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Register a new userLinear model for fast background subtraction in oligonucleotide microarrays
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One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects: 1) Correlated intensities between neighboring features in the chip and 2) sequence-dependent affinities for non-specific hybridization fitted by an extended nearest-neighbor model. The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.
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We derive herein the limiting laws for certain stationary distributions of birth-and-death processes related to the classical model of chemical adsorption-desorption reactions due to Langmuir. The model has been recently considered in the context of a hybridization reaction on an oligonucleotide DNA microarray. Our results imply that the truncated gamma- and beta- type distributions can be used as approximations to the observed distributions of the fluorescence readings of the oligo-probes on a microarray. These findings might be useful in developing new model-based, probe-specific methods of extracting target concentrations from array fluorescence readings.
Feature selection, identifying a subset of variables that are relevant for predicting a response, is an important and challenging component of many methods in statistics and machine learning. Feature selection is especially difficult and computationally intensive when the number of variables approaches or exceeds the number of samples, as is often the case for many genomic datasets. Here, we introduce a new approach -- the Bayesian Ising Approximation (BIA) -- to rapidly calculate posterior probabilities for feature relevance in L2 penalized linear regression. In the regime where the regression problem is strongly regularized by the prior, we show that computing the marginal posterior probabilities for features is equivalent to computing the magnetizations of an Ising model. Using a mean field approximation, we show it is possible to rapidly compute the feature selection path described by the posterior probabilities as a function of the L2 penalty. We present simulations and analytical results illustrating the accuracy of the BIA on some simple regression problems. Finally, we demonstrate the applicability of the BIA to high dimensional regression by analyzing a gene expression dataset with nearly 30,000 features.
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs. free energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids.
textsc{Jewel} is a fully dynamical event generator for jet evolution in a dense QCD medium, which has been validated for multiple jet and jet-like observables. Jet constituents (partons) undergo collisions with thermal partons from the medium, leading to both elastic and radiative energy loss. The recoiling medium scattering centers carry away energy and momentum from the jet. Keeping track of these recoils is essential for the description of intra-jet observables. Since the thermal component of the recoils is part of the soft background activity, comparison with data on jet observables requires the implementation of a background subtraction procedure. We will show two independent procedures through which background subtraction can be performed and discuss the impact of the medium recoil on jet shape observables and jet-background correlations. Keeping track of the medium recoil significantly improves the textsc{Jewel} description of jet shape measurements.
In this work, we present a novel background subtraction system that uses a deep Convolutional Neural Network (CNN) to perform the segmentation. With this approach, feature engineering and parameter tuning become unnecessary since the network parameters can be learned from data by training a single CNN that can handle various video scenes. Additionally, we propose a new approach to estimate background model from video. For the training of the CNN, we employed randomly 5 percent video frames and their ground truth segmentations taken from the Change Detection challenge 2014(CDnet 2014). We also utilized spatial-median filtering as the post-processing of the network outputs. Our method is evaluated with different data-sets, and the network outperforms the existing algorithms with respect to the average ranking over different evaluation metrics. Furthermore, due to the network architecture, our CNN is capable of real time processing.
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