Bayesian covariance matrix estimation using a mixture of decomposable graphical models

We present a Bayesian approach to estimating a covariance matrix by using a prior that is a mixture over all decomposable graphs, with the probability of each graph size specified by the user and graphs of equal size assigned equal probability. Most previous approaches assume that all graphs are equally probable. We show empirically that the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs in more efficiently estimating the covariance matrix. The prior requires knowing the number of decomposable graphs for each graph size and we give a simulation method for estimating these counts. We also present a Markov chain Monte Carlo method for estimating the posterior distribution of the covariance matrix that is much more efficient than current methods. Both the prior and the simulation method to evaluate the prior apply generally to any decomposable graphical model.     

Optimal designs for treatment comparisons represented by graphs

Consider an experiment for comparing a set of treatments: in each trial, one treatment is chosen and its effect determines the mean response of the trial. We examine the optimal approximate designs for the estimation of a system of treatment contrasts under this model. These designs can be used to provide optimal treatment proportions in more general models with nuisance effects. For any system of pairwise treatment comparisons, we propose to represent such a system by a graph. Then, we represent the designs by the inverses of the vertex weights in the corresponding graph and we show that the values of the eigenvalue-based optimality criteria can be expressed using the Laplacians of the vertex-weighted graphs. We provide a graph theoretic interpretation of D-, A- and E-optimality for estimating sets of pairwise comparisons. We apply the obtained graph representation to provide optimality results for these criteria as well as for ’symmetric’ systems of treatment contrasts.     

Joint response graphs and separation induced by triangular systems

Summary.  We consider joint probability distributions generated recursively in terms of univariate conditional distributions satisfying conditional independence restrictions. The independences are captured by missing edges in a directed graph. A matrix form of such a graph, called the generating edge matrix, is triangular so the distributions that are generated over such graphs are called triangular systems. We study consequences of triangular systems after grouping or reordering of the variables for analyses as chain graph models, i.e. for alternative recursive factorizations of the given density using joint conditional distributions. For this we introduce families of linear triangular equations which do not require assumptions of distributional form. The strength of the associations that are implied by such linear families for chain graph models is derived. The edge matrices of chain graphs that are implied by any triangular system are obtained by appropriately transforming the generating edge matrix. It is shown how induced independences and dependences can be studied by graphs, by edge matrix calculations and via the properties of densities. Some ways of using the results are illustrated.     

CVX‐based algorithms for constructing various optimal regression designs

CVX‐based numerical algorithms are widely and freely available for solving convex optimization problems but their applications to solve optimal design problems are limited. Using the CVX programs in MATLAB, we demonstrate their utility and flexibility over traditional algorithms in statistics for finding different types of optimal approximate designs under a convex criterion for nonlinear models. They are generally fast and easy to implement for any model and any convex optimality criterion. We derive theoretical properties of the algorithms and use them to generate new A‐, c‐, D‐ and E‐optimal designs for various nonlinear models, including multi‐stage and multi‐objective optimal designs. We report properties of the optimal designs and provide sample CVX program codes for some of our examples that users can amend to find tailored optimal designs for their problems. The Canadian Journal of Statistics 47: 374–391; 2019 © 2019 Statistical Society of Canada     

On Block Ordering of Variables in Graphical Modelling

Abstract.  In graphical modelling, the existence of substantive background knowledge on block ordering of variables is used to perform structural learning within the family of chain graphs (CGs) in which every block corresponds to an undirected graph and edges joining vertices in different blocks are directed in accordance with the ordering. We show that this practice may lead to an inappropriate restriction of the search space and introduce the concept of labelled block ordering B corresponding to a family of B - consistent CGs in which every block may be either an undirected graph or a directed acyclic graph or, more generally, a CG. In this way we provide a flexible tool for specifying subsets of chain graphs, and we observe that the most relevant subsets of CGs considered in the literature are families of B -consistent CGs for the appropriate choice of B . Structural learning within a family of B -consistent CGs requires to deal with Markov equivalence. We provide a graphical characterization of equivalence classes of B -consistent CGs, namely the B - essential graphs , as well as a procedure to construct the B -essential graph for any given equivalence class of B -consistent chain graphs. Both largest CGs and essential graphs turn out to be special cases of B -essential graphs.     

