Digital Pharmacovigilance: the medwatcher system for monitoring adverse events through automated processing of internet social media and crowdsourcing

Thesis (Ph.D.)--Boston UniversityHalf of Americans take a prescription drug, medical devices are in broad use, and population coverage for many vaccines is over 90%. Nearly all medical products carry risk of adverse events (AEs), sometimes severe. However, pre- approval trials use small populations and exclude participants by specific criteria, making them insufficient to determine the risks of a product as used in the population. Existing post-marketing reporting systems are critical, but suffer from underreporting. Meanwhile, recent years have seen an explosion in adoption of Internet services and smartphones. MedWatcher is a new system that harnesses emerging technologies for pharmacovigilance in the general population. MedWatcher consists of two components, a text-processing module, MedWatcher Social, and a crowdsourcing module, MedWatcher Personal. With the natural language processing component, we acquire public data from the Internet, apply classification algorithms, and extract AE signals. With the crowdsourcing application, we provide software allowing consumers to submit AE reports directly. Our MedWatcher Social algorithm for identifying symptoms performs with 77% precision and 88% recall on a sample of Twitter posts. Our machine learning algorithm for identifying AE-related posts performs with 68% precision and 89% recall on a labeled Twitter corpus. For zolpidem tartrate, certolizumab pegol, and dimethyl fumarate, we compared AE profiles from Twitter with reports from the FDA spontaneous reporting system. We find some concordance (Spearman's rho= 0.85, 0.77, 0.82, respectively, for symptoms at MedDRA System Organ Class level). Where the sources differ, milder effects are overrepresented in Twitter. We also compared post-marketing profiles with trial results and found little concordance. MedWatcher Personal saw substantial user adoption, receiving 550 AE reports in a one-year period, including over 400 for one device, Essure. We categorized 400 Essure reports by symptom, compared them to 129 reports from the FDA spontaneous reporting system, and found high concordance (rho = 0.65) using MedDRA Preferred Term granularity. We also compared Essure Twitter posts with MedWatcher and FDA reports, and found rho= 0.25 and 0.31 respectively. MedWatcher represents a novel pharmacoepidemiology surveillance informatics system; our analysis is the first to compare AEs across social media, direct reporting, FDA spontaneous reports, and pre-approval trials

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches

Drug Safety (DS) is a domain with significant public health and social impact. Knowledge Engineering (KE) is the Computer Science discipline elaborating on methods and tools for developing “knowledge-intensive” systems, depending on a conceptual “knowledge” schema and some kind of “reasoning” process. The present systematic and mapping review aims to investigate KE-based approaches employed for DS and highlight the introduced added value as well as trends and possible gaps in the domain. Journal articles published between 2006 and 2017 were retrieved from PubMed/MEDLINE and Web of Science® (873 in total) and filtered based on a comprehensive set of inclusion/exclusion criteria. The 80 finally selected articles were reviewed on full-text, while the mapping process relied on a set of concrete criteria (concerning specific KE and DS core activities, special DS topics, employed data sources, reference ontologies/terminologies, and computational methods, etc.). The analysis results are publicly available as online interactive analytics graphs. The review clearly depicted increased use of KE approaches for DS. The collected data illustrate the use of KE for various DS aspects, such as Adverse Drug Event (ADE) information collection, detection, and assessment. Moreover, the quantified analysis of using KE for the respective DS core activities highlighted room for intensifying research on KE for ADE monitoring, prevention and reporting. Finally, the assessed use of the various data sources for DS special topics demonstrated extensive use of dominant data sources for DS surveillance, i.e., Spontaneous Reporting Systems, but also increasing interest in the use of emerging data sources, e.g., observational healthcare databases, biochemical/genetic databases, and social media. Various exemplar applications were identified with promising results, e.g., improvement in Adverse Drug Reaction (ADR) prediction, detection of drug interactions, and novel ADE profiles related with specific mechanisms of action, etc. Nevertheless, since the reviewed studies mostly concerned proof-of-concept implementations, more intense research is required to increase the maturity level that is necessary for KE approaches to reach routine DS practice. In conclusion, we argue that efficiently addressing DS data analytics and management challenges requires the introduction of high-throughput KE-based methods for effective knowledge discovery and management, resulting ultimately, in the establishment of a continuous learning DS system

Health Misinformation in Search and Social Media

People increasingly rely on the Internet in order to search for and share health-related information. Indeed, searching for and sharing information about medical treatments are among the most frequent uses of online data. While this is a convenient and fast method to collect information, online sources may contain incorrect information that has the potential to cause harm, especially if people believe what they read without further research or professional medical advice. The goal of this thesis is to address the misinformation problem in two of the most commonly used online services: search engines and social media platforms. We examined how people use these platforms to search for and share health information. To achieve this, we designed controlled laboratory user studies and employed large-scale social media data analysis tools. The solutions proposed in this thesis can be used to build systems that better support people's health-related decisions. The techniques described in this thesis addressed online searching and social media sharing in the following manner. First, with respect to search engines, we aimed to determine the extent to which people can be influenced by search engine results when trying to learn about the efficacy of various medical treatments. We conducted a controlled laboratory study wherein we biased the search results towards either correct or incorrect information. We then asked participants to determine the efficacy of different medical treatments. Results showed that people were significantly influenced both positively and negatively by search results bias. More importantly, when the subjects were exposed to incorrect information, they made more incorrect decisions than when they had no interaction with the search results. Following from this work, we extended the study to gain insights into strategies people use during this decision-making process, via the think-aloud method. We found that, even with verbalization, people were strongly influenced by the search results bias. We also noted that people paid attention to what the majority states, authoritativeness, and content quality when evaluating online content. Understanding the effects of cognitive biases that can arise during online search is a complex undertaking because of the presence of unconscious biases (such as the search results ranking) that the think-aloud method fails to show. Moving to social media, we first proposed a solution to detect and track misinformation in social media. Using Zika as a case study, we developed a tool for tracking misinformation on Twitter. We collected 13 million tweets regarding the Zika outbreak and tracked rumors outlined by the World Health Organization and the Snopes fact-checking website. We incorporated health professionals, crowdsourcing, and machine learning to capture health-related rumors as well as clarification communications. In this way, we illustrated insights that the proposed tools provide into potentially harmful information on social media, allowing public health researchers and practitioners to respond with targeted and timely action. From identifying rumor-bearing tweets, we examined individuals on social media who are posting questionable health-related information, in particular those promoting cancer treatments that have been shown to be ineffective. Specifically, we studied 4,212 Twitter users who have posted about one of 139 ineffective ``treatments'' and compared them to a baseline of users generally interested in cancer. Considering features that capture user attributes, writing style, and sentiment, we built a classifier that is able to identify users prone to propagating such misinformation. This classifier achieved an accuracy of over 90%, providing a potential tool for public health officials to identify such individuals for preventive intervention

