intelligence
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Machine learning library written in javascript
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<h1 class="page-title">Source: genetic/population.js</h1>
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<pre class="prettyprint source linenums"><code>var events = require('events');
var utils = require('./../infrastructure/utils');
var selectionStrategies = require('./selectionStrategies');
/**
* Genetic algorithm population
* @constructor
* @param {object} options - Population options
* @param {Individual} options.baseIndividual -
* @property {object} options - Population options
*/
var Population = function (options) {
this.options = options;
this.individuals = null;
this.validateRequiredOptions();
this.setDefaultOptionsIfNotProvided();
this.initialise();
events.EventEmitter.call(this);
return this;
};
utils.inherits(Population, events.EventEmitter);
/**
* Throws an exception if a required option is missing
* @throws An exception is thrown if a required option is missing
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.validateRequiredOptions = function () {
if (!this.options) {
throw "options are required";
} else if (!this.options.baseIndividual) {
throw "option 'baseIndividual' is required";
} else if (!this.options.crossoverStrategy) {
throw "option 'crossoverStrategy' is required";
} else if (!this.options.fitnessFunction) {
throw "options 'fitnessFunction' is required";
}
return this;
};
/**
* Sets default values for options that have not been defined
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.setDefaultOptionsIfNotProvided = function () {
if (!this.options.populationSize) {
this.options.populationSize = 100;
}
if (this.options.crossoverRate === undefined) {
this.options.crossoverRate = 0.75;
}
if (this.options.mutationRate === undefined) {
this.options.mutationRate = 0.2;
}
if (!this.options.tournamentSize) {
this.options.tournamentSize = Math.ceil(this.options.populationSize * 0.05);
}
if (!this.options.selectionStrategy) {
this.options.selectionStrategy = selectionStrategies.tournament;
}
return this;
};
/**
* Creates a randomly generated population of individuals
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.initialise = function () {
this.individuals = [];
for (var i = 0; i < this.options.populationSize; i++) {
this.individuals.push(this.options.baseIndividual.createNew());
}
return this;
};
/**
* Calculates the fitness of each individual where the fitness value is null
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.evaluateFitness = function () {
for (var i = 0; i < this.individuals.length; i++) {
var individual = this.individuals[i];
if (individual.fitness === null) {
individual.fitness = this.options.fitnessFunction(individual);
}
}
return this.filterNanFitness();
};
/**
* Performs crossover using the crossoverStrategy function defined in the population options
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.crossover = function () {
this.evaluateFitness();
var limbo = [];
if (this.options.elitism) {
var elite = this.getFittestIndividuals(this.options.elitism);
for (var i = 0; i < elite.length; i++) {
limbo.push(elite[i].copy());
}
}
while (limbo.length < this.individuals.length) {
var selections = this.options.selectionStrategy(this.individuals, this.options);
if (utils.random() < this.options.crossoverRate) {
var elections = this.options.crossoverStrategy(selections, this.options);
selections = elections;
for (var i = 0; i < selections.length; i++) selections[i].fitness = null;
}
limbo = limbo.concat(selections);
}
this.individuals = limbo;
return this;
};
/**
* Mutates the population based on the mutationRate property in each individuals options
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.mutate = function () {
this.evaluateFitness();
var elite = this.options.elitism ? this.getFittestIndividuals(this.options.elitism) : null;
for (var i = 0; i < this.individuals.length; i++) {
if (!elite || elite.indexOf(this.individuals[i]) === -1) {
if (utils.random() < this.options.mutationRate) {
this.individuals[i].mutate();
}
}
}
return this;
};
/**
* Returns a specified number of individuals with the best fitness rating in the population
* @param {number} [numIndividuals=1] - The number of individuals to return
* @returns {Individual[]} An array of the fittest individuals in the population
*/
Population.prototype.getFittestIndividuals = function (numIndividuals) {
