Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. RESULTS: Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. CONCLUSIONS: Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

Sticky central limit theorems on open books

Given a probability distribution on an open book (a metric space obtained by gluing a disjoint union of copies of a half-space along their boundary hyperplanes), we define a precise concept of when the Fréchet mean (barycenter) is sticky. This nonclassical phenomenon is quantified by a law of large numbers (LLN) stating that the empirical mean eventually almost surely lies on the (codimension 1 and hence measure 0) spine that is the glued hyperplane, and a central limit theorem (CLT) stating that the limiting distribution is Gaussian and supported on the spine.We also state versions of the LLN and CLT for the cases where the mean is nonsticky (i.e., not lying on the spine) and partly sticky (i.e., is, on the spine but not sticky). © Institute of Mathematical Statistics, 2013.

Local kinetic interpretation of entropy production through reversed diffusion.

The time reversal of stochastic diffusion processes is revisited with emphasis on the physical meaning of the time-reversed drift and the noise prescription in the case of multiplicative noise. The local kinematics and mechanics of free diffusion are linked to the hydrodynamic description. These properties also provide an interpretation of the Pope-Ching formula for the steady-state probability density function along with a geometric interpretation of the fluctuation-dissipation relation. Finally, the statistics of the local entropy production rate of diffusion are discussed in the light of local diffusion properties, and a stochastic differential equation for entropy production is obtained using the Girsanov theorem for reversed diffusion. The results are illustrated for the Ornstein-Uhlenbeck process.

Influence of network topology and data collection on network inference.

We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed internal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data.

Relations, residuals, regular interiors, and relative regular equivalence

Given a relation α (a binary sociogram) and an a priori equivalence relation π, both on the same set of individuals, it is interesting to look for the largest equivalence πo that is contained in and is regular with respect to α. The equivalence relation πo is called the regular interior of π with respect to α. The computation of πo involves the left and right residuals, a concept that generalized group inverses to the algebra of relations. A polynomial-time procedure is presented (Theorem 11) and illustrated with examples. In particular, the regular interior gives meet in the lattice of regular equivalences: the regular meet of regular equivalences is the regular interior of their intersection. Finally, the concept of relative regular equivalence is defined and compared with regular equivalence.

Applications of Feller-Reuter-Riley transition functions

A Feller–Reuter–Riley function is a Markov transition function whose corresponding semigroup maps the set of the real-valued continuous functions vanishing at infinity into itself. The aim of this paper is to investigate applications of such functions in the dual problem, Markov branching processes, and the Williams-matrix. The remarkable property of a Feller–Reuter–Riley function is that it is a Feller minimal transition function with a stable q-matrix. By using this property we are able to prove that, in the theory of branching processes, the branching property is equivalent to the requirement that the corresponding transition function satisfies the Kolmogorov forward equations associated with a stable q-matrix. It follows that the probabilistic definition and the analytic definition for Markov branching processes are actually equivalent. Also, by using this property, together with the Resolvent Decomposition Theorem, a simple analytical proof of the Williams' existence theorem with respect to the Williams-matrix is obtained. The close link between the dual problem and the Feller–Reuter–Riley transition functions is revealed. It enables us to prove that a dual transition function must satisfy the Kolmogorov forward equations. A necessary and sufficient condition for a dual transition function satisfying the Kolmogorov backward equations is also provided.

Hall conditions for edge-weighted bipartite graphs

A weighted variant of Hall's condition for the existence of matchings is shown to be equivalent to the existence of a matching in a lexicographic product. This is used to introduce characterizations of those bipartite graphs whose edges may be replicated so as to yield semiregular multigraphs or, equivalently, semiregular edge-weightings. Such bipartite graphs will be called semiregularizable. Some infinite families of semiregularizable trees are described and all semiregularizable trees on at most 11 vertices are listed. Matrix analogues of some of the results are mentioned and are shown to imply some of the known characterizations of regularizable graphs.

On subspace lattices II. Continuity of Lat

We study the continuity of the map Lat sending an ultraweakly closed operator algebra to its invariant subspace lattice. We provide an example showing that Lat is in general discontinuous and give sufficient conditions for the restricted continuity of this map. As consequences we obtain that Lat is continuous on the classes of von Neumann and Arveson algebras and give a general approximative criterion for reflexivity, which extends Arvesonâ??s theorem on the reflexivity of commutative subspace lattices.

Relative energetics and structural properties of zirconia using a self-consistent tight-binding model

We describe an empirical, self-consistent, orthogonal tight-binding model for zirconia, which allows for the polarizability of the anions at dipole and quadrupole levels and for crystal field splitting of the cation d orbitals, This is achieved by mixing the orbitals of different symmetry on a site with coupling coefficients driven by the Coulomb potentials up to octapole level. The additional forces on atoms due to the self-consistency and polarizabilities are exactly obtained by straightforward electrostatics, by analogy with the Hellmann-Feynman theorem as applied in first-principles calculations. The model correctly orders the zero temperature energies of all zirconia polymorphs. The Zr-O matrix elements of the Hamiltonian, which measure covalency, make a greater contribution than the polarizability to the energy differences between phases. Results for elastic constants of the cubic and tetragonal phases and phonon frequencies of the cubic phase are also presented and compared with some experimental data and first-principles calculations. We suggest that the model will be useful for studying finite temperature effects by means of molecular dynamics.