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

The Potential of Social Media Intelligence to Improve Peoples Lives: Social Media Data for Good

In this report, developed with support from Facebook, we focus on an approach to extract public value from social media data that we believe holds the greatest potential: data collaboratives. Data collaboratives are an emerging form of public-private partnership in which actors from different sectors exchange information to create new public value. Such collaborative arrangements, for example between social media companies and humanitarian organizations or civil society actors, can be seen as possible templates for leveraging privately held data towards the attainment of public goals

Improving information accessibility using online patient drug reviews

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 85-92).We address the problem of information accessibility for patients concerned about, pharmaceutical drug side effects and experiences. We create a new corpus of online patient-provided drug reviews and present our initial experiments on that corpus. We detect biases in term distributions that show a statistically significant association between a class of cholesterol-lowering drugs called statins, and a wide range of alarming disorders, including depression, memory loss, and heart failure. We also develop an initial language model for speech recognition in the medical domain, with transcribed data on sample patient comments collected with Amazon Mechanical Turk. Our findings show that patient-reported drug experiences have great potential to empower consumers to make more informed decisions about medical drugs, and our methods will be used to increase information accessibility for consumers.by Yueyang Alice Li.M.Eng

Polycentric Information Commons: A Theory Development and Empirical Investigation

Decentralized systems online—such as open source software (OSS) development, online communities, wikis, and social media—often experience decline in participation which threatens their long-terms sustainability. Building on a rich body of research on the sustainability of physical resource systems, this dissertation presents a novel theoretical framing that addresses the sustainability issues arising in decentralized systems online and which are amplified because of their open nature. The first essay develops the theory of polycentric information commons (PIC) which conceptualizes decentralized systems online as “information commons”. The theory defines information commons, the stakeholders that participate in them, the sustainability indicators of information commons and the collective-action threats putting pressure on their long-term sustainability. Drawing on Ostrom’s factors associated with stable common pool resource systems, PIC theory specifies four polycentric governance practices that can help information commons reduce the magnitude and impact of collective-action threats while improving the information commons’ sustainability. The second essay further develops PIC theory by applying it in an empirical context of “digital activism”. Specifically, it examines the role of polycentric governance in reducing the threats to the legitimacy of digital activism—a type of information commons with an overarching objective of instigating societal change. As such, it illustrates the applicability of PIC theory in the study of digital activism. The third essay focuses on the threat of “information pollution” and its impact on open collaboration, a type of information commons dedicated to the creation of value through open participation online. It uncovers the way polycentric governance mechanism help reduce the duration of pollution events. This essay contributes to PIC theory by expanding it to the realm of operational governance in open collaboration

The Perception of Emotion from Acoustic Cues in Natural Speech

Knowledge of human perception of emotional speech is imperative for the development of emotion in speech recognition systems and emotional speech synthesis. Owing to the fact that there is a growing trend towards research on spontaneous, real-life data, the aim of the present thesis is to examine human perception of emotion in naturalistic speech. Although there are many available emotional speech corpora, most contain simulated expressions. Therefore, there remains a compelling need to obtain naturalistic speech corpora that are appropriate and freely available for research. In that regard, our initial aim was to acquire suitable naturalistic material and examine its emotional content based on listener perceptions. A web-based listening tool was developed to accumulate ratings based on large-scale listening groups. The emotional content present in the speech material was demonstrated by performing perception tests on conveyed levels of Activation and Evaluation. As a result, labels were determined that signified the emotional content, and thus contribute to the construction of a naturalistic emotional speech corpus. In line with the literature, the ratings obtained from the perception tests suggested that Evaluation (or hedonic valence) is not identified as reliably as Activation is. Emotional valence can be conveyed through both semantic and prosodic information, for which the meaning of one may serve to facilitate, modify, or conflict with the meaning of the other—particularly with naturalistic speech. The subsequent experiments aimed to investigate this concept by comparing ratings from perception tests of non-verbal speech with verbal speech. The method used to render non-verbal speech was low-pass filtering, and for this, suitable filtering conditions were determined by carrying out preliminary perception tests. The results suggested that nonverbal naturalistic speech provides sufficiently discernible levels of Activation and Evaluation. It appears that the perception of Activation and Evaluation is affected by low-pass filtering, but that the effect is relatively small. Moreover, the results suggest that there is a similar trend in agreement levels between verbal and non-verbal speech. To date it still remains difficult to determine unique acoustical patterns for hedonic valence of emotion, which may be due to inadequate labels or the incorrect selection of acoustic parameters. This study has implications for the labelling of emotional speech data and the determination of salient acoustic correlates of emotion