Automatically Detecting Failures in Natural Language Processing Tools for Online Community Text.
BACKGROUND
The prevalence and value of patient-generated health text are increasing, but processing such text remains problematic. Although existing biomedical natural language processing (NLP) tools are appealing, most were developed to process clinician- or researcher-generated text, such as clinical notes or journal articles. In addition to being constructed for different types of text, other challenges of using existing NLP include constantly changing technologies, source vocabularies, and characteristics of text. These continuously evolving challenges warrant the need for applying low-cost systematic assessment. However, the primarily accepted evaluation method in NLP, manual annotation, requires tremendous effort and time.


OBJECTIVE
The primary objective of this study is to explore an alternative approach-using low-cost, automated methods to detect failures (eg, incorrect boundaries, missed terms, mismapped concepts) when processing patient-generated text with existing biomedical NLP tools. We first characterize common failures that NLP tools can make in processing online community text. We then demonstrate the feasibility of our automated approach in detecting these common failures using one of the most popular biomedical NLP tools, MetaMap.


METHODS
Using 9657 posts from an online cancer community, we explored our automated failure detection approach in two steps: (1) to characterize the failure types, we first manually reviewed MetaMap's commonly occurring failures, grouped the inaccurate mappings into failure types, and then identified causes of the failures through iterative rounds of manual review using open coding, and (2) to automatically detect these failure types, we then explored combinations of existing NLP techniques and dictionary-based matching for each failure cause. Finally, we manually evaluated the automatically detected failures.


RESULTS
From our manual review, we characterized three types of failure: (1) boundary failures, (2) missed term failures, and (3) word ambiguity failures. Within these three failure types, we discovered 12 causes of inaccurate mappings of concepts. We used automated methods to detect almost half of 383,572 MetaMap's mappings as problematic. Word sense ambiguity failure was the most widely occurring, comprising 82.22% of failures. Boundary failure was the second most frequent, amounting to 15.90% of failures, while missed term failures were the least common, making up 1.88% of failures. The automated failure detection achieved precision, recall, accuracy, and F1 score of 83.00%, 92.57%, 88.17%, and 87.52%, respectively.


CONCLUSIONS
We illustrate the challenges of processing patient-generated online health community text and characterize failures of NLP tools on this patient-generated health text, demonstrating the feasibility of our low-cost approach to automatically detect those failures. Our approach shows the potential for scalable and effective solutions to automatically assess the constantly evolving NLP tools and source vocabularies to process patient-generated text.
Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, United States. alpark1216@gmail.com.
Albert
http://orcid.org/0000-0002-2419-0131
A
Park
Andrea L
http://orcid.org/0000-0003-4932-7314
AL
Hartzler
Jina
http://orcid.org/0000-0001-5811-9256
J
Huh
David W
http://orcid.org/0000-0001-5882-828X
DW
McDonald
Wanda
http://orcid.org/0000-0003-4035-0198
W
Pratt
D001330:Electronic Data Processing; D006801:Humans; D020407:Internet; D009323:Natural Language Processing
UMLS; automatic data processing; information extraction; natural language processing; quantitative evaluation