Browse
Submit Data
Databases
API
Help

Dataset Information

81 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A modified ant colony optimization algorithm for tumor marker gene selection.

ABSTRACT: Microarray data are often extremely asymmetric in dimensionality, such as thousands or even tens of thousands of genes but only a few hundreds of samples or less. Such extreme asymmetry between the dimensionality of genes and samples can lead to inaccurate diagnosis of disease in clinic. Therefore, it has been shown that selecting a small set of marker genes can lead to improved classification accuracy. In this paper, a simple modified ant colony optimization (ACO) algorithm is proposed to select tumor-related marker genes, and support vector machine (SVM) is used as classifier to evaluate the performance of the extracted gene subset. Experimental results on several benchmark tumor microarray datasets showed that the proposed approach produces better recognition with fewer marker genes than many other methods. It has been demonstrated that the modified ACO is a useful tool for selecting marker genes and mining high dimension data.

SUBMITTER: Yu H

PROVIDER: S-EPMC5054414 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A modified ant colony optimization algorithm for tumor marker gene selection.

Yu Hualong H Gu Guochang G Liu Haibo H Shen Jing J Zhao Jing J

Genomics, proteomics & bioinformatics 20091201 4

Microarray data are often extremely asymmetric in dimensionality, such as thousands or even tens of thousands of genes but only a few hundreds of samples or less. Such extreme asymmetry between the dimensionality of genes and samples can lead to inaccurate diagnosis of disease in clinic. Therefore, it has been shown that selecting a small set of marker genes can lead to improved classification accuracy. In this paper, a simple modified ant colony optimization (ACO) algorithm is proposed to selec ...[more]

PMID: 20172493

Similar Datasets

All-Optical Implementation of the Ant Colony Optimization Algorithm.

Project description:We report all-optical implementation of the optimization algorithm for the famous "ant colony" problem. Ant colonies progressively optimize pathway to food discovered by one of the ants through identifying the discovered route with volatile chemicals (pheromones) secreted on the way back from the food deposit. Mathematically this is an important example of graph optimization problem with dynamically changing parameters. Using an optical network with nonlinear waveguides to represent the graph and a feedback loop, we experimentally show that photons traveling through the network behave like ants that dynamically modify the environment to find the shortest pathway to any chosen point in the graph. This proof-of-principle demonstration illustrates how transient nonlinearity in the optical system can be exploited to tackle complex optimization problems directly, on the hardware level, which may be used for self-routing of optical signals in transparent communication networks and energy flow in photonic systems.

| S-EPMC4879568 | biostudies-literature

Semi-supervised associative classification using ant colony optimization algorithm.

Project description:Labeled data is the main ingredient for classification tasks. Labeled data is not always available and free. Semi-supervised learning solves the problem of labeling the unlabeled instances through heuristics. Self-training is one of the most widely-used comprehensible approaches for labeling data. Traditional self-training approaches tend to show low classification accuracy when the majority of the data is unlabeled. A novel approach named Self-Training using Associative Classification using Ant Colony Optimization (ST-AC-ACO) has been proposed in this article to label and classify the unlabeled data instances to improve self-training classification accuracy by exploiting the association among attribute values (terms) and between a set of terms and class labels of the labeled instances. Ant Colony Optimization (ACO) has been employed to construct associative classification rules based on labeled and pseudo-labeled instances. Experiments demonstrate the superiority of the proposed associative self-training approach to its competing traditional self-training approaches.

| S-EPMC8444075 | biostudies-literature

CACONET: Ant Colony Optimization (ACO) Based Clustering Algorithm for VANET.

Project description:A vehicular ad hoc network (VANET) is a wirelessly connected network of vehicular nodes. A number of techniques, such as message ferrying, data aggregation, and vehicular node clustering aim to improve communication efficiency in VANETs. Cluster heads (CHs), selected in the process of clustering, manage inter-cluster and intra-cluster communication. The lifetime of clusters and number of CHs determines the efficiency of network. In this paper a Clustering algorithm based on Ant Colony Optimization (ACO) for VANETs (CACONET) is proposed. CACONET forms optimized clusters for robust communication. CACONET is compared empirically with state-of-the-art baseline techniques like Multi-Objective Particle Swarm Optimization (MOPSO) and Comprehensive Learning Particle Swarm Optimization (CLPSO). Experiments varying the grid size of the network, the transmission range of nodes, and number of nodes in the network were performed to evaluate the comparative effectiveness of these algorithms. For optimized clustering, the parameters considered are the transmission range, direction and speed of the nodes. The results indicate that CACONET significantly outperforms MOPSO and CLPSO.

| S-EPMC4858224 | biostudies-literature

epiACO - a method for identifying epistasis based on ant Colony optimization algorithm.

