The objective of this work is to develop an automated diagnosis system that is able to predict the probability of appendicitis given a free-text emergency department (ED) note and additional structured information (e.g., lab test results). Our clinical corpus consists of about 180,000 ED notes based on ten years of patient visits to the Accident and Emergency (A&E) Department of the National University Hospital (NUH), Singapore. We propose a novel neural network approach that learns to diagnose acute appendicitis based on doctors’ free-text ED notes without any feature engineering. On a test set of 2,000 ED notes with equal number of appendicitis (positive) and non-appendicitis (negative) diagnosis and in which all the negative ED notes only consist of abdominal-related diagnosis, our model is able to achieve a promising F_0.5-score of 0.895 while ED doctors achieve F_0.5-score of 0.900. Visualization shows that our model is able to learn important features, signs, and symptoms of patients from unstructured free-text ED notes, which will help doctors to make better diagnosis.

The issue of privacy has always been a concern when clinical texts are used for research purposes. Personal health information (PHI) (such as name and identification number) needs to be removed so that patients cannot be identified. Manual anonymization is not feasible due to the large number of clinical texts to be anonymized. In this paper, we tackle the task of anonymizing clinical texts written in sentence fragments and which frequently contain symbols, abbreviations, and misspelled words. Our clinical texts therefore differ from those in the i2b2 shared tasks which are in prose form with complete sentences. Our clinical texts are also part of a structured database which contains patient name and identification number in structured fields. As such, we formulate our anonymization task as spelling variant detection, exploiting patients’ personal information in the structured fields to detect their spelling variants in clinical texts. We successfully anonymized clinical texts consisting of more than 200 million words, using minimum edit distance and regular expression patterns.