Using case-level context to classify cancer pathology reports

Shang Gao, Mohammed Alawad, Noah Schaefferkoetter, Lynne Penberthy, Xiao-Cheng Wu, Eric B Durbin, Linda Coyle, Arvind Ramanathan and Georgia Tourassi

PLOS ONE, 2020, vol. 15, issue 5, 1-21

Abstract: Individual electronic health records (EHRs) and clinical reports are often part of a larger sequence—for example, a single patient may generate multiple reports over the trajectory of a disease. In applications such as cancer pathology reports, it is necessary not only to extract information from individual reports, but also to capture aggregate information regarding the entire cancer case based off case-level context from all reports in the sequence. In this paper, we introduce a simple modular add-on for capturing case-level context that is designed to be compatible with most existing deep learning architectures for text classification on individual reports. We test our approach on a corpus of 431,433 cancer pathology reports, and we show that incorporating case-level context significantly boosts classification accuracy across six classification tasks—site, subsite, laterality, histology, behavior, and grade. We expect that with minimal modifications, our add-on can be applied towards a wide range of other clinical text-based tasks.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0232840

DOI: 10.1371/journal.pone.0232840

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