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Mayo Clinic NLP System for Patient Smoking Status Identification

Authors: Guergana K, Savova; Philip V, Ogren; Patrick H, Duffy; James D, Buntrock; Christopher G, Chute;

Mayo Clinic NLP System for Patient Smoking Status Identification

Abstract

This article describes our system entry for the 2006 I2B2 contest "Challenges in Natural Language Processing for Clinical Data" for the task of identifying the smoking status of patients. Our system makes the simplifying assumption that patient-level smoking status determination can be achieved by accurately classifying individual sentences from a patient's record. We created our system with reusable text analysis components built on the Unstructured Information Management Architecture and Weka. This reuse of code minimized the development effort related specifically to our smoking status classifier. We report precision, recall, F-score, and 95% exact confidence intervals for each metric. Recasting the classification task for the sentence level and reusing code from other text analysis projects allowed us to quickly build a classification system that performs with a system F-score of 92.64 based on held-out data tests and of 85.57 on the formal evaluation data. Our general medical natural language engine is easily adaptable to a real-world medical informatics application. Some of the limitations as applied to the use-case are negation detection and temporal resolution.

Related Organizations
Keywords

Databases, Factual, Medical Records Systems, Computerized, Smoking, Humans, Classification, Natural Language Processing

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    97
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 1%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
Powered by OpenAIRE graph
Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
97
Top 10%
Top 1%
Top 10%
bronze