Browse
Submit Data
Databases
API
Help

Dataset Information

87 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolic pathways synthesis based on ant colony optimization.

ABSTRACT: 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.

SUBMITTER: Gerard MF

PROVIDER: S-EPMC6219534 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Metabolic pathways synthesis based on ant colony optimization.

Gerard Matias F MF Stegmayer Georgina G Milone Diego H DH

Scientific reports 20181106 1

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 ...[more]

PMID: 30401873

Similar Datasets

Link Prediction based on Quantum-Inspired Ant Colony Optimization.

Project description:Incomplete or partial observations of network structures pose a serious challenge to theoretical and engineering studies of real networks. To remedy the missing links in real datasets, topology-based link prediction is introduced into the studies of various networks. Due to the complexity of network structures, the accuracy and robustness of most link prediction algorithms are not satisfying enough. In this paper, we propose a quantum-inspired ant colony optimization algorithm that integrates ant colony optimization and quantum computing to predict links in networks. Extensive experiments on both synthetic and real networks show that the accuracy and robustness of the new algorithm is competitive in respect to most of the state of the art algorithms. This result suggests that the application of intelligent optimization to link prediction is promising for boosting its accuracy and robustness.

| S-EPMC6127200 | 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

Ant colony optimization-based adjusted PID parameters: a proposed method.

Project description:The ant colony algorithm (ACA) is a heuristic algorithm that resolves the optimality problem by simulating an ant's foraging process, which finds the shortest path. The connotation of the ACA is to find the optimal solution. The Proportional Integral Derivative (PID) parameter tuning is an essential tool in the control field and includes three parameters, Kp, Ki, and Kd, to achieve the best control effect. Besides, tuning the PID parameters is closely related to finding the "optimal" solution that can be attained based on the feasible combination of the two. This article transforms the PID parameter tuning problem into an ACA that finds the optimal solution called ACA-based PID parameters tuning. Furthermore, PID control is simulated by setting the parameters of ACA, such as ant colony size, iteration times, nodes, paths, path evaluation criteria, pheromone concentration, heuristic function, weight factor, and decision function. Eventually, the two PID controller parameter tuning strategies are compared and analyzed, and the advantages and disadvantages of each are obtained. Compared with the 4:1 attenuation curve method, the proposed method can significantly reduce the MP score of the overshoot of the system, increase the time, and improve the dynamic and steady-state performance of the system, but reduce the steady-state error of the system. Therefore, the feasibility and effectiveness of the proposed method is verified.

| S-EPMC10703037 | 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

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

Self-Adjusting Ant Colony Optimization Based on Information Entropy for Detecting Epistatic Interactions.

Project description:The epistatic interactions of single nucleotide polymorphisms (SNPs) are considered to be an important factor in determining the susceptibility of individuals to complex diseases. Although many methods have been proposed to detect such interactions, the development of detection algorithm is still ongoing due to the computational burden in large-scale association studies. In this paper, to deal with the intensive computing problem of detecting epistatic interactions in large-scale datasets, a self-adjusting ant colony optimization based on information entropy (IEACO) is proposed. The algorithm can automatically self-adjust the path selection strategy according to the real-time information entropy. The performance of IEACO is compared with that of ant colony optimization (ACO), AntEpiSeeker, AntMiner, and epiACO on a set of simulated datasets and a real genome-wide dataset. The results of extensive experiments show that the proposed method is superior to the other methods.

| S-EPMC6409693 | 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

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

ACOustic: A Nature-Inspired Exploration Indicator for Ant Colony Optimization.

Project description:A statistical machine learning indicator, ACOustic, is proposed to evaluate the exploration behavior in the iterations of ant colony optimization algorithms. This idea is inspired by the behavior of some parasites in their mimicry to the queens' acoustics of their ant hosts. The parasites' reaction results from their ability to indicate the state of penetration. The proposed indicator solves the problem of robustness that results from the difference of magnitudes in the distance's matrix, especially when combinatorial optimization problems with rugged fitness landscape are applied. The performance of the proposed indicator is evaluated against the existing indicators in six variants of ant colony optimization algorithms. Instances for travelling salesman problem and quadratic assignment problem are used in the experimental evaluation. The analytical results showed that the proposed indicator is more informative and more robust.

| S-EPMC4397471 | biostudies-other

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