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Register a new userSandslash: A Two-Level Framework for Efficient Graph Pattern Mining
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Added by
Xuhao Chen
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Graph pattern mining (GPM) is used in diverse application areas including social network analysis, bioinformatics, and chemical engineering. Existing GPM frameworks either provide high-level interfaces for productivity at the cost of expressiveness or provide low-level interfaces that can express a wide variety of GPM algorithms at the cost of increased programming complexity. Moreover, existing systems lack the flexibility to explore combinations of optimizations to achieve performance competitive with hand-optimized applications. We present Sandslash, an in-memory Graph Pattern Mining (GPM) framework that uses a novel programming interface to support productive, expressive, and efficient GPM on large graphs. Sandslash provides a high-level API that needs only a specification of the GPM problem, and it implements fast subgraph enumeration, provides efficient data structures, and applies high-level optimizations automatically. To achieve performance competitive with expert-optimized implementations, Sandslash also provides a low-level API that allows users to express algorithm-specific optimizations. This enables Sandslash to support both high-productivity and high-efficiency without losing expressiveness. We evaluate Sandslash on shared-memory machines using five GPM applications and a wide range of large real-world graphs. Experimental results demonstrate that applications written using Sandslash high-level or low-level API outperforms state-of-the-art GPM systems AutoMine, Pangolin, and Peregrine on average by 13.8x, 7.9x, and 5.4x, respectively. We also show that these Sandslash applications outperform expert-optimized GPM implementations by 2.3x on average with less programming effort.
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There is growing interest in graph pattern mining (GPM) problems such as motif counting. GPM systems have been developed to provide unified interfaces for programming algorithms for these problems and for running them on parallel systems. However, existing systems may take hours to mine even simple patterns in moderate-sized graphs, which significantly limits their real-world usability. We present Pangolin, a high-performance and flexible in-memory GPM framework targeting shared-memory CPUs and GPUs. Pangolin is the first GPM system that provides high-level abstractions for GPU processing. It provides a simple programming interface based on the extend-reduce-filter model, which enables users to specify application-specific knowledge for search space pruning and isomorphism test elimination. We describe novel optimizations that exploit locality, reduce memory consumption, and mitigate the overheads of dynamic memory allocation and synchronization. Evaluation on a 28-core CPU demonstrates that Pangolin outperforms existing GPM frameworks Arabesque, RStream, and Fractal by 49x, 88x, and 80x on average, respectively. Acceleration on a V100 GPU further improves performance of Pangolin by 15x on average. Compared to state-of-the-art hand-optimized GPM applications, Pangolin provides competitive performance with less programming effort.
FP-Growth algorithm is a Frequent Pattern Min- ing (FPM) algorithm that has been extensively used to study correlations and patterns in large scale datasets. While several researchers have designed distributed memory FP-Growth algorithms, it is pivotal to consider fault tolerant FP-Growth, which can address the increasing fault rates in large scale systems. In this work, we propose a novel parallel, algorithm-level fault-tolerant FP-Growth algorithm. We leverage algorithmic properties and MPI advanced features to guarantee an O(1) space complexity, achieved by using the dataset memory space itself for checkpointing. We also propose a recovery algorithm that can use in-memory and disk-based checkpointing, though in many cases the recovery can be completed without any disk access, and incurring no memory overhead for checkpointing. We evaluate our FT algorithm on a large scale InfiniBand cluster with several large datasets using up to 2K cores. Our evaluation demonstrates excellent efficiency for checkpointing and recovery in comparison to the disk-based approach. We have also observed 20x average speed-up in comparison to Spark, establishing that a well designed algorithm can easily outperform a solution based on a general fault-tolerant programming model.
In this paper we study predictive pattern mining problems where the goal is to construct a predictive model based on a subset of predictive patterns in the database. Our main contribution is to introduce a novel method called safe pattern pruning (SPP) for a class of predictive pattern mining problems. The SPP method allows us to efficiently find a superset of all the predictive patterns in the database that are needed for the optimal predictive model. The advantage of the SPP method over existing boosting-type method is that the former can find the superset by a single search over the database, while the latter requires multiple searches. The SPP method is inspired by recent development of safe feature screening. In order to extend the idea of safe feature screening into predictive pattern mining, we derive a novel pruning rule called safe pattern pruning (SPP) rule that can be used for searching over the tree defined among patterns in the database. The SPP rule has a property that, if a node corresponding to a pattern in the database is pruned out by the SPP rule, then it is guaranteed that all the patterns corresponding to its descendant nodes are never needed for the optimal predictive model. We apply the SPP method to graph mining and item-set mining problems, and demonstrate its computational advantage.
Distributed data processing platforms such as MapReduce and Pregel have substantially simplified the design and deployment of certain classes of distributed graph analytics algorithms. However, these platforms do not represent a good match for distributed graph mining problems, as for example finding frequent subgraphs in a graph. Given an input graph, these problems require exploring a very large number of subgraphs and finding patterns that match some interestingness criteria desired by the user. These algorithms are very important for areas such as social net- works, semantic web, and bioinformatics. In this paper, we present Arabesque, the first distributed data processing platform for implementing graph mining algorithms. Arabesque automates the process of exploring a very large number of subgraphs. It defines a high-level filter-process computational model that simplifies the development of scalable graph mining algorithms: Arabesque explores subgraphs and passes them to the application, which must simply compute outputs and decide whether the subgraph should be further extended. We use Arabesques API to produce distributed solutions to three fundamental graph mining problems: frequent subgraph mining, counting motifs, and finding cliques. Our implementations require a handful of lines of code, scale to trillions of subgraphs, and represent in some cases the first available distributed solutions.
The industry and academia have proposed many distributed graph processing systems. However, the existing systems are not friendly enough for users like data analysts and algorithm engineers. On the one hand, the programing models and interfaces differ a lot in the existing systems, leading to high learning costs and program migration costs. On the other hand, these graph processing systems are tightly bound to the underlying distributed computing platforms, requiring users to be familiar with distributed computing. To improve the usability of distributed graph processing, we propose a unified distributed graph programming framework UniGPS. Firstly, we propose a unified cross-platform graph programming model VCProg for UniGPS. VCProg hides details of distributed computing from users. It is compatible with the popular graph programming models Pregel, GAS, and Push-Pull. VCProg programs can be executed by compatible distributed graph processing systems without modification, reducing the learning overheads of users. Secondly, UniGPS supports Python as the programming language. We propose an interprocess-communication-based execution environment isolation mechanism to enable Java/C++-based systems to call user-defined methods written in Python. The experimental results show that UniGPS enables users to process big graphs beyond the memory capacity of a single machine without sacrificing usability. UniGPS shows near-linear data scalability and machine scalability.
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