MSQ-Index: A Succinct Index for Fast Graph Similarity Search

TL;DR

This paper introduces MSQ-Index, a space-efficient in-memory graph similarity search index that significantly reduces memory usage and accelerates query times for large graph databases, especially in bioinformatics.

Contribution

The paper presents a novel succinct index structure based on q-gram trees with hybrid encoding, enabling scalable, fast graph similarity search on massive datasets.

Findings

Uses only 5%-15% of previous index size

Achieves 2-3 times faster query performance

Successfully scales to 25 million graphs in PubChem

Abstract

Graph similarity search has received considerable attention in many applications, such as bioinformatics, data mining, pattern recognition, and social networks. Existing methods for this problem have limited scalability because of the huge amount of memory they consume when handling very large graph databases with millions or billions of graphs. In this paper, we study the problem of graph similarity search under the graph edit distance constraint. We present a space-efficient index structure based upon the q-gram tree that incorporates succinct data structures and hybrid encoding to achieve improved query time performance with minimal space usage. Specifically, the space usage of our index requires only 5%-15% of the previous state-of-the-art indexing size on the tested data while at the same time achieving 2-3 times acceleration in query time with small data sets. We also boost the query performance by augmenting the global filter with range search, which allows us to perform a query in a reduced region. In addition, we propose two effective filters that combine degree structures and label structures. Extensive experiments demonstrate that our proposed approach is superior in space and competitive in filtering to the state-of-the-art approaches. To the best of our knowledge, our index is the first in-memory index for this problem that successfully scales to cope with the large dataset of 25 million chemical structure graphs from the PubChem dataset.