Isomorphism of graph classes related to the circular-ones property

We give a linear-time algorithm that checks for isomorphism between two 0-1 matrices that obey the circular-ones property. This algorithm leads to linear-time isomorphism algorithms for related graph classes, including Helly circular-arc graphs, \Gamma-circular-arc graphs, proper circular-arc graphs and convex-round graphs.Comment: 25 pages, 9 figure

Group testing problems in experimental molecular biology

In group testing, the task is to determine the distinguished members of a set of objects L by asking subset queries of the form ``does the subset Q of L contain a distinguished object?'' The primary biological application of group testing is for screening libraries of clones with hybridization probes. This is a crucial step in constructing physical maps and for finding genes. Group testing has also been considered for sequencing by hybridization. Another important application includes screening libraries of reagents for useful chemically active zones. This preliminary report discusses some of the constrained group testing problems which arise in biology.Comment: 7 page

PQ TREES, CONSECUTIVE ONES PROBLEM AND APPLICATIONS

A PQ tree is an advanced tree–based data structure, which represents a family of permutations on a set of elements. In this research article, we considered the significance of PQ trees and the Consecutive ones Problem to Computer Science and bioinformatics and their various applications. We also went further to demonstrate the operations of the characteristics of the Consecutive ones property by simulation, using high level programming languages. Attempt was also made at developing a PQ tree–Consecutive Ones analyzer, which could be instrumental not only as an educative tool to inquisitive students, but also serve as an important tool in developing clustering software in the field of bioinformatics and other application domains, with respect to solving real life problems

Solving the Canonical Representation and Star System Problems for Proper Circular-Arc Graphs in Log-Space

We present a logspace algorithm that constructs a canonical intersection model for a given proper circular-arc graph, where `canonical' means that models of isomorphic graphs are equal. This implies that the recognition and the isomorphism problems for this class of graphs are solvable in logspace. For a broader class of concave-round graphs, that still possess (not necessarily proper) circular-arc models, we show that those can also be constructed canonically in logspace. As a building block for these results, we show how to compute canonical models of circular-arc hypergraphs in logspace, which are also known as matrices with the circular-ones property. Finally, we consider the search version of the Star System Problem that consists in reconstructing a graph from its closed neighborhood hypergraph. We solve it in logspace for the classes of proper circular-arc, concave-round, and co-convex graphs.Comment: 19 pages, 3 figures, major revisio

Distributed Testing of Excluded Subgraphs

We study property testing in the context of distributed computing, under the classical CONGEST model. It is known that testing whether a graph is triangle-free can be done in a constant number of rounds, where the constant depends on how far the input graph is from being triangle-free. We show that, for every connected 4-node graph H, testing whether a graph is H-free can be done in a constant number of rounds too. The constant also depends on how far the input graph is from being H-free, and the dependence is identical to the one in the case of testing triangles. Hence, in particular, testing whether a graph is K_4-free, and testing whether a graph is C_4-free can be done in a constant number of rounds (where K_k denotes the k-node clique, and C_k denotes the k-node cycle). On the other hand, we show that testing K_k-freeness and C_k-freeness for k>4 appear to be much harder. Specifically, we investigate two natural types of generic algorithms for testing H-freeness, called DFS tester and BFS tester. The latter captures the previously known algorithm to test the presence of triangles, while the former captures our generic algorithm to test the presence of a 4-node graph pattern H. We prove that both DFS and BFS testers fail to test K_k-freeness and C_k-freeness in a constant number of rounds for k>4

Boolean Matrix Factorization Meets Consecutive Ones Property

Boolean matrix factorization is a natural and a popular technique for summarizing binary matrices. In this paper, we study a problem of Boolean matrix factorization where we additionally require that the factor matrices have consecutive ones property (OBMF). A major application of this optimization problem comes from graph visualization: standard techniques for visualizing graphs are circular or linear layout, where nodes are ordered in circle or on a line. A common problem with visualizing graphs is clutter due to too many edges. The standard approach to deal with this is to bundle edges together and represent them as ribbon. We also show that we can use OBMF for edge bundling combined with circular or linear layout techniques. We demonstrate that not only this problem is NP-hard but we cannot have a polynomial-time algorithm that yields a multiplicative approximation guarantee (unless P = NP). On the positive side, we develop a greedy algorithm where at each step we look for the best 1-rank factorization. Since even obtaining 1-rank factorization is NP-hard, we propose an iterative algorithm where we fix one side and and find the other, reverse the roles, and repeat. We show that this step can be done in linear time using pq-trees. We also extend the problem to cyclic ones property and symmetric factorizations. Our experiments show that our algorithms find high-quality factorizations and scale well