Developing a Prototype System for Syndromic Surveillance and Visualization Using Social Media Data.

Syndromic surveillance of emerging diseases is crucial for timely planning and execution of epidemic response from both local and global authorities. Traditional sources of information employed by surveillance systems are not only slow but also impractical for developing countries. Internet and social media provide a free source of a large amount of data which can be utilized for Syndromic surveillance. We propose developing a prototype system for gathering, storing, filtering and presenting data collected from Twitter (a popular social media platform). Since social media data is inherently noisy we describe ways to preprocess the gathered data and utilize SVM (Support Vector Machine) to identify tweets relating to influenza like symptoms. The filtered data is presented in a web application, which allows the user to explore the underlying data in both spatial and temporal dimensions

Towards cross-lingual alerting for bursty epidemic events

Background: Online news reports are increasingly becoming a source for event based early warning systems that detect natural disasters. Harnessing the massive volume of information available from multilingual newswire presents as many challenges as opportunities due to the patterns of reporting complex spatiotemporal events. Results: In this article we study the problem of utilising correlated event reports across languages. We track the evolution of 16 disease outbreaks using 5 temporal aberration detection algorithms on text-mined events classified according to disease and outbreak country. Using ProMED reports as a silver standard, comparative analysis of news data for 13 languages over a 129 day trial period showed improved sensitivity, F1 and timeliness across most models using cross-lingual events. We report a detailed case study analysis for Cholera in Angola 2010 which highlights the challenges faced in correlating news events with the silver standard. Conclusions: The results show that automated health surveillance using multilingual text mining has the potential to turn low value news into high value alerts if informed choices are used to govern the selection of models and data sources. An implementation of the C2 alerting algorithm using multilingual news is available at the BioCaster portal http://born.nii.ac.jp/?page=globalroundup

Flu Gone Viral: Syndromic Surveillance of Flu on Twitter Using Temporal Topic Models

Abstract—Surveillance of epidemic outbreaks and spread from social media is an important tool for governments and public health authorities. Machine learning techniques for nowcasting the flu have made significant inroads into correlating social media trends to case counts and prevalence of epidemics in a population. There is a disconnect between data-driven methods for forecasting flu incidence and epidemiological models that adopt a state based understanding of transitions, that can lead to sub-optimal predictions. Furthermore, models for epidemiological activity and social activity like on Twitter predict different shapes and have important differences. We propose a temporal topic model to capture hidden states of a user from his tweets and aggregate states in a geographical region for better estimation of trends. We show that our approach helps fill the gap between phenomenolog-ical methods for disease surveillance and epidemiological models. We validate this approach by modeling the flu using Twitter in multiple countries of South America. We demonstrate that our model can consistently outperform plain vocabulary assessment in flu case-count predictions, and at the same time get better flu-peak predictions than competitors. We also show that our fine-grained modeling can reconcile some contrasting behaviors between epidemiological and social models. I

Can Twitter be a source of information on allergy? Correlation of pollen counts with tweets reporting symptoms of allergic rhinoconjunctivitis and names of antihistamine drugs

Pollen forecasts are in use everywhere to inform therapeutic decisions for patients with allergic rhinoconjunctivitis (ARC). We exploited data derived from Twitter in order to identify tweets reporting a combination of symptoms consistent with a case definition of ARC and those reporting the name of an antihistamine drug. In order to increase the sensitivity of the system, we applied an algorithm aimed at automatically identifying jargon expressions related to medical terms. We compared weekly Twitter trends with National Allergy Bureau weekly pollen counts derived from US stations, and found a high correlation of the sum of the total pollen counts from each stations with tweets reporting ARC symptoms (Pearson's correlation coefficient: 0.95) and with tweets reporting antihistamine drug names (Pearson's correlation coefficient: 0.93). Longitude and latitude of the pollen stations affected the strength of the correlation. Twitter and other social networks may play a role in allergic disease surveillance and in signaling drug consumptions trends

Results from the centers for disease control and prevention's predict the 2013-2014 Influenza Season Challenge

