Computer-aided diagnosis of carotid atherosclerosis based on ultrasound image statistics, laws' texture and neural networks

Quantitative characterisation of carotid atherosclerosis and classification into symptomatic or asymptomatic is crucial in planning optimal treatment of atheromatous plaque. The computer-aided diagnosis (CAD) system described in this paper can analyse ultrasound (US) images of carotid artery and classify them into symptomatic or asymptomatic based on their echogenicity characteristics. The CAD system consists of three modules: a) the feature extraction module, where first-order statistical (FOS) features and Laws' texture energy can be estimated, b) the dimensionality reduction module, where the number of features can be reduced using analysis of variance (ANOVA), and c) the classifier module consisting of a neural network (NN) trained by a novel hybrid method based on genetic algorithms (GAs) along with the back propagation algorithm. The hybrid method is able to select the most robust features, to adjust automatically the NN architecture and to optimise the classification performance. The performance is measured by the accuracy, sensitivity, specificity and the area under the receiver-operating characteristic (ROC) curve. The CAD design and development is based on images from 54 symptomatic and 54 asymptomatic plaques. This study demonstrates the ability of a CAD system based on US image analysis and a hybrid trained NN to identify atheromatous plaques at high risk of stroke.

Matching Recall and Storage in Sequence Learning with Spiking Neural Networks

Storing and recalling spiking sequences is a general problem the brain needs to solve. It is, however, unclear what type of biologically plausible learning rule is suited to learn a wide class of spatiotemporal activity patterns in a robust way. Here we consider a recurrent network of stochastic spiking neurons composed of both visible and hidden neurons. We derive a generic learning rule that is matched to the neural dynamics by minimizing an upper bound on the Kullback–Leibler divergence from the target distribution to the model distribution. The derived learning rule is consistent with spike-timing dependent plasticity in that a presynaptic spike preceding a postsynaptic spike elicits potentiation while otherwise depression emerges. Furthermore, the learning rule for synapses that target visible neurons can be matched to the recently proposed voltage-triplet rule. The learning rule for synapses that target hidden neurons is modulated by a global factor, which shares properties with astrocytes and gives rise to testable predictions.

Improvement for detection of microcalcifications through clustering algorithms and artificial neural networks

A new method for detecting microcalcifications in regions of interest (ROIs) extracted from digitized mammograms is proposed. The top-hat transform is a technique based on mathematical morphology operations and, in this paper, is used to perform contrast enhancement of the mi-crocalcifications. To improve microcalcification detection, a novel image sub-segmentation approach based on the possibilistic fuzzy c-means algorithm is used. From the original ROIs, window-based features, such as the mean and standard deviation, were extracted; these features were used as an input vector in a classifier. The classifier is based on an artificial neural network to identify patterns belonging to microcalcifications and healthy tissue. Our results show that the proposed method is a good alternative for automatically detecting microcalcifications, because this stage is an important part of early breast cancer detection

Image sub-segmentation by PFCM and Artificial Neural Networks to detect pore space in 2D and 3D CT soil images

The image by Computed Tomography is a non-invasive alternative for observing soil structures, mainly pore space. The pore space correspond in soil data to empty or free space in the sense that no material is present there but only fluids, the fluid transport depend of pore spaces in soil, for this reason is important identify the regions that correspond to pore zones. In this paper we present a methodology in order to detect pore space and solid soil based on the synergy of the image processing, pattern recognition and artificial intelligence. The mathematical morphology is an image processing technique used for the purpose of image enhancement. In order to find pixels groups with a similar gray level intensity, or more or less homogeneous groups, a novel image sub-segmentation based on a Possibilistic Fuzzy c-Means (PFCM) clustering algorithm was used. The Artificial Neural Networks (ANNs) are very efficient for demanding large scale and generic pattern recognition applications for this reason finally a classifier based on artificial neural network is applied in order to classify soil images in two classes, pore space and solid soil respectively.

Categorical Missing Data Imputation Using Fuzzy Neural Networks with Numerical and Categorical Inputs

There are many situations where input feature vectors are incomplete and methods to tackle the problem have been studied for a long time. A commonly used procedure is to replace each missing value with an imputation. This paper presents a method to perform categorical missing data imputation from numerical and categorical variables. The imputations are based on Simpson’s fuzzy min-max neural networks where the input variables for learning and classification are just numerical. The proposed method extends the input to categorical variables by introducing new fuzzy sets, a new operation and a new architecture. The procedure is tested and compared with others using opinion poll data.

