Counting the frequencies of 3-, 4-, and 5-node undirected motifs (also know as graphlets) is widely used for understanding complex networks such as social and biology networks. However, it is a great challenge to compute these metrics for a large graph due to the intensive computation. Despite recent efforts to count triangles (i.e., 3-node undirected motif counting), little attention has been given to developing scalable tools that can be used to characterize 4- and 5-node motifs. In this paper, we develop computational efficient methods to sample and count 4- and 5- node undirected motifs. Our methods provide unbiased estimators of motif frequencies, and we derive simple and exact formulas for the variances of the estimators. Moreover, our methods are designed to fit vertex centric programming models, so they can be easily applied to current graph computing systems such as Pregel and GraphLab. We conduct experiments on a variety of real-word datasets, and experimental results show that our methods are several orders of magnitude faster than the state-of-the-art methods under the same estimation errors.
In this paper, we study the problem of computing 4- and 5-node motifs' frequencies for , which is much different from the problem of computing the number of subgraph patterns appearing in studied in @cite_2 . Recently, a lot of efforts has been devoted to design sampling methods for computing a large graph's motif concentrations @cite_13 @cite_0 @cite_8 @cite_29 @cite_1 @cite_19 . However, these methods fail to compute motif frequencies, which is more fundamental than motif concentrations. @cite_22 propose the color-coding method to reduce the computational cost of counting subgraphs. Color coding reduces the computations by coloring nodes randomly and enumerating only colorful CISes (i.e., CISes that are consisted of nodes with distinct colors), but @cite_16 reaveals that the color-coding method is not scalable and is hindered by the sheer number of colorful CISes. @cite_28 @cite_5 @cite_21 @cite_3 develop sampling methods to estimate the number of triangles of static and dynamic graphs. @cite_26 develop sampling methods to estimate 4-node undirected motifs' frequencies. However their methods are edge centric methods, which cannot be easily applied to current vertex centric graph computing systems such as GraphLab @cite_10 and GraphChi @cite_4 . Moreover, their methods fail to sample and count 5-node motifs.
@cite_26 @cite_4 @cite_22 @cite_8 @cite_28 @cite_10 @cite_29 @cite_21 @cite_1 @cite_3 @cite_0 @cite_19 @cite_2 @cite_5 @cite_16 @cite_13
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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 present a new shared-memory parallel algorithm and implementation called FASCIA for the problems of approximate sub graph counting and sub graph enumeration. The problem of sub graph counting refers to determining the frequency of occurrence of a given sub graph (or template) within a large network. This is a key graph analytic with applications in various domains. In bioinformatics, sub graph counting is used to detect and characterize local structure (motifs) in protein interaction networks. Exhaustive enumeration and exact counting is extremely compute-intensive, with running time growing exponentially with the number of vertices in the template. In this work, we apply the color coding technique to determine approximate counts of non-induced occurrences of the sub graph in the original network. Color coding gives a fixed-parameter algorithm for this problem, using a dynamic programming-based counting approach. Our new contributions are a multilevel shared-memory parallelization of the counting scheme and several optimizations to reduce the memory footprint. We show that approximate counts can be obtained for templates with up to 12 vertices, on networks with up to millions of vertices and edges. Prior work on this problem has only considered out-of-core parallelization on distributed platforms. With our new counting scheme, data layout optimizations, and multicore parallelism, we demonstrate a significant speedup over the current state-of-the-art for sub graph counting. In this paper, we study a colouring problem motivated by a practical frequency assignment problem and, up to our best knowledge, new. In wireless networks, a node interferes with other nodes, the level of interference depending on numerous parameters: distance between the nodes, geographical topography, obstacles, etc. We model this with a weighted graph (G,w) where the weight function w on the edges of G represents the noise (interference) between the two end-vertices. The total interference in a node is then the sum of all the noises of the nodes emitting on the same frequency. A weighted t-improper k-colouring of (G,w) is a k-colouring of the nodes of G (assignment of k frequencies) such that the interference at each node does not exceed the threshold t. We consider here the Weighted Improper Colouring problem which consists in determining the weighted t-improper chromatic number defined as the minimum integer k such that (G,w) admits a weighted t-improper k-colouring. We also consider the dual problem, denoted the Threshold Improper Colouring problem, where, given a number k of colours, we want to determine the minimum real t such that (G,w) admits a weighted t-improper k-colouring. We first present general upper bounds for both problems; in particular we show a generalisation of Lovasz@?s Theorem for the weighted t-improper chromatic number. Motivated by the original application, we then study a