Enumerating Maximal Bicliques from a Large Graph using MapReduce

We consider the enumeration of maximal bipartite cliques (bicliques) from a large graph, a task central to many practical data mining problems in social network analysis and bioinformatics. We present novel parallel algorithms for the MapReduce platform, and an experimental evaluation using Hadoop MapReduce. Our algorithm is based on clustering the input graph into smaller sized subgraphs, followed by processing different subgraphs in parallel. Our algorithm uses two ideas that enable it to scale to large graphs: (1) the redundancy in work between different subgraph explorations is minimized through a careful pruning of the search space, and (2) the load on different reducers is balanced through the use of an appropriate total order among the vertices. Our evaluation shows that the algorithm scales to large graphs with millions of edges and tens of mil- lions of maximal bicliques. To our knowledge, this is the first work on maximal biclique enumeration for graphs of this scale.Comment: A preliminary version of the paper was accepted at the Proceedings of the 3rd IEEE International Congress on Big Data 201

Enumerating Maximal Bicliques from a Large Graph Using MapReduce

We consider the enumeration of maximal bipartite cliques (bicliques) from a large graph, a task central to many data mining problems arising in social network analysis and bioinformatics. We present novel parallel algorithms for the MapReduce framework, and an experimental evaluation using Hadoop MapReduce. Our algorithm is based on clustering the input graph into smaller subgraphs, followed by processing different subgraphs in parallel. Our algorithm uses two ideas that enable it to scale to large graphs: (1) the redundancy in work between different subgraph explorations is minimized through a careful pruning of the search space, and (2) the load on different reducers is balanced through a task assignment that is based on an appropriate total order among the vertices. We show theoretically that our algorithm is work optimal, i.e., it performs the same total work as its sequential counterpart. We present a detailed evaluation which shows that the algorithm scales to large graphs with millions of edges and tens of millions of maximal bicliques. To our knowledge, this is the first work on maximal biclique enumeration for graphs of this scale

Tight lower bounds on the number of bicliques in false-twin-free graphs

A \emph{biclique} is a maximal bipartite complete induced subgraph of $G$. Bicliques have been studied in the last years motivated by the large number of applications. In particular, enumeration of the maximal bicliques has been of interest in data analysis. Associated with this issue, bounds on the maximum number of bicliques were given. In this paper we study bounds on the minimun number of bicliques of a graph. Since adding false-twin vertices to $G$ does not change the number of bicliques, we restrict to false-twin-free graphs. We give a tight lower bound on the minimum number bicliques for a subclass of $\{C_4$,false-twin$\}$-free graphs and for the class of $\{K_3$,false-twin$\}$-free graphs. Finally we discuss the problem for general graphs.Comment: 16 pages, 4 figue

Shared-Memory Parallel Maximal Clique Enumeration

We present shared-memory parallel methods for Maximal Clique Enumeration (MCE) from a graph. MCE is a fundamental and well-studied graph analytics task, and is a widely used primitive for identifying dense structures in a graph. Due to its computationally intensive nature, parallel methods are imperative for dealing with large graphs. However, surprisingly, there do not yet exist scalable and parallel methods for MCE on a shared-memory parallel machine. In this work, we present efficient shared-memory parallel algorithms for MCE, with the following properties: (1) the parallel algorithms are provably work-efficient relative to a state-of-the-art sequential algorithm (2) the algorithms have a provably small parallel depth, showing that they can scale to a large number of processors, and (3) our implementations on a multicore machine shows a good speedup and scaling behavior with increasing number of cores, and are substantially faster than prior shared-memory parallel algorithms for MCE.Comment: 10 pages, 3 figures, proceedings of the 25th IEEE International Conference on. High Performance Computing, Data, and Analytics (HiPC), 201

Incremental Maintenance of Maximal Cliques in a Dynamic Graph

We consider the maintenance of the set of all maximal cliques in a dynamic graph that is changing through the addition or deletion of edges. We present nearly tight bounds on the magnitude of change in the set of maximal cliques, as well as the first change-sensitive algorithms for clique maintenance, whose runtime is proportional to the magnitude of the change in the set of maximal cliques. We present experimental results showing these algorithms are efficient in practice and are faster than prior work by two to three orders of magnitude.Comment: 18 pages, 8 figure

Multipartite Graph Algorithms for the Analysis of Heterogeneous Data

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of biomolecules within an organism. This dissertation describes the design, implementation and application of graph algorithms, with the goal of seeking dense structure in data derived from omics experiments in order to detect latent associations between often heterogeneous entities, such as genes, diseases and phenotypes. Exact combinatorial solutions are developed and implemented, rather than relying on approximations or heuristics, even when problems are exceedingly large and/or difficult. Datasets on which the algorithms are applied include time series transcriptomic data from an experiment on the developing mouse cerebellum, gene expression data measuring acute ethanol response in the prefrontal cortex, and the analysis of a predicted protein-protein interaction network. A bipartite graph model is used to integrate heterogeneous data types, such as genes with phenotypes and microbes with mouse strains. The techniques are then extended to a multipartite algorithm to enumerate dense substructure in multipartite graphs, constructed using data from three or more heterogeneous sources, with applications to functional genomics. Several new theoretical results are given regarding multipartite graphs and the multipartite enumeration algorithm. In all cases, practical implementations are demonstrated to expand the frontier of computational feasibility