/// <summary>
/// Create and return a SteadyStateNeatEvolutionAlgorithm object (specific to fitness-based evaluations) ready for
/// running the
/// NEAT algorithm/search based on the given genome factory and genome list. Various sub-parts of the algorithm are
/// also constructed and connected up.
/// </summary>
/// <param name="genomeFactory">The genome factory from which to generate new genomes</param>
/// <param name="genomeList">The current genome population</param>
/// <param name="startingEvaluations">The number of evaluations that have been executed prior to the current run.</param>
/// <returns>Constructed evolutionary algorithm</returns>
public override INeatEvolutionAlgorithm<NeatGenome> CreateEvolutionAlgorithm(
IGenomeFactory<NeatGenome> genomeFactory,
List<NeatGenome> genomeList, ulong startingEvaluations)
{
FileDataLogger logger = null;
// Create distance metric. Mismatched genes have a fixed distance of 10; for matched genes the distance is their weigth difference.
IDistanceMetric distanceMetric = new ManhattanDistanceMetric(1.0, 0.0, 10.0);
ISpeciationStrategy<NeatGenome> speciationStrategy =
new ParallelKMeansClusteringStrategy<NeatGenome>(distanceMetric, ParallelOptions);
// Create complexity regulation strategy.
var complexityRegulationStrategy =
ExperimentUtils.CreateComplexityRegulationStrategy(ComplexityRegulationStrategy, Complexitythreshold);
// Initialize the logger
if (_generationalLogFile != null)
{
logger =
new FileDataLogger(_generationalLogFile);
}
// Create the evolution algorithm.
var ea = new SteadyStateNeatEvolutionAlgorithm<NeatGenome>(NeatEvolutionAlgorithmParameters,
speciationStrategy, complexityRegulationStrategy, _batchSize, _populationEvaluationFrequency,
RunPhase.Primary, logger);
// Create IBlackBox evaluator.
var mazeNavigationEvaluator = new MazeNavigationMCNSEvaluator(MaxDistanceToTarget, MaxTimesteps,
MazeVariant,
MinSuccessDistance, _behaviorCharacterizationFactory);
// Create genome decoder.
var genomeDecoder = CreateGenomeDecoder();
// Create a novelty archive.
AbstractNoveltyArchive<NeatGenome> archive =
new BehavioralNoveltyArchive<NeatGenome>(_archiveAdditionThreshold,
_archiveThresholdDecreaseMultiplier, _archiveThresholdIncreaseMultiplier,
_maxGenerationArchiveAddition, _maxGenerationsWithoutArchiveAddition);
// IGenomeEvaluator<NeatGenome> fitnessEvaluator =
// new SerialGenomeBehaviorEvaluator<NeatGenome, IBlackBox>(genomeDecoder, mazeNavigationEvaluator,
// _nearestNeighbors, archive);
IGenomeEvaluator<NeatGenome> fitnessEvaluator =
new ParallelGenomeBehaviorEvaluator<NeatGenome, IBlackBox>(genomeDecoder, mazeNavigationEvaluator,
SelectionType.SteadyState,
SearchType.MinimalCriteriaNoveltySearch,
_nearestNeighbors, archive);
// Initialize the evolution algorithm.
ea.Initialize(fitnessEvaluator, genomeFactory, genomeList, 0, MaxEvaluations, archive);
// Finished. Return the evolution algorithm
return ea;
}
/// <summary>
/// Create and return a SteadyStateNeatEvolutionAlgorithm object (specific to fitness-based evaluations) ready for
/// running the
/// NEAT algorithm/search based on the given genome factory and genome list. Various sub-parts of the algorithm are
/// also constructed and connected up.
/// </summary>
/// <param name="genomeFactory">The genome factory from which to generate new genomes</param>
/// <param name="genomeList">The current genome population</param>
/// <param name="startingEvaluations">The number of evaluations that have been executed prior to the current run.</param>
/// <returns>Constructed evolutionary algorithm</returns>
public override INeatEvolutionAlgorithm<NeatGenome> CreateEvolutionAlgorithm(
IGenomeFactory<NeatGenome> genomeFactory,
List<NeatGenome> genomeList, ulong startingEvaluations)
{
FileDataLogger logger = null;
// Create distance metric. Mismatched genes have a fixed distance of 10; for matched genes the distance is their weigth difference.
