7,458 research outputs found
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
A methodology for determining amino-acid substitution matrices from set covers
We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional forms indicating how to obtain edge weights from the set
cover and, after that, substitution-matrix elements from weighted distances on
the graph, the resulting substitution matrix can be checked for performance
against some known set of reference alignments and for given gap costs. Finding
the appropriate functional forms and gap costs can then be formulated as an
optimization problem that seeks to maximize the performance of the substitution
matrix on the reference alignment set. We give computational results on the
BAliBASE suite using a genetic algorithm for optimization. Our results indicate
that it is possible to obtain substitution matrices whose performance is either
comparable to or surpasses that of several others, depending on the particular
scenario under consideration
High Performance Frequent Subgraph Mining on Transactional Datasets
Graph data mining has been a crucial as well as inevitable area of research. Large amounts of graph data are produced in many areas, such as Bioinformatics, Cheminformatics, Social Networks, and Web etc. Scalable graph data mining methods are getting increasingly popular and necessary due to increased graph complexities. Frequent subgraph mining is one such area where the task is to find overly recurring patterns/subgraphs. To tackle this problem, many main memory-based methods were proposed, which proved to be inefficient as the data size grew exponentially over time. In the past few years several research groups have attempted to handle the frequent subgraph mining (FSM) problem in multiple ways. Many authors have tried to achieve better performance using Graphic Processing Units (GPUs) which has multi-fold improvement over in-memory while dealing with large datasets. Later, Google\u27s MapReduce model with the Hadoop framework proved to be a major breakthrough in high performance large batch processing. Although MapReduce came with many benefits, its disk I/O and non-iterative style model could not help much for FSM domain since subgraph mining process is an iterative approach. In recent years, Spark has emerged to be the De Facto industry standard with its distributed in-memory computing capability. This is a right fit solution for iterative style of programming as well. In this work, we cover how high-performance computing has helped in improving the performance tremendously in the transactional directed and undirected aspect of graphs and performance comparisons of various FSM techniques are done based on experimental results
Graph-based Modelling of Concurrent Sequential Patterns
Structural relation patterns have been introduced recently to extend the search for complex patterns often hidden behind large sequences of data. This has motivated a novel approach to sequential patterns post-processing and a corresponding data mining method was proposed for Concurrent Sequential Patterns (ConSP). This article refines the approach in the context of ConSP modelling, where a companion graph-based model is devised as an extension of previous work. Two new modelling methods are presented here together with a construction algorithm, to complete the transformation of concurrent sequential patterns to a ConSP-Graph representation. Customer orders data is used to demonstrate the effectiveness of ConSP mining while synthetic sample data highlights the strength of the modelling technique, illuminating the theories developed
A Nine Month Progress Report on an Investigation into Mechanisms for Improving Triple Store Performance
This report considers the requirement for fast, efficient, and scalable triple stores as part of the effort to produce the Semantic Web. It summarises relevant information in the major background field of Database Management Systems (DBMS), and provides an overview of the techniques currently in use amongst the triple store community. The report concludes that for individuals and organisations to be willing to provide large amounts of information as openly-accessible nodes on the Semantic Web, storage and querying of the data must be cheaper and faster than it is currently. Experiences from the DBMS field can be used to maximise triple store performance, and suggestions are provided for lines of investigation in areas of storage, indexing, and query optimisation. Finally, work packages are provided describing expected timetables for further study of these topics
Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis
Understanding protein-protein interactions is central to our understanding of
almost all complex biological processes. Computational tools exploiting rapidly
growing genomic databases to characterize protein-protein interactions are
urgently needed. Such methods should connect multiple scales from evolutionary
conserved interactions between families of homologous proteins, over the
identification of specifically interacting proteins in the case of multiple
paralogs inside a species, down to the prediction of residues being in physical
contact across interaction interfaces. Statistical inference methods detecting
residue-residue coevolution have recently triggered considerable progress in
using sequence data for quaternary protein structure prediction; they require,
however, large joint alignments of homologous protein pairs known to interact.
The generation of such alignments is a complex computational task on its own;
application of coevolutionary modeling has in turn been restricted to proteins
without paralogs, or to bacterial systems with the corresponding coding genes
being co-localized in operons. Here we show that the Direct-Coupling Analysis
of residue coevolution can be extended to connect the different scales, and
simultaneously to match interacting paralogs, to identify inter-protein
residue-residue contacts and to discriminate interacting from noninteracting
families in a multiprotein system. Our results extend the potential
applications of coevolutionary analysis far beyond cases treatable so far.Comment: Main Text 19 pages Supp. Inf. 16 page
- …