A Simpler and More Accurate AUTO-HDS Framework for Clustering and Visualization of Biological Data

In [1], the authors proposed a framework for automated clustering and visualization of biological data sets named AUTO-HDS. This letter is intended to complement that framework by showing that it is possible to get rid of a user-defined parameter in a way that the clustering stage can be implemented more accurately while having reduced computational complexity

A relaxed constant positive linear dependence constraint qualification and applications

In this work we introduce a relaxed version of the constant positive linear dependence constraint qualification (CPLD) that we call RCPLD. This development is inspired by a recent generalization of the constant rank constraint qualification by Minchenko and Stakhovski that was called RCRCQ. We show that RCPLD is enough to ensure the convergence of an augmented Lagrangian algorithm and that it asserts the validity of an error bound. We also provide proofs and counter-examples that show the relations of RCRCQ and RCPLD with other known constraint qualifications. In particular, RCPLD is strictly weaker than CPLD and RCRCQ, while still stronger than Abadie's constraint qualification. We also verify that the second order necessary optimality condition holds under RCRCQ.

Properly coloured copies and rainbow copies of large graphs with small maximum degree

Let G be a graph on n vertices with maximum degree ?. We use the Lovasz local lemma to show the following two results about colourings ? of the edges of the complete graph Kn. If for each vertex v of Kn the colouring ? assigns each colour to at most (n - 2)/(22.4?2) edges emanating from v, then there is a copy of G in Kn which is properly edge-coloured by ?. This improves on a result of Alon, Jiang, Miller, and Pritikin [Random Struct. Algorithms 23(4), 409433, 2003]. On the other hand, if ? assigns each colour to at most n/(51?2) edges of Kn, then there is a copy of G in Kn such that each edge of G receives a different colour from ?. This proves a conjecture of Frieze and Krivelevich [Electron. J. Comb. 15(1), R59, 2008]. Our proofs rely on a framework developed by Lu and Szekely [Electron. J. Comb. 14(1), R63, 2007] for applying the local lemma to random injections. In order to improve the constants in our results we use a version of the local lemma due to Bissacot, Fernandez, Procacci, and Scoppola [preprint, arXiv:0910.1824]. (c) 2011 Wiley Periodicals, Inc. Random Struct. Alg., 40, 425436, 2012

Computational tools for comparing asymmetric GARCH models via Bayes factors

In this paper we use Markov chain Monte Carlo (MCMC) methods in order to estimate and compare GARCH models from a Bayesian perspective. We allow for possibly heavy tailed and asymmetric distributions in the error term. We use a general method proposed in the literature to introduce skewness into a continuous unimodal and symmetric distribution. For each model we compute an approximation to the marginal likelihood, based on the MCMC output. From these approximations we compute Bayes factors and posterior model probabilities. (C) 2012 IMACS. Published by Elsevier B.V. All rights reserved.

A novel self consistent calculation approach for the capacitance-voltage characteristics of semiconductor quantum wire transistors based on a split-gate configuration

Purpose - The purpose of this paper is to develop an efficient numerical algorithm for the self-consistent solution of Schrodinger and Poisson equations in one-dimensional systems. The goal is to compute the charge-control and capacitance-voltage characteristics of quantum wire transistors. Design/methodology/approach - The paper presents a numerical formulation employing a non-uniform finite difference discretization scheme, in which the wavefunctions and electronic energy levels are obtained by solving the Schrodinger equation through the split-operator method while a relaxation method in the FTCS scheme ("Forward Time Centered Space") is used to solve the two-dimensional Poisson equation. Findings - The numerical model is validated by taking previously published results as a benchmark and then applying them to yield the charge-control characteristics and the capacitance-voltage relationship for a split-gate quantum wire device. Originality/value - The paper helps to fulfill the need for C-V models of quantum wire device. To do so, the authors implemented a straightforward calculation method for the two-dimensional electronic carrier density n(x,y). The formulation reduces the computational procedure to a much simpler problem, similar to the one-dimensional quantization case, significantly diminishing running time.

