Search Results for "parallel genetic algorithm" - Page 3
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Showing 244 open source projects for "parallel genetic algorithm"
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diauxic growth model ensemble
An ensemble of models showing diauxic growth behavior
...Carbon catabolite repression (CCR) is the main mechanism controlling carbohydrate uptake in bacteria, and therefore also controlling whether or not different carbon sources are metabolized in parallel or sequentially. Although described as a paradigm of the regulation of bacterial metabolism, the underlying mechanisms remain controversial. The models in the ensemble can be categorized according to regulatory, stoichiometric, and physiological constraints and differ from each other on only a single aspect. We distinguish four groups of models: (1) flux balance models that only define reaction kinetics for substrate uptake and by-product excretion, (2) kinetic models without and (3) kinetic models with regulation on the metabolic and/or genetic level, and (4) resource allocation models. -
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CUDA-MEME
Ultrafast scalable motif discovery algorithm using GPU computing
mCUDA-MEME is a well-established ultrafast scalable motif discovery algorithm based on MEME (version 4.4.0) algorithm for multiple GPUs using a hybrid combination of CUDA, MPI and OpenMP parallel programming models. This algorithm is a further extension of CUDA-MEME (based on MEME version 3.5.4) with respect to accuracy and speed and has been tested on a GPU cluster with eight compute nodes and two Fermi-based Tesla S2050 (and Tesla-based Tesla S1070) quad-GPU computing systems, running the Linux OS with the MPICH2 library. ... -
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GAKNN is a data mining software for gene annotation data. GAKNN is built with k- Nearest Neighbour algorithm optimized by the genetic algorithm. Gene annotation datasets saved under .csv or .arff formats with Gene Ontology or FunCat categorization can use GAKNN to predict gene functions.
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GA-tools
general genetic algorithms optimization fortran 95 routines
High level optimization routines in Fortran 95 for optimization problems using a genetic algorithm with elitism, steady-state-reproduction, dynamic operator scoring by merit, no-duplicates-in-population. Chromosome representation may be integer-array, real-array, permutation-array, character-array. Single objective and multi-objective maximization routines are present. Possible to incorporate own crossover and mutation operators exclusively or in addition to standard operators that are included by default. ... -
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Parallel MILC
Parallel decompression for the MILC algorithm
The MILC compression has been developed specifically for medical images and proven to be effective. This algorithm is a parallel version for the decompression phase, meant to exploit the parallel computing potential of the modern hardware. Developed with OpenCL framework (version 1.2), runs on CPU and GPU OpenCL devices. -
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cupSODA
Deterministic simulator of mass-action based models
cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA -
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PhyloPart
automated partition of phylogenetic trees
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. -
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MicroGP
A multi-purpose extensible self-adaptive evolutionary algorithm
MicroGP (µGP, ugp) is a versatile optimizer able to outperform both human experts and conventional heuristics in finding the optimal solution of hard problems. It is an evolutionary algorithm since it mimics some principles of the Neo-Darwinian paradigm. ⚠️ A new version is available on https://github.com/squillero/microgp4 -
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tsp-problem-ga-aco-comparisson
Genetic Algorithm and Ant Colony to solve the TSP problem
This project compares the classical implementation of Genetic Algorithm and Ant Colony Optimization, to solve a TSP problem. It's possible to define the number of cities to visit , and also interactively create new cities to visit in a 2D spatial panel. A total distance is given for AG and ACO solution at end. -
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Opt4J
Modular Java framework for meta-heuristic optimization
Opt4J is an open source Java-based framework for evolutionary computation. It contains a set of (multi-objective) optimization algorithms such as evolutionary algorithms (including SPEA2 and NSGA2), differential evolution, particle swarm optimization, and simulated annealing. The benchmarks that are included comprise ZDT, DTLZ, WFG, and the knapsack problem. The goal of Opt4J is to simplify the evolutionary optimization of user-defined problems as well as the implementation of arbitrary... -
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theoEA_Code
genetic algorithm for optimizing planar optical antennas
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Genetic Programming Classifier is a distributed evolutionary data classification program. It uses the ensemble method implemented under a parallel co-evolutionary Genetic Programming technique.