IDistanceMetric distanceMetric = new ManhattanDistanceMetric(1.0, 0.0, 10.0);
ISpeciationStrategy<NeatGenome> speciationStrategy =
new ParallelKMeansClusteringStrategy<NeatGenome>(distanceMetric, ParallelOptions);
// Create complexity regulation strategy.
var complexityRegulationStrategy =
ExperimentUtils.CreateComplexityRegulationStrategy(ComplexityRegulationStrategy, Complexitythreshold);
// Initialize the logger
if (_generationalLogFile != null)
{
logger =
new FileDataLogger(_generationalLogFile);
}
// Create the evolution algorithm.
var ea = new SteadyStateNeatEvolutionAlgorithm<NeatGenome>(NeatEvolutionAlgorithmParameters,
speciationStrategy, complexityRegulationStrategy, _batchSize, _populationEvaluationFrequency,
RunPhase.Primary, logger);
// Create IBlackBox evaluator.
var mazeNavigationEvaluator = new MazeNavigationRandomEvaluator(MaxDistanceToTarget, MaxTimesteps,
MazeVariant, MinSuccessDistance);
// Create genome decoder.
var genomeDecoder = CreateGenomeDecoder();
IGenomeEvaluator<NeatGenome> fitnessEvaluator =
new ParallelGenomeFitnessEvaluator<NeatGenome, IBlackBox>(genomeDecoder, mazeNavigationEvaluator,
ParallelOptions);
// Initialize the evolution algorithm.
ea.Initialize(fitnessEvaluator, genomeFactory, genomeList, null, MaxEvaluations);
// Finished. Return the evolution algorithm
return ea;
}
/// <summary>
/// Creates and returns a GenerationalNeatEvolutionAlgorithm object ready for running the NEAT algorithm/search.
/// Various sub-parts of the algorithm are also constructed and connected up. This overload accepts a pre-built genome
/// population and their associated/parent genome factory.
/// </summary>
/// <param name="genomeFactory">The NEAT genome factory.</param>
/// <param name="genomeList">The initial list of genomes.</param>
/// <returns>The NEAT evolution algorithm.</returns>
public INeatEvolutionAlgorithm<NeatGenome> CreateEvolutionAlgorithm(IGenomeFactory<NeatGenome> genomeFactory,
List<NeatGenome> genomeList)
{
FileDataLogger logger = null;
// Create distance metric. Mismatched genes have a fixed distance of 10; for matched genes the distance is their weigth difference
IDistanceMetric distanceMetric = new ManhattanDistanceMetric(1.0, 0.0, 10.0);
ISpeciationStrategy<NeatGenome> speciationStrategy =
new ParallelKMeansClusteringStrategy<NeatGenome>(distanceMetric, _parallelOptions);
// Create complexity regulation strategy
IComplexityRegulationStrategy complexityRegulationStrategy =
ExperimentUtils.CreateComplexityRegulationStrategy(_complexityRegulationStr, _complexityThreshold);
// Initialize the logger
if (_generationalLogFile != null)
{
logger =
new FileDataLogger(_generationalLogFile);
}
// Create the evolution algorithm
GenerationalNeatEvolutionAlgorithm<NeatGenome> ea =
new GenerationalNeatEvolutionAlgorithm<NeatGenome>(NeatEvolutionAlgorithmParameters, speciationStrategy,
complexityRegulationStrategy, logger);
// Create evalutor
BinaryEvolvedAutoencoderEvaluator evaluator = new BinaryEvolvedAutoencoderEvaluator(_trainingImagesFilename,
InputCount, _numImageSamples, _learningRate, _numBackpropIterations, _trainingSampleProportion);
// Create genome decoder
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder = CreateGenomeDecoder();
// Create a genome list evaluator. This packages up the genome decoder with the genome evaluator
IGenomeEvaluator<NeatGenome> innerFitnessEvaluator =
new ParallelGenomeFitnessEvaluator<NeatGenome, IBlackBox>(genomeDecoder, evaluator, _parallelOptions);
// Wrap the list evaluator in a 'selective' evaulator that will only evaluate new genomes. That is, we skip re-evaluating any genomes
// that were in the population in previous generations (elite genomes). This is determined by examining each genome's evaluation info object.
IGenomeEvaluator<NeatGenome> selectiveFitnessEvaluator = new SelectiveGenomeFitnessEvaluator<NeatGenome>(
innerFitnessEvaluator,
SelectiveGenomeFitnessEvaluator<NeatGenome>.CreatePredicate_OnceOnly());
// Initialize the evolution algorithm
ea.Initialize(selectiveFitnessEvaluator, genomeFactory, genomeList, null);
// Finished. Return the evolution algorithm
return ea;
}
/// <summary>
/// Constructs and returns a NEAT evolution algorithm, using the given genome factory and genome list.
