2,194 research outputs found
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
Classification of Occluded Objects using Fast Recurrent Processing
Recurrent neural networks are powerful tools for handling incomplete data
problems in computer vision, thanks to their significant generative
capabilities. However, the computational demand for these algorithms is too
high to work in real time, without specialized hardware or software solutions.
In this paper, we propose a framework for augmenting recurrent processing
capabilities into a feedforward network without sacrificing much from
computational efficiency. We assume a mixture model and generate samples of the
last hidden layer according to the class decisions of the output layer, modify
the hidden layer activity using the samples, and propagate to lower layers. For
visual occlusion problem, the iterative procedure emulates feedforward-feedback
loop, filling-in the missing hidden layer activity with meaningful
representations. The proposed algorithm is tested on a widely used dataset, and
shown to achieve 2 improvement in classification accuracy for occluded
objects. When compared to Restricted Boltzmann Machines, our algorithm shows
superior performance for occluded object classification.Comment: arXiv admin note: text overlap with arXiv:1409.8576 by other author
Stationary probability density of stochastic search processes in global optimization
A method for the construction of approximate analytical expressions for the
stationary marginal densities of general stochastic search processes is
proposed. By the marginal densities, regions of the search space that with high
probability contain the global optima can be readily defined. The density
estimation procedure involves a controlled number of linear operations, with a
computational cost per iteration that grows linearly with problem size
Aerospace medicine and biology: A continuing bibliography with indexes (supplement 355)
This bibliography lists 147 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during October, 1991. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance
A Plug-and-Play Image Registration Network
Deformable image registration (DIR) is an active research topic in biomedical
imaging. There is a growing interest in developing DIR methods based on deep
learning (DL). A traditional DL approach to DIR is based on training a
convolutional neural network (CNN) to estimate the registration field between
two input images. While conceptually simple, this approach comes with a
limitation that it exclusively relies on a pre-trained CNN without explicitly
enforcing fidelity between the registered image and the reference. We present
plug-and-play image registration network (PIRATE) as a new DIR method that
addresses this issue by integrating an explicit data-fidelity penalty and a CNN
prior. PIRATE pre-trains a CNN denoiser on the registration field and "plugs"
it into an iterative method as a regularizer. We additionally present PIRATE+
that fine-tunes the CNN prior in PIRATE using deep equilibrium models (DEQ).
PIRATE+ interprets the fixed-point iteration of PIRATE as a network with
effectively infinite layers and then trains the resulting network end-to-end,
enabling it to learn more task-specific information and boosting its
performance. Our numerical results on OASIS and CANDI datasets show that our
methods achieve state-of-the-art performance on DIR
Evolutionary Speech Recognition
Automatic speech recognition systems are becoming ever more common and are increasingly deployed in more variable acoustic conditions, by very different speakers. So these systems, generally conceived in a laboratory, must be robust in order to provide optimal performance in real situations. This article explores the possibility of gaining robustness by designing speech recognition systems able to auto-modify in real time, in order to adapt to the changes of acoustic environment. As a starting point, the adaptive capacities of living organisms were considered in relation to their environment. Analogues of these mechanisms were then applied to automatic speech recognition systems. It appeared to be interesting to imagine a system adapting to the changing acoustic conditions in order to remain effective regardless of its conditions of use
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Microarray image processing: A novel neural network framework
This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods.
Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.Aleppo University, Syri
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