Scalable supergraph search in large graph databases

© 2016 IEEE. Supergraph search is a fundamental problem in graph databases that is widely applied in many application scenarios. Given a graph database and a query-graph, supergraph search retrieves all data-graphs contained in the query-graph from the graph database. Most existing solutions for supergraph search follow the pruning-and-verification framework, which prunes false answers based on features in the pruning phase and performs subgraph isomorphism testings on the remaining graphs in the verification phase. However, they are not scalable to handle large-sized data-graphs and query-graphs due to three drawbacks. First, they rely on a frequent subgraph mining algorithm to select features which is expensive and cannot generate large features. Second, they require a costly verification phase. Third, they process features in a fixed order without considering their relationship to the query-graph. In this paper, we address the three drawbacks and propose new indexing and query processing algorithms. In indexing, we select features directly from the data-graphs without expensive frequent subgraph mining. The features form a feature-tree that contains all-sized features and both the cost sharing and pruning power of the features are considered. In query processing, we propose a verification-free algorithm, where the order to process features is query-dependent by considering both the cost sharing and the pruning power. We explore two optimization strategies to further improve the algorithm efficiency. The first strategy applies a lightweight graph compression technique and the second strategy optimizes the inclusion of answers. Finally, we conduct extensive performance studies on two real large datasets to demonstrate the high scalability of our algorithms

Optimization of Retrieval Algorithms on Large Scale Knowledge Graphs

Knowledge graphs have been shown to play an important role in recent knowledge mining and discovery, for example in the field of life sciences or bioinformatics. Although a lot of research has been done on the field of query optimization, query transformation and of course in storing and retrieving large scale knowledge graphs the field of algorithmic optimization is still a major challenge and a vital factor in using graph databases. Few researchers have addressed the problem of optimizing algorithms on large scale labeled property graphs. Here, we present two optimization approaches and compare them with a naive approach of directly querying the graph database. The aim of our work is to determine limiting factors of graph databases like Neo4j and we describe a novel solution to tackle these challenges. For this, we suggest a classification schema to differ between the complexity of a problem on a graph database. We evaluate our optimization approaches on a test system containing a knowledge graph derived biomedical publication data enriched with text mining data. This dense graph has more than 71M nodes and 850M relationships. The results are very encouraging and - depending on the problem - we were able to show a speedup of a factor between 44 and 3839

GraphFind: enhancing graph searching by low support data mining techniques

<p>Abstract</p> <p>Background</p> <p>Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, a key role is played by systems that search for all exact or approximate occurrences of a query graph. To deal efficiently with graph searching, advanced methods for indexing, representation and matching of graphs have been proposed.</p> <p>Results</p> <p>This paper presents GraphFind. The system implements efficient graph searching algorithms together with advanced filtering techniques that allow approximate search. It allows users to select candidate subgraphs rather than entire graphs. It implements an effective data storage based also on low-support data mining.</p> <p>Conclusions</p> <p>GraphFind is compared with Frowns, GraphGrep and gIndex. Experiments show that GraphFind outperforms the compared systems on a very large collection of small graphs. The proposed low-support mining technique which applies to any searching system also allows a significant index space reduction.</p

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Performance and scalability of indexed subgraph query processing methods

Graph data management systems have become very popular as graphs are the natural data model for many applications. One of the main problems addressed by these systems is subgraph query processing; i.e., given a query graph, return all graphs that contain the query. The naive method for processing such queries is to perform a subgraph isomorphism test against each graph in the dataset. This obviously does not scale, as subgraph isomorphism is NP-Complete. Thus, many indexing methods have been proposed to reduce the number of candidate graphs that have to underpass the subgraph isomorphism test. In this paper, we identify a set of key factors-parameters, that influence the performance of related methods: namely, the number of nodes per graph, the graph density, the number of distinct labels, the number of graphs in the dataset, and the query graph size. We then conduct comprehensive and systematic experiments that analyze the sensitivity of the various methods on the values of the key parameters. Our aims are twofold: first to derive conclusions about the algorithms’ relative performance, and, second, to stress-test all algorithms, deriving insights as to their scalability, and highlight how both performance and scalability depend on the above factors. We choose six wellestablished indexing methods, namely Grapes, CT-Index, GraphGrepSX, gIndex, Tree+∆, and gCode, as representative approaches of the overall design space, including the most recent and best performing methods. We report on their index construction time and index size, and on query processing performance in terms of time and false positive ratio. We employ both real and synthetic datasets. Specifi- cally, four real datasets of different characteristics are used: AIDS, PDBS, PCM, and PPI. In addition, we generate a large number of synthetic graph datasets, empowering us to systematically study the algorithms’ performance and scalability versus the aforementioned key parameters

A Distributed Path Query Engine for Temporal Property Graphs

Property graphs are a common form of linked data, with path queries used to traverse and explore them for enterprise transactions and mining. Temporal property graphs are a recent variant where time is a first-class entity to be queried over, and their properties and structure vary over time. These are seen in social, telecom, transit and epidemic networks. However, current graph databases and query engines have limited support for temporal relations among graph entities, no support for time-varying entities and/or do not scale on distributed resources. We address this gap by extending a linear path query model over property graphs to include intuitive temporal predicates and aggregation operators over temporal graphs. We design a distributed execution model for these temporal path queries using the interval-centric computing model, and develop a novel cost model to select an efficient execution plan from several. We perform detailed experiments of our Granite distributed query engine using both static and dynamic temporal property graphs as large as 52M vertices, 218M edges and 325M properties, and a 1600-query workload, derived from the LDBC benchmark. We often offer sub-second query latencies on a commodity cluster, which is 149x-1140x faster compared to industry-leading Neo4J shared-memory graph database and the JanusGraph / Spark distributed graph query engine. Granite also completes 100% of the queries for all graphs, compared to only 32-92% workload completion by the baseline systems. Further, our cost model selects a query plan that is within 10% of the optimal execution time in 90% of the cases. Despite the irregular nature of graph processing, we exhibit a weak-scaling efficiency >= 60% on 8 nodes and >= 40% on 16 nodes, for most query workloads.Comment: An extended version of the paper that appears in IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 202