We propose a new method for approximate Bayesian statistical inference on the basis of summary statistics. The method is suited to complex problems that arise in population genetics, extending ideas developed in this setting by earlier authors. Properties of the posterior distribution of a parameter, such as its mean or density curve, are approximated without explicit likelihood calculations. This is achieved by fitting a local-linear regression of simulated parameter values on simulated summary statistics, and then substituting the observed summary statistics into the regression equation. The method combines many of the advantages of Bayesian statistical inference with the computational efficiency of methods based on summary statistics. A key advantage of the method is that the nuisance parameters are automatically integrated out in the simulation step, so that the large numbers of nuisance parameters that arise in population genetics problems can be handled without difficulty. Simulation results indicate computational and statistical efficiency that compares favorably with those of alternative methods previously proposed in the literature. We also compare the relative efficiency of inferences obtained using methods based on summary statistics with those obtained directly from the data using MCMC.

https://www.genetics.org/content/genetics/162/4/2025.full.pdf

Approximate Bayesian computation in population genetics.

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and “ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

/pdf/inference-of-population-splits-and-mixtures-from-genome-wide-95zsqu79wu.pdf

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

Approximate Bayesian computation (ABC) methods can be used to evaluate posterior distributions without having to calculate likelihoods. In this paper, we discuss and apply an ABC method based on sequential Monte Carlo (SMC) to estimate parameters of dynamical models. We show that ABC SMC provides information about the inferability of parameters and model sensitivity to changes in parameters, and tends to perform better than other ABC approaches. The algorithm is applied to several well-known biological systems, for which parameters and their credible intervals are inferred. Moreover, we develop ABC SMC as a tool for model selection; given a range of different mathematical descriptions, ABC SMC is able to choose the best model using the standard Bayesian model selection apparatus.

/pdf/approximate-bayesian-computation-scheme-for-parameter-2fv1wot0rh.pdf

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

Machine learning (ML) encompasses a broad range of algorithms and modeling tools used for a vast array of data processing tasks, which has entered most scientific disciplines in recent years. This article reviews in a selective way the recent research on the interface between machine learning and the physical sciences. This includes conceptual developments in ML motivated by physical insights, applications of machine learning techniques to several domains in physics, and cross fertilization between the two fields. After giving a basic notion of machine learning methods and principles, examples are described of how statistical physics is used to understand methods in ML. This review then describes applications of ML methods in particle physics and cosmology, quantum many-body physics, quantum computing, and chemical and material physics. Research and development into novel computing architectures aimed at accelerating ML are also highlighted. Each of the sections describe recent successes as well as domain-specific methodology and challenges.

Machine learning and the physical sciences

Varying coefficient models are a useful extension of classical linear models. They arise naturally when one wishes to examine how regression coefficients change over different groups characterized by certain covariates such as age. The appeal of these models is that the coef .cient functions can easily be estimated via a simple local regression.This yields a simple one-step estimation procedure. We show that such a one-step method cannot be optimal when different coefficient functions admit different degrees of smoothness. This drawback can be repaired by using our proposed two-step estimation procedure.The asymptotic mean-squared error for the two-step procedure is obtained and is shown to achieve the optimal rate of convergence. A few simulation studies show that the gain by the two-step procedure can be quite substantial.The methodology is illustrated by an application to an environmental data set.

/pdf/statistical-estimation-in-varying-coefficient-models-3sk5x25vc6.pdf

Statistical estimation in varying coefficient models

The varying coefficient models are very important tool to explore the dynamic pattern in many scientific areas, such as economics, finance, politics, epidemiology, medical science, ecology and so on. They are natural extensions of classical parametric models with good interpretability and are becoming more and more popular in data analysis. Thanks to their flexibility and interpretability, in the past ten years, the varying coefficient models have experienced deep and exciting developments on methodological, theoretical and applied sides. This paper gives a selective overview on the major methodological and theoretical developments on the varying coefficient models.

https://www.intlpress.com/site/pub/files/_fulltext/journals/sii/2008/0001/0001/SII-2008-0001-0001-a015.pdf

Wenyang Zhang

Papers

Approximate Bayesian computation in population genetics.

Approximate Bayesian computation in population genetics.

Statistical estimation in varying coefficient models

Statistical Methods with Varying Coefficient Models.

Local Polynomial Fitting in Semivarying Coefficient Model