Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction Mention Extraction

Social media is an useful platform to share health-related information due to its vast reach. This makes it a good candidate for public-health monitoring tasks, specifically for pharmacovigilance. We study the problem of extraction of Adverse-Drug-Reaction (ADR) mentions from social media, particularly from twitter. Medical information extraction from social media is challenging, mainly due to short and highly information nature of text, as compared to more technical and formal medical reports. Current methods in ADR mention extraction relies on supervised learning methods, which suffers from labeled data scarcity problem. The State-of-the-art method uses deep neural networks, specifically a class of Recurrent Neural Network (RNN) which are Long-Short-Term-Memory networks (LSTMs) \cite{hochreiter1997long}. Deep neural networks, due to their large number of free parameters relies heavily on large annotated corpora for learning the end task. But in real-world, it is hard to get large labeled data, mainly due to heavy cost associated with manual annotation. Towards this end, we propose a novel semi-supervised learning based RNN model, which can leverage unlabeled data also present in abundance on social media. Through experiments we demonstrate the effectiveness of our method, achieving state-of-the-art performance in ADR mention extraction.Comment: Accepted at DTMBIO workshop, CIKM 2017. To appear in BMC Bioinformatics. Pls cite that versio

Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning

abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

UNSUPERVISED DYNAMIC TOPIC MODEL FOR EXTRACTING ADVERSE DRUG REACTION FROM HEALTH FORUMS

The relationship between drug and its side effects has been outlined in two websites: Sider and WebMD. The aim of this study was to find the association between drug and its side effects. We compared the reports of typical users of a web site called: "Ask a patient" website with reported drug side effects in reference sites such as Sider and WebMD. In addition, the typical users' comments on highly-commented drugs (Neurotic drugs, Anti-Pregnancy drugs and Gastrointestinal drugs) were analyzed, using deep learning method. To this end, typical users' comments on drugs' side effects, during last decades, were collected from the website “Ask a patient”. Then, the data on drugs were classified based on deep learning model (HAN) and the drugs' side effect. And the main topics of side effects for each group of drugs were identified and reported, through Sider and WebMD websites. Our model demonstrates its ability to accurately describe and label side effects in a temporal text corpus by a deep learning classifier which is shown to be an effective method to precisely discover the association between drugs and their side effects. Moreover, this model has the capability to immediately locate information in reference sites to recognize the side effect of new drugs, applicable for drug companies. This study suggests that the sensitivity of internet users and the diverse scientific findings are for the benefit of dis¬tinct detection of adverse effects of drugs, and deep learning would facilitate it

Adverse drug extraction in twitter data using convolutional neural network

The study of health-related topics on social media has become a useful tool for the early detection of the different adverse medical conditions. In particular, it concerns cases related to the treatment of mental diseases, as the effects of medications here often prove to be unpredictable. In our research, we use convolutional neural networks (CNN) with word2vec embedding to classify user comments on Twitter. The aim of the classification is to reveal adverse drug reactions of users. The results obtained are highly promising, showing the overall usefulness of neural network algorithms in this kind of tasks