special interference model on various grids (square, triangular, hexagonal) where a node produces a noise of intensity 1 for its neighbours and a noise of intensity 1 2 for the nodes at distance two. We derive the weighted t-improper chromatic number for all values of t. The problem of counting occurrences of query graphs in a large data graph, known as subgraph counting, is fundamental to several domains such as genomics and social network analysis. Many important special cases (e.g. triangle counting) have received significant attention. Color coding is a very general and powerful algorithmic technique for subgraph counting. Color coding has been shown to be effective in several applications, but scalable implementations are only known for the special case of tree queries (i.e. queries of treewidth one). In this paper we present the first efficient distributed implementation for color coding that goes beyond tree queries: our algorithm applies to any query graph of treewidth @math . Since tree queries can be solved in time linear in the size of the data graph, our contribution is the first step into the realm of colour coding for queries that require superlinear running time in the worst case. This superlinear complexity leads to significant load balancing problems on graphs with heavy tailed degree distributions. Our algorithm structures the computation to work around high degree nodes in the data graph, and achieves very good runtime and scalability on a diverse collection of data and query graph pairs as a result. We also provide theoretical analysis of our algorithmic techniques, showing asymptotic improvements in runtime on random graphs with power law degree distributions, a popular model for real world graphs. Detecting and counting the number of copies of certain subgraphs (also known as network motifs or graphlets) is motivated by applications in a variety of areas ranging from biology to the study of the World Wide Web. Several polynomial-time algorithms have been suggested for counting or detecting the number of occurrences of certain network motifs. However, a need for more efficient algorithms arises when the input graph is very large, as is indeed the case in many applications of motif counting. In this paper we design sublinear-time algorithms for approximating the number of copies of certain constant-size subgraphs in a graph G. That is, our algorithms do not read the whole graph, but rather query parts of the graph. Specifically, we consider algorithms that may query the degree of any vertex of their choice and may ask for any neighbor of any vertex of their choice. The main focus of this work is on the basic problem of counting the number of length-2 paths and more generally on counting the number of... Summary: Biological and engineered networks have recently been shown to display network motifs: a small set of characteristic patterns that occur much more frequently than in randomized networks with the same degree sequence. Network motifs were demonstrated to play key information processing roles in biological regulation networks. Existing algorithms for detecting network motifs act by exhaustively enumerating all subgraphs with a given number of nodes in the network. The runtime of such algorithms increases strongly with network size. Here, we present a novel algorithm that allows estimation of subgraph concentrations and detection of network motifs at a runtime that is asymptotically independent of the network size. This algorithm is based on random sampling of subgraphs. Network motifs are detected with a surprisingly small number of samples in a wide variety of networks. Our method can be applied to estimate the concentrations of larger subgraphs in larger networks than was previously possible with exhaustive enumeration algorithms. We present results for high-order motifs in several biological networks and discuss their possible functions. Availability: A software tool for estimating subgraph concentrations and detecting network motifs (mfinder 1.1) and further information is available at http: www.weizmann.ac.il mcb UriAlon This paper proposes a generalized motif-based method for detecting defects in 16 out of 17 wallpaper groups in 2D patterned texture. It assumes that most patterned texture can be decomposed into lattices and their constituents-motifs. It then utilizes the symmetry property of motifs to calculate the energy of moving subtraction and its variance among different motifs. By learning the distribution of these values over a number of defect-free patterns, boundary conditions for discerning defective and defect-free patterns can be determined. This paper presents the theoretical foundation of the method, and defines the relations between motifs and lattice, from which a new concept called energy of moving subtraction is derived using norm metric measurement between a collection of circular shift matrices of motif and itself. It has been shown in this paper that the energy of moving subtraction amplifies the defect information of the defective motif. Together with its variance, an energy-variance space is further defined where decision boundaries are drawn for classifying defective and defect-free motifs. As the 16 wallpaper groups of patterned fabric can be transformed into three major groups, the proposed method is evaluated over these three major groups, from which 160 defect-free lattices samples are used for defining the decision boundaries, with 140 defect-free and 113 defective samples used for testing. An overall detection success rate of 93.32 is achieved for the proposed