/// </summary>
/// <param name="genomeFactory">The genome factory to use for generating offspring during evolution.</param>
/// <param name="genomeList">The initial list of genomes.</param>
/// <returns>The NEAT evolution algorithm.</returns>
public INeatEvolutionAlgorithm<NeatGenome> CreateEvolutionAlgorithm(IGenomeFactory<NeatGenome> genomeFactory,
List<NeatGenome> genomeList)
{
FileDataLogger logger = null;
// Create distance metric. Mismatched genes have a fixed distance of 10; for matched genes the distance is their weigth difference.
IDistanceMetric distanceMetric = new ManhattanDistanceMetric(1.0, 0.0, 10.0);
ISpeciationStrategy<NeatGenome> speciationStrategy =
new ParallelKMeansClusteringStrategy<NeatGenome>(distanceMetric, _parallelOptions);
// Create complexity regulation strategy.
IComplexityRegulationStrategy complexityRegulationStrategy =
ExperimentUtils.CreateComplexityRegulationStrategy(_complexityRegulationStrategy, _complexityThreshold);
// Initialize the logger
if (_generationalLogFile != null)
{
logger =
new FileDataLogger(_generationalLogFile);
}
// Create the evolution algorithm.
GenerationalNeatEvolutionAlgorithm<NeatGenome> ea =
new GenerationalNeatEvolutionAlgorithm<NeatGenome>(NeatEvolutionAlgorithmParameters,
speciationStrategy, complexityRegulationStrategy, logger);
// Create black box evaluator.
ThreeParityEvaluator evaluator = new ThreeParityEvaluator();
// Create genome decoder. Decodes to a neural network packaged with an activation scheme.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder = CreateGenomeDecoder();
// Create a genome list evaluator. This packages up the genome decoder with the genome evaluator.
IGenomeEvaluator<NeatGenome> innerFitnessEvaluator =
new ParallelGenomeFitnessEvaluator<NeatGenome, IBlackBox>(genomeDecoder, evaluator, _parallelOptions);
// Wrap the list evaluator in a 'selective' evaulator that will only evaluate new genomes. That is, we skip re-evaluating any genomes
// that were in the population in previous generations (elite genomes). This is determiend by examining each genome's evaluation info object.
IGenomeEvaluator<NeatGenome> selectiveFitnessEvaluator = new SelectiveGenomeFitnessEvaluator<NeatGenome>(
innerFitnessEvaluator,
SelectiveGenomeFitnessEvaluator<NeatGenome>.CreatePredicate_OnceOnly());
// Initialize the evolution algorithm.
ea.Initialize(selectiveFitnessEvaluator, genomeFactory, genomeList);
// Finished. Return the evolution algorithm
return ea;
}
/// <summary>
/// Executes all runs of a given experiment using a configuration file as the configuration source and generated flat
/// files as the result destination.
/// </summary>
/// <param name="experimentConfigurationDirectory">The directory containing the XML experiment configuration file.</param>
/// <param name="logFileDirectory">The directory into which to write the evolution/evaluation log files.</param>
/// <param name="experimentName">The name of the experiment to execute.</param>
/// <param name="numRuns">The number of runs to execute for that experiment.</param>
/// <param name="seedPopulationFiles">The seed population XML file names.</param>
/// <param name="writeOrganismStateData">Flag indicating whether organism state data should be written to an output file.</param>
private static void ExecuteFileBasedExperiment(string experimentConfigurationDirectory, string logFileDirectory,
string experimentName,
int numRuns, string[] seedPopulationFiles, bool writeOrganismStateData)
{
// Read in the configuration files that match the given experiment name (should only be 1 file)
string[] experimentConfigurationFiles = Directory.GetFiles(experimentConfigurationDirectory,
string.Format("{0}.*", experimentName));
// Make sure there's only one configuration file that matches the experiment name
// (otherwise, we don't know for sure which configuration to use)
if (experimentConfigurationFiles.Count() != 1)
{
_executionLogger.Error(
string.Format(
"Experiment configuration ambiguous: expeted a single possible configuration, but found {0} possible configurations",
experimentConfigurationFiles.Count()));
Environment.Exit(0);
}
// Instantiate XML reader for configuration file
XmlDocument xmlConfig = new XmlDocument();
xmlConfig.Load(experimentConfigurationFiles[0]);
// Determine which experiment to execute
BaseMazeNavigationExperiment experiment = DetermineMazeNavigationExperiment(xmlConfig.DocumentElement);
