基于并行近似基序计数的复杂网络分析

George M. Slota, Kamesh Madduri
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引用次数: 32

摘要

子图计数构成了许多复杂网络分析指标的基础,包括基序和反基序发现、相对图let频率距离和图let度分布协议。确定精确的子图计数在计算上是非常昂贵的。在最近的工作中,我们提出了FASCIA,一种用于近似子图计数的共享内存并行算法和实现。FASCIA使用基于动态规划的方法,比穷举枚举要快得多,同时生成子图计数的高质量近似。然而,动态规划步骤的内存使用使我们无法将FASCIA应用于非常大的图形。本文通过图的划分和动态规划表的划分,介绍了FASCIA的分布式内存并行化。我们讨论了一种新的集体通信方案,使动态规划步骤节省内存。这些优化可以扩展到比以前大得多的网络。我们还提出了一种简单的并行化策略,用于较小网络上的分布式子图计数。新添加的功能使我们可以使用子图计数作为大型网络集合的图签名,并且我们使用各种基于子图计数的图分析来分析这个集合。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Complex Network Analysis Using Parallel Approximate Motif Counting
Subgraph counting forms the basis of many complex network analysis metrics, including motif and anti-motif finding, relative graph let frequency distance, and graph let degree distribution agreements. Determining exact subgraph counts is computationally very expensive. In recent work, we present FASCIA, a shared-memory parallel algorithm and implementation for approximate subgraph counting. FASCIA uses a dynamic programming-based approach and is significantly faster than exhaustive enumeration, while generating high-quality approximations of subgraph counts. However, the memory usage of the dynamic programming step prohibits us from applying FASCIA to very large graphs. In this paper, we introduce a distributed-memory parallelization of FASCIA by partitioning the graph and the dynamic programming table. We discuss a new collective communication scheme to make the dynamic programming step memory-efficient. These optimizations enable scaling to much larger networks than before. We also present a simple parallelization strategy for distributed subgraph counting on smaller networks. The new additions let us use subgraph counts as graph signatures for a large network collection, and we analyze this collection using various subgraph count-based graph analytics.
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