148 research outputs found
Principal manifolds and graphs in practice: from molecular biology to dynamical systems
We present several applications of non-linear data modeling, using principal
manifolds and principal graphs constructed using the metaphor of elasticity
(elastic principal graph approach). These approaches are generalizations of the
Kohonen's self-organizing maps, a class of artificial neural networks. On
several examples we show advantages of using non-linear objects for data
approximation in comparison to the linear ones. We propose four numerical
criteria for comparing linear and non-linear mappings of datasets into the
spaces of lower dimension. The examples are taken from comparative political
science, from analysis of high-throughput data in molecular biology, from
analysis of dynamical systems.Comment: 12 pages, 9 figure
Singularities of transient processes in dynamics and beyond
This note is a brief review of the analysis of long transients in dynamical
systems. The problem of long transients arose in many disciplines, from
physical and chemical kinetic to biology and even social sciences. Detailed
analysis of singularities of various `relaxation times' associated long
transients with bifurcations of -limit sets, homoclinic structures
(intersections of - and -limit sets) and other peculiarities of
dynamics. This review was stimulated by the analysis of anomalously long
transients in ecology published recently by A. Morozov and S. Petrovskii with
co-authors
Transition states and entangled mass action law
The classical approaches to the derivation of the (generalized) Mass Action
Law (MAL) assume that the intermediate transition state (i) has short life time
and (ii) is in partial equilibrium with the initial reagents of the elementary
reaction. The partial equilibrium assumption (ii) means that the reverse
decomposition of the intermediates is much faster than its transition through
other channels to the products. In this work we demonstrate how avoiding this
partial equilibrium assumption modifies the reaction rates. This kinetic
revision of transition state theory results in an effective `entanglement' of
reaction rates, which become linear combinations of different MAL expressions.Comment: Significantly extended version with more explanation, illustrations,
and reference
Fractional norms and quasinorms do not help to overcome the curse of dimensionality
The curse of dimensionality causes the well-known and widely discussed
problems for machine learning methods. There is a hypothesis that using of the
Manhattan distance and even fractional quasinorms lp (for p less than 1) can
help to overcome the curse of dimensionality in classification problems. In
this study, we systematically test this hypothesis. We confirm that fractional
quasinorms have a greater relative contrast or coefficient of variation than
the Euclidean norm l2, but we also demonstrate that the distance concentration
shows qualitatively the same behaviour for all tested norms and quasinorms and
the difference between them decays as dimension tends to infinity. Estimation
of classification quality for kNN based on different norms and quasinorms shows
that a greater relative contrast does not mean better classifier performance
and the worst performance for different databases was shown by different norms
(quasinorms). A systematic comparison shows that the difference of the
performance of kNN based on lp for p=2, 1, and 0.5 is statistically
insignificant
Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology
Technology of data visualization and data modeling is suggested. The basic of the technology is original idea of elastic net and methods of its construction and application. A short review of relevant methods has been made. The methods proposed are illustrated by applying them to the real economical, sociological and biological datasets and to some model data distributions.
The basic of the technology is original idea of elastic net - regular point approximation of some manifold that is put into the multidimensional space and has in a certain sense minimal energy. This manifold is an analogue of principal surface and serves as non-linear screen on what multidimensional data are projected.
Remarkable feature of the technology is its ability to work with and to fill gaps in data tables. Gaps are unknown or unreliable values of some features. It gives a possibility to predict plausibly values of unknown features by values of other ones. So it provides technology of constructing different prognosis systems and non-linear regressions.
The technology can be used by specialists in different fields. There are several examples of applying the method presented in the end of this paper
Possibility and Impossibility of the Entropy Balance in Lattice Boltzmann Collisions
We demonstrate that in the space of distributions operated on by lattice
Boltzmann methods that there exists a vicinity of the equilibrium where
collisions with entropy balance are possible and, at the same time, there exist
an area of nonequilibrium distributions where such collisions are impossible.
We calculate and graphically represent these areas for some simple entropic
equilibria using single relaxation time models. Therefore it is shown that the
definition of an entropic LBM is incomplete without a strategy to deal with
certain highly nonequilibrium states. Such strategies should be explicitly
stated as they may result in the production of additional entropy.Comment: v2 minor misprint correction
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