An analogue of the Magnus problem for associative algebras

We prove an analogue of Magnus theorem for associative algebras without unity over arbitrary fields. Namely, if an algebra is given by $n+k$ generators and $k$ relations and has an $n$-element system of generators, then this algebra is a free algebra of rank $n$.

Orbits of operators commuting with the Volterra operator

Asymptotic estimates of the norms of orbits of certain operators that commute with the classical Volterra operator V acting on L-P[0,1], with 1 0, but also to operators of the form phi (V), where phi is a holomorphic function at zero. The method to obtain the estimates is based on the fact that the Riemann-Liouville operator as well as the Volterra operator can be related to the Levin-Pfluger theory of holomorphic functions of completely regular growth. Different methods, such as the Denjoy-Carleman theorem, are needed to analyze the behavior of the orbits of I - cV, where c > 0. The results are applied to the study of cyclic properties of phi (V), where phi is a holomorphic function at 0.

Decompositions of spaces of measures

Let M be the Banach space of sigma-additive complex-valued measures on an abstract measurable space. We prove that any closed, with respect to absolute continuity norm-closed, linear subspace L of M is complemented and describe the unique complement, projection onto L along which has norm 1. Using this fact we prove a decomposition theorem, which includes the Jordan decomposition theorem, the generalized Radon-Nikodym theorem and the decomposition of measures into decaying and non-decaying components as particular cases. We also prove an analog of the Jessen-Wintner purity theorem for our decompositions.

Sequentially continuous non-linear fundamental systems of solutions of affine equations in locally convex spaces

According to the Mickael's selection theorem any surjective continuous linear operator from one Fr\'echet space onto another has a continuous (not necessarily linear) right inverse. Using this theorem Herzog and Lemmert proved that if $E$ is a Fr\'echet space and $T:E\to E$ is a continuous linear operator such that the Cauchy problem $\dot x=Tx$, $x(0)=x_0$ is solvable in $[0,1]$ for any $x_0\in E$, then for any $f\in C([0,1],E)$, there exists a continuos map $S:[0,1]\times E\to E$, $(t,x)\mapsto S_tx$ such that for any $x_0\in E$, the function $x(t)=S_tx_0$ is a solution of the Cauchy problem $\dot x(t)=Tx(t)+f(t)$, $x(0)=x_0$ (they call $S$ a fundamental system of solutions of the equation $\dot x=Tx+f$). We prove the same theorem, replacing "continuous" by "sequentially continuous" for locally convex spaces from a class which contains strict inductive limits of Fr\'echet spaces and strong duals of Fr\'echet--Schwarz spaces and is closed with respect to finite products and sequentially closed subspaces. The key-point of the proof is an extension of the theorem on existence of a sequentially continuous right inverse of any surjective sequentially continuous linear operator to some class of non-metrizable locally convex spaces.

On weak and strong Peano theorems

We say that the Peano theorem holds for a topological vector space $E$ if, for any continuous mapping $f : {\Bbb R}\times E \to E$ and any $(t(0), x(0))$ is an element of ${\Bbb R}\times E$, the Cauchy problem $\dot x(t) = f(t,x(t))$, $x(t(0)) = x(0)$, has a solution in some neighborhood of $t(0)$. We say that the weak version of Peano theorem holds for $E$ if, for any continuous map $f : {\Bbb R}\times E \to E$, the equation $\dot x(t) = f (t, x(t))$ has a solution on some interval. We construct an example (answering a question posed by S. G. Lobanov) of a Hausdorff locally convex topological vector space E for which the weak version of Peano theorem holds and the Peano theorem fails to hold. We also construct a Hausdorff locally convex topological vector space E for which the Peano theorem holds and any barrel in E is neither compact nor sequentially compact.

Decay measures on locally compact abelian topological groups

Source: PROCEEDINGS OF THE ROYAL SOCIETY OF EDINBURGH SECTION A-MATHEMATICS Volume: 131 Pages: 1257-1273 Part: Part 6 Published: 2001 Times Cited: 5 References: 23 Citation MapCitation Map beta Abstract: We show that the Banach space M of regular sigma-additive finite Borel complex-valued measures on a non-discrete locally compact Hausdorff topological Abelian group is the direct sum of two linear closed subspaces M-D and M-ND, where M-D is the set of measures mu is an element of M whose Fourier transform vanishes at infinity and M-ND is the set of measures mu is an element of M such that nu is not an element of MD for any nu is an element of M \ {0} absolutely continuous with respect to the variation \mu\. For any corresponding decomposition mu = mu(D) + mu(ND) (mu(D) is an element of M-D and mu(ND) is an element of M-ND) there exist a Borel set A = A(mu) such that mu(D) is the restriction of mu to A, therefore the measures mu(D) and mu(ND) are singular with respect to each other. The measures mu(D) and mu(ND) are real if mu is real and positive if mu is positive. In the case of singular continuous measures we have a refinement of Jordan's decomposition theorem. We provide series of examples of different behaviour of convolutions of measures from M-D and M-ND.