method. No other generalized approach can achieve this success rate has been reported before, and hence this result outperforms all other previously published approaches. Identifying motifs (or commonly occurring subgraphs templates) has been found to be useful in a number of applications, such as biological and social networks; they have been used to identify building blocks and functional properties, as well as to characterize the underlying networks. Enumerating subgraphs is a challenging computational problem, and all prior results have considered networks with a few thousand nodes. In this paper, we develop a parallel subgraph enumeration algorithm, ParSE, that scales to networks with millions of nodes. Our algorithm is a randomized approximation scheme, that estimates the subgraph frequency to any desired level of accuracy, and allows enumeration of a class of motifs that extends those considered in prior work. Our approach is based on parallelization of an approach called color coding, combined with a stream based partitioning. We also show that ParSE scales well with the number of processors, over a large range. Motifs in a given network are small connected subnetworks that occur in significantly higher frequencies than would be expected in random networks. They have recently gathered much attention as a concept to uncover structural design principles of complex networks. [Bioinformatics, 2004] proposed a sampling algorithm for performing the computationally challenging task of detecting network motifs. However, among other drawbacks, this algorithm suffers from a sampling bias and scales poorly with increasing subgraph size. Based on a detailed analysis of the previous algorithm, we present a new algorithm for network motif detection which overcomes these drawbacks. Furthermore, we present an efficient new approach for estimating the frequency of subgraphs in random networks that, in contrast to previous approaches, does not require the explicit generation of random networks. Experiments on a testbed of biological networks show our new algorithms to be orders of magnitude faster than previous approaches, allowing for the detection of larger motifs in bigger networks than previously possible and thus facilitating deeper insight into the field. Coloring the nodes of a graph with a small number of colors is one of the most fundamental problems in theoretical computer science. In this paper, we study graph coloring in a distributed setting. Processors of a distributed system are nodes of an undirected graph G. There is an edge between two nodes whenever the corresponding processors can directly communicate with each other. We assume that distributed coloring algorithms start with an initial m-coloring of G. In the paper, we prove new strong lower bounds for two special kinds of coloring algorithms. For algorithms which run for a single communication round---i.e., every node of the network can only send its initial color to all its neighbors---, we show that the number of colors of the computed coloring has to be at least Ω(Δ2 log2 Δ+ log log m). If such one-round algorithms are iteratively applied to reduce the number of colors step-by-step, we prove a time lower bound of Ω(Δ log2 Δ+ log*m) to obtain an O(Δ)-coloring. The best previous lower bounds for the two types of algorithms are Ω(log log m) and Ω(log*m), respectively. Many real-world domains can be represented as large node-link graphs: backbone Internet routers connect with 70,000 other hosts, mid-sized Web servers handle between 20,000 and 200,000 hyperlinked documents, and dictionaries contain millions of words defined in terms of each other. Computational manipulation of such large graphs is common, but previous tools for graph visualization have been limited to datasets of a few thousand nodes. Visual depictions of graphs and networks are external representations that exploit human visual processing to reduce the cognitive load of many tasks that require understanding of global or local structure. We assert that the two key advantages of computer-based systems for information visualization over traditional paper-based visual exposition are interactivity and scalability. We also argue that designing visualization software by taking the characteristics of a target user's task domain into account leads to systems that are more effective and scale to larger datasets than previous work. This thesis contains a detailed analysis of three specialized systems for the interactive exploration of large graphs, relating the intended tasks to the spatial layout and visual encoding choices. We present two novel algorithms for specialized layout and drawing that use quite different visual metaphors. The H3 system for visualizing the hyperlink structures of web sites scales to datasets of over 100,000 nodes by using a carefully chosen spanning tree as the layout backbone, 3D hyperbolic geometry for a Focus+Context view, and provides a fluid interactive experience through guaranteed frame rate drawing. The Constellation system features a highly specialized 2D layout intended to spatially encode domain-specific information for computational linguists checking the plausibility of a large semantic network created from dictionaries. The Planet Multicast system for displaying the tunnel topology of the Internet's multicast backbone provides a literal 3D geographic layout of arcs on a globe to help MBone maintainers find misconfigured long-distance tunnels. Each of these three systems provides a very different view of the graph structure, and we evaluate their efficacy for