Anomaly Detection in Time Series: Theoretical and Practical Improvements for Disease Outbreak Detection

The automatic collection and increasing availability of health data provides a new opportunity for techniques to monitor this information. By monitoring pre-diagnostic data sources, such as over-the-counter cough medicine sales or emergency room chief complaints of cough, there exists the potential to detect disease outbreaks earlier than traditional laboratory disease confirmation results. This research is particularly important for a modern, highly-connected society, where the onset of disease outbreak can be swift and deadly, whether caused by a naturally occurring global pandemic such as swine flu or a targeted act of bioterrorism. In this dissertation, we first describe the problem and current state of research in disease outbreak detection, then provide four main additions to the field. First, we formalize a framework for analyzing health series data and detecting anomalies: using forecasting methods to predict the next day's value, subtracting the forecast to create residuals, and finally using detection algorithms on the residuals. The formalized framework indicates the link between the forecast accuracy of the forecast method and the performance of the detector, and can be used to quantify and analyze the performance of a variety of heuristic methods. Second, we describe improvements for the forecasting of health data series. The application of weather as a predictor, cross-series covariates, and ensemble forecasting each provide improvements to forecasting health data. Third, we describe improvements for detection. This includes the use of multivariate statistics for anomaly detection and additional day-of-week preprocessing to aid detection. Most significantly, we also provide a new method, based on the CuScore, for optimizing detection when the impact of the disease outbreak is known. This method can provide an optimal detector for rapid detection, or for probability of detection within a certain timeframe. Finally, we describe a method for improved comparison of detection methods. We provide tools to evaluate how well a simulated data set captures the characteristics of the authentic series and time-lag heatmaps, a new way of visualizing daily detection rates or displaying the comparison between two methods in a more informative way

RANK-BASED TEMPO-SPATIAL CLUSTERING: A FRAMEWORK FOR RAPID OUTBREAK DETECTION USING SINGLE OR MULTIPLE DATA STREAMS

In the recent decades, algorithms for disease outbreak detection have become one of the main interests of public health practitioners to identify and localize an outbreak as early as possible in order to warrant further public health response before a pandemic develops. Today’s increased threat of biological warfare and terrorism provide an even stronger impetus to develop methods for outbreak detection based on symptoms as well as definitive laboratory diagnoses. In this dissertation work, I explore the problems of rapid disease outbreak detection using both spatial and temporal information. I develop a framework of non-parameterized algorithms which search for patterns of disease outbreak in spatial sub-regions of the monitored region within a certain period. Compared to the current existing spatial or tempo-spatial algorithm, the algorithms in this framework provide a methodology for fast searching of either univariate data set or multivariate data set. It first measures which study area is more likely to have an outbreak occurring given the baseline data and currently observed data. Then it applies a greedy searching mechanism to look for clusters with high posterior probabilities given the risk measurement for each unit area as heuristic. I also explore the performance of the proposed algorithms. From the perspective of predictive modeling, I adopt a Gamma-Poisson (GP) model to compute the probability of having an outbreak in each cluster when analyzing univariate data. I build a multinomial generalized Dirichlet (MGD) model to identify outbreak clusters from multivariate data which include the OTC data streams collected by the national retail data monitor (NRDM) and the ED data streams collected by the RODS system. Key contributions of this dissertation include 1) it introduces a rank-based tempo-spatial clustering algorithm, RSC, by utilizing greedy searching and Bayesian GP model for disease outbreak detection with comparable detection timeliness, cluster positive prediction value (PPV) and improved running time; 2) it proposes a multivariate extension of RSC (MRSC) which applies MGD model. The evaluation demonstrated the advantage that MGD model can effectively suppress the false alarms caused by elevated signals that are non-disease relevant and occur in all the monitored data streams

