Rule-based and Machine Learning Hybrid System for Patient Cohort Selection

Rui Antunes, João Figueira Silva, Arnaldo Pereira, Sérgio Matos

2019

Abstract

Clinical trials play a critical role in medical studies. However, identifying and selecting cohorts for such trials can be a troublesome task since patients must match a set of complex pre-determined criteria. Patient selection requires a manual analysis of clinical narratives in patients’ records, which is a time-consuming task for medical researchers. In this work, natural language processing (NLP) techniques were used to perform automatic patient cohort selection. The approach herein presented was developed and tested on the 2018 n2c2 Track 1 Shared-Task dataset where each patient record is annotated with 13 selection criteria. The resulting hybrid approach is based on heuristics and machine learning and attained a micro-average and macro-average F1-score of 0.8844 and 0.7271, respectively, in the n2c2 test set. Part of the source code resultant from this work is available at https://github.com/ruiantunes/2018-n2c2-track-1/.

Paper Citation

in Harvard Style

Antunes R., Silva J., Pereira A. and Matos S. (2019). Rule-based and Machine Learning Hybrid System for Patient Cohort Selection. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 5: HEALTHINF; ISBN 978-989-758-353-7, SciTePress, pages 59-67. DOI: 10.5220/0007349300590067

in Bibtex Style

@conference{healthinf19,
author={Rui Antunes and João Figueira Silva and Arnaldo Pereira and Sérgio Matos},
title={Rule-based and Machine Learning Hybrid System for Patient Cohort Selection},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 5: HEALTHINF},
year={2019},
pages={59-67},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007349300590067},
isbn={978-989-758-353-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 5: HEALTHINF
TI - Rule-based and Machine Learning Hybrid System for Patient Cohort Selection
SN - 978-989-758-353-7
AU - Antunes R.
AU - Silva J.
AU - Pereira A.
AU - Matos S.
PY - 2019
SP - 59
EP - 67
DO - 10.5220/0007349300590067
PB - SciTePress