A local 2-approximation algorithm for the vertex cover problem

We present a distributed 2-approximation algorithm for the minimum vertex cover problem. The algorithm is deterministic, and it runs in (Δ + 1)2 synchronous communication rounds, where Δ is the maximum degree of the graph. For Δ = 3, we give a 2-approximation algorithm also for the weighted version of the problem.

Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.

Compression of Weighted Graphs

We propose to compress weighted graphs (networks), motivated by the observation that large networks of social, biological, or other relations can be complex to handle and visualize. In the process also known as graph simplication, nodes and (unweighted) edges are grouped to supernodes and superedges, respectively, to obtain a smaller graph. We propose models and algorithms for weighted graphs. The interpretation (i.e. decompression) of a compressed, weighted graph is that a pair of original nodes is connected by an edge if their supernodes are connected by one, and that the weight of an edge is approximated to be the weight of the superedge. The compression problem now consists of choosing supernodes, superedges, and superedge weights so that the approximation error is minimized while the amount of compression is maximized. In this paper, we formulate this task as the 'simple weighted graph compression problem'. We then propose a much wider class of tasks under the name of 'generalized weighted graph compression problem'. The generalized task extends the optimization to preserve longer-range connectivities between nodes, not just individual edge weights. We study the properties of these problems and propose a range of algorithms to solve them, with dierent balances between complexity and quality of the result. We evaluate the problems and algorithms experimentally on real networks. The results indicate that weighted graphs can be compressed efficiently with relatively little compression error.

On the Nash-Williams′ Lemma in Graph Reconstruction Theory

A generalization of Nash-Williams′ lemma is proved for the Structure of m-uniform null (m − k)-designs. It is then applied to various graph reconstruction problems. A short combinatorial proof of the edge reconstructibility of digraphs having regular underlying undirected graphs (e.g., tournaments) is given. A type of Nash-Williams′ lemma is conjectured for the vertex reconstruction problem.

Boxicity and Poset Dimension

Let G be a simple, undirected, finite graph with vertex set V(G) and edge set E(C). A k-dimensional box is a Cartesian product of closed intervals a(1), b(1)] x a(2), b(2)] x ... x a(k), b(k)]. The boxicity of G, box(G) is the minimum integer k such that G can be represented as the intersection graph of k-dimensional boxes, i.e. each vertex is mapped to a k-dimensional box and two vertices are adjacent in G if and only if their corresponding boxes intersect. Let P = (S, P) be a poset where S is the ground set and P is a reflexive, anti-symmetric and transitive binary relation on S. The dimension of P, dim(P) is the minimum integer l such that P can be expressed as the intersection of t total orders. Let G(P) be the underlying comparability graph of P. It is a well-known fact that posets with the same underlying comparability graph have the same dimension. The first result of this paper links the dimension of a poset to the boxicity of its underlying comparability graph. In particular, we show that for any poset P, box(G(P))/(chi(G(P)) - 1) <= dim(P) <= 2box(G(P)), where chi(G(P)) is the chromatic number of G(P) and chi(G(P)) not equal 1. The second result of the paper relates the boxicity of a graph G with a natural partial order associated with its extended double cover, denoted as G(c). Let P-c be the natural height-2 poset associated with G(c) by making A the set of minimal elements and B the set of maximal elements. We show that box(G)/2 <= dim(P-c) <= 2box(G) + 4. These results have some immediate and significant consequences. The upper bound dim(P) <= 2box(G(P)) allows us to derive hitherto unknown upper bounds for poset dimension. In the other direction, using the already known bounds for partial order dimension we get the following: (I) The boxicity of any graph with maximum degree Delta is O(Delta log(2) Delta) which is an improvement over the best known upper bound of Delta(2) + 2. (2) There exist graphs with boxicity Omega(Delta log Delta). This disproves a conjecture that the boxicity of a graph is O(Delta). (3) There exists no polynomial-time algorithm to approximate the boxicity of a bipartite graph on n vertices with a factor of O(n(0.5-epsilon)) for any epsilon > 0, unless NP=ZPP.

New Approximation Algorithms for Minimum Cycle Bases of Graphs

We consider the problem of computing an approximate minimum cycle basis of an undirected non-negative edge-weighted graph G with m edges and n vertices; the extension to directed graphs is also discussed. In this problem, a {0,1} incidence vector is associated with each cycle and the vector space over F-2 generated by these vectors is the cycle space of G. A set of cycles is called a cycle basis of G if it forms a basis for its cycle space. A cycle basis where the sum of the weights of the cycles is minimum is called a minimum cycle basis of G. Cycle bases of low weight are useful in a number of contexts, e.g. the analysis of electrical networks, structural engineering, chemistry, and surface reconstruction. Although in most such applications any cycle basis can be used, a low weight cycle basis often translates to better performance and/or numerical stability. Despite the fact that the problem can be solved exactly in polynomial time, we design approximation algorithms since the performance of the exact algorithms may be too expensive for some practical applications. We present two new algorithms to compute an approximate minimum cycle basis. For any integer k >= 1, we give (2k - 1)-approximation algorithms with expected running time O(kmn(1+2/k) + mn((1+1/k)(omega-1))) and deterministic running time O(n(3+2/k) ), respectively. Here omega is the best exponent of matrix multiplication. It is presently known that omega < 2.376. Both algorithms are o(m(omega)) for dense graphs. This is the first time that any algorithm which computes sparse cycle bases with a guarantee drops below the Theta(m(omega) ) bound. We also present a 2-approximation algorithm with expected running time O(M-omega root n log n), a linear time 2-approximation algorithm for planar graphs and an O(n(3)) time 2.42-approximation algorithm for the complete Euclidean graph in the plane.

