Multiresolution signal decomposition schemes

[PNA-R9810] Interest in multiresolution techniques for signal processing and analysis is increasing steadily. An important instance of such a technique is the so-called pyramid decomposition scheme. This report proposes a general axiomatic pyramid decomposition scheme for signal analysis and synthesis. This scheme comprises the following ingredients: (i) the pyramid consists of a (finite or infinite) number of levels such that the information content decreases towards higher levels; (ii) each step towards a higher level is constituted by an (information-reducing) analysis operator, whereas each step towards a lower level is modeled by an (information-preserving) synthesis operator. One basic assumption is necessary: synthesis followed by analysis yields the identity operator, meaning that no information is lost by these two consecutive steps. In this report, several examples are described of linear as well as nonlinear (e.g., morphological) pyramid decomposition schemes. Some of these examples are known from the literature (Laplacian pyramid, morphological granulometries, skeleton decomposition) and some of them are new (morphological Haar pyramid, median pyramid). Furthermore, the report makes a distinction between single-scale and multiscale decomposition schemes (i.e. without or with sample reduction).#[PNA-R9905] In its original form, the wavelet transform is a linear tool. However, it has been increasingly recognized that nonlinear extensions are possible. A major impulse to the development of nonlinea

Multiresolution signal decomposition schemes. Part 2: Morphological wavelets

In its original form, the wavelet transform is a linear tool. However, it has been increasingly recognized that nonlinear extensions are possible. A major impulse to the development of nonlinear wavelet transforms has been given by the introduction of the lifting scheme by Sweldens. The aim of this report, which is a sequel to a previous report devoted exclusively to the pyramid transform, is to present an axiomatic framework encompassing most existing linear and nonlinear wavelet decompositions. Furthermore, it introduces some, thus far unknown, wavelets based on mathematical morphology, such as the morphological Haar wavelet, both in one and two dimensions. A general and flexible approach for the construction of nonlinear (morphological) wavelets is provided by the lifting scheme. This paper discusses one example in considerable detail, the max-lifting scheme, which has the intriguing property that it preserves local maxima in a signal over a range of scales, depending on how local or global these maxima are

A Unified Algebraic Framework for Fuzzy Image Compression and Mathematical Morphology

In this paper we show how certain techniques of image processing, having different scopes, can be joined together under a common "algebraic roof"

A morphological algorithm for improving radio-frequency interference detection

A technique is described that is used to improve the detection of radio-frequency interference in astronomical radio observatories. It is applied on a two-dimensional interference mask after regular detection in the time-frequency domain with existing techniques. The scale-invariant rank (SIR) operator is defined, which is a one-dimensional mathematical morphology technique that can be used to find adjacent intervals in the time or frequency domain that are likely to be affected by RFI. The technique might also be applicable in other areas in which morphological scale-invariant behaviour is desired, such as source detection. A new algorithm is described, that is shown to perform quite well, has linear time complexity and is fast enough to be applied in modern high resolution observatories. It is used in the default pipeline of the LOFAR observatory.Comment: Accepted for publication in A&

On the Stability and the Approximation of Branching Distribution Flows, with Applications to Nonlinear Multiple Target Filtering

We analyse the exponential stability properties of a class of measure-valued equations arising in nonlinear multi-target filtering problems. We also prove the uniform convergence properties w.r.t. the time parameter of a rather general class of stochastic filtering algorithms, including sequential Monte Carlo type models and mean eld particle interpretation models. We illustrate these results in the context of the Bernoulli and the Probability Hypothesis Density filter, yielding what seems to be the first results of this kind in this subject

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes

miRNA Regulatory Circuits in ES Cells Differentiation: A Chemical Kinetics Modeling Approach

MicroRNAs (miRNAs) play an important role in gene regulation for Embryonic Stem cells (ES cells), where they either down-regulate target mRNA genes by degradation or repress protein expression of these mRNA genes by inhibiting translation. Well known tables TargetScan and miRanda may predict quite long lists of potential miRNAs inhibitors for each mRNA gene, and one of our goals was to strongly narrow down the list of mRNA targets potentially repressed by a known large list of 400 miRNAs. Our paper focuses on algorithmic analysis of ES cells microarray data to reliably detect repressive interactions between miRNAs and mRNAs. We model, by chemical kinetics equations, the interaction architectures implementing the two basic silencing processes of miRNAs, namely “direct degradation” or “translation inhibition” of targeted mRNAs. For each pair (M,G) of potentially interacting miRMA gene M and mRNA gene G, we parameterize our associated kinetic equations by optimizing their fit with microarray data. When this fit is high enough, we validate the pair (M,G) as a highly probable repressive interaction. This approach leads to the computation of a highly selective and drastically reduced list of repressive pairs (M,G) involved in ES cells differentiation

Numerical Integration of the Master Equation in Some Models of Stochastic Epidemiology

The processes by which disease spreads in a population of individuals are inherently stochastic. The master equation has proven to be a useful tool for modeling such processes. Unfortunately, solving the master equation analytically is possible only in limited cases (e.g., when the model is linear), and thus numerical procedures or approximation methods must be employed. Available approximation methods, such as the system size expansion method of van Kampen, may fail to provide reliable solutions, whereas current numerical approaches can induce appreciable computational cost. In this paper, we propose a new numerical technique for solving the master equation. Our method is based on a more informative stochastic process than the population process commonly used in the literature. By exploiting the structure of the master equation governing this process, we develop a novel technique for calculating the exact solution of the master equation – up to a desired precision – in certain models of stochastic epidemiology. We demonstrate the potential of our method by solving the master equation associated with the stochastic SIR epidemic model. MATLAB software that implements the methods discussed in this paper is freely available as Supporting Information S1