Some results on the reconstruction problems. p-claw-free, chordal, and p4-reducible graphs

A claw is an induced subgraph isomorphic to K-1,K-3. The claw-point is the point of degree 3 in a claw. A graph is called p-claw-free when no p-cycle has a claw-point on it. It is proved that for p greater than or equal to 4, p-claw-free graphs containing at least one chordless p-cycle are edge reconstructible. It is also proved that chordal graphs are edge reconstructible. These two results together imply the edge reconstructibility of claw-free graphs. A simple proof of vertex reconstructibility of P-4-reducible graphs is also presented. (C) 1995 John Wiley and Sons, Inc.

Combinatorial Representations of Block Codes

We look at graphical descriptions of block codes known as trellises, which illustrate connections between algebra and graph theory, and can be used to develop powerful decoding algorithms. Trellis sizes for linear block codes are known to grow exponentially with the code parameters. Of considerable interest to coding theorists therefore, are more compact descriptions called tail-biting trellises which in some cases can be much smaller than any conventional trellis for the same code . We derive some interesting properties of tail-biting trellises and present a new decoding algorithm.

Acyclic edge coloring of 2-degenerate graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). A graph is called 2-degenerate if any of its induced subgraph has a vertex of degree at most 2. The class of 2-degenerate graphs properly contains seriesparallel graphs, outerplanar graphs, non - regular subcubic graphs, planar graphs of girth at least 6 and circle graphs of girth at least 5 as subclasses. It was conjectured by Alon, Sudakov and Zaks (and much earlier by Fiamcik) that a'(G)<=Delta + 2, where Delta = Delta(G) denotes the maximum degree of the graph. We prove the conjecture for 2-degenerate graphs. In fact we prove a stronger bound: we prove that if G is a 2-degenerate graph with maximum degree ?, then a'(G)<=Delta + 1. (C) 2010 Wiley Periodicals, Inc. J Graph Theory 68:1-27, 2011

Use of Vertex Index in Structure-Activity Analysis and Design of Molecules

The last few decades have witnessed application of graph theory and topological indices derived from molecular graph in structure-activity analysis. Such applications are based on regression and various multivariate analyses. Most of the topological indices are computed for the whole molecule and used as descriptors for explaining properties/activities of chemical compounds. However, some substructural descriptors in the form of topological distance based vertex indices have been found to be useful in identifying activity related substructures and in predicting pharmacological and toxicological activities of bioactive compounds. Another important aspect of drug discovery e. g. designing novel pharmaceutical candidates could also be done from the distance distribution associated with such vertex indices. In this article, we will review the development and applications of this approach both in activity prediction as well as in designing novel compounds.

Rainbow connection number and connected dominating sets

The rainbow connection number of a connected graph is the minimum number of colors needed to color its edges, so that every pair of its vertices is connected by at least one path in which no two edges are colored the same. In this article we show that for every connected graph on n vertices with minimum degree delta, the rainbow connection number is upper bounded by 3n/(delta + 1) + 3. This solves an open problem from Schiermeyer (Combinatorial Algorithms, Springer, Berlin/Hiedelberg, 2009, pp. 432437), improving the previously best known bound of 20n/delta (J Graph Theory 63 (2010), 185191). This bound is tight up to additive factors by a construction mentioned in Caro et al. (Electr J Combin 15(R57) (2008), 1). As an intermediate step we obtain an upper bound of 3n/(delta + 1) - 2 on the size of a connected two-step dominating set in a connected graph of order n and minimum degree d. This bound is tight up to an additive constant of 2. This result may be of independent interest. We also show that for every connected graph G with minimum degree at least 2, the rainbow connection number, rc(G), is upper bounded by Gc(G) + 2, where Gc(G) is the connected domination number of G. Bounds of the form diameter(G)?rc(G)?diameter(G) + c, 1?c?4, for many special graph classes follow as easy corollaries from this result. This includes interval graphs, asteroidal triple-free graphs, circular arc graphs, threshold graphs, and chain graphs all with minimum degree delta at least 2 and connected. We also show that every bridge-less chordal graph G has rc(G)?3.radius(G). In most of these cases, we also demonstrate the tightness of the bounds.

