arXiv subjects

Samuel V. Scarpino

Publications and source records attributed to Samuel V. Scarpino.

25 records · Page 2Linked to original sources

arXiv2017

Asymmetric percolation drives a double transition in sexual contact networks

Zika virus (ZIKV) exhibits unique transmission dynamics in that it is concurrently spread by a mosquito vector and through sexual contact. We show that this sexual component of ZIKV transmission induces novel processes on networks through the highly asymmetric durations of infectiousness between males and females -- it is estimated that males are infectious for periods up to ten times longer than females -- leading to an asymmetric percolation process on the network of sexual contacts. We exactly solve the properties of this asymmetric percolation on random sexual contact networks and show that this process exhibits two epidemic transitions corresponding to a core-periphery structure. This structure is not present in the underlying contact networks, which are not distinguishable from random networks, and emerges because of the asymmetric percolation. We provide an exact analytical description of this double transition and discuss the implications of our results in the context of ZIKV epidemics. Most importantly, our study suggests a bias in our current ZIKV surveillance as the community most at risk is also one of the least likely to get tested.

physics.soc-ph↗

arXiv2016

Robust estimation of inequality from binned incomes

Researchers must often estimate income inequality using data that give only the number of cases (e.g., families or households) whose incomes fall in "bins" such as $0-9,999, $10,000-14,999,..., $200,000+. We find that popular methods for estimating inequality from binned incomes are not robust in small samples, where popular methods can produce infinite, undefined, or arbitrarily large estimates. To solve these and other problems, we develop two improved estimators: the robust Pareto midpoint estimator (RPME) and the multimodel generalized beta estimator (MGBE). In a broad evaluation using US national, state, and county data from 1970 to 2009, we find that both estimators produce very good estimates of the mean and Gini, but less accurate estimates of the Theil and mean log deviation. Neither estimator is uniformly more accurate, but the RPME is much faster, which may be a consideration when many estimates must be obtained from many datasets. We have made the methods available as the rpme and mgbe commands for Stata and the binequality package for R.

stat.ME↗

arXiv2015

Prudent behaviour accelerates disease transmission

Infectious diseases often spread faster near their peak than would be predicted given early data on transmission. Despite the commonality of this phenomena, there are no known general mechanisms able to cause an exponentially spreading dis- ease to begin spreading faster. Indeed most features of real world social networks, e.g. clustering1,2 and community structure3, and of human behaviour, e.g. social distancing4 and increased hygiene5, will slow disease spread. Here, we consider a model where individuals with essential societal roles-e.g. teachers, first responders, health-care workers, etc.- who fall ill are replaced with healthy individuals. We refer to this process as relational exchange. Relational exchange is also a behavioural process, but one whose effect on disease transmission is less obvious. By incorporating this behaviour into a dynamic network model, we demonstrate that replacing individuals can accelerate disease transmission. Furthermore, we find that the effects of this process are trivial when considering a standard mass-action model, but dramatic when considering network structure. This result highlights another critical shortcoming in mass-action models, namely their inability to account for behavioural processes. Lastly, using empirical data, we find that this mechanism parsimoniously explains observed patterns across more than seventeen years of influenza and dengue virus data. We anticipate that our findings will advance the emerging field of disease forecasting and will better inform public health decision making during outbreaks.

q-bio.QM↗

arXiv2015

A message-passing approach for recurrent-state epidemic models on networks

Epidemic processes are common out-of-equilibrium phenomena of broad interdisciplinary interest. Recently, dynamic message-passing (DMP) has been proposed as an efficient algorithm for simulating epidemic models on networks, and in particular for estimating the probability that a given node will become infectious at a particular time. To date, DMP has been applied exclusively to models with one-way state changes, as opposed to models like SIS (susceptible-infectious-susceptible) and SIRS (susceptible-infectious-recovered-susceptible) where nodes can return to previously inhabited states. Because many real-world epidemics can exhibit such recurrent dynamics, we propose a DMP algorithm for complex, recurrent epidemic models on networks. Our approach takes correlations between neighboring nodes into account while preventing causal signals from backtracking to their immediate source, and thus avoids "echo chamber effects" where a pair of adjacent nodes each amplify the probability that the other is infectious. We demonstrate that this approach well approximates results obtained from Monte Carlo simulation and that its accuracy is often superior to the pair approximation (which also takes second-order correlations into account). Moreover, our approach is more computationally efficient than the pair approximation, especially for complex epidemic models: the number of variables in our DMP approach grows as $2mk$ where $m$ is the number of edges and $k$ is the number of states, as opposed to $mk^2$ for the pair approximation. We suspect that the resulting reduction in computational effort, as well as the conceptual simplicity of DMP, will make it a useful tool in epidemic modeling, especially for inference tasks where there is a large parameter space to explore.

physics.soc-ph↗

arXiv2014

multiDimBio: An R Package for the Design, Analysis, and Visualization of Systems Biology Experiments

The past decade has witnessed a dramatic increase in the size and scope of biological and behavioral experiments. These experiments are providing an unprecedented level of detail and depth of data. However, this increase in data presents substantial statistical and graphical hurdles to overcome, namely how to distinguish signal from noise and how to visualize multidimensional results. Here we present a series of tools designed to support a research project from inception to publication. We provide implementation of dimension reduction techniques and visualizations that function well with the types of data often seen in animal behavior studies. This package is designed to be used with experimental data but can also be used for experimental design and sample justification. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques.

q-bio.QM↗

arXiv2014

Epidemiological consequences of an ineffective Bordetella pertussis vaccine

The recent increase in Bordetella pertussis incidence (whooping cough) presents a challenge to global health. Recent studies have called into question the effectiveness of acellular B. pertussis vaccination in reducing transmission. Here we examine the epidemiological consequences of an ineffective B. pertussis vaccine. Using a dynamic transmission model, we find that: 1) an ineffective vaccine can account for the observed increase in B. pertussis incidence; 2) asymptomatic infections can bias surveillance and upset situational awareness of B. pertussis; and 3) vaccinating individuals in close contact with infants too young to receive vaccine (so called "cocooning" unvaccinated children) may be ineffective. Our results have important implications for B. pertussis vaccination policy and paint a complicated picture for achieving herd immunity and possible B. pertussis eradication.

q-bio.PE↗

arXiv2012

Estimation with Binned Data

Variables such as household income are sometimes binned, so that we only know how many households fall in each of several bins such as $0-10,000, $10,000-15,000, or $200,000+. We provide a SAS macro that estimates the mean and variance of binned data by fitting the extended generalized gamma (EGG) distribution, the power normal (PN) distribution, and a new distribution that we call the power logistic (PL). The macro also implements a "best-of-breed" estimator that chooses from among the EGG, PN, and PL estimates on the basis of likelihood and finite variance. We test the macro by estimating the mean family and household incomes of approximately 13,000 US school districts between 1970 and 2009. The estimates have negligible bias (0-2%) and a root mean squared error of just 3-6%. The estimates compare favorably with estimates obtained by fitting the Dagum, generalized beta (GB2), or logspline distributions.

stat.ME↗