6,343 research outputs found
Winner-Relaxing Self-Organizing Maps
A new family of self-organizing maps, the Winner-Relaxing Kohonen Algorithm,
is introduced as a generalization of a variant given by Kohonen in 1991. The
magnification behaviour is calculated analytically. For the original variant a
magnification exponent of 4/7 is derived; the generalized version allows to
steer the magnification in the wide range from exponent 1/2 to 1 in the
one-dimensional case, thus provides optimal mapping in the sense of information
theory. The Winner Relaxing Algorithm requires minimal extra computations per
learning step and is conveniently easy to implement.Comment: 14 pages (6 figs included). To appear in Neural Computatio
ASPECT: A spectra clustering tool for exploration of large spectral surveys
We present the novel, semi-automated clustering tool ASPECT for analysing
voluminous archives of spectra. The heart of the program is a neural network in
form of Kohonen's self-organizing map. The resulting map is designed as an icon
map suitable for the inspection by eye. The visual analysis is supported by the
option to blend in individual object properties such as redshift, apparent
magnitude, or signal-to-noise ratio. In addition, the package provides several
tools for the selection of special spectral types, e.g. local difference maps
which reflect the deviations of all spectra from one given input spectrum (real
or artificial). ASPECT is able to produce a two-dimensional topological map of
a huge number of spectra. The software package enables the user to browse and
navigate through a huge data pool and helps him to gain an insight into
underlying relationships between the spectra and other physical properties and
to get the big picture of the entire data set. We demonstrate the capability of
ASPECT by clustering the entire data pool of 0.6 million spectra from the Data
Release 4 of the Sloan Digital Sky Survey (SDSS). To illustrate the results
regarding quality and completeness we track objects from existing catalogues of
quasars and carbon stars, respectively, and connect the SDSS spectra with
morphological information from the GalaxyZoo project.Comment: 15 pages, 14 figures; accepted for publication in Astronomy and
Astrophysic
Magnification Control in Self-Organizing Maps and Neural Gas
We consider different ways to control the magnification in self-organizing
maps (SOM) and neural gas (NG). Starting from early approaches of magnification
control in vector quantization, we then concentrate on different approaches for
SOM and NG. We show that three structurally similar approaches can be applied
to both algorithms: localized learning, concave-convex learning, and winner
relaxing learning. Thereby, the approach of concave-convex learning in SOM is
extended to a more general description, whereas the concave-convex learning for
NG is new. In general, the control mechanisms generate only slightly different
behavior comparing both neural algorithms. However, we emphasize that the NG
results are valid for any data dimension, whereas in the SOM case the results
hold only for the one-dimensional case.Comment: 24 pages, 4 figure
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
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