A unified approach to known and unknown cases of Berge's conjecture

Berge's elegant dipath partition conjecture from 1982 states that in a dipath partition P of the vertex set of a digraph minimizing , there exists a collection Ck of k disjoint independent sets, where each dipath P?P meets exactly min{|P|, k} of the independent sets in C. This conjecture extends Linial's conjecture, the GreeneKleitman Theorem and Dilworth's Theorem for all digraphs. The conjecture is known to be true for acyclic digraphs. For general digraphs, it is known for k=1 by the GallaiMilgram Theorem, for k?? (where ?is the number of vertices in the longest dipath in the graph), by the GallaiRoy Theorem, and when the optimal path partition P contains only dipaths P with |P|?k. Recently, it was proved (Eur J Combin (2007)) for k=2. There was no proof that covers all the known cases of Berge's conjecture. In this article, we give an algorithmic proof of a stronger version of the conjecture for acyclic digraphs, using network flows, which covers all the known cases, except the case k=2, and the new, unknown case, of k=?-1 for all digraphs. So far, there has been no proof that unified all these cases. This proof gives hope for finding a proof for all k.

Acyclic Edge Coloring of Triangle-Free Planar Graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). It was conjectured by Alon, Sudakov and Zaks (and much earlier by Fiamcik) that a'(G) ? ? + 2, where ? = ?(G) denotes the maximum degree of the graph. If every induced subgraph H of G satisfies the condition |E(H)| ? 2|V(H)|-1, we say that the graph G satisfies Property A. In this article, we prove that if G satisfies Property A, then a'(G) ? ? + 3. Triangle-free planar graphs satisfy Property A. We infer that a'(G) ? ? + 3, if G is a triangle-free planar graph. Another class of graph which satisfies Property A is 2-fold graphs (union of two forests). (C) 2011 Wiley Periodicals, Inc. J Graph Theory

On the Erdos-Szekeres n-interior point problem

The n-interior point variant of the Erdos-Szekeres problem is to show the following: For any n, n-1, every point set in the plane with sufficient number of interior points contains a convex polygon containing exactly n-interior points. This has been proved only for n-3. In this paper, we prove it for pointsets having atmost logarithmic number of convex layers. We also show that any pointset containing atleast n interior points, there exists a 2-convex polygon that contains exactly n-interior points.

Inferring biochemical routes from biochemical networks

Metabolism is a defining feature of life, and its study is important to understand how a cell works, alterations that lead to disease and for applications in drug discovery. From a systems perspective, metabolism can be represented as a network that captures all the metabolites as nodes and the inter-conversions among pairs of them as edges. Such an abstraction enables the networks to be studied by applying graph theory, particularly, to infer the flow of chemical information in the networks by identifying relevant metabolic pathways. In this study, different weighting schemes are used to illustrate that appropriately weighted networks can capture the quantitative cellular dynamics quite accurately. Thus, the networks now combine the elegance and simplicity of representation of the system and ease of analysing metabolic graphs. Metabolic routes or paths determined by this therefore are likely to be more biologically meaningful. The usefulness of the approach is demonstrated with two examples, first for understanding bacterial stress response and second for studying metabolic alterations that occurs in cancer cells.

Topics in randomized numerical linear algebra

This thesis studies three classes of randomized numerical linear algebra algorithms, namely: (i) randomized matrix sparsification algorithms, (ii) low-rank approximation algorithms that use randomized unitary transformations, and (iii) low-rank approximation algorithms for positive-semidefinite (PSD) matrices.

Randomized matrix sparsification algorithms set randomly chosen entries of the input matrix to zero. When the approximant is substituted for the original matrix in computations, its sparsity allows one to employ faster sparsity-exploiting algorithms. This thesis contributes bounds on the approximation error of nonuniform randomized sparsification schemes, measured in the spectral norm and two NP-hard norms that are of interest in computational graph theory and subset selection applications.

Low-rank approximations based on randomized unitary transformations have several desirable properties: they have low communication costs, are amenable to parallel implementation, and exploit the existence of fast transform algorithms. This thesis investigates the tradeoff between the accuracy and cost of generating such approximations. State-of-the-art spectral and Frobenius-norm error bounds are provided.

The last class of algorithms considered are SPSD "sketching" algorithms. Such sketches can be computed faster than approximations based on projecting onto mixtures of the columns of the matrix. The performance of several such sketching schemes is empirically evaluated using a suite of canonical matrices drawn from machine learning and data analysis applications, and a framework is developed for establishing theoretical error bounds.

In addition to studying these algorithms, this thesis extends the Matrix Laplace Transform framework to derive Chernoff and Bernstein inequalities that apply to all the eigenvalues of certain classes of random matrices. These inequalities are used to investigate the behavior of the singular values of a matrix under random sampling, and to derive convergence rates for each individual eigenvalue of a sample covariance matrix.

