding vectors), an unsupervised learning-based tool, to find standardized clinical terminologies for queries, such as a hospital’s own codes. By incorporating both string matching methods and term embedding vectors generated by BioBERT (bidirectional encoder representations from transformers for biomedical text mining), it utilizes both structural and contextual information to calculate similarity measures between source and target terms. Compared to previous term mapping methods, MARIE shows improved mapping accuracy. Furthermore, it can be easily expanded to incorporate any string matching or term embedding methods. Without requiring any additional model training, it is not only effective, but also a practical term mapping method for text data standardization and pre-processing.