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)

A Partitioning Algorithm for Maximum Common Subgraph Problems

We introduce a new branch and bound algorithm for the maximum common subgraph and maximum common connected subgraph problems which is based around vertex labelling and partitioning. Our method in some ways resembles a traditional constraint programming approach, but uses a novel compact domain store and supporting inference algorithms which dramatically reduce the memory and computation requirements during search, and allow better dual viewpoint ordering heuristics to be calculated cheaply. Experiments show a speedup of more than an order of magnitude over the state of the art, and demonstrate that we can operate on much larger graphs without running out of memory

Quantum Query Complexity of Subgraph Isomorphism and Homomorphism

Let $H$ be a fixed graph on $n$ vertices. Let $f_H(G) = 1$ iff the input graph $G$ on $n$ vertices contains $H$ as a (not necessarily induced) subgraph. Let $\alpha_H$ denote the cardinality of a maximum independent set of $H$. In this paper we show: $$Q(f_H) = \Omega\left(\sqrt{\alpha_H \cdot n}\right),$$ where $Q(f_H)$ denotes the quantum query complexity of $f_H$. As a consequence we obtain a lower bounds for $Q(f_H)$ in terms of several other parameters of $H$ such as the average degree, minimum vertex cover, chromatic number, and the critical probability. We also use the above bound to show that $Q(f_H) = \Omega(n^{3/4})$ for any $H$, improving on the previously best known bound of $\Omega(n^{2/3})$. Until very recently, it was believed that the quantum query complexity is at least square root of the randomized one. Our $\Omega(n^{3/4})$ bound for $Q(f_H)$ matches the square root of the current best known bound for the randomized query complexity of $f_H$, which is $\Omega(n^{3/2})$ due to Gr\"oger. Interestingly, the randomized bound of $\Omega(\alpha_H \cdot n)$ for $f_H$ still remains open. We also study the Subgraph Homomorphism Problem, denoted by $f_{[H]}$, and show that $Q(f_{[H]}) = \Omega(n)$. Finally we extend our results to the $3$-uniform hypergraphs. In particular, we show an $\Omega(n^{4/5})$ bound for quantum query complexity of the Subgraph Isomorphism, improving on the previously known $\Omega(n^{3/4})$ bound. For the Subgraph Homomorphism, we obtain an $\Omega(n^{3/2})$ bound for the same.Comment: 16 pages, 2 figure

Between Subgraph Isomorphism and Maximum Common Subgraph

When a small pattern graph does not occur inside a larger target graph, we can ask how to find "as much of the pattern as possible" inside the target graph. In general, this is known as the maximum common subgraph problem, which is much more computationally challenging in practice than subgraph isomorphism. We introduce a restricted alternative, where we ask if all but k vertices from the pattern can be found in the target graph. This allows for the development of slightly weakened forms of certain invariants from subgraph isomorphism which are based upon degree and number of paths. We show that when k is small, weakening the invariants still retains much of their effectiveness. We are then able to solve this problem on the standard problem instances used to benchmark subgraph isomorphism algorithms, despite these instances being too large for current maximum common subgraph algorithms to handle. Finally, by iteratively increasing k, we obtain an algorithm which is also competitive for the maximum common subgraph

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

Frequent Subgraph Mining in Outerplanar Graphs

In recent years there has been an increased interest in frequent pattern discovery in large databases of graph structured objects. While the frequent connected subgraph mining problem for tree datasets can be solved in incremental polynomial time, it becomes intractable for arbitrary graph databases. Existing approaches have therefore resorted to various heuristic strategies and restrictions of the search space, but have not identified a practically relevant tractable graph class beyond trees. In this paper, we define the class of so called tenuous outerplanar graphs, a strict generalization of trees, develop a frequent subgraph mining algorithm for tenuous outerplanar graphs that works in incremental polynomial time, and evaluate the algorithm empirically on the NCI molecular graph dataset