Formulação teórica dos fundamentos da otimização global topográfica com análise de desempenho e aplicações à estabilidade de fases de misturas termodinâmicas

Métodos de otimização que utilizam condições de otimalidade de primeira e/ou segunda ordem são conhecidos por serem eficientes. Comumente, esses métodos iterativos são desenvolvidos e analisados à luz da análise matemática do espaço euclidiano n-dimensional, cuja natureza é de caráter local. Consequentemente, esses métodos levam a algoritmos iterativos que executam apenas as buscas locais. Assim, a aplicação de tais algoritmos para o cálculo de minimizadores globais de uma função não linear,especialmente não-convexas e multimodais, depende fortemente da localização dos pontos de partida. O método de Otimização Global Topográfico é um algoritmo de agrupamento, que utiliza uma abordagem baseada em conceitos elementares da teoria dos grafos, a fim de gerar bons pontos de partida para os métodos de busca local, a partir de pontos distribuídos de modo uniforme no interior da região viável. Este trabalho tem dois objetivos. O primeiro é realizar uma nova abordagem sobre método de Otimização Global Topográfica, onde, pela primeira vez, seus fundamentos são formalmente descritos e suas propriedades básicas são matematicamente comprovadas. Neste contexto, propõe-se uma fórmula semi-empírica para calcular o parâmetro chave deste algoritmo de agrupamento, e, usando um método robusto e eficiente de direções viáveis por pontos-interiores, estendemos o uso do método de Otimização Global Topográfica a problemas com restrições de desigualdade. O segundo objetivo é a aplicação deste método para a análise de estabilidade de fase em misturas termodinâmicas,o qual consiste em determinar se uma dada mistura se apresenta em uma ou mais fases. A solução deste problema de otimização global é necessária para o cálculo do equilíbrio de fases, que é um problema de grande importância em processos da engenharia, como, por exemplo, na separação por destilação, em processos de extração e simulação da recuperação terciária de petróleo, entre outros. Além disso, afim de ter uma avaliação inicial do potencial dessa técnica, primeiro vamos resolver 70 problemas testes, e então comparar o desempenho do método proposto aqui com o solver MIDACO, um poderoso software recentemente introduzido no campo da otimização global.

Otimização global topográfica aplicada a problemas de otimização com restrições de igualdade e desigualdade

Os métodos de otimização que adotam condições de otimalidade de primeira e/ou segunda ordem são eficientes e normalmente esses métodos iterativos são desenvolvidos e analisados através da análise matemática do espaço euclidiano n-dimensional, o qual tem caráter local. Esses métodos levam a algoritmos iterativos que são usados para o cálculo de minimizadores globais de uma função não linear, principalmente não-convexas e multimodais, dependendo da posição dos pontos de partida. Método de Otimização Global Topográfico é um algoritmo de agrupamento, o qual é fundamentado nos conceitos elementares da teoria dos grafos, com a finalidade de gerar bons pontos de partida para os métodos de busca local, com base nos pontos distribuídos de modo uniforme no interior da região viável. Este trabalho tem como objetivo a aplicação do método de Otimização Global Topográfica junto com um método robusto e eficaz de direções viáveis por pontos-interiores a problemas de otimização que tem restrições de igualdade e/ou desigualdade lineares e/ou não lineares, que constituem conjuntos viáveis com interiores não vazios. Para cada um destes problemas, é representado também um hiper-retângulo compreendendo cada conjunto viável, onde os pontos amostrais são gerados.

Modular Organization in a Cell: Concepts and Applications

Network biology is conceptualized as an interdisciplinary field, lying at the intersection among graph theory, statistical mechanics and biology. Great efforts have been made to promote the concept of network biology and its various applications in life s

algorithms for computing weak bisimulation equivalence

IEEE Comp Soc, IFIP, Tianjin Normal Univ

Study on QSPR of alcohols with a novel edge connectivity index F-m

A novel edge degree f(i) for heteroatom and multiple bonds in molecular graph is derived on the basis of the edge degree delta(e(r)). A novel edge connectivity index F-m is introduced. The multiple linear regression by using the edge connectivity index F-m and alcohol-type parameter delta, alcohol-distance parameter L can provide high-quality QSPR models for the normal boiling points (BPs), molar volumes (MVs), molar refraction (MRs), water solubility(log(1/S)) and octanol/water partition (logP) of alcohols with up to 17 non-hydrogen atoms. The results imply that these physical properties may be expressed as a liner combination of the edge connectivity index and alcohol-type parameter, 6, alcohol-distance parameter, L. For the models of the five properties, the correlation coefficient r and the standard errors are 0.9969,3.022; 0.9993, 1.504; 0.9992, 0.446; 0.9924,0.129 and 0.9973,0.123 for BPs, MVs, MRs, log(1/S) and logP, respectively. The cross-validation by using the leave-one-out method demonstrates the models to be highly reliable from the point of view of statistics.