Structural matching of 2D electrophoresis gels using deformed graphs

2D electrophoresis is a well-known method for protein separation which is extremely useful in the field of proteomics. Each spot in the image represents a protein accumulation and the goal is to perform a differential analysis between pairs of images to study changes in protein content. It is thus necessary to register two images by finding spot correspondences. Although it may seem a simple task, generally, the manual processing of this kind of images is very cumbersome, especially when strong variations between corresponding sets of spots are expected (e.g. strong non-linear deformations and outliers). In order to solve this problem, this paper proposes a new quadratic assignment formulation together with a correspondence estimation algorithm based on graph matching which takes into account the structural information between the detected spots. Each image is represented by a graph and the task is to find a maximum common subgraph. Successful experimental results using real data are presented, including an extensive comparative performance evaluation with ground-truth data. (C) 2010 Elsevier B.V. All rights reserved.

Template-based quadrilateral meshing

Generating quadrilateral meshes is a highly non-trivial task, as design decisions are frequently driven by specific application demands. Automatic techniques can optimize objective quality metrics, such as mesh regularity, orthogonality, alignment and adaptivity; however, they cannot make subjective design decisions. There are a few quad meshing approaches that offer some mechanisms to include the user in the mesh generation process; however, these techniques either require a large amount of user interaction or do not provide necessary or easy to use inputs. Here, we propose a template-based approach for generating quad-only meshes from triangle surfaces. Our approach offers a flexible mechanism to allow external input, through the definition of alignment features that are respected during the mesh generation process. While allowing user inputs to support subjective design decisions, our approach also takes into account objective quality metrics to produce semi-regular, quad-only meshes that align well to desired surface features. Published by Elsevier Ltd.

Approximation algorithms and hardness results for the clique packing problem

For a fixed family F of graphs, an F-packing in a graph G is a set of pairwise vertex-disjoint subgraphs of G, each isomorphic to an element of F. Finding an F-packing that maximizes the number of covered edges is a natural generalization of the maximum matching problem, which is just F = {K(2)}. In this paper we provide new approximation algorithms and hardness results for the K(r)-packing problem where K(r) = {K(2), K(3,) . . . , K(r)}. We show that already for r = 3 the K(r)-packing problem is APX-complete, and, in fact, we show that it remains so even for graphs with maximum degree 4. On the positive side, we give an approximation algorithm with approximation ratio at most 2 for every fixed r. For r = 3, 4, 5 we obtain better approximations. For r = 3 we obtain a simple 3/2-approximation, achieving a known ratio that follows from a more involved algorithm of Halldorsson. For r = 4, we obtain a (3/2 + epsilon)-approximation, and for r = 5 we obtain a (25/14 + epsilon)-approximation. (C) 2008 Elsevier B.V. All rights reserved.

An algorithmic Friedman-Pippenger theorem on tree embeddings and applications

An (n, d)-expander is a graph G = (V, E) such that for every X subset of V with vertical bar X vertical bar <= 2n - 2 we have vertical bar Gamma(G)(X) vertical bar >= (d + 1) vertical bar X vertical bar. A tree T is small if it has at most n vertices and has maximum degree at most d. Friedman and Pippenger (1987) proved that any ( n; d)- expander contains every small tree. However, their elegant proof does not seem to yield an efficient algorithm for obtaining the tree. In this paper, we give an alternative result that does admit a polynomial time algorithm for finding the immersion of any small tree in subgraphs G of (N, D, lambda)-graphs Lambda, as long as G contains a positive fraction of the edges of Lambda and lambda/D is small enough. In several applications of the Friedman-Pippenger theorem, including the ones in the original paper of those authors, the (n, d)-expander G is a subgraph of an (N, D, lambda)-graph as above. Therefore, our result suffices to provide efficient algorithms for such previously non-constructive applications. As an example, we discuss a recent result of Alon, Krivelevich, and Sudakov (2007) concerning embedding nearly spanning bounded degree trees, the proof of which makes use of the Friedman-Pippenger theorem. We shall also show a construction inspired on Wigderson-Zuckerman expander graphs for which any sufficiently dense subgraph contains all trees of sizes and maximum degrees achieving essentially optimal parameters. Our algorithmic approach is based on a reduction of the tree embedding problem to a certain on-line matching problem for bipartite graphs, solved by Aggarwal et al. (1996).