A Bayesian Network Model for Spatio-Temporal Event Surveillance

Event surveillance involves analyzing a region in order to detect patterns that are indicative of some event of interest. An example is the monitoring of information about emergency department visits to detect a disease outbreak. Spatial event surveillance involves analyzing spatial patterns of evidence that are indicative of the event of interest. A special case of spatial event surveillance is spatial cluster detection, which searches for subregions in which the count of an event of interest is higher than expected. Temporal event surveillance involves monitoring for emerging temporal patterns. Spatio-temporal event surveillance involves joint spatial and temporal monitoring.When the events observed are of direct interest, then analyzing counts of those events is generally the preferred approach. However, in event surveillance we often only observe events that are indirectly related to the events of interest. For example, during an influenza outbreak, we may only have information about the chief complaints of patients who visited emergency departments. In this situation, a better surveillance approach may be to model the relationships among the events of interest and those observed.I developed a high-level Bayesian network architecture that represents a class of spatial event surveillance models, which I call BayesNet-S. I also developed an architecture that represents a class of temporal event surveillance models called BayesNet-T. These Bayesian network architectures are combined into a single architecture that represents a class of spatio-temporal models called BayesNet-ST. Using these architectures, it is often possible to construct a temporal, spatial, or spatio-temporal model from an existing Bayesian network event-surveillance model that is non-spatial and non-temporal. My general hypothesis is that when an existing model is extended to incorporate space and time, event surveillance will be improved.PANDA-CDCA (PC) (Cooper et al., 2007) is a non-temporal, non-spatial disease outbreak detection system. I extended PC both spatially and temporally. My specific hypothesis is that each of the spatial and temporal extensions of PC will perform outbreak detection better than does PC, and that the combined use of the spatial and temporal extensions will perform better than either extension alone.The experimental results obtained in this research support this hypothesis

BAYESIAN MODELING OF ANOMALIES DUE TO KNOWN AND UNKNOWN CAUSES

Bayesian modeling of unknown causes of events is an important and pervasive problem. However, it has received relatively little research attention. In general, an intelligent agent (or system) has only limited causal knowledge of the world. Therefore, the agent may well be experiencing the influences of causes outside its model. For example, a clinician may be seeing a patient with a virus that is new to humans; the HIV virus was at one time such an example. It is important that clinicians be able to recognize that a patient is presenting with an unknown disease. In general, intelligent agents (or systems) need to recognize under uncertainty when they are likely to be experiencing influences outside their realm of knowledge. This dissertation investigates Bayesian modeling of unknown causes of events in the context of disease-outbreak detection.The dissertation introduces a Bayesian approach that models and detects (1) known diseases (e.g., influenza and anthrax) by using informative prior probabilities, (2) unknown diseases (e.g., a new, highly contagious respiratory virus that has never been seen before) by using relatively non-informative prior probabilities and (3) partially-known diseases (e.g., a disease that has characteristics of an influenza-like illness) by using semi-informative prior probabilities. I report the results of simulation experiments which support that this modeling method can improve the detection of new disease outbreaks in a population. A key contribution of this dissertation is that it introduces a Bayesian approach for jointly modeling both known and unknown causes of events. Such modeling has broad applicability in artificial intelligence in general and biomedical informatics applications in particular, where the space of known causes of outcomes of interest is seldom complete

Bayesian prediction of an epidemic curve

AbstractAn epidemic curve is a graph in which the number of new cases of an outbreak disease is plotted against time. Epidemic curves are ordinarily constructed after the disease outbreak is over. However, a good estimate of the epidemic curve early in an outbreak would be invaluable to health care officials. Currently, techniques for predicting the severity of an outbreak are very limited. As far as predicting the number of future cases, ordinarily epidemiologists simply make an educated guess as to how many people might become affected. We develop a model for estimating an epidemic curve early in an outbreak, and we show results of experiments testing its accuracy

International Society for Disease Surveillance Conference 2011: Building the Future of Public Health Surveillance: Building the Future of Public Health Surveillance

Daniel Reidpath - ORCID: 0000-0002-8796-0420 https://orcid.org/0000-0002-8796-04204pubpub1117

Report on DIMACS Working Group Meeting: Mathematical Sciences Methods for the Study of Deliberate Releases of Biological Agents and their Consequences

