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At least 91 records · Page 5Linked to original sources

Sparsity vs. Statistical Independence in Adaptive Signal Representations: A Case Study of the Spike Process

Finding a basis/coordinate system that can efficiently represent an input data stream by viewing them as realizations of a stochastic process is of tremendous importance in many fields including data compression and computational neuroscience. Two popular measures of such efficiency of a basis are sparsity (measured by the expected $\ell^p$ norm, $0 < p \leq 1$) and statistical independence (measured by the mutual information). Gaining deeper understanding of their intricate relationship, however, remains elusive. Therefore, we chose to study a simple synthetic stochastic process called the spike process, which puts a unit impulse at a random location in an $n$-dimensional vector for each realization. For this process, we obtained the following results: 1) The standard basis is the best both in terms of sparsity and statistical independence if $n \geq 5$ and the search of basis is restricted within all possible orthonormal bases in $R^n$; 2) If we extend our basis search in all possible invertible linear transformations in $R^n$, then the best basis in statistical independence differs from the one in sparsity; 3) In either of the above, the best basis in statistical independence is not unique, and there even exist those which make the inputs completely dense; 4) There is no linear invertible transformation that achieves the true statistical independence for $n > 2$.

math.NA↗

A Note on Applications of Support Vector Machine

We describe in a rudimentary fashion how SVM(support vector machine) plays the role of classifier in a mathematical setting. We then discuss its application in the study of multiple SNP(single nucleotide polymorphism) variations. Also presented is a set of preliminary test results with clinical data.

math.OC↗

The Generalized Spike Process, Sparsity, and Statistical Independence

A basis under which a given set of realizations of a stochastic process can be represented most sparsely (the so-called best sparsifying basis (BSB)) and the one under which such a set becomes as less statistically dependent as possible (the so-called least statistically-dependent basis (LSDB)) are important for data compression and have generated interests among computational neuroscientists as well as applied mathematicians. Here we consider these bases for a particularly simple stochastic process called ``generalized spike process'', which puts a single spike--whose amplitude is sampled from the standard normal distribution--at a random location in the zero vector of length $\ndim$ for each realization. Unlike the ``simple spike process'' which we dealt with in our previous paper and whose amplitude is constant, we need to consider the kurtosis-maximizing basis (KMB) instead of the LSDB due to the difficulty of evaluating differential entropy and mutual information of the generalized spike process. By computing the marginal densities and moments, we prove that: 1) the BSB and the KMB selects the standard basis if we restrict our basis search within all possible orthonormal bases in ${\mathbb R}^n$; 2) if we extend our basis search to all possible volume-preserving invertible linear transformations, then the BSB exists and is again the standard basis whereas the KMB does not exist. Thus, the KMB is rather sensitive to the orthonormality of the transformations under consideration whereas the BSB is insensitive to that. Our results once again support the preference of the BSB over the LSDB/KMB for data compression applications as our previous work did.

math.PR↗

Stochastic spatial models of plant diseases

I present three models of plant--pathogen interactions. The models are stochastic and spatially explicit at the scale of individual plants. For each model, I use a version of pair approximation or moment closure along with a separation of timescales argument to determine the effects of spatial clustering on threshold structure. By computing the spatial structure early in an invasion, I find explicit corrections to mean field theory. In the first chapter, I present a lattice model of a disease that is not directly lethal to its host, but affects its ability to compete with neighbors. I use a type of pair approximation to determine conditions for invasions and coexistence. In the second chapter, I study a basic SIR epidemic point process in continuous space. I implement a multiplicative moment closure scheme to compute the threshold transmission rate as a function of spatial parameters. In the final chapter, I model the evolution of pathogen resistance when two plant species share a pathogen. Evolution may lead to non--resistance by a host that finds the disease to be a useful weapon. I use a lattice model with the ordinary pair approximation assumption to study phenotypic evolution via repeated invasions by novel strains.

math.NA↗

Efficient pooling designs for library screening

We describe efficient methods for screening clone libraries, based on pooling schemes which we call ``random $k$-sets designs''. In these designs, the pools in which any clone occurs are equally likely to be any possible selection of $k$ from the $v$ pools. The values of $k$ and $v$ can be chosen to optimize desirable properties. Random $k$-sets designs have substantial advantages over alternative pooling schemes: they are efficient, flexible, easy to specify, require fewer pools, and have error-correcting and error-detecting capabilities. In addition, screening can often be achieved in only one pass, thus facilitating automation. For design comparison, we assume a binomial distribution for the number of ``positive'' clones, with parameters $n$, the number of clones, and $c$, the coverage. We propose the expected number of {\em resolved positive} clones---clones which are definitely positive based upon the pool assays---as a criterion for the efficiency of a pooling design. We determine the value of $k$ which is optimal, with respect to this criterion, as a function of $v$, $n$ and $c$. We also describe superior $k$-sets designs called $k$-sets packing designs. As an illustration, we discuss a robotically implemented design for a 2.5-fold-coverage, human chromosome 16 YAC library of $n=1,298$ clones. We also estimate the probability each clone is positive, given the pool-assay data and a model for experimental errors.

math.CO↗

VLSI layouts and DNA physical mappings

We show that an important problem ($k$-ICG) in computational biology is equivalent to a colored version of a well-known graph layout problem ($k$-CVS).

math.CO↗

Large deviations for the Fleming-Viot process with neutral mutation and selection

Large deviation principles are established for the Fleming-Viot processes with neutral mutation and selection, and the corresponding equilibrium measures as the sampling rate goes to 0. All results are first proved for the finite allele model, and then generalized, through the projective limit technique, to the infinite allele model. Explicit expressions are obtained for the rate functions.