Ciratefi: An RST-invariant template matching with extension to color images

Template matching is a technique widely used for finding patterns in digital images. A good template matching should be able to detect template instances that have undergone geometric transformations. In this paper, we proposed a grayscale template matching algorithm named Ciratefi, invariant to rotation, scale, translation, brightness and contrast and its extension to color images. We introduce CSSIM (color structural similarity) for comparing the similarity of two color image patches and use it in our algorithm. We also describe a scheme to determine automatically the appropriate parameters of our algorithm and use pyramidal structure to improve the scale invariance. We conducted several experiments to compare grayscale and color Ciratefis with SIFT, C-color-SIFT and EasyMatch algorithms in many different situations. The results attest that grayscale and color Ciratefis are more accurate than the compared algorithms and that color-Ciratefi outperforms grayscale Ciratefi most of the time. However, Ciratefi is slower than the other algorithms.

PARALLEL ALGORITHMS FOR MAXIMAL CLIQUES IN CIRCLE GRAPHS AND UNRESTRICTED DEPTH SEARCH

We present parallel algorithms on the BSP/CGM model, with p processors, to count and generate all the maximal cliques of a circle graph with n vertices and m edges. To count the number of all the maximal cliques, without actually generating them, our algorithm requires O(log p) communication rounds with O(nm/p) local computation time. We also present an algorithm to generate the first maximal clique in O(log p) communication rounds with O(nm/p) local computation, and to generate each one of the subsequent maximal cliques this algorithm requires O(log p) communication rounds with O(m/p) local computation. The maximal cliques generation algorithm is based on generating all maximal paths in a directed acyclic graph, and we present an algorithm for this problem that uses O(log p) communication rounds with O(m/p) local computation for each maximal path. We also show that the presented algorithms can be extended to the CREW PRAM model.

Algorithms for Maximum Independent Set in Convex Bipartite Graphs

A bipartite graph G = (V, W, E) is convex if there exists an ordering of the vertices of W such that, for each v. V, the neighbors of v are consecutive in W. We describe both a sequential and a BSP/CGM algorithm to find a maximum independent set in a convex bipartite graph. The sequential algorithm improves over the running time of the previously known algorithm and the BSP/CGM algorithm is a parallel version of the sequential one. The complexity of the algorithms does not depend on |W|.

Algorithms for two-dimensional cutting stock and strip packing problems using dynamic programming and column generation

We investigate several two-dimensional guillotine cutting stock problems and their variants in which orthogonal rotations are allowed. We first present two dynamic programming based algorithms for the Rectangular Knapsack (RK) problem and its variants in which the patterns must be staged. The first algorithm solves the recurrence formula proposed by Beasley; the second algorithm - for staged patterns - also uses a recurrence formula. We show that if the items are not so small compared to the dimensions of the bin, then these algorithms require polynomial time. Using these algorithms we solved all instances of the RK problem found at the OR-LIBRARY, including one for which no optimal solution was known. We also consider the Two-dimensional Cutting Stock problem. We present a column generation based algorithm for this problem that uses the first algorithm above mentioned to generate the columns. We propose two strategies to tackle the residual instances. We also investigate a variant of this problem where the bins have different sizes. At last, we study the Two-dimensional Strip Packing problem. We also present a column generation based algorithm for this problem that uses the second algorithm above mentioned where staged patterns are imposed. In this case we solve instances for two-, three- and four-staged patterns. We report on some computational experiments with the various algorithms we propose in this paper. The results indicate that these algorithms seem to be suitable for solving real-world instances. We give a detailed description (a pseudo-code) of all the algorithms presented here, so that the reader may easily implement these algorithms. (c) 2007 Elsevier B.V. All rights reserved.

Análises do matching de identidade generalizado por contingências de três e quatro termos: implicações para equivalência de estímulos

A expansão da tríplice continência em unidades com quatro ou mais elementos abriu novas perspectivas para a compreensão de comportamentos complexos, como a emergência de respostas que derivam da formação de classes de estímulos equivalentes e que modelam comportamentos simbólicos e conceituais. Na investigação experimental, o procedimento de matching to sample tem sido frequentemente empregado para estabelecer discriminações condicionais. Em particular, a obtenção do matching de identidade generalizado é considerada demonstrativa da aquisição dos conceitos de igualdade e diferença. Segundo argumentamos, o fato de se buscar a compreensão desses conceitos a partir de processos discriminativos condicionais pode ter sido responsável pelos frequentes fracassos em demonstrá-los em sujeitos não humanos. A falta de correspondência entre os processos discriminativos responsáveis por estabelecer a relação de reflexividade entre estímulos que formam classes equivalentes e o matching de identidade generalizado, nesse sentido, é aqui revista ao longo de estudos empíricos e discutida com respeito às suas implicações.

