We address the problem of computing the distribution of induced connected subgraphs, aka \emph{graphlets} or \emph{motifs}, in large graphs. The current state-of-the-art algorithms estimate the motif counts via uniform sampling, by leveraging the color coding technique by Alon, Yuster and Zwick. In this work we extend the applicability of this approach, by introducing a set of algorithmic optimizations and techniques that reduce the running time and space usage of color coding and improve the accuracy of the counts. To this end, we first show how to optimize color coding to efficiently build a compact table of a representative subsample of all graphlets in the input graph. For $8$-node motifs, we can build such a table in one hour for a graph with $65$M nodes and $1.8$B edges, which is $2000$ times larger than the state of the art. We then introduce a novel adaptive sampling scheme that breaks the "additive error barrier" of uniform sampling, guaranteeing multiplicative approximations instead of just additive ones. This allows us to count not only the most frequent motifs, but also extremely rare ones. For instance, on one graph we accurately count nearly $10.000$ distinct $8$-node motifs whose relative frequency is so small that uniform sampling would literally take centuries to find them. Our results show that color coding is still the most promising approach to scalable motif counting.
Pattern counting in graphs is fundamental to network science tasks, and there are many scalable methods for approximating counts of small patterns, often called motifs, in large graphs. However, modern graph datasets now contain richer structure, and incorporating temporal information in particular has become a critical part of network analysis. Temporal motifs, which are generalizations of small subgraph patterns that incorporate temporal ordering on edges, are an emerging part of the network analysis toolbox. However, there are no algorithms for fast estimation of temporal motifs counts; mor…
We introduce Tiered Sampling, a novel technique for approximate counting sparse motifs in massive graphs whose edges are observed in a stream. Our technique requires only a single pass on the data and uses a memory of fixed size $M$, which can be magnitudes smaller than the number of edges. Our methods addresses the challenging task of counting sparse motifs - sub-graph patterns that have low probability to appear in a sample of $M$ edges in the graph, which is the maximum amount of data available to the algorithms in each step. To obtain an unbiased and low variance estimate of the count we p…
A $k$-motif (or graphlet) is a subgraph on $k$ nodes in a graph or network. Counting of motifs in complex networks has been a well-studied problem in network analysis of various real-word graphs arising from the study of social networks and bioinformatics. In particular, the triangle counting problem has received much attention due to its significance in understanding the behavior of social networks. Similarly, subgraphs with more than 3 nodes have received much attention recently. While there have been successful methods developed on this problem, most of the existing algorithms are not scala…
A great variety of complex systems, from user interactions in communication networks to transactions in financial markets, can be modeled as temporal graphs consisting of a set of vertices and a series of timestamped and directed edges. Temporal motifs are generalized from subgraph patterns in static graphs which consider edge orderings and durations in addition to topologies. Counting the number of occurrences of temporal motifs is a fundamental problem for temporal network analysis. However, existing methods either cannot support temporal motifs or suffer from performance issues. Moreover, t…
Hunan University（湖南大学）；National University of Singapore（新加坡国立大学）；Singapore Management University（新加坡管理大学）；Alibaba-Zhejiang University Joint Research Institute of Frontier Technologies（阿里巴巴-浙江大学前沿技术联合研究院）
A great variety of complex systems ranging from user interactions in communication networks to transactions in financial markets can be modeled as temporal graphs, which consist of a set of vertices and a series of timestamped and directed edges. Temporal motifs in temporal graphs are generalized from subgraph patterns in static graphs which take into account edge orderings and durations in addition to structures. Counting the number of occurrences of temporal motifs is a fundamental problem for temporal network analysis. However, existing methods either cannot support temporal motifs or suffe…
We consider the problem of sampling and approximately counting an arbitrary given motif $H$ in a graph $G$, where access to $G$ is given via queries: degree, neighbor, and pair, as well as uniform edge sample queries. Previous algorithms for these tasks were based on a decomposition of $H$ into a collection of odd cycles and stars, denoted $\mathcal{D}^*(H)=\{O_{k_1}, \ldots, O_{k_q}, S_{p_1}, \ldots, S_{p_\ell}\}$. These algorithms were shown to be optimal for the case where $H$ is a clique or an odd-length cycle, but no other lower bounds were known. We present a new algorithm for sampling a…
