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

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 114 ◽  
Author(s):  
Boxin Guan ◽  
Yuhai Zhao
Keyword(s):  
Ant Colony Optimization ◽  
Information Entropy ◽  
Large Scale ◽  
Association Studies ◽  
Detection Algorithm ◽  
Path Selection ◽  
Ant Colony ◽  
Selection Strategy ◽  
Nucleotide Polymorphisms ◽  
Epistatic Interactions

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.

scholarly journals QALPA- An Efficient QoS Aware Hybrid Localization Model Using Particle Swarm Optimization and Ant Colony Optimization for Cognitive Wireless Sensor Networks

2021 ◽  
Vol 14 (1) ◽  
pp. 270-280
Author(s):  
Abhijit Halkai ◽  
◽  
Sujatha Terdal ◽  
Keyword(s):  
Particle Swarm Optimization ◽  
Sensor Networks ◽  
Ant Colony Optimization ◽  
Large Scale ◽  
Cluster Head ◽  
Particle Swarm ◽  
Base Station ◽  
Ant Colony ◽  
Swarm Optimization ◽  
Localization Model

A sensor network operates wirelessly and transmits detected information to the base station. The sensor is a small sized device, it is battery-powered with some electrical components, and the protocols should operate efficiently in such least resource availability. Here, we propose a novel improved framework in large scale applications where the huge numbers of sensors are distributed over an area. The designed protocol will address the issues that arise during its communication and give a consistent seamless communication system. The process of reasoning and learning in cognitive sensors guarantees data delivery in the network. Localization in Scarce and dense sensor networks is achieved by efficient cluster head election and route selection which are indeed based on cognition, improved Particle Swarm Optimization, and improved Ant Colony Optimization algorithms. Factors such as mobility, use of sensor buffer, power management, and defects in channels have been identified and solutions are presented in this research to build an accurate path based on the network context. The achieved results in extensive simulation prove that the proposed scheme outperforms ESNA, NETCRP, and GAECH algorithms in terms of Delay, Network lifetime, Energy consumption.

scholarly journals Secure large-scale genome-wide association studies using homomorphic encryption

2020 ◽  
Vol 117 (21) ◽  
pp. 11608-11613 ◽  
Author(s):  
Marcelo Blatt ◽  
Alexander Gusev ◽  
Yuriy Polyakov ◽  
Shafi Goldwasser
Keyword(s):  
Large Scale ◽  
Homomorphic Encryption ◽  
Association Studies ◽  
Genome Wide Association ◽  
Single Server ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
User Interactions ◽  
Individual Level ◽  
Genome Wide

Genome-wide association studies (GWASs) seek to identify genetic variants associated with a trait, and have been a powerful approach for understanding complex diseases. A critical challenge for GWASs has been the dependence on individual-level data that typically have strict privacy requirements, creating an urgent need for methods that preserve the individual-level privacy of participants. Here, we present a privacy-preserving framework based on several advances in homomorphic encryption and demonstrate that it can perform an accurate GWAS analysis for a real dataset of more than 25,000 individuals, keeping all individual data encrypted and requiring no user interactions. Our extrapolations show that it can evaluate GWASs of 100,000 individuals and 500,000 single-nucleotide polymorphisms (SNPs) in 5.6 h on a single server node (or in 11 min on 31 server nodes running in parallel). Our performance results are more than one order of magnitude faster than prior state-of-the-art results using secure multiparty computation, which requires continuous user interactions, with the accuracy of both solutions being similar. Our homomorphic encryption advances can also be applied to other domains where large-scale statistical analyses over encrypted data are needed.

scholarly journals Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation

2019 ◽  
Vol 48 (D1) ◽  
pp. D659-D667 ◽  
Author(s):  
Wenqian Yang ◽  
Yanbo Yang ◽  
Cecheng Zhao ◽  
Kun Yang ◽  
Dongyang Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Whole Genome Resequencing ◽  
Missing Genotypes

Abstract Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs) and thus can be widely used in large-scale genome-wide association studies (GWASs) using relatively inexpensive and low-density SNP arrays. However, most animals except humans lack high-quality reference panels, which greatly limits the application of genotype imputation in animals. To overcome this limitation, we developed Animal-ImputeDB, which is dedicated to collecting genotype data and whole-genome resequencing data of nonhuman animals from various studies and databases. A computational pipeline was developed to process different types of raw data to construct reference panels. Finally, 13 high-quality reference panels including ∼400 million SNPs from 2265 samples were constructed. In Animal-ImputeDB, an easy-to-use online tool consisting of two popular imputation tools was designed for the purpose of genotype imputation. Collectively, Animal-ImputeDB serves as an important resource for animal genotype imputation and will greatly facilitate research on animal genomic selection and genetic improvement.