Bayesian online algorithms for learning in discrete Hidden Markov Models

We propose and analyze two different Bayesian online algorithms for learning in discrete Hidden Markov Models and compare their performance with the already known Baldi-Chauvin Algorithm. Using the Kullback-Leibler divergence as a measure of generalization we draw learning curves in simplified situations for these algorithms and compare their performances.

Intermediate motions and dipolar couplings as studied by Lee-Goldburg cross-polarization NMR: Hartmann-Hahn matching profiles

In this article, we evaluate the use of simple Lee-Goldburg cross-polarization (LG-CP) NMR experiments for obtaining quantitative information of molecular motion in the intermediate regime. In particular, we introduce the measurement of Hartmann-Hahn matching profiles for the assessment of heteronuclear dipolar couplings as well as dynamics as a reliable and robust alternative to the more common analysis of build-up curves. We have carried out dynamic spin dynamics simulations in order to test the method's sensitivity to intermediate motion and address its limitations concerning possible experimental imperfections. We further demonstrate the successful use of simple theoretical concepts, most prominently Anderson-Weiss (AW) theory, to analyze the data. We further propose an alternative way to estimate activation energies of molecular motions, based upon the acquisition of only two LG-CP spectra per temperature at different temperatures. As experimental tests, molecular jumps in imidazole methyl sulfonate, trimethylsulfoxonium iodide, and bisphenol A polycarbonate were investigated with the new method.

On the k-restricted structure ratio in planar and outerplanar graphs

A planar k-restricted structure is a simple graph whose blocks are planar and each has at most k vertices. Planar k-restricted structures are used by approximation algorithms for Maximum Weight Planar Subgraph, which motivates this work. The planar k-restricted ratio is the infimum, over simple planar graphs H, of the ratio of the number of edges in a maximum k-restricted structure subgraph of H to the number edges of H. We prove that, as k tends to infinity, the planar k-restricted ratio tends to 1/2. The same result holds for the weighted version. Our results are based on analyzing the analogous ratios for outerplanar and weighted outerplanar graphs. Here both ratios tend to 1 as k goes to infinity, and we provide good estimates of the rates of convergence, showing that they differ in the weighted from the unweighted case.

Node-Depth Encoding and Multiobjective Evolutionary Algorithm Applied to Large-Scale Distribution System Reconfiguration

The power loss reduction in distribution systems (DSs) is a nonlinear and multiobjective problem. Service restoration in DSs is even computationally hard since it additionally requires a solution in real-time. Both DS problems are computationally complex. For large-scale networks, the usual problem formulation has thousands of constraint equations. The node-depth encoding (NDE) enables a modeling of DSs problems that eliminates several constraint equations from the usual formulation, making the problem solution simpler. On the other hand, a multiobjective evolutionary algorithm (EA) based on subpopulation tables adequately models several objectives and constraints, enabling a better exploration of the search space. The combination of the multiobjective EA with NDE (MEAN) results in the proposed approach for solving DSs problems for large-scale networks. Simulation results have shown the MEAN is able to find adequate restoration plans for a real DS with 3860 buses and 632 switches in a running time of 0.68 s. Moreover, the MEAN has shown a sublinear running time in function of the system size. Tests with networks ranging from 632 to 5166 switches indicate that the MEAN can find network configurations corresponding to a power loss reduction of 27.64% for very large networks requiring relatively low running time.

GOOAL: A routine based on Genetic Algorithms to track harmonics in electric power systems

Voltage and current waveforms of a distribution or transmission power system are not pure sinusoids. There are distortions in these waveforms that can be represented as a combination of the fundamental frequency, harmonics and high frequency transients. This paper presents a novel approach to identifying harmonics in power system distorted waveforms. The proposed method is based on Genetic Algorithms, which is an optimization technique inspired by genetics and natural evolution. GOOAL, a specially designed intelligent algorithm for optimization problems, was successfully implemented and tested. Two kinds of representations concerning chromosomes are utilized: binary and real. The results show that the proposed method is more precise than the traditional Fourier Transform, especially considering the real representation of the chromosomes.

Hybrid Algorithms for Routing and Assignment Wavelengths in Optical Networks

This paper presents a strategy for the solution of the WDM optical networks planning. Specifically, the problem of Routing and Wavelength Allocation (RWA) in order to minimize the amount of wavelengths used. In this case, the problem is known as the Min-RWA. Two meta-heuristics (Tabu Search and Simulated Annealing) are applied to take solutions of good quality and high performance. The key point is the degradation of the maximum load on the virtual links in favor of minimization of number of wavelengths used; the objective is to find a good compromise between the metrics of virtual topology (load in Gb/s) and of the physical topology (quantity of wavelengths). The simulations suggest good results when compared to some existing in the literature.