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

Journal of the American Medical Informatics Association : JAMIA
Azadeh NikfarjamGraciela Gonzalez

Abstract

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. 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. ADRMine outperforms several strong baseline systems in the ADR extracti...Continue Reading

References

Jul 3, 2004·BMJ : British Medical Journal·Munir PirmohamedAlasdair M Breckenridge
Mar 1, 2006·BMC Bioinformatics·Richard Tzong-Han TsaiWen-Lian Hsu
May 13, 2006·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Lorna Hazell, Saad A W Shakir
Sep 18, 2007·European Journal of Clinical Pharmacology·E C G van GeffenE R Heerdink
Mar 1, 2008·Journal of the American Medical Informatics Association : JAMIA·Qing Zeng-TreitlerAziz Boxwala
Oct 9, 2009·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Lise AagaardEbba Holme Hansen
Jan 21, 2010·Molecular Systems Biology·Michael KuhnPeer Bork
Feb 10, 2011·Bioinformatics·Minlie HuangXiaoyan Zhu
Aug 9, 2011·Journal of Biomedical Informatics·Adrian BentonJohn H Holmes
May 3, 2012·Clinical Pharmacology and Therapeutics·R HarpazC Friedman
Dec 22, 2012·Journal of Biomedical Semantics·Harsha GurulingappaLuca Toldo
Mar 8, 2013·Journal of the American Medical Informatics Association : JAMIA·Ryen W WhiteEric Horvitz
Dec 19, 2013·Journal of Pharmacology & Pharmacotherapeutics·Janet SultanaGianluca Trifirò
Sep 12, 2014·Database : the Journal of Biological Databases and Curation·Ehsan EmadzadehGraciela Gonzalez

❮ Previous
Next ❯

Citations

Jan 23, 2016·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Gregory E PowellNabarun Dasgupta
Jun 21, 2015·Journal of Medical Internet Research·Rachel Lynn KendraLisa Gandy
May 4, 2016·Database : the Journal of Biological Databases and Curation·Saber A AkhondiJan A Kors
Jul 2, 2016·Journal of Biomedical Informatics·Ioannis KorkontzelosGraciela H Gonzalez
Aug 9, 2016·Journal of the American Medical Informatics Association : JAMIA·Kirk RobertsPatricia Flatley Brennan
Nov 2, 2015·Journal of the American Medical Informatics Association : JAMIA·Chen LinGuergana K Savova
Aug 15, 2015·British Journal of Clinical Pharmacology·Su GolderYoon K Loke
Jul 7, 2015·British Journal of Clinical Pharmacology·Richard SloaneMunir Pirmohamed
Sep 20, 2019·BMC Bioinformatics·Tongxuan ZhangYijia Zhang
Nov 30, 2018·PloS One·Jorge Carrillo-de-AlbornozLaura Plaza
Oct 3, 2018·Journal of the American Medical Informatics Association : JAMIA·Abeed SarkerGraciela Gonzalez-Hernandez
Oct 5, 2018·Expert Opinion on Drug Safety·Irma ConvertinoMarco Tuccori
May 10, 2017·Briefings in Bioinformatics·Riccardo MiottoJoel T Dudley
Jun 4, 2019·Frontiers in Pharmacology·Pantelis NatsiavasVassilis Koutkias
Nov 7, 2019·Briefings in Bioinformatics·Tianlin ZhangYing Liu
Jan 4, 2017·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Carrie E PierceNabarun Dasgupta
Feb 7, 2019·Journal of Medical Internet Research·Chi-Shiang WangJung-Hsien Chiang
Jul 16, 2019·Genomics & Informatics·Mina GachlooJingbo Xia
Feb 27, 2017·JMIR Public Health and Surveillance·Shinichi MatsudaYoichiro Takahashi
Nov 1, 2017·Journal of Medical Internet Research·Abeed SarkerGraciela Gonzalez
Apr 25, 2019·Computational and Mathematical Methods in Medicine·Voldemaras ŽitkusMarcin Woźniak
May 5, 2017·JMIR Public Health and Surveillance·Nestor AlvaroNigel Collier
May 11, 2018·JMIR Public Health and Surveillance·Danushka BollegalaMunir Pirmohamed
Jul 9, 2020·Genomics & Informatics·Ramya Tekumalla, Juan M Banda
Jun 15, 2019·Journal of the American Medical Informatics Association : JAMIA·Meizhi JuSophia Ananiadou
Aug 15, 2018·Journal of Cheminformatics·Paul ThompsonSophia Ananiadou
Sep 1, 2018·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Karen SmithGraciela Gonzalez-Hernandez
Apr 14, 2019·Journal of the American Medical Informatics Association : JAMIA·Anne CocosAaron J Masino
May 16, 2019·Journal of the American Medical Informatics Association : JAMIA·Arjun MaggeGraciela Gonzalez-Hernandez
Nov 9, 2019·BMC Medical Informatics and Decision Making·Jia RongHua Wang
Oct 12, 2018·Clinical Pharmacology and Therapeutics·Juergen SchmiderPatrick M Caubel
Jan 17, 2019·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Abhyuday JagannathaHong Yu
Jan 17, 2019·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Alec B ChapmanOlga V Patterson
Feb 13, 2019·Psychological Medicine·Adrian B R ShatteSamantha J Teague

❮ Previous
Next ❯

Software Mentioned

DailyStrength
Ubuntu
SIDER
DS
MedHelp
Word2vec
COSTART
MetaMap
PatientsLikeMe
CRFsuite

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.