Independent component analysis of microarray data in the study of endometrial cancer.

Gene microarray technology is highly effective in screening for differential gene expression and has hence become a popular tool in the molecular investigation of cancer. When applied to tumours, molecular characteristics may be correlated with clinical features such as response to chemotherapy. Exploitation of the huge amount of data generated by microarrays is difficult, however, and constitutes a major challenge in the advancement of this methodology. Independent component analysis (ICA), a modern statistical method, allows us to better understand data in such complex and noisy measurement environments. The technique has the potential to significantly increase the quality of the resulting data and improve the biological validity of subsequent analysis. We performed microarray experiments on 31 postmenopausal endometrial biopsies, comprising 11 benign and 20 malignant samples. We compared ICA to the established methods of principal component analysis (PCA), Cyber-T, and SAM. We show that ICA generated patterns that clearly characterized the malignant samples studied, in contrast to PCA. Moreover, ICA improved the biological validity of the genes identified as differentially expressed in endometrial carcinoma, compared to those found by Cyber-T and SAM. In particular, several genes involved in lipid metabolism that are differentially expressed in endometrial carcinoma were only found using this method. This report highlights the potential of ICA in the analysis of microarray data.

Autonomous extraction of optimal flame fronts in OH planar laser-induced fluorescence images.

The location of a flame front is often taken as the point of maximum OH gradient. Planar laser-induced fluorescence of OH can be used to obtain the flame front by extracting the points of maximum gradient. This operation is typically performed using an edge detection algorithm. The choice of operating parameters a priori poses significant problems of robustness when handling images with a range of signal-to-noise ratios. A statistical method of parameter selection originating in the image processing literature is detailed, and its merit for this application is demonstrated. A reduced search space method is proposed to decrease computational cost and render the technique viable for large data sets. This gives nearly identical output to the full method. These methods demonstrate substantial decreases in data rejection compared to the use of a priori parameters. These methods are viable for any application where maximum gradient contours must be accurately extracted from images of species or temperature, even at very low signal-to-noise ratios.

Dynamics of in-plane arch rocking: An energy approach

This study employs an analytical model to describe the rocking response of a masonry arch to in-plane seismic loading. Through evaluation of the rate of energy input to the system, the model reveals the ground motions that cause maximum rocking amplification. An experimental investigation of small-scale masonry arches subjected to past earthquake time histories is used to evaluate the analytical model and to explore arch rocking behaviour. The results demonstrate that rocking amplification can occur, but is highly sensitive to slight variations in the ground motion. Thus, the accuracy to which the arch response can be predicted is brought into perspective. The concept that the primary impulse of an expected ground motion is fundamentally important in predicting arch collapse is evaluated in light of the developed energy approach. Finally, a statistical method is proposed for predicting the probability of arch collapse during seismic loading.

Bayesian inference for multidimensional NMR image reconstruction

Reconstruction of an image from a set of projections has been adapted to generate multidimensional nuclear magnetic resonance (NMR) spectra, which have discrete features that are relatively sparsely distributed in space. For this reason, a reliable reconstruction can be made from a small number of projections. This new concept is called Projection Reconstruction NMR (PR-NMR). In this paper, multidimensional NMR spectra are reconstructed by Reversible Jump Markov Chain Monte Carlo (RJMCMC). This statistical method generates samples under the assumption that each peak consists of a small number of parameters: position of peak centres, peak amplitude, and peak width. In order to find the number of peaks and shape, RJMCMC has several moves: birth, death, merge, split, and invariant updating. The reconstruction schemes are tested on a set of six projections derived from the three-dimensional 700 MHz HNCO spectrum of a protein HasA.

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/.

Efficient parametric uncertainty analysis within the hybrid Finite Element/Statistical Energy Analysis method

This paper is concerned with the development of efficient algorithms for propagating parametric uncertainty within the context of the hybrid Finite Element/Statistical Energy Analysis (FE/SEA) approach to the analysis of complex vibro-acoustic systems. This approach models the system as a combination of SEA subsystems and FE components; it is assumed that the FE components have fully deterministic properties, while the SEA subsystems have a high degree of randomness. The method has been recently generalised by allowing the FE components to possess parametric uncertainty, leading to two ensembles of uncertainty: a non-parametric one (SEA subsystems) and a parametric one (FE components). The SEA subsystems ensemble is dealt with analytically, while the effect of the additional FE components ensemble can be dealt with by Monte Carlo Simulations. However, this approach can be computationally intensive when applied to complex engineering systems having many uncertain parameters. Two different strategies are proposed: (i) the combination of the hybrid FE/SEA method with the First Order Reliability Method which allows the probability of the non-parametric ensemble average of a response variable exceeding a barrier to be calculated and (ii) the combination of the hybrid FE/SEA method with Laplace's method which allows the evaluation of the probability of a response variable exceeding a limit value. The proposed approaches are illustrated using two built-up plate systems with uncertain properties and the results are validated against direct integration, Monte Carlo simulations of the FE and of the hybrid FE/SEA models. © 2013 Elsevier Ltd.

An approximate likelihood method for estimating static parameters in multi-target tracking models

This paper considers a class of dynamic Spatial Point Processes (PP) that evolves over time in a Markovian fashion. This Markov in time PP is hidden and observed indirectly through another PP via thinning, displacement and noise. This statistical model is important for Multi object Tracking applications and we present an approximate likelihood based method for estimating the model parameters. The work is supported by an extensive numerical study.

Statistical energy analysis of a built-up structure excited through its stiffening members

A new method of analysing high frequency vibrations in stiffened structures requires the calculation of a "power absorbing impedance matrix" for each plate in the system. The present paper is concerned with formulating this matrix by using point collocation in conjunction with basis functions representing incoming cylindrical waves. Key numerical issues are highlighted by considering the special case of a membrane, rather than a plate, and conclusions are made regarding the utility of the method.

Statistical image modelling using interscale phase relationships of complex wavelet coefficients

A novel method for modelling the statistics of 2D photographic images useful in image restoration is defined. The new method is based on the Dual Tree Complex Wavelet Transform (DT-CWT) but a phase rotation is applied to the coefficients to create complex coefficients whose phase is shift-invariant at multiscale edge and ridge features. This is in addition to the magnitude shift invariance achieved by the DT-CWT. The increased correlation between coefficients adjacent in space and scale provides an improved mechanism for signal estimation. © 2006 IEEE.

The Modeling of Ion Implantation in a Three-Layer Structure Using the Method of Dose Matching

The method of modeling ion implantation in a multilayer target using moments of a statistical distribution and numerical integration for dose calculation in each target layer is applied to the modelling of As⁺ in poly-Si/SiO2/Si. Good agreement with experiment is obtained. Copyright © 1985 by The Institute of Electrical and Electronics Engineers, Inc.

Statistical user simulation with a hidden agenda

Recent work in the area of probabilistic user simulation for training statistical dialogue managers has investigated a new agenda-based user model and presented preliminary experiments with a handcrafted model parameter set. Training the model on dialogue data is an important next step, but non-trivial since the user agenda states are not observable in data and the space of possible states and state transitions is intractably large. This paper presents a summary-space mapping which greatly reduces the number of state transitions and introduces a tree-based method for representing the space of possible agenda state sequences. Treating the user agenda as a hidden variable, the forward/backward algorithm can then be successfully applied to iteratively estimate the model parameters on dialogue data. © 2007 Association for Computational Linguistics.