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Sched-SPM
A C++ schedule generator based on Genetic Algorithm and Hill Climbing
Sched-SPM is a C++ schedule generator for software project staffing and rescheduling based on Genetic Algorithm (GA) and Hill Climbing (HC). This preliminary tool is mainly for academic purpose. It is implemented with GALib (http://lancet.mit.edu/ga/), an open-source toolkit of Genetic Algorithms in various platforms including Unix and Windows. The input and output files of the software are required as XML format. The input file includes tasks' and employees' information according to predefined file format. ... -
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MORO can conveniently analyze the relationship between network modularity and robustness. We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation. In particular, to ensure the robustness algorithm’s applicability to large-scale networks, we implemented it as a parallel algorithm by using the OpenCL library. A batch-mode simulation function was also developed to verify whether an observed relationship between modularity and robustness is conserved in a large set of randomly structured networks. ...
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Parallel Quicksort with MPI
Parallel Quicksort with MPI
...The main aim of this study is to implement the QuickSort algorithm using the Open MPI library and therefore compare the sequential with the parallel execution. -
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GA-EoC
GeneticAlgorithm-based search for Heterogeneous Ensemble Combinations
...To enhance classification performances, we propose an ensemble of classifiers that combine the classification outputs of base classifiers using the simplest and largely used majority voting approach. Instead of creating the ensemble using all base classifiers, we have implemented a genetic algorithm (GA) to search for the best combination from heterogeneous base classifiers. The classification performances achieved by the proposed method method on the chosen datasets are promising. -
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REDHORSE
Software suite for the analysis of haploid hybrids using NGS
...We therefore designed a software suite called REDHORSE that takes genomic alignments as input, extracts meaningful markers and generates MSAs that are the inputs to existing RD algorithms. In addition, REDHORSE implements a custom RD algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is portable and platform independent suite that provides efficient analysis of genetic crosses based on NGS data. -
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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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GeneticAlgorithms
Framework for using the Genetic Algorithms optimization heuristic.
GeneticAlgorithms is a simple and lightweight framework to implement an optimization heuristic following the Genetic Algorithms model. A genetic algorithm mimics the natural processes of evolution, selection and "survival of the fittest". This framework is intuitive and good integrated with Java 1.5 SDK and later. -
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libCudaOptimize
A Parallel Optimization library with CUDA
LibCudaOptimize is a GPU-based open source library that allows you to run state-of-the-art bio-inspired optimization heuristics in parallel to optimize a fitness function, introduce a new optimization algorithm, or easily modify/extend existing ones. -
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CUDA-Quicksort
CUDA-Quicksort: A GPU-based implementation of the quicksort algorithm
CUDA-quicksort is a GPU-based implementation of the quicksort algorithm. CUDA-quicksort is designed to exploit the power computing of modern NVIDIA GPUs. "Two GPU-based implementations of the quicksort were presented in literature: the GPU-quicksort, a compute-unified device architecture (CUDA) iterative implementation, and the CUDA dynamic parallel (CDP) quicksort, a recursive implementation provided by NVIDIA Corporation."[*]. -
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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Java CoreWars Evolver
A Java based, pMars compatible, CoreWars simulator with GA
A Java based, pMars compatible, CoreWars simulator with Genetic Algorithm warrior evolver functionality. Java 8 is needed. See [Wiki:Tutorial] -
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COMRAD-MPI
Compression of Large Genomic Datasets using Parallel Computing
COMRAD-MPI is a parallel computing algorithm for reducing the computational time for compressing the large genomic data sets based on COMRAD algorithm. It captures the long range repeat redundancies in large genomes there by providing a way to compress the large DNA data set. Three stages- Substitution, Clean up and Huffman encoding have been parallelized using message passing library. -
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis.
