On the Galois Lattice of Bipartite Distance Hereditary Graphs

We give a complete characterization of bipartite graphs hav- ing tree-like Galois lattices. We prove that the poset obtained by deleting bottom and top elements from the Galois lattice of a bipartite graph is tree-like if and only if the graph is a Bipartite Distance Hereditary graph. We show that the lattice can be realized as the containment relation among directed paths in an arborescence. Moreover, a compact encoding of Bipartite Distance Hereditary graphs is proposed, that allows optimal time computation of neighborhood intersections and maximal bicliques

A tight relation between series--parallel graphs and bipartite distance hereditary graphs

Bandelt and Mulder’s structural characterization of bipartite distance hereditary graphs asserts that such graphs can be built inductively starting from a single vertex and by re17 peatedly adding either pendant vertices or twins (i.e., vertices with the same neighborhood as an existing one). Dirac and Duffin’s structural characterization of 2–connected series–parallel graphs asserts that such graphs can be built inductively starting from a single edge by adding either edges in series or in parallel. In this paper we give an elementary proof that the two constructions are the same construction when bipartite graphs are viewed as the fundamental graphs of a graphic matroid. We then apply the result to re-prove known results concerning bipartite distance hereditary graphs and series–parallel graphs and to provide a new class of polynomially-solvable instances for the integer multi-commodity flow of maximum valu

Formal Concept Analysis Applications in Bioinformatics

Bioinformatics is an important field that seeks to solve biological problems with the help of computation. One specific field in bioinformatics is that of genomics, the study of genes and their functions. Genomics can provide valuable analysis as to the interaction between how genes interact with their environment. One such way to measure the interaction is through gene expression data, which determines whether (and how much) a certain gene activates in a situation. Analyzing this data can be critical for predicting diseases or other biological reactions. One method used for analysis is Formal Concept Analysis (FCA), a computing technique based in partial orders that allows the user to examine the structural properties of binary data based on which subsets of the data set depend on each other. This thesis surveys, in breadth and depth, the current literature related to the use of FCA for bioinformatics, with particular focus on gene expression data. This includes descriptions of current data management techniques specific to FCA, such as lattice reduction, discretization, and variations of FCA to account for different data types. Advantages and shortcomings of using FCA for genomic investigations, as well as the feasibility of using FCA for this application are addressed. Finally, several areas for future doctoral research are proposed. Adviser: Jitender S. Deogu

Solving Hard Graph Problems with Combinatorial Computing and Optimization

Many problems arising in graph theory are difficult by nature, and finding solutions to large or complex instances of them often require the use of computers. As some such problems are $NP$-hard or lie even higher in the polynomial hierarchy, it is unlikely that efficient, exact algorithms will solve them. Therefore, alternative computational methods are used. Combinatorial computing is a branch of mathematics and computer science concerned with these methods, where algorithms are developed to generate and search through combinatorial structures in order to determine certain properties of them. In this thesis, we explore a number of such techniques, in the hopes of solving specific problem instances of interest. Three separate problems are considered, each of which is attacked with different methods of combinatorial computing and optimization. The first, originally proposed by ErdH{o}s and Hajnal in 1967, asks to find the Folkman number $F_e(3,3;4)$, defined as the smallest order of a $K_4$-free graph that is not the union of two triangle-free graphs. A notoriously difficult problem associated with Ramsey theory, the best known bounds on it prior to this work were $19 leq F_e(3,3;4) leq 941$. We improve the upper bound to $F_e(3,3;4) leq 786$ using a combination of known methods and the Goemans-Williamson semi-definite programming relaxation of MAX-CUT. The second problem of interest is the Ramsey number $R(C_4,K_m)$, which is the smallest $n$ such that any $n$-vertex graph contains a cycle of length four or an independent set of order $m$. With the help of combinatorial algorithms, we determine $R(C_4,K_9)=30$ and $R(C_4,K_{10})=36$ using large-scale computations on the Open Science Grid. Finally, we explore applications of the well-known Lenstra-Lenstra-Lov\u27{a}sz (LLL) algorithm, a polynomial-time algorithm that, when given a basis of a lattice, returns a basis for the same lattice with relatively short vectors. The main result of this work is an application to graph domination, where certain hard instances are solved using this algorithm as a heuristic