Maximum Series-Parallel Subgraph

Consider the NP-hard problem of, given a simple graph G, to find a series-parallel subgraph of G with the maximum number of edges. The algorithm that, given a connected graph G, outputs a spanning tree of G, is a 1/2-approximation. Indeed, if n is the number of vertices in G, any spanning tree in G has n-1 edges and any series-parallel graph on n vertices has at most 2n-3 edges. We present a 7/12 -approximation for this problem and results showing the limits of our approach.

Edge Colourings of Graphs Avoiding Monochromatic Matchings of a Given Size

Let k and l be positive integers. With a graph G, we associate the quantity c(k,l)(G), the number of k-colourings of the edge set of G with no monochromatic matching of size l. Consider the function c(k,l) : N --> N given by c(k,l)(n) = max {c(k,l)(G): vertical bar V(G)vertical bar = n}, the maximum of c(k,l)(G) over all graphs G on n vertices. In this paper, we determine c(k,l)(n) and the corresponding extremal graphs for all large n and all fixed values of k and l.

Fuzzy Connectedness Image Segmentation in Graph Cut Formulation: A Linear-Time Algorithm and a Comparative Analysis

A deep theoretical analysis of the graph cut image segmentation framework presented in this paper simultaneously translates into important contributions in several directions. The most important practical contribution of this work is a full theoretical description, and implementation, of a novel powerful segmentation algorithm, GC(max). The output of GC(max) coincides with a version of a segmentation algorithm known as Iterative Relative Fuzzy Connectedness, IRFC. However, GC(max) is considerably faster than the classic IRFC algorithm, which we prove theoretically and show experimentally. Specifically, we prove that, in the worst case scenario, the GC(max) algorithm runs in linear time with respect to the variable M=|C|+|Z|, where |C| is the image scene size and |Z| is the size of the allowable range, Z, of the associated weight/affinity function. For most implementations, Z is identical to the set of allowable image intensity values, and its size can be treated as small with respect to |C|, meaning that O(M)=O(|C|). In such a situation, GC(max) runs in linear time with respect to the image size |C|. We show that the output of GC(max) constitutes a solution of a graph cut energy minimization problem, in which the energy is defined as the a"" (a) norm ayenF (P) ayen(a) of the map F (P) that associates, with every element e from the boundary of an object P, its weight w(e). This formulation brings IRFC algorithms to the realm of the graph cut energy minimizers, with energy functions ayenF (P) ayen (q) for qa[1,a]. Of these, the best known minimization problem is for the energy ayenF (P) ayen(1), which is solved by the classic min-cut/max-flow algorithm, referred to often as the Graph Cut algorithm. We notice that a minimization problem for ayenF (P) ayen (q) , qa[1,a), is identical to that for ayenF (P) ayen(1), when the original weight function w is replaced by w (q) . Thus, any algorithm GC(sum) solving the ayenF (P) ayen(1) minimization problem, solves also one for ayenF (P) ayen (q) with qa[1,a), so just two algorithms, GC(sum) and GC(max), are enough to solve all ayenF (P) ayen (q) -minimization problems. We also show that, for any fixed weight assignment, the solutions of the ayenF (P) ayen (q) -minimization problems converge to a solution of the ayenF (P) ayen(a)-minimization problem (ayenF (P) ayen(a)=lim (q -> a)ayenF (P) ayen (q) is not enough to deduce that). An experimental comparison of the performance of GC(max) and GC(sum) algorithms is included. This concentrates on comparing the actual (as opposed to provable worst scenario) algorithms' running time, as well as the influence of the choice of the seeds on the output.