On kuhnels 9-vertex complex projective plane

We present an elementary combinatorial proof of the existence and uniqueness of the 9-vertex triangulation of C P2. The original proof of existence, due to Kuhnel, as well as the original proof of uniqueness, due to Kuhnel and Lassmann, were based on extensive computer search. Recently Arnoux and Marin have used cohomology theory to present a computer-free proof. Our proof has the advantage of displaying a canonical copy of the affine plane over the three-element field inside this complex in terms of which the entire complex has a very neat and short description. This explicates the full automorphism group of the Kuhnel complex as a subgroup of the automorphism group of this affine plane. Our method also brings out the rich combinatorial structure inside this complex.

Some results and approaches for reconstruction conjectures

Tutte (1979) proved that the disconnected spanning subgraphs of a graph can be reconstructed from its vertex deck. This result is used to prove that if we can reconstruct a set of connected graphs from the shuffled edge deck (SED) then the vertex reconstruction conjecture is true. It is proved that a set of connected graphs can be reconstructed from the SED when all the graphs in the set are claw-free or all are P-4-free. Such a problem is also solved for a large subclass of the class of chordal graphs. This subclass contains maximal outerplanar graphs. Finally, two new conjectures, which imply the edge reconstruction conjecture, are presented. Conjecture 1 demands a construction of a stronger k-edge hypomorphism (to be defined later) from the edge hypomorphism. It is well known that the Nash-Williams' theorem applies to a variety of structures. To prove Conjecture 2, we need to incorporate more graph theoretic information in the Nash-Williams' theorem.

Chordal Bipartite Graphs with High Boxicity

The boxicity of a graph G is defined as the minimum integer k such that G is an intersection graph of axis-parallel k-dimensional boxes. Chordal bipartite graphs are bipartite graphs that do not contain an induced cycle of length greater than 4. It was conjectured by Otachi, Okamoto and Yamazaki that chordal bipartite graphs have boxicity at most 2. We disprove this conjecture by exhibiting an infinite family of chordal bipartite graphs that have unbounded boxicity.

The existence of homeomorphic subgraphs in chordal graphs

We establish conditions for the existence, in a chordal graph, of subgraphs homeomorphic to K-n (n greater than or equal to 3), K-m,K-n (m,n greater than or equal to 2), and wheels W-r (r greater than or equal to 3). Using these results, we develop a simple linear time algorithm for testing planarity of chordal graphs. We also show how these results lead to simple polynomial time algorithms for the Fixed Subgraph Homeomorphism problem on chordal graphs for some special classes of pattern graphs.

Acyclic Edge-Coloring of Planar Graphs

A proper edge-coloring with the property that every cycle contains edges of at least three distinct colors is called an acyclic edge-coloring. The acyclic chromatic index of a graph G, denoted. chi'(alpha)(G), is the minimum k such that G admits an acyclic edge-coloring with k colors. We conjecture that if G is planar and Delta(G) is large enough, then chi'(alpha) (G) = Delta (G). We settle this conjecture for planar graphs with girth at least 5. We also show that chi'(alpha) (G) <= Delta (G) + 12 for all planar G, which improves a previous result by Fiedorowicz, Haluszczak, and Narayan Inform. Process. Lett., 108 (2008), pp. 412-417].

Boxicity of Line Graphs

The boxicity of a graph H, denoted by View the MathML source, is the minimum integer k such that H is an intersection graph of axis-parallel k-dimensional boxes in View the MathML source. In this paper we show that for a line graph G of a multigraph, View the MathML source, where Δ(G) denotes the maximum degree of G. Since G is a line graph, Δ(G)≤2(χ(G)−1), where χ(G) denotes the chromatic number of G, and therefore, View the MathML source. For the d-dimensional hypercube Qd, we prove that View the MathML source. The question of finding a nontrivial lower bound for View the MathML source was left open by Chandran and Sivadasan in [L. Sunil Chandran, Naveen Sivadasan, The cubicity of Hypercube Graphs. Discrete Mathematics 308 (23) (2008) 5795–5800]. The above results are consequences of bounds that we obtain for the boxicity of a fully subdivided graph (a graph that can be obtained by subdividing every edge of a graph exactly once).

Percolation and Connectivity in AB Random Geometric Graphs

Given two independent Poisson point processes ©(1);©(2) in Rd, the AB Poisson Boolean model is the graph with points of ©(1) as vertices and with edges between any pair of points for which the intersection of balls of radius 2r centred at these points contains at least one point of ©(2). This is a generalization of the AB percolation model on discrete lattices. We show the existence of percolation for all d ¸ 2 and derive bounds for a critical intensity. We also provide a characterization for this critical intensity when d = 2. To study the connectivity problem, we consider independent Poisson point processes of intensities n and cn in the unit cube. The AB random geometric graph is de¯ned as above but with balls of radius r. We derive a weak law result for the largest nearest neighbour distance and almost sure asymptotic bounds for the connectivity threshold.