Profinite and Asymptotic Group Theory

[no abstract available

Hard Mathematical Problems in Cryptography and Coding Theory

In this thesis, we are concerned with certain interesting computationally hard problems and the complexities of their associated algorithms. All of these problems share a common feature in that they all arise from, or have applications to, cryptography, or the theory of error correcting codes. Each chapter in the thesis is based on a stand-alone paper which attacks a particular hard problem. The problems and the techniques employed in attacking them are described in detail. The first problem concerns integer factorization: given a positive integer $N$. the problem is to find the unique prime factors of $N$. This problem, which was historically of only academic interest to number theorists, has in recent decades assumed a central importance in public-key cryptography. We propose a method for factorizing a given integer using a graph-theoretic algorithm employing Binary Decision Diagrams (BDD). The second problem that we consider is related to the classification of certain naturally arising classes of error correcting codes, called self-dual additive codes over the finite field of four elements, $GF(4)$. We address the problem of classifying self-dual additive codes, determining their weight enumerators, and computing their minimum distance. There is a natural relation between self-dual additive codes over $GF(4)$ and graphs via isotropic systems. Utilizing the properties of the corresponding graphs, and again employing Binary Decision Diagrams (BDD) to compute the weight enumerators, we can obtain a theoretical speed up of the previously developed algorithm for the classification of these codes. The third problem that we investigate deals with one of the central issues in cryptography, which has historical origins in the theory of geometry of numbers, namely the shortest vector problem in lattices. One method which is used both in theory and practice to solve the shortest vector problem is by enumeration algorithms. Lattice enumeration is an exhaustive search whose goal is to find the shortest vector given a lattice basis as input. In our work, we focus on speeding up the lattice enumeration algorithm, and we propose two new ideas to this end. The shortest vector in a lattice can be written as ${\bf s} = v_1{\bf b}_1+v_2{\bf b}_2+\ldots+v_n{\bf b}_n$. where $v_i \in \mathbb{Z}$ are integer coefficients and ${\bf b}_i$ are the lattice basis vectors. We propose an enumeration algorithm, called hybrid enumeration, which is a greedy approach for computing a short interval of possible integer values for the coefficients $v_i$ of a shortest lattice vector. Second, we provide an algorithm for estimating the signs $+$ or $-$ of the coefficients $v_1,v_2,\ldots,v_n$ of a shortest vector ${\bf s}=\sum_{i=1}^{n} v_i{\bf b}_i$. Both of these algorithms results in a reduction in the number of nodes in the search tree. Finally, the fourth problem that we deal with arises in the arithmetic of the class groups of imaginary quadratic fields. We follow the results of Soleng and Gillibert pertaining to the class numbers of some sequence of imaginary quadratic fields arising in the arithmetic of elliptic and hyperelliptic curves and compute a bound on the effective estimates for the orders of class groups of a family of imaginary quadratic number fields. That is, suppose $f(n)$ is a sequence of positive numbers tending to infinity. Given any positive real number $L$. an effective estimate is to find the smallest positive integer $N = N(L)$ depending on $L$ such that $f(n) > L$ for all $n > N$. In other words, given a constant $M > 0$. we find a value $N$ such that the order of the ideal class $I_n$ in the ring $R_n$ (provided by the homomorphism in Soleng's paper) is greater than $M$ for any $n>N$. In summary, in this thesis we attack some hard problems in computer science arising from arithmetic, geometry of numbers, and coding theory, which have applications in the mathematical foundations of cryptography and error correcting codes

An extensive English language bibliography on graph theory and its applications

Bibliography on graph theory and its application