Leveraging medical context to recommend semantically similar terms for chart reviews

BMC Medical Informatics and Decision Making

Cheng Ye¹  Daniel Fabbri²  Bradley A. Malin³ 

[1] Department of Computer Science, Vanderbilt University, PMB 351679, 2301 Vanderbilt Place, 37235-1679, Nashville, TN, USA;Department of Computer Science, Vanderbilt University, PMB 351679, 2301 Vanderbilt Place, 37235-1679, Nashville, TN, USA;Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA;Department of Computer Science, Vanderbilt University, PMB 351679, 2301 Vanderbilt Place, 37235-1679, Nashville, TN, USA;Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA;Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA;

关键词: Electronic medical records;    Data science;    Chart reviews;    Clinically similar terms;    Vector space model;   

DOI  :  10.1186/s12911-021-01724-2

来源: Springer

【 摘 要 】

BackgroundInformation retrieval (IR) help clinicians answer questions posed to large collections of electronic medical records (EMRs), such as how best to identify a patient’s cancer stage. One of the more promising approaches to IR for EMRs is to expand a keyword query with similar terms (e.g., augmenting cancer with mets). However, there is a large range of clinical chart review tasks, such that fixed sets of similar terms is insufficient. Current language models, such as Bidirectional Encoder Representations from Transformers (BERT) embeddings, do not capture the full non-textual context of a task. In this study, we present new methods that provide similar terms dynamically by adjusting with the context of the chart review task.MethodsWe introduce a vector space for medical-context in which each word is represented by a vector that captures the word’s usage in different medical contexts (e.g., how frequently cancer is used when ordering a prescription versus describing family history) beyond the context learned from the surrounding text. These vectors are transformed into a vector space for customizing the set of similar terms selected for different chart review tasks. We evaluate the vector space model with multiple chart review tasks, in which supervised machine learning models learn to predict the preferred terms of clinically knowledgeable reviewers. To quantify the usefulness of the predicted similar terms to a baseline of standard word2vec embeddings, we measure (1) the prediction performance of the medical-context vector space model using the area under the receiver operating characteristic curve (AUROC) and (2) the labeling effort required to train the models.ResultsThe vector space outperformed the baseline word2vec embeddings in all three chart review tasks with an average AUROC of 0.80 versus 0.66, respectively. Additionally, the medical-context vector space significantly reduced the number of labels required to learn and predict the preferred similar terms of reviewers. Specifically, the labeling effort was reduced to 10% of the entire dataset in all three tasks.ConclusionsThe set of preferred similar terms that are relevant to a chart review task can be learned by leveraging the medical context of the task.

【 授权许可】

CC BY