A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

A stochastic algorithm for probabilistic independent component analysis

The decomposition of a sample of images on a relevant subspace is a recurrent problem in many different fields from Computer Vision to medical image analysis. We propose in this paper a new learning principle and implementation of the generative decomposition model generally known as noisy ICA (for independent component analysis) based on the SAEM algorithm, which is a versatile stochastic approximation of the standard EM algorithm. We demonstrate the applicability of the method on a large range of decomposition models and illustrate the developments with experimental results on various data sets.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS499 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Towards Effective Codebookless Model for Image Classification

The bag-of-features (BoF) model for image classification has been thoroughly studied over the last decade. Different from the widely used BoF methods which modeled images with a pre-trained codebook, the alternative codebook free image modeling method, which we call Codebookless Model (CLM), attracted little attention. In this paper, we present an effective CLM that represents an image with a single Gaussian for classification. By embedding Gaussian manifold into a vector space, we show that the simple incorporation of our CLM into a linear classifier achieves very competitive accuracy compared with state-of-the-art BoF methods (e.g., Fisher Vector). Since our CLM lies in a high dimensional Riemannian manifold, we further propose a joint learning method of low-rank transformation with support vector machine (SVM) classifier on the Gaussian manifold, in order to reduce computational and storage cost. To study and alleviate the side effect of background clutter on our CLM, we also present a simple yet effective partial background removal method based on saliency detection. Experiments are extensively conducted on eight widely used databases to demonstrate the effectiveness and efficiency of our CLM method

Inferring the photometric and size evolution of galaxies from image simulations

Current constraints on models of galaxy evolution rely on morphometric catalogs extracted from multi-band photometric surveys. However, these catalogs are altered by selection effects that are difficult to model, that correlate in non trivial ways, and that can lead to contradictory predictions if not taken into account carefully. To address this issue, we have developed a new approach combining parametric Bayesian indirect likelihood (pBIL) techniques and empirical modeling with realistic image simulations that reproduce a large fraction of these selection effects. This allows us to perform a direct comparison between observed and simulated images and to infer robust constraints on model parameters. We use a semi-empirical forward model to generate a distribution of mock galaxies from a set of physical parameters. These galaxies are passed through an image simulator reproducing the instrumental characteristics of any survey and are then extracted in the same way as the observed data. The discrepancy between the simulated and observed data is quantified, and minimized with a custom sampling process based on adaptive Monte Carlo Markov Chain methods. Using synthetic data matching most of the properties of a CFHTLS Deep field, we demonstrate the robustness and internal consistency of our approach by inferring the parameters governing the size and luminosity functions and their evolutions for different realistic populations of galaxies. We also compare the results of our approach with those obtained from the classical spectral energy distribution fitting and photometric redshift approach.Our pipeline infers efficiently the luminosity and size distribution and evolution parameters with a very limited number of observables (3 photometric bands). When compared to SED fitting based on the same set of observables, our method yields results that are more accurate and free from systematic biases.Comment: 24 pages, 12 figures, accepted for publication in A&

Deep SimNets

We present a deep layered architecture that generalizes convolutional neural networks (ConvNets). The architecture, called SimNets, is driven by two operators: (i) a similarity function that generalizes inner-product, and (ii) a log-mean-exp function called MEX that generalizes maximum and average. The two operators applied in succession give rise to a standard neuron but in "feature space". The feature spaces realized by SimNets depend on the choice of the similarity operator. The simplest setting, which corresponds to a convolution, realizes the feature space of the Exponential kernel, while other settings realize feature spaces of more powerful kernels (Generalized Gaussian, which includes as special cases RBF and Laplacian), or even dynamically learned feature spaces (Generalized Multiple Kernel Learning). As a result, the SimNet contains a higher abstraction level compared to a traditional ConvNet. We argue that enhanced expressiveness is important when the networks are small due to run-time constraints (such as those imposed by mobile applications). Empirical evaluation validates the superior expressiveness of SimNets, showing a significant gain in accuracy over ConvNets when computational resources at run-time are limited. We also show that in large-scale settings, where computational complexity is less of a concern, the additional capacity of SimNets can be controlled with proper regularization, yielding accuracies comparable to state of the art ConvNets