39,759 research outputs found
Temporal patterns of gene expression via nonmetric multidimensional scaling analysis
Motivation: Microarray experiments result in large scale data sets that
require extensive mining and refining to extract useful information. We have
been developing an efficient novel algorithm for nonmetric multidimensional
scaling (nMDS) analysis for very large data sets as a maximally unsupervised
data mining device. We wish to demonstrate its usefulness in the context of
bioinformatics. In our motivation is also an aim to demonstrate that
intrinsically nonlinear methods are generally advantageous in data mining.
Results: The Pearson correlation distance measure is used to indicate the
dissimilarity of the gene activities in transcriptional response of cell
cycle-synchronized human fibroblasts to serum [Iyer et al., Science vol. 283,
p83 (1999)]. These dissimilarity data have been analyzed with our nMDS
algorithm to produce an almost circular arrangement of the genes. The temporal
expression patterns of the genes rotate along this circular arrangement. If an
appropriate preparation procedure may be applied to the original data set,
linear methods such as the principal component analysis (PCA) could achieve
reasonable results, but without data preprocessing linear methods such as PCA
cannot achieve a useful picture. Furthermore, even with an appropriate data
preprocessing, the outcomes of linear procedures are not as clearcut as those
by nMDS without preprocessing.Comment: 11 pages, 6 figures + online only 2 color figures, submitted to
Bioinformatic
Binary Particle Swarm Optimization based Biclustering of Web usage Data
Web mining is the nontrivial process to discover valid, novel, potentially
useful knowledge from web data using the data mining techniques or methods. It
may give information that is useful for improving the services offered by web
portals and information access and retrieval tools. With the rapid development
of biclustering, more researchers have applied the biclustering technique to
different fields in recent years. When biclustering approach is applied to the
web usage data it automatically captures the hidden browsing patterns from it
in the form of biclusters. In this work, swarm intelligent technique is
combined with biclustering approach to propose an algorithm called Binary
Particle Swarm Optimization (BPSO) based Biclustering for Web Usage Data. The
main objective of this algorithm is to retrieve the global optimal bicluster
from the web usage data. These biclusters contain relationships between web
users and web pages which are useful for the E-Commerce applications like web
advertising and marketing. Experiments are conducted on real dataset to prove
the efficiency of the proposed algorithms
A Survey on Soft Subspace Clustering
Subspace clustering (SC) is a promising clustering technology to identify
clusters based on their associations with subspaces in high dimensional spaces.
SC can be classified into hard subspace clustering (HSC) and soft subspace
clustering (SSC). While HSC algorithms have been extensively studied and well
accepted by the scientific community, SSC algorithms are relatively new but
gaining more attention in recent years due to better adaptability. In the
paper, a comprehensive survey on existing SSC algorithms and the recent
development are presented. The SSC algorithms are classified systematically
into three main categories, namely, conventional SSC (CSSC), independent SSC
(ISSC) and extended SSC (XSSC). The characteristics of these algorithms are
highlighted and the potential future development of SSC is also discussed.Comment: This paper has been published in Information Sciences Journal in 201
Improving clustering with metabolic pathway data
Background: It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally related patterns to propose hypotheses for their behavior and the biological processes involved. Therefore, this knowledge is used only as a second step, after data are just clustered according to their expression patterns. Thus, it could be very useful to be able to improve the clustering of biological data by incorporating prior knowledge into the cluster formation itself, in order to enhance the biological value of the clusters.
Results: A novel training algorithm for clustering is presented, which evaluates the biological internal connections of the data points while the clusters are being formed. Within this training algorithm, the calculation of distances among data points and neurons centroids includes a new term based on information from well-known metabolic pathways. The standard self-organizing map (SOM) training versus the biologically-inspired SOM (bSOM) training were tested with two real data sets of transcripts and metabolites from Solanum lycopersicum and Arabidopsis thaliana species. Classical data mining validation measures were used to evaluate the clustering solutions obtained by both algorithms. Moreover, a new measure that takes into account the biological connectivity of the clusters was applied. The results of bSOM show important improvements in the convergence and performance for the proposed clustering method in comparison to standard SOM training, in particular, from the application point of view.
Conclusions: Analyses of the clusters obtained with bSOM indicate that including biological information during training can certainly increase the biological value of the clusters found with the proposed method. It is worth to highlight that this fact has effectively improved the results, which can simplify their further analysis.Fil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Lopez, Mariana Gabriela. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Carrari, Fernando Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentin
Revisiting Numerical Pattern Mining with Formal Concept Analysis
In this paper, we investigate the problem of mining numerical data in the
framework of Formal Concept Analysis. The usual way is to use a scaling
procedure --transforming numerical attributes into binary ones-- leading either
to a loss of information or of efficiency, in particular w.r.t. the volume of
extracted patterns. By contrast, we propose to directly work on numerical data
in a more precise and efficient way, and we prove it. For that, the notions of
closed patterns, generators and equivalent classes are revisited in the
numerical context. Moreover, two original algorithms are proposed and used in
an evaluation involving real-world data, showing the predominance of the
present approach
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A niching memetic algorithm for simultaneous clustering and feature selection
Clustering is inherently a difficult task, and is made even more difficult when the selection of relevant features is also an issue. In this paper we propose an approach for simultaneous clustering and feature selection using a niching memetic algorithm. Our approach (which we call NMA_CFS) makes feature selection an integral part of the global clustering search procedure and attempts to overcome the problem of identifying less promising locally optimal solutions in both clustering and feature selection, without making any a priori assumption about the number of clusters. Within the NMA_CFS procedure, a variable composite representation is devised to encode both feature selection and cluster centers with different numbers of clusters. Further, local search operations are introduced to refine feature selection and cluster centers encoded in the chromosomes. Finally, a niching method is integrated to preserve the population diversity and prevent premature convergence. In an experimental evaluation we demonstrate the effectiveness of the proposed approach and compare it with other related approaches, using both synthetic and real data
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