Stochastic trapping in a solvable model of on-line independent component analysis

Previous analytical studies of on-line Independent Component Analysis (ICA) learning rules have focussed on asymptotic stability and efficiency. In practice the transient stages of learning will often be more significant in determining the success of an algorithm. This is demonstrated here with an analysis of a Hebbian ICA algorithm which can find a small number of non-Gaussian components given data composed of a linear mixture of independent source signals. An idealised data model is considered in which the sources comprise a number of non-Gaussian and Gaussian sources and a solution to the dynamics is obtained in the limit where the number of Gaussian sources is infinite. Previous stability results are confirmed by expanding around optimal fixed points, where a closed form solution to the learning dynamics is obtained. However, stochastic effects are shown to stabilise otherwise unstable sub-optimal fixed points. Conditions required to destabilise one such fixed point are obtained for the case of a single non-Gaussian component, indicating that the initial learning rate \eta required to successfully escape is very low (\eta = O(N^{-2}) where N is the data dimension) resulting in very slow learning typically requiring O(N^3) iterations. Simulations confirm that this picture holds for a finite system.Comment: 17 pages, 3 figures. To appear in Neural Computatio

Analysis of Natural Gradient Descent for Multilayer Neural Networks

Natural gradient descent is a principled method for adapting the parameters of a statistical model on-line using an underlying Riemannian parameter space to redefine the direction of steepest descent. The algorithm is examined via methods of statistical physics which accurately characterize both transient and asymptotic behavior. A solution of the learning dynamics is obtained for the case of multilayer neural network training in the limit of large input dimension. We find that natural gradient learning leads to optimal asymptotic performance and outperforms gradient descent in the transient, significantly shortening or even removing plateaus in the transient generalization performance which typically hamper gradient descent training.Comment: 14 pages including figures. To appear in Physical Review

The Shadow of a Doubt: a play in three acts by Edith Wharton

No abstract available

BayesBinMix: an R Package for Model Based Clustering of Multivariate Binary Data

The BayesBinMix package offers a Bayesian framework for clustering binary data with or without missing values by fitting mixtures of multivariate Bernoulli distributions with an unknown number of components. It allows the joint estimation of the number of clusters and model parameters using Markov chain Monte Carlo sampling. Heated chains are run in parallel and accelerate the convergence to the target posterior distribution. Identifiability issues are addressed by implementing label switching algorithms. The package is demonstrated and benchmarked against the Expectation-Maximization algorithm using a simulation study as well as a real dataset.Comment: Accepted to the R Journal. The package is available on CRAN: https://CRAN.R-project.org/package=BayesBinMi

The Dynamics of a Genetic Algorithm for a Simple Learning Problem

A formalism for describing the dynamics of Genetic Algorithms (GAs) using methods from statistical mechanics is applied to the problem of generalization in a perceptron with binary weights. The dynamics are solved for the case where a new batch of training patterns is presented to each population member each generation, which considerably simplifies the calculation. The theory is shown to agree closely to simulations of a real GA averaged over many runs, accurately predicting the mean best solution found. For weak selection and large problem size the difference equations describing the dynamics can be expressed analytically and we find that the effects of noise due to the finite size of each training batch can be removed by increasing the population size appropriately. If this population resizing is used, one can deduce the most computationally efficient size of training batch each generation. For independent patterns this choice also gives the minimum total number of training patterns used. Although using independent patterns is a very inefficient use of training patterns in general, this work may also prove useful for determining the optimum batch size in the case where patterns are recycled.Comment: 28 pages, 4 Postscript figures. Latex using IOP macros ioplppt and iopl12 which are included. To appear in Journal of Physics A. Also available at ftp://ftp.cs.man.ac.uk/pub/ai/jls/GAlearn.ps.gz and http://www.cs.man.ac.uk/~jl

Bayesian estimation of Differential Transcript Usage from RNA-seq data

Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene expression of a transcript. The contribution of this paper is to: (a) extend the use of cjBitSeq to the DTU context, a previously introduced Bayesian model which is originally designed for identifying changes in overall expression levels and (b) propose a Bayesian version of DRIMSeq, a frequentist model for inferring DTU. cjBitSeq is a read based model and performs fully Bayesian inference by MCMC sampling on the space of latent state of each transcript per gene. BayesDRIMSeq is a count based model and estimates the Bayes Factor of a DTU model against a null model using Laplace's approximation. The proposed models are benchmarked against the existing ones using a recent independent simulation study as well as a real RNA-seq dataset. Our results suggest that the Bayesian methods exhibit similar performance with DRIMSeq in terms of precision/recall but offer better calibration of False Discovery Rate.Comment: Revised version, accepted to Statistical Applications in Genetics and Molecular Biolog

The Shadow of a Doubt: discovering a new work by Edith Wharton

No abstract available