55 pages, 1 article*Report on DIMACS Working Group Meeting: Mathematical Sciences Methods for the Study of Deliberate Releases of Biological Agents and their Consequences* (Castillo-Chavez, Carlos; Roberts, Fred S.) 55 page

Syndromic surveillance: reports from a national conference, 2003

Overview of Syndromic Surveillance -- What is Syndromic Surveillance? -- Linking Better Surveillance to Better Outcomes -- Review of the 2003 National Syndromic Surveillance Conference - Lessons Learned and Questions To Be Answered -- -- System Descriptions -- New York City Syndromic Surveillance Systems -- Syndrome and Outbreak Detection Using Chief-Complaint Data - Experience of the Real-Time Outbreak and Disease Surveillance Project -- Removing a Barrier to Computer-Based Outbreak and Disease Surveillance - The RODS Open Source Project -- National Retail Data Monitor for Public Health Surveillance -- National Bioterrorism Syndromic Surveillance Demonstration Program -- Daily Emergency Department Surveillance System - Bergen County, New Jersey -- Hospital Admissions Syndromic Surveillance - Connecticut, September 2001-November 2003 -- BioSense - A National Initiative for Early Detection and Quantification of Public Health Emergencies -- Syndromic Surveillance at Hospital Emergency Departments - Southeastern Virginia -- -- Research Methods -- Bivariate Method for Spatio-Temporal Syndromic Surveillance -- Role of Data Aggregation in Biosurveillance Detection Strategies with Applications from ESSENCE -- Scan Statistics for Temporal Surveillance for Biologic Terrorism -- Approaches to Syndromic Surveillance When Data Consist of Small Regional Counts -- Algorithm for Statistical Detection of Peaks - Syndromic Surveillance System for the Athens 2004 Olympic Games -- Taming Variability in Free Text: Application to Health Surveillance -- Comparison of Two Major Emergency Department-Based Free-Text Chief-Complaint Coding Systems -- How Many Illnesses Does One Emergency Department Visit Represent? Using a Population-Based Telephone Survey To Estimate the Syndromic Multiplier -- Comparison of Office Visit and Nurse Advice Hotline Data for Syndromic Surveillance - Baltimore-Washington, D.C., Metropolitan Area, 2002 -- Progress in Understanding and Using Over-the-Counter Pharmaceuticals for Syndromic Surveillance -- -- Evaluation -- Evaluation Challenges for Syndromic Surveillance - Making Incremental Progress -- Measuring Outbreak-Detection Performance By Using Controlled Feature Set Simulations -- Evaluation of Syndromic Surveillance Systems - Design of an Epidemic Simulation Model -- Benchmark Data and Power Calculations for Evaluating Disease Outbreak Detection Methods -- Bio-ALIRT Biosurveillance Detection Algorithm Evaluation -- ESSENCE II and the Framework for Evaluating Syndromic Surveillance Systems -- Conducting Population Behavioral Health Surveillance by Using Automated Diagnostic and Pharmacy Data Systems -- Evaluation of an Electronic General-Practitioner-Based Syndromic Surveillance System -- National Symptom Surveillance Using Calls to a Telephone Health Advice Service - United Kingdom, December 2001-February 2003 -- Field Investigations of Emergency Department Syndromic Surveillance Signals - New York City -- Should We Be Worried? Investigation of Signals Generated by an Electronic Syndromic Surveillance System - Westchester County, New York -- -- Public Health Practice -- Public Health Information Network - Improving Early Detection by Using a Standards-Based Approach to Connecting Public Health and Clinical Medicine -- Information System Architectures for Syndromic Surveillance -- Perspective of an Emergency Physician Group as a Data Provider for Syndromic Surveillance -- SARS Surveillance Project - Internet-Enabled Multiregion Surveillance for Rapidly Emerging Disease -- Health Information Privacy and Syndromic Surveillance SystemsPapers from the second annual National Syndromic Surveillance Conference convened by the New York City Department of Health and Mental Hygiene, the New York Academy of Medicine, and the CDC in New York City during Oct. 23-24, 2003. Published as the September 24, 2004 supplement to vol. 53 of MMWR. Morbidity and mortality weekly report.1571461