What Do Patients Say About Their Disease Symptoms? Deep Multilabel Text Classification With Human-in-the-Loop Curation for Automatic Labeling of Patient Self Reports of Problems

Abstract

The USA Food and Drug Administration has accorded increasing importance to patient-reported problems in clinical and research settings. In this paper, we explore one of the largest online datasets comprising 170,141 open-ended self-reported responses (called "verbatims") from patients with Parkinson's (PwPs) to questions about what bothers them about their Parkinson's Disease and how it affects their daily functioning, also known as the Parkinson's Disease Patient Report of Problems. Classifying such verbatims into multiple clinically relevant symptom categories is an important problem and requires multiple steps - expert curation, a multi-label text classification (MLTC) approach and large amounts of labelled training data. Further, human annotation of such large datasets is tedious and expensive. We present a novel solution to this problem where we build a baseline dataset using 2,341 (of the 170,141) verbatims annotated by nine curators including clinical experts and PwPs. We develop a rules based linguistic-dictionary using NLP techniques and graph database-based expert phrase-query system to scale the annotation to the remaining cohort generating the machine annotated dataset, and finally build a Keras-Tensorflow based MLTC model for both datasets. The machine annotated model significantly outperforms the baseline model with a F1-score of 95% across 65 symptom categories on a held-out test set.