2,682 research outputs found
Efficient mining of discriminative molecular fragments
Frequent pattern discovery in structured data is receiving
an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset
Dynamic load balancing for the distributed mining of molecular structures
In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of
methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the
past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially
render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to
discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no
reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic
partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated
load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer
Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed
approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable
for large-scale, multi-domain, heterogeneous environments, such as computational grids
Shared-Memory Parallel Maximal Clique Enumeration
We present shared-memory parallel methods for Maximal Clique Enumeration
(MCE) from a graph. MCE is a fundamental and well-studied graph analytics task,
and is a widely used primitive for identifying dense structures in a graph. Due
to its computationally intensive nature, parallel methods are imperative for
dealing with large graphs. However, surprisingly, there do not yet exist
scalable and parallel methods for MCE on a shared-memory parallel machine. In
this work, we present efficient shared-memory parallel algorithms for MCE, with
the following properties: (1) the parallel algorithms are provably
work-efficient relative to a state-of-the-art sequential algorithm (2) the
algorithms have a provably small parallel depth, showing that they can scale to
a large number of processors, and (3) our implementations on a multicore
machine shows a good speedup and scaling behavior with increasing number of
cores, and are substantially faster than prior shared-memory parallel
algorithms for MCE.Comment: 10 pages, 3 figures, proceedings of the 25th IEEE International
Conference on. High Performance Computing, Data, and Analytics (HiPC), 201
Efficient Subgraph Matching on Billion Node Graphs
The ability to handle large scale graph data is crucial to an increasing
number of applications. Much work has been dedicated to supporting basic graph
operations such as subgraph matching, reachability, regular expression
matching, etc. In many cases, graph indices are employed to speed up query
processing. Typically, most indices require either super-linear indexing time
or super-linear indexing space. Unfortunately, for very large graphs,
super-linear approaches are almost always infeasible. In this paper, we study
the problem of subgraph matching on billion-node graphs. We present a novel
algorithm that supports efficient subgraph matching for graphs deployed on a
distributed memory store. Instead of relying on super-linear indices, we use
efficient graph exploration and massive parallel computing for query
processing. Our experimental results demonstrate the feasibility of performing
subgraph matching on web-scale graph data.Comment: VLDB201
Core Decomposition in Multilayer Networks: Theory, Algorithms, and Applications
Multilayer networks are a powerful paradigm to model complex systems, where
multiple relations occur between the same entities. Despite the keen interest
in a variety of tasks, algorithms, and analyses in this type of network, the
problem of extracting dense subgraphs has remained largely unexplored so far.
In this work we study the problem of core decomposition of a multilayer
network. The multilayer context is much challenging as no total order exists
among multilayer cores; rather, they form a lattice whose size is exponential
in the number of layers. In this setting we devise three algorithms which
differ in the way they visit the core lattice and in their pruning techniques.
We then move a step forward and study the problem of extracting the
inner-most (also known as maximal) cores, i.e., the cores that are not
dominated by any other core in terms of their core index in all the layers.
Inner-most cores are typically orders of magnitude less than all the cores.
Motivated by this, we devise an algorithm that effectively exploits the
maximality property and extracts inner-most cores directly, without first
computing a complete decomposition.
Finally, we showcase the multilayer core-decomposition tool in a variety of
scenarios and problems. We start by considering the problem of densest-subgraph
extraction in multilayer networks. We introduce a definition of multilayer
densest subgraph that trades-off between high density and number of layers in
which the high density holds, and exploit multilayer core decomposition to
approximate this problem with quality guarantees. As further applications, we
show how to utilize multilayer core decomposition to speed-up the extraction of
frequent cross-graph quasi-cliques and to generalize the community-search
problem to the multilayer setting
Similarity-Aware Spectral Sparsification by Edge Filtering
In recent years, spectral graph sparsification techniques that can compute
ultra-sparse graph proxies have been extensively studied for accelerating
various numerical and graph-related applications. Prior nearly-linear-time
spectral sparsification methods first extract low-stretch spanning tree from
the original graph to form the backbone of the sparsifier, and then recover
small portions of spectrally-critical off-tree edges to the spanning tree to
significantly improve the approximation quality. However, it is not clear how
many off-tree edges should be recovered for achieving a desired spectral
similarity level within the sparsifier. Motivated by recent graph signal
processing techniques, this paper proposes a similarity-aware spectral graph
sparsification framework that leverages efficient spectral off-tree edge
embedding and filtering schemes to construct spectral sparsifiers with
guaranteed spectral similarity (relative condition number) level. An iterative
graph densification scheme is introduced to facilitate efficient and effective
filtering of off-tree edges for highly ill-conditioned problems. The proposed
method has been validated using various kinds of graphs obtained from public
domain sparse matrix collections relevant to VLSI CAD, finite element analysis,
as well as social and data networks frequently studied in many machine learning
and data mining applications
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