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

The Michaelis-Menten-Stueckelberg Theorem

We study chemical reactions with complex mechanisms under two assumptions: (i) intermediates are present in small amounts (this is the quasi-steady-state hypothesis or QSS) and (ii) they are in equilibrium relations with substrates (this is the quasiequilibrium hypothesis or QE). Under these assumptions, we prove the generalized mass action law together with the basic relations between kinetic factors, which are sufficient for the positivity of the entropy production but hold even without microreversibility, when the detailed balance is not applicable. Even though QE and QSS produce useful approximations by themselves, only the combination of these assumptions can render the possibility beyond the "rarefied gas" limit or the "molecular chaos" hypotheses. We do not use any a priori form of the kinetic law for the chemical reactions and describe their equilibria by thermodynamic relations. The transformations of the intermediate compounds can be described by the Markov kinetics because of their low density ({\em low density of elementary events}). This combination of assumptions was introduced by Michaelis and Menten in 1913. In 1952, Stueckelberg used the same assumptions for the gas kinetics and produced the remarkable semi-detailed balance relations between collision rates in the Boltzmann equation that are weaker than the detailed balance conditions but are still sufficient for the Boltzmann $H$-theorem to be valid. Our results are obtained within the Michaelis-Menten-Stueckelbeg conceptual framework.Comment: 54 pages, the final version; correction of a misprint in Attachment

Generation of Explicit Knowledge from Empirical Data through Pruning of Trainable Neural Networks

This paper presents a generalized technology of extraction of explicit knowledge from data. The main ideas are 1) maximal reduction of network complexity (not only removal of neurons or synapses, but removal all the unnecessary elements and signals and reduction of the complexity of elements), 2) using of adjustable and flexible pruning process (the pruning sequence shouldn't be predetermined - the user should have a possibility to prune network on his own way in order to achieve a desired network structure for the purpose of extraction of rules of desired type and form), and 3) extraction of rules not in predetermined but any desired form. Some considerations and notes about network architecture and training process and applicability of currently developed pruning techniques and rule extraction algorithms are discussed. This technology, being developed by us for more than 10 years, allowed us to create dozens of knowledge-based expert systems. In this paper we present a generalized three-step technology of extraction of explicit knowledge from empirical data.Comment: 9 pages, The talk was given at the IJCNN '99 (Washington DC, July 1999

Elastic principal manifolds and their practical applications

Principal manifolds serve as useful tool for many practical applications. These manifolds are defined as lines or surfaces passing through "the middle" of data distribution. We propose an algorithm for fast construction of grid approximations of principal manifolds with given topology. It is based on analogy of principal manifold and elastic membrane. The first advantage of this method is a form of the functional to be minimized which becomes quadratic at the step of the vertices position refinement. This makes the algorithm very effective, especially for parallel implementations. Another advantage is that the same algorithmic kernel is applied to construct principal manifolds of different dimensions and topologies. We demonstrate how flexibility of the approach allows numerous adaptive strategies like principal graph constructing, etc. The algorithm is implemented as a C++ package elmap and as a part of stand-alone data visualization tool VidaExpert, available on the web. We describe the approach and provide several examples of its application with speed performance characteristics.Comment: 26 pages, 10 figures, edited final versio

PCA Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes

Multidimensional data distributions can have complex topologies and variable local dimensions. To approximate complex data, we propose a new type of low-dimensional ``principal object'': a principal cubic complex. This complex is a generalization of linear and non-linear principal manifolds and includes them as a particular case. To construct such an object, we combine a method of topological grammars with the minimization of an elastic energy defined for its embedment into multidimensional data space. The whole complex is presented as a system of nodes and springs and as a product of one-dimensional continua (represented by graphs), and the grammars describe how these continua transform during the process of optimal complex construction. The simplest case of a topological grammar (``add a node'', ``bisect an edge'') is equivalent to the construction of ``principal trees'', an object useful in many practical applications. We demonstrate how it can be applied to the analysis of bacterial genomes and for visualization of cDNA microarray data using the ``metro map'' representation. The preprint is supplemented by animation: ``How the topological grammar constructs branching principal components (AnimatedBranchingPCA.gif)''.Comment: 19 pages, 8 figure

Lyapunov-like Conditions of Forward Invariance and Boundedness for a Class of Unstable Systems

We provide Lyapunov-like characterizations of boundedness and convergence of non-trivial solutions for a class of systems with unstable invariant sets. Examples of systems to which the results may apply include interconnections of stable subsystems with one-dimensional unstable dynamics or critically stable dynamics. Systems of this type arise in problems of nonlinear output regulation, parameter estimation and adaptive control. In addition to providing boundedness and convergence criteria the results allow to derive domains of initial conditions corresponding to solutions leaving a given neighborhood of the origin at least once. In contrast to other works addressing convergence issues in unstable systems, our results require neither input-output characterizations for the stable part nor estimates of convergence rates. The results are illustrated with examples, including the analysis of phase synchronization of neural oscillators with heterogenous coupling