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.
Vassilevska and Williams @cite_4 studied the problem of finding and counting individual non-induced subgraphs. Their results depend on the size @math of the independent set in the pattern graph and rely on efficient computations of matrix permanents and not on fast matrix multiplication techniques like some other approaches. If we restrict the problem to counting small patterns and therefore treat @math and @math as small constants, their approach counts a non-induced pattern in @math time. This is an improvement over a simple enumeration when @math . Kowaluk @cite_10 also improved on the result of Vassilevska and Williams when @math . @cite_3 developed algorithms for counting non-induced cycles with 3 to 7 nodes in @math , where @math represents the exponent of matrix multiplication algorithms.
@cite_10 @cite_4 @cite_3
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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... 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. The ability to find and count subgraphs of a given network is an important non trivial task with multidisciplinary applicability. Discovering network motifs or computing graphlet signatures are two examples of methodologies that at their core rely precisely on the subgraph counting problem. Here we present the g-trie, a data-structure specifically designed for discovering subgraph frequencies. We produce a tree that encapsulates the structure of the entire graph set, taking advantage of common topologies in the same way a prefix tree takes advantage of common prefixes. This avoids redundancy in the representation of the graphs, thus allowing for both memory and computation time savings. We introduce a specialized canonical labeling designed to highlight common substructures and annotate the g-trie with a set of conditional rules that break symmetries, avoiding repetitions in the computation. We introduce a novel algorithm that takes as input a set of small graphs and is able to efficiently find and count them as induced subgraphs of a larger network. We perform an extensive empirical evaluation of our algorithms, focusing on efficiency and scalability on a set of diversified complex networks. Results show that g-tries are able to clearly outperform previously existing algorithms by at least one order of magnitude. The subgraph isomorphism problem involves deciding whether a copy of a pattern graph occurs inside a larger target graph. The non-induced version allows extra edges in the target, whilst the induced version does not. Although both variants are NP-complete, algorithms inspired by constraint programming can operate comfortably on many real-world problem instances with thousands of vertices. However, they cannot handle arbitrary instances of this size. We show how to generate " really hard " random instances for subgraph isomorphism problems, which are computationally challenging with a couple of hundred vertices in the target, and only twenty pattern vertices. For the non-induced version of the problem, these instances lie on a satisfiable unsatisfiable phase transition, whose location we can predict; for the induced variant, much richer behaviour is observed, and constrained-ness gives a better measure of difficulty than does proximity to a phase transition. These results have practical consequences: we explain why the widely researched " filter verify " indexing technique used in graph databases is founded upon a misunderstanding of the empirical hardness of NP-complete problems, and cannot be beneficial when paired with any reasonable subgraph isomorphism algorithm.