2,562 research outputs found
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
Subgraph Pattern Matching over Uncertain Graphs with Identity Linkage Uncertainty
There is a growing need for methods which can capture uncertainties and
answer queries over graph-structured data. Two common types of uncertainty are
uncertainty over the attribute values of nodes and uncertainty over the
existence of edges. In this paper, we combine those with identity uncertainty.
Identity uncertainty represents uncertainty over the mapping from objects
mentioned in the data, or references, to the underlying real-world entities. We
propose the notion of a probabilistic entity graph (PEG), a probabilistic graph
model that defines a distribution over possible graphs at the entity level. The
model takes into account node attribute uncertainty, edge existence
uncertainty, and identity uncertainty, and thus enables us to systematically
reason about all three types of uncertainties in a uniform manner. We introduce
a general framework for constructing a PEG given uncertain data at the
reference level and develop highly efficient algorithms to answer subgraph
pattern matching queries in this setting. Our algorithms are based on two novel
ideas: context-aware path indexing and reduction by join-candidates, which
drastically reduce the query search space. A comprehensive experimental
evaluation shows that our approach outperforms baseline implementations by
orders of magnitude
FPGA-based Query Acceleration for Non-relational Databases
Database management systems are an integral part of today’s everyday life. Trends like smart applications, the internet of things, and business and social networks require applications to deal efficiently with data in various data models close to the underlying domain. Therefore, non-relational database systems provide a wide variety of database models, like graphs and documents. However, current non-relational database systems face performance challenges due to the end of Dennard scaling and therefore performance scaling of CPUs. In the meanwhile, FPGAs have gained traction as accelerators for data management.
Our goal is to tackle the performance challenges of non-relational database
systems with FPGA acceleration and, at the same time, address design challenges of FPGA acceleration itself. Therefore, we split this thesis up into two main lines of work: graph processing and flexible data processing.
Because of the lacking benchmark practices for graph processing accelerators, we propose GraphSim. GraphSim is able to reproduce runtimes of these accelerators based on a memory access model of the approach. Through this simulation environment, we extract three performance-critical accelerator properties: asynchronous graph processing, compressed graph data structure, and multi-channel memory. Since these accelerator properties have not been combined in one system, we propose GraphScale. GraphScale is the first scalable, asynchronous graph processing accelerator working on a compressed graph and outperforms all state-of-the-art graph processing accelerators.
Focusing on accelerator flexibility, we propose PipeJSON as the first FPGA-based JSON parser for arbitrary JSON documents. PipeJSON is able to achieve
parsing at line-speed, outperforming the fastest, vectorized parsers for CPUs. Lastly, we propose the subgraph query processing accelerator GraphMatch which outperforms state-of-the-art CPU systems for subgraph query processing and is able to flexibly switch queries during runtime in a matter of clock cycles
Question Answering with Subgraph Embeddings
This paper presents a system which learns to answer questions on a broad
range of topics from a knowledge base using few hand-crafted features. Our
model learns low-dimensional embeddings of words and knowledge base
constituents; these representations are used to score natural language
questions against candidate answers. Training our system using pairs of
questions and structured representations of their answers, and pairs of
question paraphrases, yields competitive results on a competitive benchmark of
the literature
cuTS: Scaling Subgraph Isomorphism on Distributed Multi-GPU Systems Using Trie Based Data Structure
Subgraph isomorphism is a pattern-matching algorithm widely used in many domains such as chem-informatics, bioinformatics, databases, and social network analysis. It is computationally expensive and is a proven NP-hard problem. The massive parallelism in GPUs is well suited for solving subgraph isomorphism. However, current GPU implementations are far from the achievable performance. Moreover, the enormous memory requirement of current approaches limits the problem size that can be handled. This work analyzes the fundamental challenges associated with processing subgraph isomorphism on GPUs and develops an efficient GPU implementation. We also develop a GPU-friendly trie-based data structure to drastically reduce the intermediate storage space requirement, enabling large benchmarks to be processed. We also develop the first distributed sub-graph isomorphism algorithm for GPUs. Our experimental evaluation demonstrates the efficacy of our approach by comparing the execution time and number of cases that can be handled against the state-of-the-art GPU implementations
Entropy-scaling search of massive biological data
Many datasets exhibit a well-defined structure that can be exploited to
design faster search tools, but it is not always clear when such acceleration
is possible. Here, we introduce a framework for similarity search based on
characterizing a dataset's entropy and fractal dimension. We prove that
searching scales in time with metric entropy (number of covering hyperspheres),
if the fractal dimension of the dataset is low, and scales in space with the
sum of metric entropy and information-theoretic entropy (randomness of the
data). Using these ideas, we present accelerated versions of standard tools,
with no loss in specificity and little loss in sensitivity, for use in three
domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics
(MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search
(esFragBag, 10x speedup of FragBag). Our framework can be used to achieve
"compressive omics," and the general theory can be readily applied to data
science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo
- …