5,326 research outputs found
Efficient Subgraph Similarity Search on Large Probabilistic Graph Databases
Many studies have been conducted on seeking the efficient solution for
subgraph similarity search over certain (deterministic) graphs due to its wide
application in many fields, including bioinformatics, social network analysis,
and Resource Description Framework (RDF) data management. All these works
assume that the underlying data are certain. However, in reality, graphs are
often noisy and uncertain due to various factors, such as errors in data
extraction, inconsistencies in data integration, and privacy preserving
purposes. Therefore, in this paper, we study subgraph similarity search on
large probabilistic graph databases. Different from previous works assuming
that edges in an uncertain graph are independent of each other, we study the
uncertain graphs where edges' occurrences are correlated. We formally prove
that subgraph similarity search over probabilistic graphs is #P-complete, thus,
we employ a filter-and-verify framework to speed up the search. In the
filtering phase,we develop tight lower and upper bounds of subgraph similarity
probability based on a probabilistic matrix index, PMI. PMI is composed of
discriminative subgraph features associated with tight lower and upper bounds
of subgraph isomorphism probability. Based on PMI, we can sort out a large
number of probabilistic graphs and maximize the pruning capability. During the
verification phase, we develop an efficient sampling algorithm to validate the
remaining candidates. The efficiency of our proposed solutions has been
verified through extensive experiments.Comment: VLDB201
Any-k: Anytime Top-k Tree Pattern Retrieval in Labeled Graphs
Many problems in areas as diverse as recommendation systems, social network
analysis, semantic search, and distributed root cause analysis can be modeled
as pattern search on labeled graphs (also called "heterogeneous information
networks" or HINs). Given a large graph and a query pattern with node and edge
label constraints, a fundamental challenge is to nd the top-k matches ac-
cording to a ranking function over edge and node weights. For users, it is di
cult to select value k . We therefore propose the novel notion of an any-k
ranking algorithm: for a given time budget, re- turn as many of the top-ranked
results as possible. Then, given additional time, produce the next lower-ranked
results quickly as well. It can be stopped anytime, but may have to continues
until all results are returned. This paper focuses on acyclic patterns over
arbitrary labeled graphs. We are interested in practical algorithms that
effectively exploit (1) properties of heterogeneous networks, in particular
selective constraints on labels, and (2) that the users often explore only a
fraction of the top-ranked results. Our solution, KARPET, carefully integrates
aggressive pruning that leverages the acyclic nature of the query, and
incremental guided search. It enables us to prove strong non-trivial time and
space guarantees, which is generally considered very hard for this type of
graph search problem. Through experimental studies we show that KARPET achieves
running times in the order of milliseconds for tree patterns on large networks
with millions of nodes and edges.Comment: To appear in WWW 201
Geo-Social Group Queries with Minimum Acquaintance Constraint
The prosperity of location-based social networking services enables
geo-social group queries for group-based activity planning and marketing. This
paper proposes a new family of geo-social group queries with minimum
acquaintance constraint (GSGQs), which are more appealing than existing
geo-social group queries in terms of producing a cohesive group that guarantees
the worst-case acquaintance level. GSGQs, also specified with various spatial
constraints, are more complex than conventional spatial queries; particularly,
those with a strict NN spatial constraint are proved to be NP-hard. For
efficient processing of general GSGQ queries on large location-based social
networks, we devise two social-aware index structures, namely SaR-tree and
SaR*-tree. The latter features a novel clustering technique that considers both
spatial and social factors. Based on SaR-tree and SaR*-tree, efficient
algorithms are developed to process various GSGQs. Extensive experiments on
real-world Gowalla and Dianping datasets show that our proposed methods
substantially outperform the baseline algorithms based on R-tree.Comment: This is the preprint version that is accepted by the Very Large Data
Bases Journa
TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system
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