Project description:BACKGROUND:Identifying epistasis or epistatic interactions, which refer to nonlinear interaction effects of single nucleotide polymorphisms (SNPs), is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Though many works have been done for identifying epistatic interactions, due to their methodological and computational challenges, the algorithmic development is still ongoing. RESULTS:In this study, a method epiACO is proposed to identify epistatic interactions, which based on ant colony optimization algorithm. Highlights of epiACO are the introduced fitness function Svalue, path selection strategies, and a memory based strategy. The Svalue leverages the advantages of both mutual information and Bayesian network to effectively and efficiently measure associations between SNP combinations and the phenotype. Two path selection strategies, i.e., probabilistic path selection strategy and stochastic path selection strategy, are provided to adaptively guide ant behaviors of exploration and exploitation. The memory based strategy is designed to retain candidate solutions found in the previous iterations, and compare them to solutions of the current iteration to generate new candidate solutions, yielding a more accurate way for identifying epistasis. CONCLUSIONS:Experiments of epiACO and its comparison with other recent methods epiMODE, TEAM, BOOST, SNPRuler, AntEpiSeeker, AntMiner, MACOED, and IACO are performed on both simulation data sets and a real data set of age-related macular degeneration. Results show that epiACO is promising in identifying epistasis and might be an alternative to existing methods.

| S-EPMC5500974 | biostudies-literature

An ant colony optimization based feature selection for web page classification.

Project description:The increased popularity of the web has caused the inclusion of huge amount of information to the web, and as a result of this explosive information growth, automated web page classification systems are needed to improve search engines' performance. Web pages have a large number of features such as HTML/XML tags, URLs, hyperlinks, and text contents that should be considered during an automated classification process. The aim of this study is to reduce the number of features to be used to improve runtime and accuracy of the classification of web pages. In this study, we used an ant colony optimization (ACO) algorithm to select the best features, and then we applied the well-known C4.5, naive Bayes, and k nearest neighbor classifiers to assign class labels to web pages. We used the WebKB and Conference datasets in our experiments, and we showed that using the ACO for feature selection improves both accuracy and runtime performance of classification. We also showed that the proposed ACO based algorithm can select better features with respect to the well-known information gain and chi square feature selection methods.

| S-EPMC4127204 | biostudies-other

An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle.

Project description:BackgroundDistance matrix methods constitute a major family of phylogenetic estimation methods, and the minimum evolution (ME) principle (aiming at recovering the phylogeny with shortest length) is one of the most commonly used optimality criteria for estimating phylogenetic trees. The major difficulty for its application is that the number of possible phylogenies grows exponentially with the number of taxa analyzed and the minimum evolution principle is known to belong to the NRho- hard class of problems.ResultsIn this paper, we introduce an Ant Colony Optimization (ACO) algorithm to estimate phylogenies under the minimum evolution principle. ACO is an optimization technique inspired from the foraging behavior of real ant colonies. This behavior is exploited in artificial ant colonies for the search of approximate solutions to discrete optimization problems.ConclusionWe show that the ACO algorithm is potentially competitive in comparison with state-of-the-art algorithms for the minimum evolution principle. This is the first application of an ACO algorithm to the phylogenetic estimation problem.

| S-EPMC2211314 | biostudies-literature

An improved ant colony optimization algorithm based on context for tourism route planning.

Project description:To solve the problem of one-sided pursuit of the shortest distance but ignoring the tourist experience in the process of tourism route planning, an improved ant colony optimization algorithm is proposed for tourism route planning. Contextual information of scenic spots significantly effect people's choice of tourism destination, so the pheromone update strategy is combined with the contextual information such as weather and comfort degree of the scenic spot in the process of searching the global optimal route, so that the pheromone update tends to the path suitable for tourists. At the same time, in order to avoid falling into local optimization, the sub-path support degree is introduced. The experimental results show that the optimized tourism route has greatly improved the tourist experience, the route distance is shortened by 20.5% and the convergence speed is increased by 21.2% compared with the basic algorithm, which proves that the improved algorithm is notably effective.

| S-EPMC8445481 | biostudies-literature

A novel algorithm for parameter estimation of Hidden Markov Model inspired by Ant Colony Optimization.

Project description:HMM is a powerful method to model data in various fields. Estimation of Hidden Markov Model parameters is an NP-Hard problem. We propose a heuristic algorithm called "AntMarkov" to improve the efficiency of estimating HMM parameters. We compared our method with four algorithms. The comparison was conducted on 5 different simulated datasets with different features. For further evaluation, we analyzed the performance of algorithms on the prediction of protein secondary structures problem. The results demonstrate that our algorithm obtains better results with respect to the results of the other algorithms in terms of time efficiency and the amount of similarity of estimated parameters to the original parameters and log-likelihood. The source code of our algorithm is available in https://github.com/emdadi/HMMPE.

| S-EPMC6422281 | biostudies-literature

VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization.

Project description:The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.

| S-EPMC8199267 | biostudies-literature

Metabolic pathways synthesis based on ant colony optimization.

Project description:One of the current challenges in bioinformatics is to discover new ways to transform a set of compounds into specific products. The usual approach is finding the reactions to synthesize a particular product, from a given substrate, by means of classical searching algorithms. However, they have three main limitations: difficulty in handling large amounts of reactions and compounds; absence of a step that verifies the availability of substrates; and inability to find branched pathways. We present here a novel bio-inspired algorithm for synthesizing linear and branched metabolic pathways. It allows relating several compounds simultaneously, ensuring the availability of substrates for every reaction in the solution. Comparisons with classical searching algorithms and other recent metaheuristic approaches show clear advantages of this proposal, fully recovering well-known pathways. Furthermore, solutions found can be analyzed in a simple way through graphical representations on the web.

| S-EPMC6219534 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data