12,680 research outputs found
A Novel Genetic Algorithm using Helper Objectives for the 0-1 Knapsack Problem
The 0-1 knapsack problem is a well-known combinatorial optimisation problem.
Approximation algorithms have been designed for solving it and they return
provably good solutions within polynomial time. On the other hand, genetic
algorithms are well suited for solving the knapsack problem and they find
reasonably good solutions quickly. A naturally arising question is whether
genetic algorithms are able to find solutions as good as approximation
algorithms do. This paper presents a novel multi-objective optimisation genetic
algorithm for solving the 0-1 knapsack problem. Experiment results show that
the new algorithm outperforms its rivals, the greedy algorithm, mixed strategy
genetic algorithm, and greedy algorithm + mixed strategy genetic algorithm
Fast and scalable inference of multi-sample cancer lineages.
Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee
An efficient null space inexact Newton method for hydraulic simulation of water distribution networks
Null space Newton algorithms are efficient in solving the nonlinear equations
arising in hydraulic analysis of water distribution networks. In this article,
we propose and evaluate an inexact Newton method that relies on partial updates
of the network pipes' frictional headloss computations to solve the linear
systems more efficiently and with numerical reliability. The update set
parameters are studied to propose appropriate values. Different null space
basis generation schemes are analysed to choose methods for sparse and
well-conditioned null space bases resulting in a smaller update set. The Newton
steps are computed in the null space by solving sparse, symmetric positive
definite systems with sparse Cholesky factorizations. By using the constant
structure of the null space system matrices, a single symbolic factorization in
the Cholesky decomposition is used multiple times, reducing the computational
cost of linear solves. The algorithms and analyses are validated using medium
to large-scale water network models.Comment: 15 pages, 9 figures, Preprint extension of Abraham and Stoianov, 2015
(https://dx.doi.org/10.1061/(ASCE)HY.1943-7900.0001089), September 2015.
Includes extended exposition, additional case studies and new simulations and
analysi
Optimal Placement of Phasor Measurement Units for Power Systems Using Genetic Algorithm
Power grids require monitoring to operate with high efficiency while minimizing the chances of having a failure. However, current monitoring scheme which consists of SCADA (Supervisory Control and Data Acquisition), accompanied with conventional meters distributed throughout the grid, is no longer sufficient to maintain an acceptable operation of the grid. This is evident from the multiple failures and blackouts that happened and are still happening in grids worldwide. This issue became more severe due to systems being operated near their limits (to reduce costs and due to the increase in electricity demands), as well as, the addition of renewable energy sources, which usually have abrupt changes. Smart grids were introduced as a solution to this issue by the inclusion of Wide Area Monitoring System (WAMS), which is mainly based on Phasor Measurement Units (PMU), which are measurement devices that provides synchronized time stamped measurements with high sending rate which significantly improves the monitoring of the grid. However, PMUs are relatively expensive (considering both direct and indirect costs incurred). Thus, it is desired to know the minimum number of PMUs required for achieving certain monitoring criteria. Thus, Optimal PMU Placement (OPP) formulates an optimization problem to solve this issue. In the literature of OPP, multiple objectives and constraints are considered, based on desired criteria. In this thesis, a review of OPP is made, followed by the application of selected algorithms (Integer Linear Programming and Genetic Algorithm) on various test systems as a verification and then applying it to Qatar Grid, to compare between different considerations as well as gain insight about the possible PMU placements for Qatar Grid. The contribution of this thesis is introducing a modified fitness function for the Genetic Algorithm that provides more diverse results than previous papers, while incorporating for various considerations like Zero Injection Buses, Conventional Measurements and current branch limit. It also analyzes the results of current branch limit and provides new plots describing their effects
De novo construction of polyploid linkage maps using discrete graphical models
Linkage maps are used to identify the location of genes responsible for
traits and diseases. New sequencing techniques have created opportunities to
substantially increase the density of genetic markers. Such revolutionary
advances in technology have given rise to new challenges, such as creating
high-density linkage maps. Current multiple testing approaches based on
pairwise recombination fractions are underpowered in the high-dimensional
setting and do not extend easily to polyploid species. We propose to construct
linkage maps using graphical models either via a sparse Gaussian copula or a
nonparanormal skeptic approach. Linkage groups (LGs), typically chromosomes,
and the order of markers in each LG are determined by inferring the conditional
independence relationships among large numbers of markers in the genome.
Through simulations, we illustrate the utility of our map construction method
and compare its performance with other available methods, both when the data
are clean and contain no missing observations and when data contain genotyping
errors and are incomplete. We apply the proposed method to two genotype
datasets: barley and potato from diploid and polypoid populations,
respectively. Our comprehensive map construction method makes full use of the
dosage SNP data to reconstruct linkage map for any bi-parental diploid and
polyploid species. We have implemented the method in the R package netgwas.Comment: 25 pages, 7 figure
Multifactorial Evolutionary Algorithm For Clustered Minimum Routing Cost Problem
Minimum Routing Cost Clustered Tree Problem (CluMRCT) is applied in various
fields in both theory and application. Because the CluMRCT is NP-Hard, the
approximate approaches are suitable to find the solution for this problem.
Recently, Multifactorial Evolutionary Algorithm (MFEA) has emerged as one of
the most efficient approximation algorithms to deal with many different kinds
of problems. Therefore, this paper studies to apply MFEA for solving CluMRCT
problems. In the proposed MFEA, we focus on crossover and mutation operators
which create a valid solution of CluMRCT problem in two levels: first level
constructs spanning trees for graphs in clusters while the second level builds
a spanning tree for connecting among clusters. To reduce the consuming
resources, we will also introduce a new method of calculating the cost of
CluMRCT solution. The proposed algorithm is experimented on numerous types of
datasets. The experimental results demonstrate the effectiveness of the
proposed algorithm, partially on large instance
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