Spanning trees and identifiability of a single-factor model

The aim of this paper is to propose conditions for exploring the class of identifiable Gaussian models with one latent variable. In particular, we focus attention on the topological structure of the complementary graph of the residuals. These conditions are mainly based on the presence of odd cycles and bridge edges in the complementary graph. We propose to use the spanning tree representation of the graph and the associated matrix of fundamental cycles. In this way it is possible to obtain an algorithm able to establish in advance whether modifying the graph corresponding to an identifiable model, the resulting graph still denotes identifiability.     

On the Exponential Decay Rate of the Tail of a Discrete Probability Distribution

Abstract

We give a sufficient condition for the exponential decay of the tail of a discrete probability distribution π = (π _n ) _n≥0 in the sense that lim _n→∞(1/n) log∑ _i>n π _i  = ?θ with 0 < θ < ∞. We focus on analytic properties of the probability generating function of a discrete probability distribution, especially, the radius of convergence and the number of poles on the circle of convergence. Furthermore, we give an example of an M/G/1 type Markov chain such that the tail of its stationary distribution does not decay exponentially.     

An ADMM with continuation algorithm for non-convex SICA-penalized regression in high dimensions

The smooth integration of counting and absolute deviation (SICA) penalty has been demonstrated theoretically and practically to be effective in non-convex penalization for variable selection. However, solving the non-convex optimization problem associated with the SICA penalty when the number of variables exceeds the sample size remains to be enriched due to the singularity at the origin and the non-convexity of the SICA penalty function. In this paper, we develop an efficient and accurate alternating direction method of multipliers with continuation algorithm for solving the SICA-penalized least squares problem in high dimensions. We establish the convergence property of the proposed algorithm under some mild regularity conditions and study the corresponding Karush–Kuhn–Tucker optimality condition. A high-dimensional Bayesian information criterion is developed to select the optimal tuning parameters. We conduct extensive simulations studies to evaluate the efficiency and accuracy of the proposed algorithm, while its practical usefulness is further illustrated with a high-dimensional microarray study.     

Experimental designs for detecting synergy and antagonism between two drugs in a pre‐clinical study

The identification of synergistic interactions between combinations of drugs is an important area within drug discovery and development. Pre‐clinically, large numbers of screening studies to identify synergistic pairs of compounds can often be ran, necessitating efficient and robust experimental designs. We consider experimental designs for detecting interaction between two drugs in a pre‐clinical in vitro assay in the presence of uncertainty of the monotherapy response. The monotherapies are assumed to follow the Hill equation with common lower and upper asymptotes, and a common variance. The optimality criterion used is the variance of the interaction parameter. We focus on ray designs and investigate two algorithms for selecting the optimum set of dose combinations. The first is a forward algorithm in which design points are added sequentially. This is found to give useful solutions in simple cases but can lack robustness when knowledge about the monotherapy parameters is insufficient. The second algorithm is a more pragmatic approach where the design points are constrained to be distributed log‐normally along the rays and monotherapy doses. We find that the pragmatic algorithm is more stable than the forward algorithm, and even when the forward algorithm has converged, the pragmatic algorithm can still out‐perform it. Practically, we find that good designs for detecting an interaction have equal numbers of points on monotherapies and combination therapies, with those points typically placed in positions where a 50% response is expected. More uncertainty in monotherapy parameters leads to an optimal design with design points that are more spread out. Copyright © 2015 John Wiley & Sons, Ltd.     

Degree-based goodness-of-fit tests for heterogeneous random graph models: Independent and exchangeable cases

The degrees are a classical and relevant way to study the topology of a network. They can be used to assess the goodness of fit for a given random graph model. In this paper, we introduce goodness-of-fit tests for two classes of models. First, we consider the case of independent graph models such as the heterogeneous Erdös-Rényi model in which the edges have different connection probabilities. Second, we consider a generic model for exchangeable random graphs called the W-graph. The stochastic block model and the expected degree distribution model fall within this framework. We prove the asymptotic normality of the degree mean square under these independent and exchangeable models and derive formal tests. We study the power of the proposed tests and we prove the asymptotic normality under specific sparsity regimes. The tests are illustrated on real networks from social sciences and ecology, and their performances are assessed via a simulation study.     

Mixed Graphical Models with Missing Data and the Partial Imputation EM Algorithm

In this paper we discuss graphical models for mixed types of continuous and discrete variables with incomplete data. We use a set of hyperedges to represent an observed data pattern. A hyperedge is a set of variables observed for a group of individuals. In a mixed graph with two types of vertices and two types of edges, dots and circles represent discrete and continuous variables respectively. A normal graph represents a graphical model and a hypergraph represents an observed data pattern. In terms of the mixed graph, we discuss decomposition of mixed graphical models with incomplete data, and we present a partial imputation method which can be used in the EM algorithm and the Gibbs sampler to speed their convergence. For a given mixed graphical model and an observed data pattern, we try to decompose a large graph into several small ones so that the original likelihood can be factored into a product of likelihoods with distinct parameters for small graphs. For the case that a graph cannot be decomposed due to its observed data pattern, we can impute missing data partially so that the graph can be decomposed.     

Metrics and barycenters for point pattern data

We introduce the transport–transform and the relative transport–transform metrics between finite point patterns on a general space, which provide a unified framework for earlier point pattern metrics, in particular the generalized spike time and the normalized and unnormalized optimal subpattern assignment metrics. Our main focus is on barycenters, i.e., minimizers of a q-th-order Fréchet functional with respect to these metrics. We present a heuristic algorithm that terminates in a local minimum and is shown to be fast and reliable in a simulation study. The algorithm serves as a general plug-in method that can be applied to point patterns on any state space where an appropriate algorithm for solving the location problem for individual points is available. We present applications to geocoded data of crimes in Euclidean space and on a street network, illustrating that barycenters serve as informative summary statistics. Our work is a first step toward statistical inference in covariate-based models of repeated point pattern observations.     

Label‐ and Level‐Invariant Graphical Log‐Linear Models

We introduce two types of graphical log‐linear models: label‐ and level‐invariant models for triangle‐free graphs. These models generalise symmetry concepts in graphical log‐linear models and provide a tool with which to model symmetry in the discrete case. A label‐invariant model is category‐invariant and is preserved after permuting some of the vertices according to transformations that maintain the graph, whereas a level‐invariant model equates expected frequencies according to a given set of permutations. These new models can both be seen as instances of a new type of graphical log‐linear model termed the restricted graphical log‐linear model, or RGLL, in which equality restrictions on subsets of main effects and first‐order interactions are imposed. Their likelihood equations and graphical representation can be obtained from those derived for the RGLL models.     

Stochastic relaxation,Gibbs distributions and the Bayesian restoration of images*

We make an analogy between images and statistical mechanics systems. Pixel gray levels and the presence and orientation of edges are viewed as states of atoms or molecules in a lattice-like physical system. The assignment of an energy function in the physical system determines its Gibbs distribution. Because of the Gibbs distribution, Markov random field (MRF) equivalence, this assignment also determines an MRF image model. The energy function is a more convenient and natural mechanism for embodying picture attributes than are the local characteristics of the MRF. For a range of degradation mechanisms, including blurring, non-linear deformations, and multiplicative or additive noise, the posterior distribution is an MRF with a structure akin to the image model. By the analogy, the posterior distribution defines another (imaginary) physical system. Gradual temperature reduction in the physical system isolates low-energy states (‘annealing’), or what is the same thing, the most probable states under the Gibbs distribution. The analogous operation under the posterior distribution yields the maximum a posteriori (MAP) estimate of the image given the degraded observations. The result is a highly parallel ‘relaxation’ algorithm for MAP estimation. We establish convergence properties of the algorithm and we experiment with some simple pictures, for which good restorations are obtained at low signal-to-noise ratios.     

A modified ziggurat algorithm for generating exponentially and normally distributed pseudorandom numbers

The ziggurat algorithm is a very fast rejection sampling method for generating pseudorandom numbers (PRNs) from statistical distributions. In the algorithm, rectangular sampling domains are layered on top of each other (resembling a ziggurat) to encapsulate the desired probability density function. Random values within these layers are sampled and then returned if they lie beneath the graph of the probability density function. Here, we present an implementation where ziggurat layers reside completely beneath the probability density function, thereby eliminating the need for any rejection test within the ziggurat layers. In the new algorithm, small overhanging segments of probability density remain to the right of each ziggurat layer, which can be efficiently sampled with triangularly shaped sampling domains. Median runtimes of the new algorithm for exponential and normal variates is reduced to 58% and 53%, respectively (collective range: 41–93%). An accessible C library, along with extensions into Python and MATLAB/Octave are provided.     

Tail Probability of Low-Priority Queue Length in a Discrete-Time Priority BMAP/PH/1 Queue

ABSTRACT

We investigate the tail probability of the queue length of low-priority class for a discrete-time priority BMAP/PH/1 queue that consists of two priority classes, with BMAP (Batch Markovian Arrival Process) arrivals of high-priority class and MAP (Markovian Arrival Process) arrivals of low-priority class. A sufficient condition under which this tail probability has the asymptotically geometric property is derived. A method is designed to compute the asymptotic decay rate if the asymptotically geometric property holds. For the case when the BMAP for high-priority class is the superposition of a number of MAP's, though the parameter matrices representing the BMAP is huge in dimension, the sufficient condition is numerically easy to verify and the asymptotic decay rate can be computed efficiently.     

Cytometry inference through adaptive atomic deconvolution

In this paper, we consider a statistical estimation problem known as atomic deconvolution. Introduced in reliability, this model has a direct application when considering biological data produced by flow cytometers. From a statistical point of view, we aim at inferring the percentage of cells expressing the selected molecule and the probability distribution function associated with its fluorescence emission. We propose here an adaptive estimation procedure based on a previous deconvolution procedure introduced by Es, Gugushvili, and Spreij [(2008), ‘Deconvolution for an atomic distribution’, Electronic Journal of Statistics, 2, 265–297] and Gugushvili, Es, and Spreij [(2011), ‘Deconvolution for an atomic distribution: rates of convergence’, Journal of Nonparametric Statistics, 23, 1003–1029]. For both estimating the mixing parameter and the mixing density automatically, we use the Lepskii method based on the optimal choice of a bandwidth using a bias-variance decomposition. We then derive some convergence rates that are shown to be minimax optimal (up to some log terms) in Sobolev classes. Finally, we apply our algorithm on the simulated and real biological data.     

MAP segmentation in Bayesian hidden Markov models: a case study

We consider the problem of estimating the maximum posterior probability (MAP) state sequence for a finite state and finite emission alphabet hidden Markov model (HMM) in the Bayesian setup, where both emission and transition matrices have Dirichlet priors. We study a training set consisting of thousands of protein alignment pairs. The training data is used to set the prior hyperparameters for Bayesian MAP segmentation. Since the Viterbi algorithm is not applicable any more, there is no simple procedure to find the MAP path, and several iterative algorithms are considered and compared. The main goal of the paper is to test the Bayesian setup against the frequentist one, where the parameters of HMM are estimated using the training data.     

Sequential Monte Carlo for counting vertex covers in general graphs

In this paper we describe a sequential importance sampling (SIS) procedure for counting the number of vertex covers in general graphs. The optimal SIS proposal distribution is the uniform over a suitably restricted set, but is not implementable. We will consider two proposal distributions as approximations to the optimal. Both proposals are based on randomization techniques. The first randomization is the classic probability model of random graphs, and in fact, the resulting SIS algorithm shows polynomial complexity for random graphs. The second randomization introduces a probabilistic relaxation technique that uses Dynamic Programming. The numerical experiments show that the resulting SIS algorithm enjoys excellent practical performance in comparison with existing methods. In particular the method is compared with cachet—an exact model counter, and the state of the art SampleSearch, which is based on Belief Networks and importance sampling.     

Maximum Likelihood Estimation in Gaussian Chain Graph Models under the Alternative Markov Property

Abstract.  The Andersson–Madigan–Perlman (AMP) Markov property is a recently proposed alternative Markov property (AMP) for chain graphs. In the case of continuous variables with a joint multivariate Gaussian distribution, it is the AMP rather than the earlier introduced Lauritzen–Wermuth–Frydenberg Markov property that is coherent with data-generation by natural block-recursive regressions. In this paper, we show that maximum likelihood estimates in Gaussian AMP chain graph models can be obtained by combining generalized least squares and iterative proportional fitting to an iterative algorithm. In an appendix, we give useful convergence results for iterative partial maximization algorithms that apply in particular to the described algorithm.