Search Results for "parallel genetic algorithm" - Page 3
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Showing 317 open source projects for "parallel genetic algorithm"
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GAVGA
A Genetic Algorithm for Viral Genome Assembly
GAVGA is a Genetic Algorithm for Viral Genome Assembly. It can be used in the assembly of small genomes, like viral ones. -
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UmUTracker
A MATLAB program for 2D particle tracking or 3D DHM based tracking.
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing long video sequences acquired by either light microscopy or digital holography microscopy (DHM). Our program finds the 2D particle center position using an isosceles triangle transform and the axial position by a fast implementation of Rayleigh-Sommerfeld numerical reconstruction algorithm using a one dimensional radial intensity profile. *Updates v1.1: 2017/11/21- Bug... -
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Recursive Directory Removal
Recursive Directory Removal
https://github.com/mhisoft/rdpro -
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CUBiBit
Tool to search binary biclusters on CUDA-enabled GPUs
...It is able to exploit the parallel capabilities of manycore NVIDIA GPUS. It also makes use of C++11 multithreading support to accelerate one phase of the algorithm on several CPU cores. -
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Solid Python
A comprehensive gradient-free optimization framework written in Python
Solid is a Python framework for gradient-free optimization. It contains basic versions of many of the most common optimization algorithms that do not require the calculation of gradients, and allows for very rapid development using them. -
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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
...By default, the class "GeneticCode" generates alternative genetic codes, with the reqirement of block structure, and, optionally, with the assumption of stereochemical or biosynthetic models (to impose the assumption of the adaptive model, simply filter the codes using the error_cost() function). See Appendix in Makukov & shCherbak (2017) for the description of the algorithm. The code requires Qt 5. -
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Swift AI
The Swift machine learning library
Swift AI is a high-performance deep learning library written entirely in Swift. We currently offer support for all Apple platforms, with Linux support coming soon. Swift AI includes a collection of common tools used for artificial intelligence and scientific applications. A flexible, fully-connected neural network with support for deep learning. Optimized specifically for Apple hardware, using advanced parallel processing techniques. We've created some example projects to demonstrate the... -
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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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Sched-Resched
A C++ schedule generator based on Genetic Algorithm and Hill Climbing
Sched-Sched is a C++ schedule generator for software project staffing and rescheduling based on Genetic Algorithm (GA) and Hill Climbing (HC). 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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theoEA_Code
genetic algorithm for optimizing planar optical antennas
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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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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.
