Search results for "algorithms"
showing 10 items of 1716 documents
Impact of chaotic dynamics on the performance of metaheuristic optimization algorithms : An experimental analysis
2022
Random mechanisms including mutations are an internal part of evolutionary algorithms, which are based on the fundamental ideas of Darwin's theory of evolution as well as Mendel's theory of genetic heritage. In this paper, we debate whether pseudo-random processes are needed for evolutionary algorithms or whether deterministic chaos, which is not a random process, can be suitably used instead. Specifically, we compare the performance of 10 evolutionary algorithms driven by chaotic dynamics and pseudo-random number generators using chaotic processes as a comparative study. In this study, the logistic equation is employed for generating periodical sequences of different lengths, which are use…
A new paradigm for pattern classification: Nearest Border Techniques
2013
Published version of a chapter in the book: AI 2013: Advances in Artificial Intelligence. Also available from the publisher at: http://dx.doi.org/10.1007/978-3-319-03680-9_44 There are many paradigms for pattern classification. As opposed to these, this paper introduces a paradigm that has not been reported in the literature earlier, which we shall refer to as the Nearest Border (NB) paradigm. The philosophy for developing such a NB strategy is as follows: Given the training data set for each class, we shall first attempt to create borders for each individual class. After that, we advocate that testing is accomplished by assigning the test sample to the class whose border it lies closest to…
Variability of Classification Results in Data with High Dimensionality and Small Sample Size
2021
The study focuses on the analysis of biological data containing information on the number of genome sequences of intestinal microbiome bacteria before and after antibiotic use. The data have high dimensionality (bacterial taxa) and a small number of records, which is typical of bioinformatics data. Classification models induced on data sets like this usually are not stable and the accuracy metrics have high variance. The aim of the study is to create a preprocessing workflow and a classification model that can perform the most accurate classification of the microbiome into groups before and after the use of antibiotics and lessen the variability of accuracy measures of the classifier. To ev…
Evaluation of enantioselective binding of fluoxetine to human serum albumin by ultrafiltration and CE - Experimental design and quality considerations
2012
Several pharmacokinetic processes are affected by enantioselectivity (ES). At the level of distribution, protein binding (PB) is one of the most important. The enantioselective binding of fluoxetine (FLX) to HSA has been evaluated in this work by ultrafiltration of FLX–HSA mixtures and chiral analysis of unbound fractions by EKC-CD. PB, affinity constants (K) and ES were obtained for both enantiomers of FLX. In order to improve the consistency of the estimations, the evaluation of affinity constants of each enantiomer was performed using two designs, one keeping constant the total concentration of protein and varying the total concentration of the enantiomers, and the other in the opposite …
Efficient unsupervised clustering for spatial bird population analysis along the Loire river
2015
International audience; This paper focuses on application and comparison of Non Linear Dimensionality Reduction (NLDR) methods on natural high dimensional bird communities dataset along the Loire River (France). In this context, biologists usually use the well-known PCA in order to explain the upstream-downstream gradient.Unfortunately this method was unsuccessful on this kind of nonlinear dataset.The goal of this paper is to compare recent NLDR methods coupled with different data transformations in order to find out the best approach. Results show that Multiscale Jensen-Shannon Embedding (Ms JSE) outperform all over methods in this context.
SMART: Unique splitting-while-merging framework for gene clustering
2014
© 2014 Fa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named "splitting merging awareness tactics" (SMART), which does not require any a priori knowledge of either the number …
Computation Cluster Validation in the Big Data Era
2017
Data-driven class discovery, i.e., the inference of cluster structure in a dataset, is a fundamental task in Data Analysis, in particular for the Life Sciences. We provide a tutorial on the most common approaches used for that task, focusing on methodologies for the prediction of the number of clusters in a dataset. Although the methods that we present are general in terms of the data for which they can be used, we offer a case study relevant for Microarray Data Analysis.
GenClust: A genetic algorithm for clustering gene expression data
2005
Abstract Background Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. Results GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, …
Calcification is not the Achilles' heel of cold-water corals in an acidifying ocean
2015
Ocean acidification is thought to be a major threat to coral reefs: laboratory evidence and CO2 seep research has shown adverse effects on many coral species, although a few are resilient. There are concerns that cold-water corals are even more vulnerable as they live in areas where aragonite saturation (?ara) is lower than in the tropics and is falling rapidly due to CO2 emissions. Here, we provide laboratory evidence that net (gross calcification minus dissolution) and gross calcification rates of three common cold-water corals, Caryophyllia smithii, Dendrophyllia cornigera, and Desmophyllum dianthus, are not affected by pCO2 levels expected for 2100 (pCO2 1058 ?atm, ?ara 1.29), and nor a…
Neural networks with non-uniform embedding and explicit validation phase to assess Granger causality
2015
A challenging problem when studying a dynamical system is to find the interdependencies among its individual components. Several algorithms have been proposed to detect directed dynamical influences between time series. Two of the most used approaches are a model-free one (transfer entropy) and a model-based one (Granger causality). Several pitfalls are related to the presence or absence of assumptions in modeling the relevant features of the data. We tried to overcome those pitfalls using a neural network approach in which a model is built without any a priori assumptions. In this sense this method can be seen as a bridge between model-free and model-based approaches. The experiments perfo…