7,428 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
Stationary States of NLS on Star Graphs
We consider a generalized nonlinear Schr\"odinger equation (NLS) with a power
nonlinearity |\psi|^2\mu\psi, of focusing type, describing propagation on the
ramified structure given by N edges connected at a vertex (a star graph). To
model the interaction at the junction, it is there imposed a boundary condition
analogous to the \delta potential of strength \alpha on the line, including as
a special case (\alpha=0) the free propagation. We show that nonlinear
stationary states describing solitons sitting at the vertex exist both for
attractive (\alpha0, a
potential barrier) interaction. In the case of sufficiently strong attractive
interaction at the vertex and power nonlinearity \mu<2, including the standard
cubic case, we characterize the ground state as minimizer of a constrained
action and we discuss its orbital stability. Finally we show that in the free
case, for even N only, the stationary states can be used to construct traveling
waves on the graph.Comment: Revised version, 5 pages, 2 figure
Data complexity measured by principal graphs
How to measure the complexity of a finite set of vectors embedded in a
multidimensional space? This is a non-trivial question which can be approached
in many different ways. Here we suggest a set of data complexity measures using
universal approximators, principal cubic complexes. Principal cubic complexes
generalise the notion of principal manifolds for datasets with non-trivial
topologies. The type of the principal cubic complex is determined by its
dimension and a grammar of elementary graph transformations. The simplest
grammar produces principal trees.
We introduce three natural types of data complexity: 1) geometric (deviation
of the data's approximator from some "idealized" configuration, such as
deviation from harmonicity); 2) structural (how many elements of a principal
graph are needed to approximate the data), and 3) construction complexity (how
many applications of elementary graph transformations are needed to construct
the principal object starting from the simplest one).
We compute these measures for several simulated and real-life data
distributions and show them in the "accuracy-complexity" plots, helping to
optimize the accuracy/complexity ratio. We discuss various issues connected
with measuring data complexity. Software for computing data complexity measures
from principal cubic complexes is provided as well.Comment: Computers and Mathematics with Applications, in pres
Scaling and Universality in City Space Syntax: between Zipf and Matthew
We report about universality of rank-integration distributions of open spaces
in city space syntax similar to the famous rank-size distributions of cities
(Zipf's law). We also demonstrate that the degree of choice an open space
represents for other spaces directly linked to it in a city follows a power law
statistic. Universal statistical behavior of space syntax measures uncovers the
universality of the city creation mechanism. We suggest that the observed
universality may help to establish the international definition of a city as a
specific land use pattern.Comment: 24 pages, 5 *.eps figure
Bond-Propagation Algorithm for Thermodynamic Functions in General 2D Ising Models
Recently, we developed and implemented the bond propagation algorithm for
calculating the partition function and correlation functions of random bond
Ising models in two dimensions. The algorithm is the fastest available for
calculating these quantities near the percolation threshold. In this paper, we
show how to extend the bond propagation algorithm to directly calculate
thermodynamic functions by applying the algorithm to derivatives of the
partition function, and we derive explicit expressions for this transformation.
We also discuss variations of the original bond propagation procedure within
the larger context of Y-Delta-Y-reducibility and discuss the relation of this
class of algorithm to other algorithms developed for Ising systems. We conclude
with a discussion on the outlook for applying similar algorithms to other
models.Comment: 12 pages, 10 figures; submitte
"Clumpiness" Mixing in Complex Networks
Three measures of clumpiness of complex networks are introduced. The measures
quantify how most central nodes of a network are clumped together. The
assortativity coefficient defined in a previous study measures a similar
characteristic, but accounts only for the clumpiness of the central nodes that
are directly connected to each other. The clumpiness coefficient defined in the
present paper also takes into account the cases where central nodes are
separated by a few links. The definition is based on the node degrees and the
distances between pairs of nodes. The clumpiness coefficient together with the
assortativity coefficient can define four classes of network. Numerical
calculations demonstrate that the classification scheme successfully
categorizes 30 real-world networks into the four classes: clumped assortative,
clumped disassortative, loose assortative and loose disassortative networks.
The clumpiness coefficient also differentiates the Erdos-Renyi model from the
Barabasi-Albert model, which the assortativity coefficient could not
differentiate. In addition, the bounds of the clumpiness coefficient as well as
the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure
"Clumpiness" Mixing in Complex Networks
Three measures of clumpiness of complex networks are introduced. The measures
quantify how most central nodes of a network are clumped together. The
assortativity coefficient defined in a previous study measures a similar
characteristic, but accounts only for the clumpiness of the central nodes that
are directly connected to each other. The clumpiness coefficient defined in the
present paper also takes into account the cases where central nodes are
separated by a few links. The definition is based on the node degrees and the
distances between pairs of nodes. The clumpiness coefficient together with the
assortativity coefficient can define four classes of network. Numerical
calculations demonstrate that the classification scheme successfully
categorizes 30 real-world networks into the four classes: clumped assortative,
clumped disassortative, loose assortative and loose disassortative networks.
The clumpiness coefficient also differentiates the Erdos-Renyi model from the
Barabasi-Albert model, which the assortativity coefficient could not
differentiate. In addition, the bounds of the clumpiness coefficient as well as
the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure
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