Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach

Background: Electronic health records store large amounts of patient clinical data. Despite efforts to structure patient data, clinical notes containing rich patient information remain stored as free text, greatly limiting its exploitation. This includes family history, which is highly relevant for applications such as diagnosis and prognosis. Objective: This study aims to develop automatic strategies for annotating family history information in clinical notes, focusing not only on the extraction of relevant entities such as family members and disease mentions but also on the extraction of relations between the identified entities. Methods: This study extends a previous contribution for the 2019 track on family history extraction from national natural language processing clinical challenges by improving a previously developed rule-based engine, using deep learning (DL) approaches for the extraction of entities from clinical notes, and combining both approaches in a hybrid end-to-end system capable of successfully extracting family member and observation entities and the relations between those entities. Furthermore, this study analyzes the impact of factors such as the use of external resources and different types of embeddings in the performance of DL models. Results: The approaches developed were evaluated in a first task regarding entity extraction and in a second task concerning relation extraction. The proposed DL approach improved observation extraction, obtaining F-1 scores of 0.8688 and 0.7907 in the training and test sets, respectively. However, DL approaches have limitations in the extraction of family members. The rule-based engine was adjusted to have higher generalizing capability and achieved family member extraction F-1 scores of 0.8823 and 0.8092 in the training and test sets, respectively. The resulting hybrid system obtained F-1 scores of 0.8743 and 0.7979 in the training and test sets, respectively. For the second task, the original evaluator was adjusted to perform a more exact evaluation than the original one, and the hybrid system obtained F-1 scores of 0.6480 and 0.5082 in the training and test sets, respectively. Conclusions: We evaluated the impact of several factors on the performance of DL models, and we present an end-to-end system for extracting family history information from clinical notes, which can help in the structuring and reuse of this type of information. The final hybrid solution is provided in a publicly available code repository.