Dataset Information

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

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 nontechnical, 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 (CRFs). ADRMine utilizes a variety of features, including a novel feature for modeling words' semantic similarities. The similarities are modeled by clustering words based on unsupervised, pretrained 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.

SUBMITTER: Nikfarjam A

PROVIDER: S-EPMC4457113 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Nikfarjam Azadeh A Sarker Abeed A O'Connor Karen K Ginn Rachel R Gonzalez Graciela G

Journal of the American Medical Informatics Association : JAMIA 20150309 3

<h4>Objective</h4>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 nontechnical, descriptive, and challenging to extract. There has been limited progress in addressing th ...[more]

PMID: 25755127

Similar Datasets

Project description:BackgroundKnowledge about adverse drug reactions (ADRs) in the population is limited because of underreporting, which hampers surveillance and assessment of drug safety. Therefore, gathering accurate information that can be retrieved from clinical notes about the incidence of ADRs is of great relevance. However, manual labeling of these notes is time-consuming, and automatization can improve the use of free-text clinical notes for the identification of ADRs. Furthermore, tools for language processing in languages other than English are not widely available.ObjectiveThe aim of this study is to design and evaluate a method for automatic extraction of medication and Adverse Drug Reaction Identification in Clinical Notes (ADRIN).MethodsDutch free-text clinical notes (N=277,398) and medication registrations (N=499,435) from the Cardiology Centers of the Netherlands database were used. All clinical notes were used to develop word embedding models. Vector representations of word embedding models and string matching with a medical dictionary (Medical Dictionary for Regulatory Activities [MedDRA]) were used for identification of ADRs and medication in a test set of clinical notes that were manually labeled. Several settings, including search area and punctuation, could be adjusted in the prototype to evaluate the optimal version of the prototype.ResultsThe ADRIN method was evaluated using a test set of 988 clinical notes written on the stop date of a drug. Multiple versions of the prototype were evaluated for a variety of tasks. Binary classification of ADR presence achieved the highest accuracy of 0.84. Reduced search area and inclusion of punctuation improved performance, whereas incorporation of the MedDRA did not improve the performance of the pipeline.ConclusionsThe ADRIN method and prototype are effective in recognizing ADRs in Dutch clinical notes from cardiac diagnostic screening centers. Surprisingly, incorporation of the MedDRA did not result in improved identification on top of word embedding models. The implementation of the ADRIN tool may help increase the identification of ADRs, resulting in better care and saving substantial health care costs.

Project description:BackgroundThe exponential growth of location-based social media (LBSM) data has ushered in novel prospects for investigating the urban food environment in health geography research. However, previous studies have primarily relied on word dictionaries with a limited number of food words and employed common-sense categorizations to determine the healthiness of those words. To enhance the analysis of the urban food environment using LBSM data, it is crucial to develop a more comprehensive list of food-related words. Within the context, this study delves into the exploration of expanding food-related words along with their associated energy densities.MethodsThis study addresses the aforementioned research gap by introducing a novel methodology for expanding the food-related word dictionary and predicting energy densities. Seed words are generated from official and crowdsourced food composition databases, and new food words are discovered by clustering food words within the word embedding space using the Gaussian mixture model. Machine learning models are employed to predict the energy density classifications of these food words based on their feature vectors. To ensure a thorough exploration of the prediction problem, ten widely used machine learning models are evaluated.ResultsThe approach successfully expands the food-related word dictionary and accurately predicts food energy density (reaching 91.62%.). Through a comparison of the newly expanded dictionary with the initial seed words and an analysis of Yelp reviews in the city of Toronto, we observe significant improvements in identifying food words and gaining a deeper understanding of the food environment.ConclusionsThis study proposes a novel method to expand food-related vocabulary and predict the food energy density based on machine learning and word embedding. This method makes a valuable contribution to building a more comprehensive list of food words that can be used in geography and public health studies by mining geotagged social media data.

Dataset Information

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

Objective

Methods

Results

Conclusion

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets