Ancestral Inference in Population Genetics Models with Selection (with Discussion)

A new algorithm is presented for exact simulation from the conditional distribution of the genealogical history of a sample, given the composition of the sample, for population genetics models with general diploid selection. The method applies to the usual diffusion approximation of evolution at a single locus, in a randomly mating population of constant size, for mutation models in which the distribution of the type of a mutant does not depend on the type of the progenitor allele; this includes any model with only two alleles. The new method is applied to ancestral inference for the two‐allele case, both with genic selection and heterozygote advantage and disadvantage, where one of the alleles is assumed to have resulted from a unique mutation event. The paper describes how the method could be used for inference when data are also available at neutral markers linked to the locus under selection. It also informally describes and constructs the non‐neutral Fleming–Viot measure‐valued diffusion.     

Graphical models for skew-normal variates

This paper explores the usefulness of the multivariate skew-normal distribution in the context of graphical models. A slight extension of the family recently discussed by Azzalini & Dalla Valle (1996 ) and Azzalini & Capitanio (1999 ) is described, the main motivation being the additional property of closure under conditioning. After considerations of the main probabilistic features, the focus of the paper is on the construction of conditional independence graphs for skew-normal variables. Necessary and sufficient conditions for conditional independence are stated, and the admissible structures of a graph under restriction on univariate marginal distribution are studied. Finally, parameter estimation is considered. It is shown how the factorization of the likelihood function according to a graph can be rearranged in order to obtain a parameter based factorization.     

Bayesian phylogenetic inference from animal mitochondrial genome arrangements

Summary. The determination of evolutionary relationships is a fundamental problem in evolutionary biology. Genome arrangement data are potentially more informative than deoxyribonucleic acid sequence data for inferring evolutionary relationships between distantly related taxa. We describe a Bayesian framework for phylogenetic inference from mitochondrial genome arrangement data using Markov chain Monte Carlo methods. We apply the method to assess evolutionary relationships between eight animal phyla.     

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.     

Density estimation for samples satisfying a certain absolute regularity condition

Let {ξ_i} be an absolutely regular sequence of identically distributed random variables having common density function f(x). Let H_k(x,y) (k=1, 2,…) be a sequence of Borel-measurable functions and f_n(x)=n^?1(H_n(x,ξ₁)+…+H_n(x,ξ_n)) the empirical density function. In this paper, the asymptotic property of the probability P(sup_x|f_n(x)?f(x)|>ε) (n→∞) is studied.     

CAD在位置量规设计中的应用

本文介绍了位置量规设计原理及计算公式，陈述了位置量计算机辅助设计系统的总体设计及软、硬件构成，同时介绍了为加快绘图速度对图形输入板菜单进行重新编制的方法。     

THE CONVERGENCE RATE OF SEQUENTIAL FIXED-WIDTH CONFIDENCE INTERVALS FOR REGULAR FUNCTIONALS

Let X₁X₂,.be i.i.d. random variables and let U_n= (n r)^-1S?^(n,r) h (X_i1,., X_ir,) be a U-statistic with EU_n= v, v unknown. Assume that g(X₁) =E[h(X₁,.,X_r) - v |X₁]has a strictly positive variance s?². Further, let a be such that φ(a) - φ(-a) =α for fixed α, 0 < α < 1, where φ is the standard normal d.f., and let S²_n be the Jackknife estimator of n Var U_n. Consider the stopping times N(d)= min {n: S²_n: + n^-1≤²a^-2},d > 0, and a confidence interval for v of length 2d,of the form I_n,d= [U_n,-d, Un + d]. We assume that Var U_n is unknown, and hence, no fixed sample size method is available for finding a confidence interval for v of prescribed width 2d and prescribed coverage probability α Turning to a sequential procedure, let I_N(d),d be a sequence of sequential confidence intervals for v. The asymptotic consistency of this procedure, i.e. lim_{d → 0}P(v ∈ I_N(d),d)=α follows from Sproule (1969). In this paper, the rate at which |P(v ∈ I_N(d),d) converges to α is investigated. We obtain that |P(v ∈ I_N(d),d) - α| = 0 (d^{1/2-(1+k)/2(1+m)}), d → 0, where K = max {0,4 - m}, under the condition that E|h(X₁, X_r)|^m < ∞m > 2. This improves and extends recent results of Ghosh & DasGupta (1980) and Mukhopadhyay (1981).     

Two Variations of the Minimum Steiner Problem

Given a set S of starting vertices and a set T of terminating vertices in a graph G = (V,E) with non-negative weights on edges, the minimum Steiner network problem is to find a subgraph of G with the minimum total edge weight. In such a subgraph, we require that for each vertex s S and t T, there is a path from s to a terminating vertex as well as a path from a starting vertex to t. This problem can easily be proven NP-hard. For solving the minimum Steiner network problem, we first present an algorithm that runs in time and space that both are polynomial in n with constant degrees, but exponential in |S|+|T|, where n is the number of vertices in G. Then we present an algorithm that uses space that is quadratic in n and runs in time that is polynomial in n with a degree O(max {max {|S|,|T|}–2,min {|S|,|T|}–1}). In spite of this degree, we prove that the number of Steiner vertices in our solution can be as large as |S|+|T|–2. Our algorithm can enumerate all possible optimal solutions. The input graph G can either be undirected or directed acyclic. We also give a linear time algorithm for the special case when min {|S|,|T|} = 1 and max {|S|,|T|} = 2.The minimum union paths problem is similar to the minimum Steiner network problem except that we are given a set H of hitting vertices in G in addition to the sets of starting and terminating vertices. We want to find a subgraph of G with the minimum total edge weight such that the conditions required by the minimum Steiner network problem are satisfied as well as the condition that every hitting vertex is on a path from a starting vertex to a terminating vertex. Furthermore, G must be directed acyclic. For solving the minimum union paths problem, we also present algorithms that have a time and space tradeoff similar to algorithms for the minimum Steiner network problem. We also give a linear time algorithm for the special case when |S| = 1, |T| = 1 and |H| = 2.An extended abstract of part of this paper appears in Hsu et al. (1996).Supported in part by the National Science Foundation under Grants CCR-9309743 and INT-9207212, and by the Office of Naval Research under Grant No. N00014-93-1-0272.Supported in part by the National Science Council, Taiwan, ROC, under Grant No. NSC-83-0408-E-001-021.     

A GALTON-WATSON BRANCHING PROCESS IN VARYING ENVIRONMENTS WITH ESSENTIALLY CONSTANT OFFSPRING MEANS AND TWO RATES OF GROWTH1

A Galton-Watson process in varying environments (Z_n), with essentially constant offspring means, i.e. E(Z_n)/mⁿ→α∈(0, ∞), and exactly two rates of growth is constructed. The underlying sample space Ω can be decomposed into parts A and B such that (Z_n)_n grows like 2ⁿon A and like mⁿon B (m > 4).