scholarly journals Genetically Predicted Circulating Concentrations of Micronutrients and Risk of Amyotrophic Lateral Sclerosis: A Mendelian Randomization Study

2022 ◽  
Vol 12 ◽  
Author(s):  
Changqing Mu ◽  
Yating Zhao ◽  
Chen Han ◽  
Dandan Tian ◽  
Na Guo ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Large Scale ◽  
Mendelian Randomization ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Inverse Variance ◽  
Effective Role ◽  
Copper Zinc ◽  
Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive and devastating neurodegenerative disease with increasing incidence and high mortality, resulting in a considerable socio-economic burden. Till now, plenty of studies have explored the potential relationship between circulating levels of various micronutrients and ALS risk. However, the observations remain equivocal and controversial. Thus, we conducted a two-sample Mendelian randomization (MR) study to investigate the causality between circulating concentrations of 9 micronutrients, including retinol, folate acid, vitamin B12, B6 and C, calcium, copper, zinc as well as magnesium, and ALS susceptibility. In our analysis, several single nucleotide polymorphisms were collected as instrumental variables from large-scale genome-wide association studies of these 9 micronutrients. Then, inverse variance weighted (IVW) approach as well as alternative MR-Egger regression, weighted median and MR-pleiotropy residual sum and outlier (MR-PRESSO) analyses were performed to evaluate causal estimates. The results from IVW analysis showed that there was no causal relationship of 9 micronutrients with ALS risk. Meanwhile, the three complementary approaches obtained similar results. Thus, our findings indicated that supplementation of these 9 micronutrients may not play a clinically effective role in preventing the occurrence of ALS.

scholarly journals Pleiotropy of Alzheimer’s Disease and Educational Attainment: Insights from the Summary Statistics

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 986-986
Author(s):  
Yury Loika ◽  
Elena Loiko ◽  
Irina Culminskaya ◽  
Alexander Kulminski
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Educational Attainment ◽  
Large Scale ◽  
Association Studies ◽  
Epidemiological Studies ◽  
Genome Wide Association Studies ◽  
Summary Statistics ◽  
Nucleotide Polymorphisms ◽  
Omnibus Test

Abstract Epidemiological studies report beneficial associations of higher educational attainment (EDU) with Alzheimer’s disease (AD). Prior genome-wide association studies (GWAS) also reported variants associated with AD and EDU separately. The analysis of pleiotropic predisposition to these phenotypes may shed light on EDU-related protection against AD. We examined pleiotropic predisposition to AD and EDU using Fisher’s method and omnibus test applied to summary statistics for single nucleotide polymorphisms (SNPs) associated with AD and EDU in large-scale univariate GWAS at suggestive-effect (5×10-8

scholarly journals A Novel Approach to Comparative Analysis of Legacy and Nature Inspired Ant Colony Optimization based Routing Protocol in MANET

2019 ◽  
Vol 54 (4) ◽  
Author(s):  
Ibrahim Ahmed Alameri
Keyword(s):  
Ant Colony Optimization ◽  
Routing Protocols ◽  
Large Scale ◽  
Ad Hoc ◽  
Mobile Ad Hoc Network ◽  
Ant Colony ◽  
Novel Approach ◽  
Manet Routing ◽  
Mobile Ad Hoc ◽  
Hoc Networks

Performance, scalability, Quality of Service (QoS), users’ response, etc. of any network depends upon the efficient network design and communication technologies being exploited. Mobile Ad hoc Networks (MANETs) have become widespread due to their zero-configuration requirements, scalability, maintenance and adaptable nature to cater varying requirements. The core process of any network is routing which is performed by routing protocols. Routing protocols play a crucial role to enhance and improve the performance indicators of any network. Traditional MANET routing protocols have been failed to address growing demands of wireless mobile ad hoc network. In this paper we study and compare a nature inspired Ant Colony Optimization (ACO) algorithm with legacy of MANET protocols. Simulation results show that ACO algorithm has high potential to be used in large scale MANET or other wireless networks. We compared ACO with proactive and reactive routing protocols because despite of their weaknesses these types of protocols are still being used in different and same wireless arrangements.

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