Impact of noise on a dynamical system: prediction and uncertainties from a swarm-optimized neural network

In this study, an artificial neural network (ANN) based on particle swarm optimization (PSO) was developed for the time series prediction. The hybrid ANN+PSO algorithm was applied on Mackey--Glass chaotic time series in the short-term $x(t+6)$. The performance prediction was evaluated and compared with another studies available in the literature. Also, we presented properties of the dynamical system via the study of chaotic behaviour obtained from the predicted time series. Next, the hybrid ANN+PSO algorithm was complemented with a Gaussian stochastic procedure (called {\it stochastic} hybrid ANN+PSO) in order to obtain a new estimator of the predictions, which also allowed us to compute uncertainties of predictions for noisy Mackey--Glass chaotic time series. Thus, we studied the impact of noise for several cases with a white noise level ($\sigma_{N}$) from 0.01 to 0.1.Comment: 11 pages, 8 figure

Genetic algorithm-neural network: feature extraction for bioinformatics data.

With the advance of gene expression data in the bioinformatics field, the questions which frequently arise, for both computer and medical scientists, are which genes are significantly involved in discriminating cancer classes and which genes are significant with respect to a specific cancer pathology. Numerous computational analysis models have been developed to identify informative genes from the microarray data, however, the integrity of the reported genes is still uncertain. This is mainly due to the misconception of the objectives of microarray study. Furthermore, the application of various preprocessing techniques in the microarray data has jeopardised the quality of the microarray data. As a result, the integrity of the findings has been compromised by the improper use of techniques and the ill-conceived objectives of the study. This research proposes an innovative hybridised model based on genetic algorithms (GAs) and artificial neural networks (ANNs), to extract the highly differentially expressed genes for a specific cancer pathology. The proposed method can efficiently extract the informative genes from the original data set and this has reduced the gene variability errors incurred by the preprocessing techniques. The novelty of the research comes from two perspectives. Firstly, the research emphasises on extracting informative features from a high dimensional and highly complex data set, rather than to improve classification results. Secondly, the use of ANN to compute the fitness function of GA which is rare in the context of feature extraction. Two benchmark microarray data have been taken to research the prominent genes expressed in the tumour development and the results show that the genes respond to different stages of tumourigenesis (i.e. different fitness precision levels) which may be useful for early malignancy detection. The extraction ability of the proposed model is validated based on the expected results in the synthetic data sets. In addition, two bioassay data have been used to examine the efficiency of the proposed model to extract significant features from the large, imbalanced and multiple data representation bioassay data

Memetic micro-genetic algorithms for cancer data classification

Fast and precise medical diagnosis of human cancer is crucial for treatment decisions. Gene selection consists of identifying a set of informative genes from microarray data to allow high predictive accuracy in human cancer classification. This task is a combinatorial search problem, and optimisation methods can be applied for its resolution. In this paper, two memetic micro-genetic algorithms (MμV1 and MμV2) with different hybridisation approaches are proposed for feature selection of cancer microarray data. Seven gene expression datasets are used for experimentation. The comparison with stochastic state-of-the-art optimisation techniques concludes that problem-dependent local search methods combined with micro-genetic algorithms improve feature selection of cancer microarray data.Fil: Rojas, Matias Gabriel. Universidad Nacional de Lujan. Centro de Investigacion Docencia y Extension En Tecnologias de la Informacion y Las Comunicaciones.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Olivera, Ana Carolina. Universidad Nacional de Cuyo. Facultad de Ingeniería; Argentina. Universidad Nacional de Lujan. Centro de Investigacion Docencia y Extension En Tecnologias de la Informacion y Las Comunicaciones.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Carballido, Jessica Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Vidal, Pablo Javier. Universidad Nacional de Cuyo. Facultad de Ingeniería; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentin

Predicting stable gravel-bed river hydraulic geometry: A test of novel, advanced, hybrid data mining algorithms

Accurate prediction of stable alluvial hydraulic geometry, in which erosion and sedimentation are in equilibrium, is one of the most difficult but critical topics in the field of river engineering. Data mining algorithms have been gaining more attention in this field due to their high performance and flexibility. However, an understanding of the potential for these algorithms to provide fast, cheap, and accurate predictions of hydraulic geometry is lacking. This study provides the first quantification of this potential. Using at-a-station field data, predictions of flow depth, water-surface width and longitudinal water surface slope are made using three standalone data mining techniques -, Instance-based Learning (IBK), KStar, Locally Weighted Learning (LWL) - along with four types of novel hybrid algorithms in which the standalone models are trained with Vote, Attribute Selected Classifier (ASC), Regression by Discretization (RBD), and Cross-validation Parameter Selection (CVPS) algorithms (Vote-IBK, Vote-Kstar, Vote-LWL, ASC-IBK, ASC-Kstar, ASC-LWL, RBD-IBK, RBD-Kstar, RBD-LWL, CVPS-IBK, CVPS-Kstar, CVPS-LWL). Through a comparison of their predictive performance and a sensitivity analysis of the driving variables, the results reveal: (1) Shield stress was the most effective parameter in the prediction of all geometry dimensions; (2) hybrid models had a higher prediction power than standalone data mining models, empirical equations and traditional machine learning algorithms; (3) Vote-Kstar model had the highest performance in predicting depth and width, and ASC-Kstar in estimating slope, each providing very good prediction performance. Through these algorithms, the hydraulic geometry of any river can potentially be predicted accurately and with ease using just a few, readily available flow and channel parameters. Thus, the results reveal that these models have great potential for use in stable channel design in data poor catchments, especially in developing nations where technical modelling skills and understanding of the hydraulic and sediment processes occurring in the river system may be lacking

Detecting and comparing non-coding RNAs in the high-throughput era.

