Graphlet analysis is an approach to network analysis that is particularly popular in bioinformatics. We show how to set up a system of linear equations that relate the orbit counts and can be used in an algorithm that is significantly faster than the existing approaches based on direct enumeration of graphlets. The algorithm requires existence of a vertex with certain properties; we show that such vertex exists for graphlets of arbitrary size, except for complete graphs and @math , which are treated separately. Empirical analysis of running time agrees with the theoretical results.
Some approaches exploit the relations between the numbers of occurrences of induced subgraphs in a graph. Kloks . @cite_2 showed how to construct a system of equations that allows computing the number of occurrences of all six possible induced four-node subgraphs if we know the count of any of them. The time complexity of setting up the system equals the time complexity of multiplying two square matrices of size @math . Kowaluk @cite_10 generalized the result by Kloks to counting subgraph patterns of arbitrary size. Their solution depends on the size of the independent set in the pattern graph and relies on fast matrix multiplication techniques. They also provide an analysis of their approach on sparse graphs, where they avoid matrix multiplications and derive the time bounds in terms of the number of edges in the graph.
@cite_10 @cite_2
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The complexity of the subgraph isomorphism problem where the pattern graph is of fixed size is well known to depend on the topology of the pattern graph. For instance, the larger the maximum independent set of the pattern graph is the more efficient algorithms are known. The situation seems to be substantially different in the case of induced subgraph isomorphism for pattern graphs of fixed size. We present two results which provide evidence that no topology of an induced subgraph of fixed size can be easier to detect or count than an independent set of related size. We show that: Any fixed pattern graph that has a maximum independent set of size k that is disjoint from other maximum independent sets is not easier to detect as an induced subgraph than an independent set of size k. It follows in particular that an induced path on k vertices is not easier to detect than an independent set on ⌈k 2 ⌉ vertices, and that an induced even cycle on k vertices is not easier to detect than an independent set on k 2 vertices. In view of linear time upper bounds on induced paths of length three and four, our lower bound is tight. Similar corollaries hold for the detection of induced complete bipartite graphs and induced complete split graphs. For an arbitrary pattern graph H on k vertices with no isolated vertices, there is a simple subdivision of H, resulting from splitting each edge into a path of length four and attaching a distinct path of length three at each vertex of degree one, that is not easier to detect or count than an independent set on k vertices, respectively. Finally, we show that the so called diamond, paw and C 4 are not easier to detect as induced subgraphs than an independent set on three vertices. We present a general technique for detecting and counting small subgraphs. It consists of forming special linear combinations of the numbers of occurrences of different induced subgraphs of fixed size in a graph. These combinations can be efficiently computed by rectangular matrix multiplication. Our two main results utilizing the technique are as follows. Let @math be a fixed graph with @math vertices and an independent set of size @math 1. Detecting if an @math -vertex graph contains a (not necessarily induced) subgraph isomorphic to @math can be done in time @math , where @math is the exponent of fast arithmetic matrix multiplication of an @math matrix by an @math matrix. 2. When @math counting the number of (not necessarily induced) subgraphs isomorphic to @math can be done in the same time, i.e., in time @math It follows in particular that we can count the nu... We introduce graph motif parameters, a class of graph parameters that depend only on the frequencies of constant-size induced subgraphs. Classical works by Lovasz show that many interesting quantities have this form, including, for fixed graphs H, the number of H-copies (induced or not) in an input graph G, and the number of homomorphisms from H to G. We use the framework of graph motif parameters to obtain faster algorithms for counting subgraph copies of fixed graphs H in host graphs G. More precisely, for graphs H on k edges, we show how to count subgraph copies of H in time kO(k)· n0.174k + o(k) by a surprisingly simple algorithm. This improves upon previously known running times, such as O(n0.91k + c) time for k-edge matchings or O(n0.46k + c) time for k-cycles. Furthermore, we prove a general complexity dichotomy for evaluating graph motif parameters: Given a class C of such parameters, we consider the problem of evaluating f e C on input graphs G, parameterized by the number of induced subgraphs that f depends upon. For every recursively enumerable class C, we prove the above problem to be either FPT or #W[1]-hard, with an explicit dichotomy criterion. This allows us to recover known dichotomies for counting subgraphs, induced subgraphs, and homomorphisms in a uniform and simplified way, together with improved lower bounds. Finally, we extend graph motif parameters to colored subgraphs and prove a complexity trichotomy: For vertex-colored graphs H and G, where H is from a fixed class of graphs, we want to count color-preserving H-copies in G. We show that this problem is either polynomial-time solvable or FPT or #W[1]-hard, and that the FPT cases indeed need FPT time under reasonable assumptions. We consider the problem of counting, in a given graph, the number of induced k-vertex subgraphs which have an even number of edges, and also the complementary problem of counting the k-vertex induced subgraphs having an odd number of edges. We demonstrate that both problems are #W[1]-hard when parameterised by k, in fact proving a somewhat stronger result about counting subgraphs with a property that only holds for some subset of k-vertex subgraphs which have an even (respectively odd) number of edges. On the other hand, we show that each of the problems admits an FPTRAS. These approximation schemes are based on a surprising structural result, which exploits ideas from Ramsey theory.