Tracking Dengue Epidemics using Twitter Content Classification and Topic Modelling

Detecting and preventing outbreaks of mosquito-borne diseases such as Dengue and Zika in Brasil and other tropical regions has long been a priority for governments in affected areas. Streaming social media content, such as Twitter, is increasingly being used for health vigilance applications such as flu detection. However, previous work has not addressed the complexity of drastic seasonal changes on Twitter content across multiple epidemic outbreaks. In order to address this gap, this paper contrasts two complementary approaches to detecting Twitter content that is relevant for Dengue outbreak detection, namely supervised classification and unsupervised clustering using topic modelling. Each approach has benefits and shortcomings. Our classifier achieves a prediction accuracy of about 80\% based on a small training set of about 1,000 instances, but the need for manual annotation makes it hard to track seasonal changes in the nature of the epidemics, such as the emergence of new types of virus in certain geographical locations. In contrast, LDA-based topic modelling scales well, generating cohesive and well-separated clusters from larger samples. While clusters can be easily re-generated following changes in epidemics, however, this approach makes it hard to clearly segregate relevant tweets into well-defined clusters.Comment: Procs. SoWeMine - co-located with ICWE 2016. 2016, Lugano, Switzerlan

What's unusual in online disease outbreak news?

Background: Accurate and timely detection of public health events of international concern is necessary to help support risk assessment and response and save lives. Novel event-based methods that use the World Wide Web as a signal source offer potential to extend health surveillance into areas where traditional indicator networks are lacking. In this paper we address the issue of systematically evaluating online health news to support automatic alerting using daily disease-country counts text mined from real world data using BioCaster. For 18 data sets produced by BioCaster, we compare 5 aberration detection algorithms (EARS C2, C3, W2, F-statistic and EWMA) for performance against expert moderated ProMED-mail postings. Results: We report sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), mean alerts/100 days and F1, at 95% confidence interval (CI) for 287 ProMED-mail postings on 18 outbreaks across 14 countries over a 366 day period. Results indicate that W2 had the best F1 with a slight benefit for day of week effect over C2. In drill down analysis we indicate issues arising from the granular choice of country-level modeling, sudden drops in reporting due to day of week effects and reporting bias. Automatic alerting has been implemented in BioCaster available from http://born.nii.ac.jp. Conclusions: Online health news alerts have the potential to enhance manual analytical methods by increasing throughput, timeliness and detection rates. Systematic evaluation of health news aberrations is necessary to push forward our understanding of the complex relationship between news report volumes and case numbers and to select the best performing features and algorithms

Global disease monitoring and forecasting with Wikipedia

Infectious disease is a leading threat to public health, economic stability, and other key social structures. Efforts to mitigate these impacts depend on accurate and timely monitoring to measure the risk and progress of disease. Traditional, biologically-focused monitoring techniques are accurate but costly and slow; in response, new techniques based on social internet data such as social media and search queries are emerging. These efforts are promising, but important challenges in the areas of scientific peer review, breadth of diseases and countries, and forecasting hamper their operational usefulness. We examine a freely available, open data source for this use: access logs from the online encyclopedia Wikipedia. Using linear models, language as a proxy for location, and a systematic yet simple article selection procedure, we tested 14 location-disease combinations and demonstrate that these data feasibly support an approach that overcomes these challenges. Specifically, our proof-of-concept yields models with $r^2$ up to 0.92, forecasting value up to the 28 days tested, and several pairs of models similar enough to suggest that transferring models from one location to another without re-training is feasible. Based on these preliminary results, we close with a research agenda designed to overcome these challenges and produce a disease monitoring and forecasting system that is significantly more effective, robust, and globally comprehensive than the current state of the art.Comment: 27 pages; 4 figures; 4 tables. Version 2: Cite McIver & Brownstein and adjust novelty claims accordingly; revise title; various revisions for clarit

Epidemiological Prediction using Deep Learning

Department of Mathematical SciencesAccurate and real-time epidemic disease prediction plays a significant role in the health system and is of great importance for policy making, vaccine distribution and disease control. From the SIR model by Mckendrick and Kermack in the early 1900s, researchers have developed a various mathematical model to forecast the spread of disease. With all attempt, however, the epidemic prediction has always been an ongoing scientific issue due to the limitation that the current model lacks flexibility or shows poor performance. Owing to the temporal and spatial aspect of epidemiological data, the problem fits into the category of time-series forecasting. To capture both aspects of the data, this paper proposes a combination of recent Deep Leaning models and applies the model to ILI (influenza like illness) data in the United States. Specifically, the graph convolutional network (GCN) model is used to capture the geographical feature of the U.S. regions and the gated recurrent unit (GRU) model is used to capture the temporal dynamics of ILI. The result was compared with the Deep Learning model proposed by other researchers, demonstrating the proposed model outperforms the previous methods.clos

Addendum to Informatics for Health 2017: Advancing both science and practice

This article presents presentation and poster abstracts that were mistakenly omitted from the original publication

Point-of-Care Ultrasound Assessment of Tropical Infectious Diseases—A Review of Applications and Perspectives

The development of good quality and affordable ultrasound machines has led to the establishment and implementation of numerous point-of-care ultrasound (POCUS) protocols in various medical disciplines. POCUS for major infectious diseases endemic in tropical regions has received less attention, despite its likely even more pronounced benefit for populations with limited access to imaging infrastructure. Focused assessment with sonography for HIV-associated TB (FASH) and echinococcosis (FASE) are the only two POCUS protocols for tropical infectious diseases, which have been formally investigated and which have been implemented in routine patient care today. This review collates the available evidence for FASH and FASE, and discusses sonographic experiences reported for urinary and intestinal schistosomiasis, lymphatic filariasis, viral hemorrhagic fevers, amebic liver abscess, and visceral leishmaniasis. Potential POCUS protocols are suggested and technical as well as training aspects in the context of resource-limited settings are reviewed. Using the focused approach for tropical infectious diseases will make ultrasound diagnosis available to patients who would otherwise have very limited or no access to medical imaging

A sentiment-based filteration and data analysis framework for social media

This paper describes a framework that explains the processes involved in the filteration and analysis of data for user generated content in social media.Previous researches have put their focus in leveraging high quality data from social media data stream, but there are many opportunities that need to be explored.This paper proposes a sentiment-based filteration and data analysis framework in identifying relevant information from data generated by users in social media.Based on the textual contents generated and spread through social media, it is assumed that each of the set of text streams/corpora might carry a sentiment associated with it regardless of its polarity bias. Due to this, the proposed framework introduces the idea of data filtering that exploits information and sentiment captured in text while at the same time adapts text analysis methods overcoming the noisy and unstructured nature of social media textual content