this.evaluateFitness();
var self = this;
this.evaluateFitness();
if (!numIndividuals) numIndividuals = 1;
return this.individuals.sort(function (a, b) {
if (a.fitness === null && b.fitness === null) {
return 0;
} else if (a.fitness === null) {
return -1;
} else if (b.fitness === null) {
return 1;
} else {
return self.options.isMinimise ? a.fitness - b.fitness : b.fitness - a.fitness;
}
}).slice(0, numIndividuals);
};
/**
* Calculate the average fitness of all individuals in the population (exluding infinite values)
* @returns {number} Average fitness of the population
*/
Population.prototype.getAverageFitness = function () {
this.evaluateFitness();
var sum = 0;
for (var i = 0; i < this.individuals.length; i++) {
if (isFinite(this.individuals[i].fitness)) {
sum += this.individuals[i].fitness;
}
};
return sum / this.individuals.length;
};
/**
* Applies a single iteration of crossover and mutation to the population
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.step = function () {
return this.evaluateFitness().crossover().mutate().evaluateFitness();
};
/**
* Trains the population over a specified number of generations
* @param {number} numGenerations - The number of generations to train the population over
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.train = function (numGenerations) {
if (numGenerations <= 0) {
throw "'numGenerations' must greater than 0";
} else {
for (var i = 0; i < numGenerations; i++) {
this.step();
this.emit('generationCompleted', this, i);
}
}
this.emit('trainingCompleted', this);
return this;
};
/**
* Subsitutes an individuals fitness to positive or negative infinity if it isNaN
* @returns {Population} Reference to current object for chaining
*/
Population.prototype.filterNanFitness = function () {
var value = this.options.isMinimise ? Number.POSITIVE_INFINITY : Number.NEGATIVE_INFINITY;
for (var i = 0; i < this.individuals.length; i++) {
var individual = this.individuals[i];
if (isNaN(individual.fitness)) {
individual.fitness = value
}
}
return this;
};
exports.Population = Population;</code></pre>
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<h2><a href="index.html">Index</a></h2><h3>Classes</h3><ul><li><a href="Individual.html">Individual</a></li><li><a href="LinearConditionalNode.html">LinearConditionalNode</a></li><li><a href="LinearFunctionNode.html">LinearFunctionNode</a></li><li><a href="LinearGPNode.html">LinearGPNode</a></li><li><a href="LinearIndividual.html">LinearIndividual</a></li><li><a href="Population.html">Population</a></li><li><a href="RegisterReference.html">RegisterReference</a></li><li><a href="RegisterSet.html">RegisterSet</a></li></ul><h3>Global</h3><ul><li><a href="global.html#alphabet">alphabet</a></li><li><a href="global.html#arrayEqual">arrayEqual</a></li><li><a href="global.html#binaryNumber">binaryNumber</a></li><li><a href="global.html#binaryString">binaryString</a></li><li><a href="global.html#createCalculation">createCalculation</a></li><li><a href="global.html#createConstant">createConstant</a></li><li><a href="global.html#createInput">createInput</a></li><li><a href="global.html#createOutput">createOutput</a></li><li><a href="global.html#formatString">formatString</a></li><li><a href="global.html#fpEqual">fpEqual</a></li><li><a href="global.html#inherits">inherits</a></li><li><a href="global.html#linearNode">linearNode</a></li><li><a href="global.html#onePointFixed">onePointFixed</a></li><li><a href="global.html#onePointVariable">onePointVariable</a></li><li><a href="global.html#randBetween">randBetween</a></li><li><a href="global.html#random">random</a></li><li><a href="global.html#randomNumber">randomNumber</a></li><li><a href="global.html#rank">rank</a></li><li><a href="global.html#rouletteWheel">rouletteWheel</a></li><li><a href="global.html#selectRandom">selectRandom</a></li><li><a href="global.html#swapGenes">swapGenes</a></li><li><a href="global.html#tournament">tournament</a></li><li><a href="global.html#twoPointFixed">twoPointFixed</a></li><li><a href="global.html#twoPointVariable">twoPointVariable</a></li><li><a href="global.html#uniform">uniform</a></li><li><a href="global.html#validateFixedLength">validateFixedLength</a></li><li><a href="global.html#validateMinimumLength">validateMinimumLength</a></li><li><a href="global.html#validateVariableLength">validateVariableLength</a></li></ul>
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