Computing subgraph frequencies is a fundamental task that lies at the core of several network analysis methodologies, such as network motifs and graphlet-based metrics, which have been widely used to categorize and compare networks from multiple domains. Counting subgraphs is however computationally very expensive and there has been a large body of work on efficient algorithms and strategies to make subgraph counting feasible for larger subgraphs and networks. This survey aims precisely to provide a comprehensive overview of the existing methods for subgraph counting. Our main contribution is …
Counting the number of occurrences of small connected subgraphs, called temporal motifs, has become a fundamental primitive for the analysis of temporal networks, whose edges are annotated with the time of the event they represent. One of the main complications in studying temporal motifs is the large number of motifs that can be built even with a limited number of vertices or edges. As a consequence, since in many applications motifs are employed for exploratory analyses, the user needs to iteratively select and analyze several motifs that represent different aspects of the network, resulting…
Estimating the frequency of sub-graphs is of importance for many tasks, including sub-graph isomorphism, kernel-based anomaly detection, and network structure analysis. While multiple algorithms were proposed for full enumeration or sampling-based estimates, these methods fail in very large graphs. Recent advances in parallelization allow for estimates of total sub-graphs counts in very large graphs. The task of counting the frequency of each sub-graph associated with each vertex also received excellent solutions for undirected graphs. However, there is currently no good solution for very larg…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper, we explore the opportunities for parallelization of the exact and inexact matches and present an efficient SIMD solution for the Occ portion of the algorithm. Our implementation computes all eight Occ values required for the inexact match algorithm step in a single pass. We showcase the algorithm performance in a multi-core genome aligner and discuss effects…
We introduce graph motif parameters, a class of graph parameters that depend only on the frequencies of constant-size induced subgraphs. Classical works by Lovász 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 $G$. Using the framework of graph motif parameters, we obtain faster algorithms for counting subgraph copies of fixed graphs $H$ in host graphs $G$: For graphs $H$ on $k$ edges, we show how to count subgraph copies of $H$ in time $k^{O(k)}\c…
Many real-world applications give rise to large heterogeneous networks where nodes and edges can be of any arbitrary type (e.g., user, web page, location). Special cases of such heterogeneous graphs include homogeneous graphs, bipartite, k-partite, signed, labeled graphs, among many others. In this work, we generalize the notion of network motifs to heterogeneous networks. In particular, small induced typed subgraphs called typed graphlets (heterogeneous network motifs) are introduced and shown to be the fundamental building blocks of complex heterogeneous networks. Typed graphlets are a power…
A streaming model is one where data items arrive over long period of time, either one item at a time or in bursts. Typical tasks include computing various statistics over a sliding window of some fixed time-horizon. What makes the streaming model interesting is that as the time progresses, old items expire and new ones arrive. One of the simplest and central tasks in this model is sampling. That is, the task of maintaining up to $k$ uniformly distributed items from a current time-window as old items expire and new ones arrive. We call sampling algorithms {\bf succinct} if they use provably opt…
The identification and counting of small graph patterns, called network motifs, is a fundamental primitive in the analysis of networks, with application in various domains, from social networks to neuroscience. Several techniques have been designed to count the occurrences of motifs in static networks, with recent work focusing on the computational challenges provided by large networks. Modern networked datasets contain rich information, such as the time at which the events modeled by the networks edges happened, which can provide useful insights into the process modeled by the network. The an…
Clique counting is a fundamental task in network analysis, and even the simplest setting of $3$-cliques (triangles) has been the center of much recent research. Getting the count of $k$-cliques for larger $k$ is algorithmically challenging, due to the exponential blowup in the search space of large cliques. But a number of recent applications (especially for community detection or clustering) use larger clique counts. Moreover, one often desires \textit{local} counts, the number of $k$-cliques per vertex/edge. Our main result is Pivoter, an algorithm that exactly counts the number of $k$-cliqu…
We study the problem of approximately counting cliques and near cliques in a graph, where the access to the graph is only available through crawling its vertices; thus typically seeing only a small portion of it. This model, known as the random walk model or the neighborhood query model has been introduced recently and captures real-life scenarios in which the entire graph is too massive to be stored as a whole or be scanned entirely and sampling vertices independently is non-trivial in it. We introduce DeMEtRIS: Dense Motif Estimation through Random Incident Sampling. This method provides a s…