In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes and of the finding that many of these transcripts are involved in key cellular functions. In this context, accurately detecting and comparing RNA sequences has become important. Aligning nucleotide sequences is a key requisite when searching for homologous genes. Accurate alignments reveal evolutionary relationships, conserved regions and more generally any biologically relevant pattern. Comparing RNA molecules is, however, a challenging task. The nucleotide alphabet is simpler and therefore less informative than that of amino-acids. Moreover for many non-coding RNAs, evolution is likely to be mostly constrained at the structural level and not at the sequence level. This results in very poor sequence conservation impeding comparison of these molecules. These difficulties define a context where new methods are urgently needed in order to exploit experimental results to their full potential. This review focuses on the comparative genomics of non-coding RNAs in the context of new sequencing technologies and especially dealing with two extremely important and timely research aspects: the development of new methods to align RNAs and the analysis of high-throughput data

Genetic algorithm-neural network : feature extraction for bioinformatics data

With the advance of gene expression data in the bioinformatics field, the questions which frequently arise, for both computer and medical scientists, are which genes are significantly involved in discriminating cancer classes and which genes are significant with respect to a specific cancer pathology. Numerous computational analysis models have been developed to identify informative genes from the microarray data, however, the integrity of the reported genes is still uncertain. This is mainly due to the misconception of the objectives of microarray study. Furthermore, the application of various preprocessing techniques in the microarray data has jeopardised the quality of the microarray data. As a result, the integrity of the findings has been compromised by the improper use of techniques and the ill-conceived objectives of the study. This research proposes an innovative hybridised model based on genetic algorithms (GAs) and artificial neural networks (ANNs), to extract the highly differentially expressed genes for a specific cancer pathology. The proposed method can efficiently extract the informative genes from the original data set and this has reduced the gene variability errors incurred by the preprocessing techniques. The novelty of the research comes from two perspectives. Firstly, the research emphasises on extracting informative features from a high dimensional and highly complex data set, rather than to improve classification results. Secondly, the use of ANN to compute the fitness function of GA which is rare in the context of feature extraction. Two benchmark microarray data have been taken to research the prominent genes expressed in the tumour development and the results show that the genes respond to different stages of tumourigenesis (i.e. different fitness precision levels) which may be useful for early malignancy detection. The extraction ability of the proposed model is validated based on the expected results in the synthetic data sets. In addition, two bioassay data have been used to examine the efficiency of the proposed model to extract significant features from the large, imbalanced and multiple data representation bioassay data.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Optimisation of a weightless neural network using particle swarms

Among numerous pattern recognition methods the neural network approach has been the subject of much research due to its ability to learn from a given collection of representative examples. This thesis is concerned with the design of weightless neural networks, which decompose a given pattern into several sets of n points, termed n-tuples. Considerable research has shown that by optimising the input connection mapping of such n-tuple networks classification performance can be improved significantly. In this thesis the application of a population-based stochastic optimisation technique, known as Particle Swarm Optimisation (PSO), to the optimisation of the connectivity pattern of such “n-tuple” classifiers is explored. The research was aimed at improving the discriminating power of the classifier in recognising handwritten characters by exploiting more efficient learning strategies. The proposed "learning" scheme searches for ‘good’ input connections of the n-tuples in the solution space and shrinks the search area step by step. It refines its search by attracting the particles to positions with good solutions in an iterative manner. Every iteration the performance or fitness of each input connection is evaluated, so a reward and punishment based fitness function was modelled for the task. The original PSO was refined by combining it with other bio-inspired approaches like Self-Organized Criticality and Nearest Neighbour Interactions. The hybrid algorithms were adapted for the n-tuple system and the performance was measured in selecting better connectivity patterns. The Genetic Algorithm (GA) has been shown to be accomplishing the same goals as the PSO, so the performances and convergence properties of the GA were compared against the PSO to optimise input connections. Experiments were conducted to evaluate the proposed methods by applying the trained classifiers to recognise handprinted digits from a widely used database. Results revealed the superiority of the particle swarm optimised training for the n-tuples over other algorithms including the GA. Low particle velocity in PSO was favourable for exploring more areas in the solution space and resulted in better recognition rates. Use of hybridisation was helpful and one of the versions of the hybrid PSO was found to be the best performing algorithm in finding the optimum set of input maps for the n-tuple network

A survey on metaheuristics for stochastic combinatorial optimization

Metaheuristics are general algorithmic frameworks, often nature-inspired, designed to solve complex optimization problems, and they are a growing research area since a few decades. In recent years, metaheuristics are emerging as successful alternatives to more classical approaches also for solving optimization problems that include in their mathematical formulation uncertain, stochastic, and dynamic information. In this paper metaheuristics such as Ant Colony Optimization, Evolutionary Computation, Simulated Annealing, Tabu Search and others are introduced, and their applications to the class of Stochastic Combinatorial Optimization Problems (SCOPs) is thoroughly reviewed. Issues common to all metaheuristics, open problems, and possible directions of research are proposed and discussed. In this survey, the reader familiar to metaheuristics finds also pointers to classical algorithmic approaches to optimization under uncertainty, and useful informations to start working on this problem domain, while the reader new to metaheuristics should find a good tutorial in those metaheuristics that are currently being applied to optimization under uncertainty, and motivations for interest in this fiel

Simulated Annealing

The book contains 15 chapters presenting recent contributions of top researchers working with Simulated Annealing (SA). Although it represents a small sample of the research activity on SA, the book will certainly serve as a valuable tool for researchers interested in getting involved in this multidisciplinary field. In fact, one of the salient features is that the book is highly multidisciplinary in terms of application areas since it assembles experts from the fields of Biology, Telecommunications, Geology, Electronics and Medicine