Approximately Counting Embeddings into Random Graphs

Let H be a graph, and let C_H(G) be the number of (subgraph isomorphic) copies of H contained in a graph G. We investigate the fundamental problem of estimating C_H(G). Previous results cover only a few specific instances of this general problem, for example, the case when H has degree at most one (monomer-dimer problem). In this paper, we present the first general subcase of the subgraph isomorphism counting problem which is almost always efficiently approximable. The results rely on a new graph decomposition technique. Informally, the decomposition is a labeling of the vertices such that every edge is between vertices with different labels and for every vertex all neighbors with a higher label have identical labels. The labeling implicitly generates a sequence of bipartite graphs which permits us to break the problem of counting embeddings of large subgraphs into that of counting embeddings of small subgraphs. Using this method, we present a simple randomized algorithm for the counting problem. For all decomposable graphs H and all graphs G, the algorithm is an unbiased estimator. Furthermore, for all graphs H having a decomposition where each of the bipartite graphs generated is small and almost all graphs G, the algorithm is a fully polynomial randomized approximation scheme. We show that the graph classes of H for which we obtain a fully polynomial randomized approximation scheme for almost all G includes graphs of degree at most two, bounded-degree forests, bounded-length grid graphs, subdivision of bounded-degree graphs, and major subclasses of outerplanar graphs, series-parallel graphs and planar graphs, whereas unbounded-length grid graphs are excluded.Comment: Earlier version appeared in Random 2008. Fixed an typo in Definition 3.

Graph Isomorphism for unit square graphs

In the past decades for more and more graph classes the Graph Isomorphism Problem was shown to be solvable in polynomial time. An interesting family of graph classes arises from intersection graphs of geometric objects. In this work we show that the Graph Isomorphism Problem for unit square graphs, intersection graphs of axis-parallel unit squares in the plane, can be solved in polynomial time. Since the recognition problem for this class of graphs is NP-hard we can not rely on standard techniques for geometric graphs based on constructing a canonical realization. Instead, we develop new techniques which combine structural insights into the class of unit square graphs with understanding of the automorphism group of such graphs. For the latter we introduce a generalization of bounded degree graphs which is used to capture the main structure of unit square graphs. Using group theoretic algorithms we obtain sufficient information to solve the isomorphism problem for unit square graphs.Comment: 31 pages, 6 figure

Faster Algorithms for the Maximum Common Subtree Isomorphism Problem

The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in general graphs. Confining to trees renders polynomial time algorithms possible and is of fundamental importance for approaches on more general graph classes. Various variants of this problem in trees have been intensively studied. We consider the general case, where trees are neither rooted nor ordered and the isomorphism is maximum w.r.t. a weight function on the mapped vertices and edges. For trees of order $n$ and maximum degree $\Delta$ our algorithm achieves a running time of $\mathcal{O}(n^2\Delta)$ by exploiting the structure of the matching instances arising as subproblems. Thus our algorithm outperforms the best previously known approaches. No faster algorithm is possible for trees of bounded degree and for trees of unbounded degree we show that a further reduction of the running time would directly improve the best known approach to the assignment problem. Combining a polynomial-delay algorithm for the enumeration of all maximum common subtree isomorphisms with central ideas of our new algorithm leads to an improvement of its running time from $\mathcal{O}(n^6+Tn^2)$ to $\mathcal{O}(n^3+Tn\Delta)$, where $n$ is the order of the larger tree, $T$ is the number of different solutions, and $\Delta$ is the minimum of the maximum degrees of the input trees. Our theoretical results are supplemented by an experimental evaluation on synthetic and real-world instances

Maximum common subgraph isomorphism algorithms for the matching of chemical structures

The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks

On retracts, absolute retracts, and folds in cographs

Let G and H be two cographs. We show that the problem to determine whether H is a retract of G is NP-complete. We show that this problem is fixed-parameter tractable when parameterized by the size of H. When restricted to the class of threshold graphs or to the class of trivially perfect graphs, the problem becomes tractable in polynomial time. The problem is also soluble when one cograph is given as an induced subgraph of the other. We characterize absolute retracts of cographs.Comment: 15 page

Surface Split Decompositions and Subgraph Isomorphism in Graphs on Surfaces

The Subgraph Isomorphism problem asks, given a host graph G on n vertices and a pattern graph P on k vertices, whether G contains a subgraph isomorphic to P. The restriction of this problem to planar graphs has often been considered. After a sequence of improvements, the current best algorithm for planar graphs is a linear time algorithm by Dorn (STACS '10), with complexity $2^{O(k)} O(n)$. We generalize this result, by giving an algorithm of the same complexity for graphs that can be embedded in surfaces of bounded genus. At the same time, we simplify the algorithm and analysis. The key to these improvements is the introduction of surface split decompositions for bounded genus graphs, which generalize sphere cut decompositions for planar graphs. We extend the algorithm for the problem of counting and generating all subgraphs isomorphic to P, even for the case where P is disconnected. This answers an open question by Eppstein (SODA '95 / JGAA '99)