the intended task. We generalize these findings in our analysis of the importance of interactivity and specialization for graph visualization systems that are effective and scalable. We present a simple generation procedure which turns out to be an effective source of very hard cases for graph 3-colorability. The graphs distributed according to this generation procedure are much denser in very hard cases than previously reported for the same problem size. The coloring cost for these instances is also orders of magnitude bigger. This ability is issued from the fact that the procedure favors-inside the class of graphs with given connectivity and free of 4-cliques-the generation of graphs with relatively few paths of length three (that we call 3-paths). There is a critical value of the ratio between the number of 3-paths and the number of edges, independent of the number of nodes, which separates the graphs having the same connectivity in two regions: one contains almost all graphs free of 4-cliques while the other contains almost no such graphs. The generated very hard cases are near this phase transition, and have a regular structure, witnessed by the low variance in node degrees, as opposite to the random graphs. This regularity in the graph structure seems to confuse the coloring algorithm by inducing an uniform search space, with no clue for the search. A new scheme to sample signals defined on the nodes of a graph is proposed. The underlying assumption is that such signals admit a sparse representation in a frequency domain related to the structure of the graph, which is captured by the so-called graph-shift operator. Instead of using the value of the signal observed at a subset of nodes to recover the signal in the entire graph, the sampling scheme proposed here uses as input observations taken at a single node. The observations correspond to sequential applications of the graph-shift operator, which are linear combinations of the information gathered by the neighbors of the node. When the graph corresponds to a directed cycle (which is the support of time-varying signals), our method is equivalent to the classical sampling in the time domain. When the graph is more general, we show that the Vandermonde structure of the sampling matrix, critical when sampling time-varying signals, is preserved. Sampling and interpolation are analyzed first in the absence of noise, and then noise is considered. We then study the recovery of the sampled signal when the specific set of frequencies that is active is not known. Moreover, we present a more general sampling scheme, under which, either our aggregation approach or the alternative approach of sampling a graph signal by observing the value of the signal at a subset of nodes can be both viewed as particular cases. Numerical experiments illustrating the results in both synthetic and real-world graphs close the paper. Numerous graph mining applications rely on detecting subgraphs which are large near-cliques. Since formulations that are geared towards finding large near-cliques are hard and frequently inapproximable due to connections with the Maximum Clique problem, the poly-time solvable densest subgraph problem which maximizes the average degree over all possible subgraphs "lies at the core of large scale data mining" [10]. However, frequently the densest subgraph problem fails in detecting large near-cliques in networks. In this work, we introduce the k-clique densest subgraph problem, k ≥ 2. This generalizes the well studied densest subgraph problem which is obtained as a special case for k=2. For k=3 we obtain a novel formulation which we refer to as the triangle densest subgraph problem: given a graph G(V,E), find a subset of vertices S* such that τ(S*)=max limitsS ⊆ V t(S) |S|, where t(S) is the number of triangles induced by the set S. On the theory side, we prove that for any k constant, there exist an exact polynomial time algorithm for the k-clique densest subgraph problem . Furthermore, we propose an efficient 1 k-approximation algorithm which generalizes the greedy peeling algorithm of Asahiro and Charikar [8,18] for k=2. Finally, we show how to implement efficiently this peeling framework on MapReduce for any k ≥ 3, generalizing the work of Bahmani, Kumar and Vassilvitskii for the case k=2 [10]. On the empirical side, our two main findings are that (i) the triangle densest subgraph is consistently closer to being a large near-clique compared to the densest subgraph and (ii) the peeling approximation algorithms for both k=2 and k=3 achieve on real-world networks approximation ratios closer to 1 rather than the pessimistic 1 k guarantee. An interesting consequence of our work is that triangle counting, a well-studied computational problem in the context of social network analysis can be used to detect large near-cliques. Finally, we evaluate our proposed method on a popular graph mining application. Counting the frequency of small subgraphs is a fundamental technique in network analysis across various domains, most notably in bioinformatics and social networks. The special case of triangle counting has received much attention. Getting results for 4-vertex patterns is highly challenging, and there are few practical results known that can scale to massive sizes. Indeed, even a highly tuned enumeration code takes more than a day on a graph with millions of edges. Most previous work that runs for truly massive graphs employ clusters and massive parallelization. We provide a sampling algorithm that provably and accurately approximates the frequencies of all 4-vertex