math.PR↗

Effect of Mutation and Recombination on the Genotype-Phenotype Map

The effect of genetic operators other than selection, such as mutation and recombination, on the genotype-phenotype map is considered. In particular, when the genotypic fitness landscape exhibits a ``symmetry'', i.e. many genotypes corresponding to the same phenotype have equal fitness values, it is shown that such operators can break this symmetry. The consequences of this ``induced symmetry breaking'' are investigated. Specifically, it is shown that it generically leads to an increase in order or self-organization in the system and to the phenomenon of orthogenesis. Additionally, it is shown that it potentially leads to a more robust evolution circumventing some of the problems of brittleness. The above points are supported by explicit, analytic results associated with some simple one and two-locus models and also by some much more complicated numerical simulations.

nlin.AO↗

Competing Populations in Flows with Chaotic Mixing

We investigate the effects of spatial heterogeneity on the coexistence of competing species in the case when the heterogeneity is dynamically generated by environmental flows with chaotic mixing properties. We show that one of the effects of chaotic advection on the passively advected species (such as phytoplankton, or self-replicating macromolecules) is the possibility of coexistence of more species than that limited by the number of niches they occupy. We derive a novel set of dynamical equations for competing populations.

nlin.CD↗

Modelling Food Webs

We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species according to some simple rule. The second class are dynamical models, which include the population dynamics of several interacting species. We focus on the question of the stability of such webs. The third class are species assembly models and evolutionary models, which build webs starting from a few species by adding new species through a process of "invasion" (assembly models) or "speciation" (evolutionary models). Evolutionary models are found to be capable of building large stable webs.

nlin.AO↗

Spatial Patterns in Chemically and Biologically Reacting Flows

We present here a number of processes, inspired by concepts in Nonlinear Dynamics such as chaotic advection and excitability, that can be useful to understand generic behaviors in chemical or biological systems in fluid flows. Emphasis is put on the description of observed plankton patchiness in the sea. The linearly decaying tracer, and excitable kinetics in a chaotic flow are mainly the models described. Finally, some warnings are given about the difficulties in modeling discrete individuals (such as planktonic organisms) in terms of continuous concentration fields.

nlin.CD↗

Survival in the replicator model: Dynamics and statistics

We study the multi-species replicator model with linear fitness and random fitness matrices of various classes. By means of numerical resolution of the replicator equations, we determine the survival probability of a species in terms of its average interaction with the rest of the system. The role of the interaction pattern of the ecosystem in defining survival and extinction probabilities is emphasized.

nlin.AO↗

Cancer Detection via Determination of Fractal Cell Dimension

We utilize the fractal dimension of the perimeter surface of cell sections as a new observable to characterize cells of different types. We propose that it is possible to distinguish cancerous from healthy cells with the aid of this new approach. As a first application we show that it is possible to perform this distinction between patients with hairy-cell lymphocytic leukemia and those with normal blood lymphocytes.

patt-sol↗

Two boundary model for freezing front propagation in biological tissue

The response of the living tissue to the effects of strong heating or cooling can cause the blood flow rate to vary by an order of magnitude. A mathematical model for the freezing of living tissue is formulated which takes into account the nonlocal temperature dependence of the blood flow rate when the temperature distribution in the tissue is substantially nonuniform, as in cryosurgery.

patt-sol↗

Optimal Mutation Rates in Dynamic Environments

In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments. A model with multiple fitness coding loci tracking a moving fitness peak is developed and an analytical expression for the optimal mutation rate is derived. Surprisingly it turns out that the optimal mutation rate per genome is approximately independent of genome length, something that also has been observed in nature. Simulations confirm the theoretical predictions. We also suggest an explanation for the difference in mutation frequency between RNA and DNA based organisms.

physics.bio-ph↗

Evolution: The Case of the Glyceraldehyde-3-Phosphate Dehydrogenase Gene

The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) catalyses the decomposition of glucose. The gene that produces the GAPDH is therefore present in a wide class of organisms. We show that for this gene the average value of the fluctuations in nucleotide distribution in the codons, normalized to strand bias, provides a reasonable measure of how the gene has evolved in time.

physics.bio-ph↗

Nonlinear Dynamics in the Binary DNA/RNA Coding Problem

The presence of low dimensional chaos in the protein secondary structures, using the binary coded $α$-helices and $β$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the purine/pyrimidine and strong/wea k H - bond classification sheme, of binary numbers to the nucleotides was made. We have found that this assignment leads to different averaged fractal dimensions for $α$-helices and $β$-sheets. When embedded in the two dimensional phase space the binary string structures show the attractor type behavior which depends on the value of the time lag parameter.

physics.bio-ph↗

Elastic wave propagation along DNA

It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA can alter signal transmission. The overall effect is a method of signal processing by DNA binding proteins that creates a "cellular communications network". The propagation of small amplitude disturbances through DNA is treated according to the mechanical theory of elastic rods. According to the theory four types of mechanical waves affecting extension(compression), twist, bend or shear can propagate through DNA. Each type of wave has unique characteristic properties. Disturbances affecting all wave types can propagate independently of each other. Using a linear approximation to the theory of motion of elastic rods, the dispersion of these waves is investigated. The phase velocities of the waves lies in the range 5-8 angstroms/ps using constants suitable for a description of DNA. The dispersion of all wave types of arbitrary wave length is investigated for a straight, twisted rod. Based on these findings, we propose all-atom numerical simulations of DNA to investigate the propagation of these waves as an alternative measure of the wave velocity and dispersion analysis.

physics.bio-ph↗