Extracting Lifestyle Factors for Alzheimer's Disease from Clinical Notes Using Deep Learning with Weak Supervision

• URL: http://arxiv.org/abs/2101.09244v2
• Date: Mon, 25 Jan 2021 03:42:00 GMT
• Title: Extracting Lifestyle Factors for Alzheimer's Disease from Clinical Notes Using Deep Learning with Weak Supervision
• Authors: Zitao Shen, Yoonkwon Yi, Anusha Bompelli, Fang Yu, Yanshan Wang, Rui Zhang
• Abstract summary: The objective of the study was to demonstrate the feasibility of natural language processing (NLP) models to classify lifestyle factors. We performed two case studies: physical activity and excessive diet, in order to validate the effectiveness of BERT models. The proposed approach leveraging weak supervision could significantly increase the sample size.
• Score: 9.53786612243512
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Since no effective therapies exist for Alzheimer's disease (AD), prevention has become more critical through lifestyle factor changes and interventions. Analyzing electronic health records (EHR) of patients with AD can help us better understand lifestyle's effect on AD. However, lifestyle information is typically stored in clinical narratives. Thus, the objective of the study was to demonstrate the feasibility of natural language processing (NLP) models to classify lifestyle factors (e.g., physical activity and excessive diet) from clinical texts. We automatically generated labels for the training data by using a rule-based NLP algorithm. We conducted weak supervision for pre-trained Bidirectional Encoder Representations from Transformers (BERT) models on the weakly labeled training corpus. These models include the BERT base model, PubMedBERT(abstracts + full text), PubMedBERT(only abstracts), Unified Medical Language System (UMLS) BERT, Bio BERT, and Bio-clinical BERT. We performed two case studies: physical activity and excessive diet, in order to validate the effectiveness of BERT models in classifying lifestyle factors for AD. These models were compared on the developed Gold Standard Corpus (GSC) on the two case studies. The PubmedBERT(Abs) model achieved the best performance for physical activity, with its precision, recall, and F-1 scores of 0.96, 0.96, and 0.96, respectively. Regarding classifying excessive diet, the Bio BERT model showed the highest performance with perfect precision, recall, and F-1 scores. The proposed approach leveraging weak supervision could significantly increase the sample size, which is required for training the deep learning models. The study also demonstrates the effectiveness of BERT models for extracting lifestyle factors for Alzheimer's disease from clinical notes.

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