A Biased Topic Modeling Approach for Case Control Study from Health Related Social Media Postings

abstract: Online social networks are the hubs of social activity in cyberspace, and using them to exchange knowledge, experiences, and opinions is common. In this work, an advanced topic modeling framework is designed to analyse complex longitudinal health information from social media with minimal human annotation, and Adverse Drug Events and Reaction (ADR) information is extracted and automatically processed by using a biased topic modeling method. This framework improves and extends existing topic modelling algorithms that incorporate background knowledge. Using this approach, background knowledge such as ADR terms and other biomedical knowledge can be incorporated during the text mining process, with scores which indicate the presence of ADR being generated. A case control study has been performed on a data set of twitter timelines of women that announced their pregnancy, the goals of the study is to compare the ADR risk of medication usage from each medication category during the pregnancy. In addition, to evaluate the prediction power of this approach, another important aspect of personalized medicine was addressed: the prediction of medication usage through the identification of risk groups. During the prediction process, the health information from Twitter timeline, such as diseases, symptoms, treatments, effects, and etc., is summarized by the topic modelling processes and the summarization results is used for prediction. Dimension reduction and topic similarity measurement are integrated into this framework for timeline classification and prediction. This work could be applied to provide guidelines for FDA drug risk categories. Currently, this process is done based on laboratory results and reported cases. Finally, a multi-dimensional text data warehouse (MTD) to manage the output from the topic modelling is proposed. Some attempts have been also made to incorporate topic structure (ontology) and the MTD hierarchy. Results demonstrate that proposed methods show promise and this system represents a low-cost approach for drug safety early warning.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Linking social media, medical literature, and clinical notes using deep learning.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts

Information Retrieval of Opioid Dependence Medications Reviews from Health-Related Social Media

Social media provides a convenient platform for patients to share their drug usage experience with others; consequently, health researchers can leverage this potential data to gain valuable information about users’ drug satisfaction. Since the 1990s, opioid drug abuse has become a national crisis. In order to reduce the dependency of opioids, several drugs have been presented to the market, but little is known about patient satisfaction with these treatments. Sentiment analysis is a method to measure and interpret patients’ satisfaction. In the first phase of this study, we aimed to utilize social media posts to predict patients’ sentiment towards opioid dependency treatment. We focused on Suboxone, a well-known opioid dependence medication, as our targeted treatment and Drugs.com, an online healthcare forum as our data source. For the purpose of our analysis, we first collected 1,532 posts to create a training dataset, split the posts to sentences, and annotated 1100 sentences for sentiment analysis. To predict patients’ sentiment, we extracted features from patients’ posts, including bigrams, trigrams, and features extracted from topic modeling. To develop the prediction model, we used two machine learning methods, Naïve Bayes and SVM, for predicting sentiment. We achieved the best performance using SVM, getting an accuracy of 61% for SVM. In the second phase of this study, we also aimed to understand the behavior of the patients toward the targeted medication. To accomplish this goal, we used the Health Belief Model (HBM), a social psychological model that describes and predicts patients’ health-related attitudes in action, benefit, barrier, and threat categories, for predicting such behavior from patients’ reviews. We also utilized the same combinations of features and machine learning methods that we used in the first phase of the study, and the best accuracy performance was 47% for the SVM classifier as compared to 43% as our baseline