arXiv subjects
Publications and source records attributed to Susan Holmes.
Many casinos routinely use mechanical card shuffling machines. We were asked to evaluate a new product, a shelf shuffler. This leads to new probability, new combinatorics and to some practical advice which was adopted by the manufacturer. The interplay between theory, computing, and real-world application is developed.
We develop algorithms for sampling from a probability distribution on a submanifold embedded in Rn. Applications are given to the evaluation of algorithms in 'Topological Statistics'; to goodness of fit tests in exponential families and to Neyman's smooth test. This article is partially expository, giving an introduction to the tools of geometric measure theory.
Today's data-heavy research environment requires the integration of different sources of information into structured data sets that can not be analyzed as simple matrices. We introduce an old technique, known in the European data analyses circles as the Duality Diagram Approach, put to new uses through the use of a variety of metrics and ways of combining different diagrams together. This issue of the Annals of Applied Statistics contains contemporary examples of how this approach provides solutions to hard problems in data integration. We present here the genesis of the technique and how it can be seen as a precursor of the modern kernel based approaches.
We work out the graph limit theory for dense interval graphs. The theory developed departs from the usual description of a graph limit as a symmetric function $W(x,y)$ on the unit square, with $x$ and $y$ uniform on the interval $(0,1)$. Instead, we fix a $W$ and change the underlying distribution of the coordinates $x$ and $y$. We find choices such that our limits are continuous. Connections to random interval graphs are given, including some examples. We also show a continuity result for the chromatic number and clique number of interval graphs. Some results on uniqueness of the limit description are given for general graph limits.
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and `generalizability' of these summaries. This paper provides an implementation of the geometric distance between trees developed by Billera, Holmes and Vogtmann (2001) [BHV] equally applicable to phylogenetic trees and hieirarchical clustering trees, and shows some of the applications in statistical inference for which this distance can be useful. In particular, since BHV have shown that the space of trees is negatively curved (a CAT(0) space), a natural representation of a collection of trees is a tree. We compare this representation to the Euclidean approximations of treespace made available through Multidimensional Scaling of the matrix of distances between trees. We also provide applications of the distances between trees to hierarchical clustering trees constructed from microarrays. Our method gives a new way of evaluating the influence both of certain columns (positions, variables or genes) and of certain rows (whether species, observations or arrays).
We provide an explanation of the main ideas underlying Götze's main result in using Stein's method. We also provide detailed derivations of various intermediate estimates. Curiously, we are led to a different dimensional dependence of the constant than that given Götze's paper. We would like to dedicate this to Charles Stein on the occasion of his 90th birthday.
We study the limit theory of large threshold graphs and apply this to a variety of models for random threshold graphs. The results give a nice set of examples for the emerging theory of graph limits.
Classical multidimensional scaling (MDS) is a method for visualizing high-dimensional point clouds by mapping to low-dimensional Euclidean space. This mapping is defined in terms of eigenfunctions of a matrix of interpoint dissimilarities. In this paper we analyze in detail multidimensional scaling applied to a specific dataset: the 2005 United States House of Representatives roll call votes. Certain MDS and kernel projections output ``horseshoes'' that are characteristic of dimensionality reduction techniques. We show that, in general, a latent ordering of the data gives rise to these patterns when one only has local information. That is, when only the interpoint distances for nearby points are known accurately. Our results provide a rigorous set of results and insight into manifold learning in the special case where the manifold is a curve.
This paper presents exploratory techniques for multivariate data, many of them well known to French statisticians and ecologists, but few well understood in North American culture. We present the general framework of duality diagrams which encompasses discriminant analysis, correspondence analysis and principal components, and we show how this framework can be generalized to the regression of graphs on covariates.