A marker-and-cell approach to free surface 2-D multiphase flows

This work describes a methodology to simulate free surface incompressible multiphase flows. This novel methodology allows the simulation of multiphase flows with an arbitrary number of phases, each of them having different densities and viscosities. Surface and interfacial tension effects are also included. The numerical technique is based on the GENSMAC front-tracking method. The velocity field is computed using a finite-difference discretization of a modification of the NavierStokes equations. These equations together with the continuity equation are solved for the two-dimensional multiphase flows, with different densities and viscosities in the different phases. The governing equations are solved on a regular Eulerian grid, and a Lagrangian mesh is employed to track free surfaces and interfaces. The method is validated by comparing numerical with analytic results for a number of simple problems; it was also employed to simulate complex problems for which no analytic solutions are available. The method presented in this paper has been shown to be robust and computationally efficient. Copyright (c) 2012 John Wiley & Sons, Ltd.

An in-depth analysis of the HIV-1/AIDS dynamics by comprehensive mathematical modeling

This work presents major results from a novel dynamic model intended to deterministically represent the complex relation between HIV-1 and the human immune system. The novel structure of the model extends previous work by representing different host anatomic compartments under a more in-depth cellular and molecular immunological phenomenology. Recently identified mechanisms related to HIV-1 infection as well as other well known relevant mechanisms typically ignored in mathematical models of HIV-1 pathogenesis and immunology, such as cell-cell transmission, are also addressed. (C) 2011 Elsevier Ltd. All rights reserved.

Weak quasi-randomness for uniform hypergraphs

We study quasi-random properties of k-uniform hypergraphs. Our central notion is uniform edge distribution with respect to large vertex sets. We will find several equivalent characterisations of this property and our work can be viewed as an extension of the well known Chung-Graham-Wilson theorem for quasi-random graphs. Moreover, let K(k) be the complete graph on k vertices and M(k) the line graph of the graph of the k-dimensional hypercube. We will show that the pair of graphs (K(k),M(k)) has the property that if the number of copies of both K(k) and M(k) in another graph G are as expected in the random graph of density d, then G is quasi-random (in the sense of the Chung-Graham-Wilson theorem) with density close to d. (C) 2011 Wiley Periodicals, Inc. Random Struct. Alg., 40, 1-38, 2012

Semilinear functional difference equations with infinite delay

We obtain boundedness and asymptotic behavior of solutions for semilinear functional difference equations with infinite delay. Applications to Volterra difference equations with infinite delay are shown. (C) 2011 Elsevier Ltd. All rights reserved.

The boundedness of penalty parameters in an augmented Lagrangian method with constrained subproblems

Augmented Lagrangian methods are effective tools for solving large-scale nonlinear programming problems. At each outer iteration, a minimization subproblem with simple constraints, whose objective function depends on updated Lagrange multipliers and penalty parameters, is approximately solved. When the penalty parameter becomes very large, solving the subproblem becomes difficult; therefore, the effectiveness of this approach is associated with the boundedness of the penalty parameters. In this paper, it is proved that under more natural assumptions than the ones employed until now, penalty parameters are bounded. For proving the new boundedness result, the original algorithm has been slightly modified. Numerical consequences of the modifications are discussed and computational experiments are presented.

A new enrichment space for the treatment of discontinuous pressures in multi-fluid flows

In this work, a new enrichment space to accommodate jumps in the pressure field at immersed interfaces in finite element formulations, is proposed. The new enrichment adds two degrees of freedom per element that can be eliminated by means of static condensation. The new space is tested and compared with the classical P1 space and to the space proposed by Ausas et al (Comp. Meth. Appl. Mech. Eng., Vol. 199, 10191031, 2010) in several problems involving jumps in the viscosity and/or the presence of singular forces at interfaces not conforming with the element edges. The combination of this enrichment space with another enrichment that accommodates discontinuities in the pressure gradient has also been explored, exhibiting excellent results in problems involving jumps in the density or the volume forces. Copyright (c) 2011 John Wiley & Sons, Ltd.

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.