Reduced synchronization persistence in neural networks derived from atm-deficient mice

Many neurodegenerative diseases are characterized by malfunction of the DNA damage response. Therefore, it is important to understand the connection between system level neural network behavior and DNA. Neural networks drawn from genetically engineered animals, interfaced with micro-electrode arrays allowed us to unveil connections between networks’ system level activity properties and such genome instability. We discovered that Atm protein deficiency, which in humans leads to progressive motor impairment, leads to a reduced synchronization persistence compared to wild type synchronization, after chemically imposed DNA damage. Not only do these results suggest a role for DNA stability in neural network activity, they also establish an experimental paradigm for empirically determining the role a gene plays on the behavior of a neural network.

Pollutant concentrations and Meteorological data classification by Neural Networks

This paper present an environmental contingency forecasting tool based on Neural Networks (NN). Forecasting tool analyzes every hour and daily Sulphur Dioxide (SO2) concentrations and Meteorological data time series. Pollutant concentrations and meteorological variables are self-organized applying a Self-organizing Map (SOM) NN in different classes. Classes are used in training phase of a General Regression Neural Network (GRNN) classifier to provide an air quality forecast. In this case a time series set obtained from Environmental Monitoring Network (EMN) of the city of Salamanca, Guanajuato, México is used. Results verify the potential of this method versus other statistical classification methods and also variables correlation is solved.

Data Mining with Enhanced Neural Networks-CMMSE

Abstract This paper presents a new method to extract knowledge from existing data sets, that is, to extract symbolic rules using the weights of an Artificial Neural Network. The method has been applied to a neural network with special architecture named Enhanced Neural Network (ENN). This architecture improves the results that have been obtained with multilayer perceptron (MLP). The relationship among the knowledge stored in the weights, the performance of the network and the new implemented algorithm to acquire rules from the weights is explained. The method itself gives a model to follow in the knowledge acquisition with ENN.

Bus line classification using neural networks

Grouping urban bus routes is necessary when there are evidences of significant differences among them. In Jiménez et al. (2013), a reduced sample of routes was grouped into clusters utilizing kinematic measured data. As a further step, in this paper, the remaining urban bus routes of a city, for which no kinematic measurements are available, are classified. For such purpose we use macroscopic geographical and functional variables to describe each route, while the clustering process is performed by means of a neural network. Limitations caused by reduced training samples are solved using the bootstrap method.

Multiplexing QKD systems in Conventional Optical Networks

Current QKD designs try to keep the quantum channel as error free as possible by using a separate physical medium for this purpose. In the most common case, this means the exclusive use of an optical fiber for the quantum channel, precluding its use for any other purpose. In current optical networks, the fiber is the single most expensive element and this poses a major problem from a cost and availability point of view. Sharing the fiber is thus mandatory for the widespread adoption of QKD. The objective of this communication is to propose a general scheme and present some preliminary measurements of a metropolitan area network (MAN) designed to multiplex of the order of 64 addressable quantum channels and the associated QKD classical service signals on a single dark fibre. It uses as much existing components and infraestructure as possible in an attempt to simultaneously lower most of the practical barriers for the adoption of QKD.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Overtopping of harbour breakwaters: a comparison of semi-empirical equations, neural networks, and physical model tests

This paper reports extensive tests of empirical equations developed by different authors for harbour breakwater overtopping. First, the existing equations are compiled and evaluated as tools for estimating the overtopping rates on sloping and vertical breakwaters. These equations are then tested using the data obtained in a number of laboratory studies performed in the Centre for Harbours and Coastal Studies of the CEDEX, Spain. It was found that the recommended application ranges of the empirical equations typically deviate from those revealed in the experimental tests. In addition, a neural network model developed within the European CLASH Project is tested. The wind effects on overtopping are also assessed using a reduced scale physical model

Peptide design by artificial neural networks and computer-based evolutionary search

A technique for systematic peptide variation by a combination of rational and evolutionary approaches is presented. The design scheme consists of five consecutive steps: (i) identification of a “seed peptide” with a desired activity, (ii) generation of variants selected from a physicochemical space around the seed peptide, (iii) synthesis and testing of this biased library, (iv) modeling of a quantitative sequence-activity relationship by an artificial neural network, and (v) de novo design by a computer-based evolutionary search in sequence space using the trained neural network as the fitness function. This strategy was successfully applied to the identification of novel peptides that fully prevent the positive chronotropic effect of anti-β1-adrenoreceptor autoantibodies from the serum of patients with dilated cardiomyopathy. The seed peptide, comprising 10 residues, was derived by epitope mapping from an extracellular loop of human β1-adrenoreceptor. A set of 90 peptides was synthesized and tested to provide training data for neural network development. De novo design revealed peptides with desired activities that do not match the seed peptide sequence. These results demonstrate that computer-based evolutionary searches can generate novel peptides with substantial biological activity.