The use of mixture density networks in the emulation of complex epidemiological individual-based models

Complex, highly-computational, individual-based models are abundant in epidemiology. For epidemics such as macro-parasitic diseases, detailed modelling of human behaviour and pathogen life-cycle are required in order to produce accurate results. This can often lead to models that are computationally-expensive to analyse and perform model fitting, and often require many simulation runs in order to build up sufficient statistics. Emulation can provide a more computationally-efficient output of the individual-based model, by approximating it using a statistical model. Previous work has used Gaussian processes (GPs) in order to achieve this, but these can not deal with multi-modal, heavy-tailed, or discrete distributions. Here, we introduce the concept of a mixture density network (MDN) in its application in the emulation of epidemiological models. MDNs incorporate both a mixture model and a neural network to provide a flexible tool for emulating a variety of models and outputs. We develop an MDN emulation methodology and demonstrate its use on a number of simple models incorporating both normal, gamma and beta distribution outputs. We then explore its use on the stochastic SIR model to predict the final size distribution and infection dynamics. MDNs have the potential to faithfully reproduce multiple outputs of an individual-based model and allow for rapid analysis from a range of users. As such, an open-access library of the method has been released alongside this manuscript

SPADE4: Sparsity and Delay Embedding based Forecasting of Epidemics

Predicting the evolution of diseases is challenging, especially when the data availability is scarce and incomplete. The most popular tools for modelling and predicting infectious disease epidemics are compartmental models. They stratify the population into compartments according to health status and model the dynamics of these compartments using dynamical systems. However, these predefined systems may not capture the true dynamics of the epidemic due to the complexity of the disease transmission and human interactions. In order to overcome this drawback, we propose Sparsity and Delay Embedding based Forecasting (SPADE4) for predicting epidemics. SPADE4 predicts the future trajectory of an observable variable without the knowledge of the other variables or the underlying system. We use random features model with sparse regression to handle the data scarcity issue and employ Takens' delay embedding theorem to capture the nature of the underlying system from the observed variable. We show that our approach outperforms compartmental models when applied to both simulated and real data.Comment: 24 pages, 13 figures, 2 table

A Bayesian generative neural network framework for epidemic inference problems

The reconstruction of missing information in epidemic spreading on contact networks can be essential in the prevention and containment strategies. The identification and warning of infectious but asymptomatic individuals (i.e., contact tracing), the well-known patient-zero problem, or the inference of the infectivity values in structured populations are examples of significant epidemic inference problems. As the number of possible epidemic cascades grows exponentially with the number of individuals involved and only an almost negligible subset of them is compatible with the observations (e.g., medical tests), epidemic inference in contact networks poses incredible computational challenges. We present a new generative neural networks framework that learns to generate the most probable infection cascades compatible with observations. The proposed method achieves better (in some cases, significantly better) or comparable results with existing methods in all problems considered both in synthetic and real contact networks. Given its generality, clear Bayesian and variational nature, the presented framework paves the way to solve fundamental inference epidemic problems with high precision in small and medium-sized real case scenarios such as the spread of infections in workplaces and hospitals

Cascading Behavior in Large Blog Graphs

How do blogs cite and influence each other? How do such links evolve? Does the popularity of old blog posts drop exponentially with time? These are some of the questions that we address in this work. Our goal is to build a model that generates realistic cascades, so that it can help us with link prediction and outlier detection. Blogs (weblogs) have become an important medium of information because of their timely publication, ease of use, and wide availability. In fact, they often make headlines, by discussing and discovering evidence about political events and facts. Often blogs link to one another, creating a publicly available record of how information and influence spreads through an underlying social network. Aggregating links from several blog posts creates a directed graph which we analyze to discover the patterns of information propagation in blogspace, and thereby understand the underlying social network. Not only are blogs interesting on their own merit, but our analysis also sheds light on how rumors, viruses, and ideas propagate over social and computer networks. Here we report some surprising findings of the blog linking and information propagation structure, after we analyzed one of the largest available datasets, with 45,000 blogs and ~ 2.2 million blog-postings. Our analysis also sheds light on how rumors, viruses, and ideas propagate over social and computer networks. We also present a simple model that mimics the spread of information on the blogosphere, and produces information cascades very similar to those found in real life