Diego Lab : Biomedical Informatics Lab at ASU


Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features

Azadeh Nikfarjam, Abeed Sarker, Karen O Connor, Rachel Ginn, Graciela Gonzalez

Department of Biomedical Informatics, Arizona State University, Scottsdale, USA

 

Abstract

    Objective:
    Social media is becoming increasingly popular as a platform for sharing personal health-related information. This information can be utilized for public health monitoring tasks, particularly for pharmacovigilance, via the use of Natural Language Processing (NLP) techniques. However, the language in social media is highly informal, and user-expressed medical concepts are often non-technical, descriptive, and challenging to extract. There has been limited progress in addressing these challenges, and thus far, advanced machine learning-based NLP techniques have been underutilized. Our objective is to design a machine learning-based approach to extract mentions of adverse drug reactions (ADRs) from highly informal text in social media.
    Methods:
    We introduce ADRMine, a machine learning-based concept extraction system that uses Conditional Random Fields (CRF). ADRMine utilizes a variety of features, including a novel feature for modeling words semantic similarities. The similarities are modeled by clustering the words based on unsupervised, pre-trained word representation vectors (embeddings), generated from unlabeled user posts in social media using a deep learning technique.
    Results:
    ADRMine outperforms several strong baseline systems in the ADR extraction task by achieving an F-measure of 0.82. Feature analysis demonstrates that the proposed word cluster features significantly improve extraction performance.
    Conclusion:
    It is possible to extract complex medical concepts, with relatively high performance, from informal, user-generated content. Our approach is particularly scalable, suitable for social media mining, as it relies on large volumes of unlabeled data, thus diminishing the need for large, annotated training data sets.

Last Update: 11, Mar 2015

 

Quick Download:
Paper (PDF)
ADR Lexicon
Drug names
Word clusters
Word Embeddings
Downloads:
Twitter Corpus
ADRMine

 

Contact Information:
Azadeh Nikfarjam
Email:
anikfarj@asu.edu
Phone:
+1 480-295-9138