Machine learning is a branch of computer science that has the potential to transform epidemiologic sciences. Amid a growing focus on "Big Data," it offers epidemiologists new tools to tackle problems for which classical methods are not well-suited. In order to critically evaluate the value of integrating machine learning algorithms and existing methods, however, it is essential to address language and technical barriers between the two fields that can make it difficult for epidemiologists to read and assess machine learning studies. Here, we provide an overview of the concepts and terminology used in machine learning literature, which encompasses a diverse set of tools with goals ranging from prediction to classification to clustering. We provide a brief introduction to 5 common machine learning algorithms and 4 ensemble-based approaches. We then summarize epidemiologic applications of machine learning techniques in the published literature. We recommend approaches to incorporate machine learning in epidemiologic research and discuss opportunities and challenges for integrating machine learning and existing epidemiologic research methods. Machine learning is a branch of computer science that broadly aims to enable computers to "learn" without being directly programmed (1). It has origins in the artificial intelligence movement of the 1950s and emphasizes practical objectives and applications, particularly prediction and optimization. Computers "learn" in machine learning by improving their performance at tasks through "experience" (2, p. xv). In practice, "experience" usually means fitting to data; hence, there is not a clear boundary between machine learning and statistical approaches. Indeed, whether a given methodology is considered "machine learning" or "statistical" often reflects its history as much as genuine differences, and many algorithms (e.g., least absolute shrinkage and selection operator (LASSO), stepwise regression) may or may not be considered machine learning depending on who you ask. Still, despite methodological similarities, machine learning is philosophically and practically distinguishable. At the liberty of (considerable) oversimplification, machine learning generally emphasizes predictive accuracy over hypothesis-driven inference, usually focusing on large, high-dimensional (i.e., having many covariates) data sets (3, 4). Regardless of the precise distinction between approaches, in practice, machine learning offers epidemiologists important tools. In particular, a growing focus on "Big Data" emphasizes problems and data sets for which machine learning algorithms excel while more commonly used statistical approaches struggle. This primer provides a basic introduction to machine learning with the aim of providing readers a foundation for critically reading studies based on these methods and a jumping-off point for those interested in using machine learning techniques in epidemiologic research.
Recently, the Centers for Disease Control and Prevention (CDC) has worked with other federal agencies to identify counties with increasing coronavirus disease 2019 (COVID-19) incidence (hotspots) and offers support to local health departments to limit the spread of the disease. Understanding the spatio-temporal dynamics of hotspot events is of great importance to support policy decisions and prevent large-scale outbreaks. This paper presents a spatio-temporal Bayesian framework for early detection of COVID-19 hotspots (at the county level) in the United States. We assume both the observed number of cases and hotspots depend on a class of latent random variables, which encode the underlying spatio-temporal dynamics of the transmission of COVID-19. Such latent variables follow a zero-mean Gaussian process, whose covariance is specified by a non-stationary kernel function. The most salient feature of our kernel function is that deep neural networks are introduced to enhance the model's representative power while still enjoying the interpretability of the kernel. We derive a sparse model and fit the model using a variational learning strategy to circumvent the computational intractability for large data sets. Our model demonstrates better interpretability and superior hotspot-detection performance compared to other baseline methods.
Epidemiology models are central in understanding and controlling large scale pandemics. Several epidemiology models require simulation-based inference such as Approximate Bayesian Computation (ABC) to fit their parameters to observations. ABC inference is highly amenable to efficient hardware acceleration. In this work, we develop parallel ABC inference of a stochastic epidemiology model for COVID-19. The statistical inference framework is implemented and compared on Intel Xeon CPU, NVIDIA Tesla V100 GPU and the Graphcore Mk1 IPU, and the results are discussed in the context of their computational architectures. Results show that GPUs are 4x and IPUs are 30x faster than Xeon CPUs. Extensive performance analysis indicates that the difference between IPU and GPU can be attributed to higher communication bandwidth, closeness of memory to compute, and higher compute power in the IPU. The proposed framework scales across 16 IPUs, with scaling overhead not exceeding 8% for the experiments performed. We present an example of our framework in practice, performing inference on the epidemiology model across three countries, and giving a brief overview of the results.
In these applications, one often can only observe or use selected components of the data for decisionmaking due to the capacity limitation in data acquisition, transmission, processing, or storage. For instance, the sensor devices might have limited battery powers; thus, one might want to use a subset of sensors per time step over a long period instead of using full sensors simultaneously over a short period. Likewise, while sensing is usually cheap, the communication bandwidth is often limited from remote sensors to the fusion center that makes a global decision. The fusion center might prioritize certain local sensors to send local information for decision making. Also, in many applications such as quality engineering or biosurveillance, one faces the design issue and needs to decide which variables or patients to be measured to detect the defect or disease outbreak more efficiently. This paper aims to investigate how to efficiently real-time monitor high-dimensional streaming data under resource constraints.
