Scoring Disease-Medication Associations using Advanced NLP, Machine Learning, and Multiple Content Sources

Bharath Dandala, Murthy Devarakonda, Mihaela Bornea, Christopher Nielson


Abstract
Effective knowledge resources are critical for developing successful clinical decision support systems that alleviate the cognitive load on physicians in patient care. In this paper, we describe two new methods for building a knowledge resource of disease to medication associations. These methods use fundamentally different content and are based on advanced natural language processing and machine learning techniques. One method uses distributional semantics on large medical text, and the other uses data mining on a large number of patient records. The methods are evaluated using 25,379 unique disease-medication pairs extracted from 100 de-identified longitudinal patient records of a large multi-provider hospital system. We measured recall (R), precision (P), and F scores for positive and negative association prediction, along with coverage and accuracy. While individual methods performed well, a combined stacked classifier achieved the best performance, indicating the limitations and unique value of each resource and method. In predicting positive associations, the stacked combination significantly outperformed the baseline (a distant semi-supervised method on large medical text), achieving F scores of 0.75 versus 0.55 on the pairs seen in the patient records, and F scores of 0.69 and 0.35 on unique pairs.
Anthology ID:
W16-5114
Volume:
Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM2016)
Month:
December
Year:
2016
Address:
Osaka, Japan
Venue:
WS
SIG:
Publisher:
The COLING 2016 Organizing Committee
Note:
Pages:
125–133
Language:
URL:
https://www.aclweb.org/anthology/W16-5114
DOI:
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PDF:
http://aclanthology.lst.uni-saarland.de/W16-5114.pdf