Application of The Method of Elastic Maps In Analysis of Genetic Texts

Abstract - Method of elastic maps ( http://cogprints.ecs.soton.ac.uk/archive/00003088/ and http://cogprints.ecs.soton.ac.uk/archive/00003919/ ) allows us to construct efficiently 1D, 2D and 3D non-linear approximations to the principal manifolds with different topology (piece of plane, sphere, torus etc.) and to project data onto it. We describe the idea of the method and demonstrate its applications in analysis of genetic sequences. The animated 3D-scatters are available on our web-site: http://www.ihes.fr/~zinovyev/7clusters/ We found the universal cluster structure of genetic sequences, and demonstrated the thin structure of these clusters for coding regions. This thin structure is related to different translational efficiency

The General Approximation Theorem

A general approximation theorem is proved. It uniformly envelopes both the classical Stone theorem and approximation of functions of several variables by means of superpositions and linear combinations of functions of one variable. This theorem is interpreted as a statement on universal approximating possibilities ( approximating omnipotence ) of arbitrary nonlinearity. For the neural networks, our result states that the function of neuron activation must be nonlinear, and nothing els

High Order Orthogonal Tensor Networks: Information Capacity and Reliability

Neural networks based on construction of orthogonal projectors in the tensor power of space of signals are described. A sharp estimate of their ultimate information capacity is obtained. The number of stored prototype patterns (prototypes) can many times exceed the number of neurons. A comparison with the error control codes is mad

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

The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Back-propagation of accuracy

In this paper we solve the problem: how to determine maximal allowable errors, possible for signals and parameters of each element of a network proceeding from the condition that the vector of output signals of the network should be calculated with given accuracy? "Back-propagation of accuracy" is developed to solve this problem. The calculation of allowable errors for each element of network by back-propagation of accuracy is surprisingly similar to a back-propagation of error, because it is the backward signals motion, but at the same time it is very different because the new rules of signals transformation in the passing back through the elements are different. The method allows us to formulate the requirements to the accuracy of calculations and to the realization of technical devices, if the requirements to the accuracy of output signals of the network are known.Comment: 4 pages, 5 figures, The talk given on ICNN97 (The 1997 IEEE International Conference on Neural Networks, Houston, USA

Linking the hydrodynamic and kinetic description of a dissipative relativistic conformal theory

We use the entropy production variational method to associate a one particle distribution function to the assumed known energy-momentum and entropy currents describing a relativistic conformal fluid. Assuming a simple form for the collision operator we find this one particle distribution function explicitly, and show that this method of linking the hydro and kinetic description is a non trivial generalization of Grad's ansatz. The resulting constitutive relations are the same as in the conformal dissipative type theories discussed in J. Peralta-Ramos and E. Calzetta, Phys. Rev. D {\bfseries 80}, 126002 (2009). Our results may prove useful in the description of freeze-out in ultrarelativistic heavy-ion collisions.Comment: v2: 23 pages, no figures, accepted in Phys. Rev.

Thermodynamic Tree: The Space of Admissible Paths

Is a spontaneous transition from a state x to a state y allowed by thermodynamics? Such a question arises often in chemical thermodynamics and kinetics. We ask the more formal question: is there a continuous path between these states, along which the conservation laws hold, the concentrations remain non-negative and the relevant thermodynamic potential G (Gibbs energy, for example) monotonically decreases? The obvious necessary condition, G(x)\geq G(y), is not sufficient, and we construct the necessary and sufficient conditions. For example, it is impossible to overstep the equilibrium in 1-dimensional (1D) systems (with n components and n-1 conservation laws). The system cannot come from a state x to a state y if they are on the opposite sides of the equilibrium even if G(x) > G(y). We find the general multidimensional analogue of this 1D rule and constructively solve the problem of the thermodynamically admissible transitions. We study dynamical systems, which are given in a positively invariant convex polyhedron D and have a convex Lyapunov function G. An admissible path is a continuous curve along which $G$ does not increase. For x,y from D, x\geq y (x precedes y) if there exists an admissible path from x to y and x \sim y if x\geq y and y\geq x. The tree of G in D is a quotient space D/~. We provide an algorithm for the construction of this tree. In this algorithm, the restriction of G onto the 1-skeleton of $D$ (the union of edges) is used. The problem of existence of admissible paths between states is solved constructively. The regions attainable by the admissible paths are described.Comment: Extended version, 31 page, 9 figures, 69 cited references, many minor correction

Decay and coherence of two-photon excited yellow ortho-excitons in Cu2O

Photoluminescence excitation spectroscopy has revealed a novel, highly efficient two-photon excitation method to produce a cold, uniformly distributed high density excitonic gas in bulk cuprous oxide. A study of the time evolution of the density, temperature and chemical potential of the exciton gas shows that the so called quantum saturation effect that prevents Bose-Einstein condensation of the ortho-exciton gas originates from an unfavorable ratio between the cooling and recombination rates. Oscillations observed in the temporal decay of the ortho-excitonic luminescence intensity are discussed in terms of polaritonic beating. We present the semiclassical description of polaritonic oscillations in linear and non-linear optical processes.Comment: 14 pages, 12 figure