pattern subgraphs. Our algorithm is based on a novel technique of 3-path sampling and a special pruning scheme to decrease the variance in estimates. We provide theoretical proofs for the accuracy of our algorithm, and give formal bounds for the error and confidence of our estimates. We perform a detailed empirical study and show that our algorithm provides estimates within 1 relative error for all subpatterns (over a large class of test graphs), while being orders of magnitude faster than enumeration and other sampling based algorithms. Our algorithm takes less than a minute (on a single commodity machine) to process an Orkut social network with 300 million edges. For many random constraint satisfaction problems, by now there exist asymptotically tight estimates of the largest constraint density for which solutions exist. At the same time, for many of these problems, all known polynomial-time algorithms stop finding solutions at much smaller densities. For example, it is well-known that it is easy to color a random graph using twice as many colors as its chromatic number. Indeed, some of the simplest possible coloring algorithms achieve this goal. Given the simplicity of those algorithms, one would expect room for improvement. Yet, to date, no algorithm is known that uses (2 - epsiv)chi colors, in spite of efforts by numerous researchers over the years. In view of the remarkable resilience of this factor of 2 against every algorithm hurled at it, we find it natural to inquire into its origin. We do so by analyzing the evolution of the set of k-colorings of a random graph, viewed as a subset of 1,...,k n, as edges are added. We prove that the factor of 2 corresponds in a precise mathematical sense to a phase transition in the geometry of this set. Roughly speaking, we prove that the set of k-colorings looks like a giant ball for k ges 2chi, but like an error-correcting code for k les (2 - epsiv)chi. We also prove that an analogous phase transition occurs both in random k-SAT and in random hypergraph 2-coloring. And that for each of these three problems, the location of the transition corresponds to the point where all known polynomial-time algorithms fail. To prove our results we develop a general technique that allows us to establish rigorously much of the celebrated 1-step replica-symmetry-breaking hypothesis of statistical physics for random CSPs. Network motifs are statistically overrepresented sub-structures (sub-graphs) in a network, and have been recognized as ‘the simple building blocks of complex networks’. Study of biological network motifs may reveal answers to many important biological questions. The main difficulty in detecting larger network motifs in biological networks lies in the facts that the number of possible sub-graphs increases exponentially with the network or motif size (node counts, in general), and that no known polynomial-time algorithm exists in deciding if two graphs are topologically equivalent. This article discusses the biological significance of network motifs, the motivation behind solving the motif-finding problem, and strategies to solve the various aspects of this problem. A simple classification scheme is designed to analyze the strengths and weaknesses of several existing algorithms. Experimental results derived from a few comparative studies in the literature are discussed, with conclusions that lead to future research directions. The problem of locating motifs in real-valued, multivariate time series data involves the discovery of sets of recurring patterns embedded in the time series. Each set is composed of several non-overlapping subsequences and constitutes a motif because all of the included subsequences are similar. The ability to automatically discover such motifs allows intelligent systems to form endogenously meaningful representations of their environment through unsupervised sensor analysis. In this paper, we formulate a unifying view of motif discovery as a problem of locating regions of high density in the space of all time series subsequences. Our approach is efficient (sub-quadratic in the length of the data), requires fewer user-specified parameters than previous methods, and naturally allows variable length motif occurrences and non-linear temporal warping. We evaluate the performance of our approach using four data sets from different domains including on-body inertial sensors and speech. We study deterministic, distributed algorithms for two weak variants of the standard graph coloring problem. We consider defective colorings, i.e., colorings where nodes of a color class may induce a graph of maximum degree d for some parameter d>0. We also look at colorings where a minimum number of multi-chromatic edges is required. For an integer k>0, we call a coloring k-partially proper if every node v has at least min k,deg(v) neighbors with a different color. We show that for all d∈ 1,...,Δ , it is possible to compute a O(Δ2 d2)-coloring with defect d in time O(log*n) where Δ is the largest degree of the network graph. Similarly, for all k∈ 1,...,Δ , a k-partially proper O(k2)-coloring can be computed in O(log*n) rounds. As an application of our weak defective coloring algorithm, we obtain a faster deterministic algorithm for the standard vertex coloring problem on graphs with moderate degrees. We show that in time O(Δ+log*n), a (Δ+1)-coloring can be computed, a task for which the best previous algorithm required time O(Δ*log(Δ) + log*n). The same result holds for the problem of computing a maximal independent set. 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.