Background: Early insights into the timing of the start, peak, and intensity of the influenza season could be useful in planning influenza prevention and control activities. To encourage development and innovation in influenza forecasting, the Centers for Disease Control and Prevention (CDC) organized a challenge to predict the 2013-14 Unites States influenza season. Methods: Challenge contestants were asked to forecast the start, peak, and intensity of the 2013-2014 influenza season at the national level and at any or all Health and Human Services (HHS) region level(s). The challenge ran from December 1, 2013-March 27, 2014; contestants were required to submit 9 biweekly forecasts at the national level to be eligible. The selection of the winner was based on expert evaluation of the methodology used to make the prediction and the accuracy of the prediction as judged against the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). Results: Nine teams submitted 13 forecasts for all required milestones. The first forecast was due on December 2, 2013; 3/13 forecasts received correctly predicted the start of the influenza season within one week, 1/13 predicted the peak within 1 week, 3/13 predicted the peak ILINet percentage within 1 %, and 4/13 predicted the season duration within 1 week. For the prediction due on December 19, 2013, the number of forecasts that correctly forecasted the peak week increased to 2/13, the peak percentage to 6/13, and the duration of the season to 6/13. As the season progressed, the forecasts became more stable and were closer to the season milestones. Conclusion: Forecasting has become technically feasible, but further efforts are needed to improve forecast accuracy so that policy makers can reliably use these predictions. CDC and challenge contestants plan to build upon the methods developed during this contest to improve the accuracy of influenza forecasts. © 2016 The Author(s)

Efficient Text Classification with Linear Regression Using a Combination of Predictors for Flu Outbreak Detection

Early prediction of disease outbreaks and seasonal epidemics such as Influenza may reduce their impact on daily lives. Today, the web can be used for surveillance of diseases.Search engines and Social Networking Sites can be used to track trends of different diseases more quickly than government agencies such as Center of Disease Control and Prevention(CDC). Today, Social Networking Sites (SNS) are widely used by diverse demographic populations. Thus, SNS data can be used effectively to track disease outbreaks and provide necessary warnings. Although the generated data of microblogging sites is valuable for real time analysis and outbreak predictions, the volume is huge. Therefore, one of the main challenges in analyzing this huge volume of data is to find the best approach for accurate analysis in an efficient time. Regardless of the analysis time, many studies show only the accuracy of applying different machine learning approaches. Current SNS-based flu detection and prediction frameworks apply conventional machine learning approaches that require lengthy training and testing, which is not the optimal solution for new outbreaks with new signs and symptoms. The aim of this study is to propose an efficient and accurate framework that uses SNS data to track disease outbreaks and provide early warnings, even for newest outbreaks accurately. The presented framework of outbreak prediction consists of three main modules: text classification, mapping, and linear regression for weekly flu rate predictions. The text classification module utilizes the features of sentiment analysis and predefined keyword occurrences. Various classifiers, including FastText and six conventional machine learning algorithms, are evaluated to identify the most efficient and accurate one for the proposed framework. The text classifiers have been trained and tested using a pre-labeled dataset of flu-related and unrelated Twitter postings. The selected text classifier is then used to classify over 8,400,000 tweet documents. The flu-related documents are then mapped ona weekly basis using a mapping module. Lastly, the mapped results are passed together with historical Center for Disease Control and Prevention (CDC) data to a linear regression module for weekly flu rate predictions. The evaluation of flu tweet classification shows that FastText together with the extracted features, has achieved accurate results with anF-measure value of 89.9% in addition to its efficiency. Therefore, FastText has been chosen to be the classification module to work together with the other modules in the proposed framework, including the linear regression module, for flu trend predictions. The prediction results are compared with the available recent data from CDC as the ground truth and show a strong correlation of 96.2%

Enhancing Drug Overdose Mortality Surveillance through Natural Language Processing and Machine Learning

Epidemiological surveillance is key to monitoring and assessing the health of populations. Drug overdose surveillance has become an increasingly important part of public health practice as overdose morbidity and mortality has increased due in large part to the opioid crisis. Monitoring drug overdose mortality relies on death certificate data, which has several limitations including timeliness and the coding structure used to identify specific substances that caused death. These limitations stem from the need to analyze the free-text cause-of-death sections of the death certificate that are completed by the medical certifier during death investigation. Other fields, including clinical sciences, have utilized natural language processing (NLP) methods to gain insight from free-text data, but thus far, adoption of NLP methods in epidemiological surveillance has been limited. Through a narrative review of NLP methods currently used in public health surveillance and the integration of two NLP tasks, classification and named entity recognition, this dissertation enhances the capabilities of public health practitioners and researchers to perform drug overdose mortality surveillance. This dissertation advances both surveillance science and public health practice by integrating methods from bioinformatics into the surveillance pipeline which provides more timely and increased quality overdose mortality surveillance, which is essential to guiding effective public health response to the continuing drug overdose epidemic