Baker, Antoine, Biazzo, Indaco, Braunstein, Alfredo, Catania, Giovanni, Dall'Asta, Luca, Ingrosso, Alessandro, Krzakala, Florent, Mazza, Fabio, Mézard, Marc, Muntoni, Anna Paola, Refinetti, Maria, Mannelli, Stefano Sarao, Zdeborová, Lenka
Contact-tracing is an essential tool in order to mitigate the impact of pandemic such as the COVID-19. In order to achieve efficient and scalable contact-tracing in real time, digital devices can play an important role. While a lot of attention has been paid to analyzing the privacy and ethical risks of the associated mobile applications, so far much less research has been devoted to optimizing their performance and assessing their impact on the mitigation of the epidemic. We develop Bayesian inference methods to estimate the risk that an individual is infected. This inference is based on the list of his recent contacts and their own risk levels, as well as personal information such as results of tests or presence of syndromes. We propose to use probabilistic risk estimation in order to optimize testing and quarantining strategies for the control of an epidemic. Our results show that in some range of epidemic spreading (typically when the manual tracing of all contacts of infected people becomes practically impossible, but before the fraction of infected people reaches the scale where a lockdown becomes unavoidable), this inference of individuals at risk could be an efficient way to mitigate the epidemic. Our approaches translate into fully distributed algorithms that only require communication between individuals who have recently been in contact. Such communication may be encrypted and anonymized and thus compatible with privacy preserving standards. We conclude that probabilistic risk estimation is capable to enhance performance of digital contact tracing and should be considered in the currently developed mobile applications. Identifying, calling, testing, and if needed quarantining the recent contacts of an individual who has just been tested positive is the standard route for limiting the transmission of a highly contagious virus.
The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. While standard methods exist, they work best at coarse-grained national or state scales with abundant data, and struggle to accommodate the partial observability and sparse data common at finer scales (e.g., individual schools or towns). For example, case counts may be sparse when only a small fraction of infections are caught by a testing program. Or, whether an infected individual tests positive may depend on the kind of test and the point in time when they are tested. We propose a Bayesian framework which accommodates partial observability in a principled manner. Our model places a Gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. For example, our framework can accommodate a variety of kinds of tests (viral RNA, antibody, antigen, etc.) and sampling schemes (e.g., longitudinal or cross-sectional screening). Inference in this framework is complicated by the presence of tens or hundreds of thousands of discrete latent variables. To address this challenge, we propose an efficient stochastic variational inference method which relies on a novel gradient estimator for the variational objective. Experimental results for an example motivated by COVID-19 show that our method produces an accurate and well-calibrated posterior, while standard methods for estimating the reproduction number can fail badly.
Model selection is a fundamental part of Bayesian statistical inference; a widely used tool in the field of epidemiology. Simple methods such as Akaike Information Criterion are commonly used but they do not incorporate the uncertainty of the model's parameters, which can give misleading choices when comparing models with similar fit to the data. One approach to model selection in a more rigorous way that uses the full posterior distributions of the models is to compute the ratio of the normalising constants (or model evidence), known as Bayes factors. These normalising constants integrate the posterior distribution over all parameters and balance over and under fitting. However, normalising constants often come in the form of intractable, high-dimensional integrals, therefore special probabilistic techniques need to be applied to correctly estimate the Bayes factors. One such method is thermodynamic integration (TI), which can be used to estimate the ratio of two models' evidence by integrating over a continuous path between the two un-normalised densities. In this paper we introduce a variation of the TI method, here referred to as referenced TI, which computes a single model's evidence in an efficient way by using a reference density such as a multivariate normal - where the normalising constant is known. We show that referenced TI, an asymptotically exact Monte Carlo method of calculating the normalising constant of a single model, in practice converges to the correct result much faster than other competing approaches such as the method of power posteriors. We illustrate the implementation of the algorithm on informative 1- and 2-dimensional examples, and apply it to a popular linear regression problem, and use it to select parameters for a model of the COVID-19 epidemic in South Korea.
Contemporary Epidemiological Surveillance (ES) relies heavily on data analytics. These analytics are critical input for pandemics preparedness networks; however, this input is not integrated into a form suitable for decision makers or experts in preparedness. A decision support system (DSS) with Computational Intelligence (CI) tools is required to bridge the gap between epidemiological model of evidence and expert group decision. We argue that such DSS shall be a cognitive dynamic system enabling the CI and human expert to work together. The core of such DSS must be based on machine reasoning techniques such as probabilistic inference, and shall be capable of estimating risks, reliability and biases in decision making.
This paper presents a multivariate functional data statistical approach, for spatiotemporal prediction of COVID-19 mortality counts. Specifically, spatial heterogeneous nonlinear parametric functional regression trend model fitting is first implemented. Classical and Bayesian infinite-dimensional log-Gaussian linear residual correlation analysis is then applied. The nonlinear regression predictor of the mortality risk is combined with the plug-in predictor of the multiplicative error term. An empirical model ranking, based on random K-fold validation, is established for COVID-19 mortality risk forecasting and assessment, involving Machine Learning (ML) models, and the adopted Classical and Bayesian semilinear estimation approach. This empirical analysis also determines the ML models favored by the spatial multivariate Functional Data Analysis (FDA) framework. The results could be extrapolated to other countries.
Events are occurrences in specific locations, time, and semantics that nontrivially impact either our society or the nature, such as civil unrest, system failures, and epidemics. It is highly desirable to be able to anticipate the occurrence of such events in advance in order to reduce the potential social upheaval and damage caused. Event prediction, which has traditionally been prohibitively challenging, is now becoming a viable option in the big data era and is thus experiencing rapid growth. There is a large amount of existing work that focuses on addressing the challenges involved, including heterogeneous multi-faceted outputs, complex dependencies, and streaming data feeds. Most existing event prediction methods were initially designed to deal with specific application domains, though the techniques and evaluation procedures utilized are usually generalizable across different domains. However, it is imperative yet difficult to cross-reference the techniques across different domains, given the absence of a comprehensive literature survey for event prediction. This paper aims to provide a systematic and comprehensive survey of the technologies, applications, and evaluations of event prediction in the big data era. First, systematic categorization and summary of existing techniques are presented, which facilitate domain experts' searches for suitable techniques and help model developers consolidate their research at the frontiers. Then, comprehensive categorization and summary of major application domains are provided. Evaluation metrics and procedures are summarized and standardized to unify the understanding of model performance among stakeholders, model developers, and domain experts in various application domains. Finally, open problems and future directions for this promising and important domain are elucidated and discussed.