// Execute the experiment for the specified number of runs
for (int runIdx = 0; runIdx < numRuns; runIdx++)
{
// Initialize the data loggers for the given run
IDataLogger evolutionDataLogger =
new FileDataLogger(string.Format("{0}\\{1} - Run{2} - Evolution.csv", logFileDirectory,
experimentName,
runIdx + 1));
IDataLogger evaluationDataLogger = writeOrganismStateData
? new FileDataLogger(string.Format("{0}\\{1} - Run{2} - Evaluation.csv", logFileDirectory,
experimentName,
runIdx + 1))
: null;
// Initialize new experiment
experiment.Initialize(experimentName, xmlConfig.DocumentElement, evolutionDataLogger,
evaluationDataLogger);
_executionLogger.Info(string.Format("Initialized experiment {0}.", experiment.GetType()));
// This will hold the number of evaluations executed for each "attempt" of the EA within the current run
ulong curEvaluations = 0;
// This will hold the number of restarts of the algorithm
int curRestarts = 0;
do
{
IGenomeFactory<NeatGenome> genomeFactory;
List<NeatGenome> genomeList;
// If there were seed population files specified, read them in
if (seedPopulationFiles != null)
{
// Open and load population XML file.
using (XmlReader xr = XmlReader.Create(seedPopulationFiles[runIdx]))
{
genomeList = experiment.LoadPopulation(xr);
}
// Grab the specified genome factory on the first genome in the list
genomeFactory = genomeList[0].GenomeFactory;
}
// Otherwise, generate the starting population
else
{
// Create a new genome factory
genomeFactory = experiment.CreateGenomeFactory();
// Generate the initial population
genomeList = genomeFactory.CreateGenomeList(experiment.SeedGenomeCount, 0);
}
_executionLogger.Info(string.Format("Loaded [{0}] genomes as initial population.", genomeList.Count));
_executionLogger.Info("Kicking off Experiment initialization/execution");
// Kick off the experiment run
RunExperiment(genomeFactory, genomeList, experimentName, experiment, numRuns, runIdx, curEvaluations);
// Increment the evaluations
curEvaluations = _ea.CurrentEvaluations;
// Increment the restart count
curRestarts++;
} while (_ea.StopConditionSatisfied == false && experiment.MaxRestarts >= curRestarts);
// Close the data loggers
evolutionDataLogger.Close();
evaluationDataLogger?.Close();
}
}
/// <summary>
/// Executes all runs of a given coevolution experiment using a configuration file as the configuration source and
/// generated flat files as the result destination.
/// </summary>
/// <param name="experimentConfigurationDirectory">The directory containing the XML experiment configuration file.</param>
/// <param name="logFileDirectory">The directory into which to write the evolution/evaluation log files.</param>
/// <param name="seedMazePath">The path to the XML maze genome file or directory containing XML maze genome files.</param>
/// <param name="experimentName">The name of the experiment to execute.</param>
/// <param name="numRuns">The number of runs to execute for that experiment.</param>
/// <param name="startFromRun">The run to start from (1 by default).</param>
private static void ExecuteFileBasedCoevolutionExperiment(string experimentConfigurationDirectory,
string logFileDirectory, string seedMazePath,
string experimentName,
int numRuns, int startFromRun)
{
// Read in the configuration files that match the given experiment name (should only be 1 file)
string[] experimentConfigurationFiles = Directory.GetFiles(experimentConfigurationDirectory,
string.Format("{0}.*", experimentName));
// Make sure there's only one configuration file that matches the experiment name
// (otherwise, we don't know for sure which configuration to use)
if (experimentConfigurationFiles.Count() != 1)
{
_executionLogger.Error(
string.Format(
"Experiment configuration ambiguous: expeted a single possible configuration, but found {0} possible configurations",
experimentConfigurationFiles.Count()));
Environment.Exit(0);
}
// Instantiate XML reader for configuration file
XmlDocument xmlConfig = new XmlDocument();
xmlConfig.Load(experimentConfigurationFiles[0]);
// Determine which experiment to execute
BaseCoevolutionMazeNavigationExperiment experiment =
DetermineCoevolutionMazeNavigationExperiment(xmlConfig.DocumentElement);
// Execute the experiment for the specified number of runs
for (int runIdx = startFromRun; runIdx <= numRuns; runIdx++)
{
// Initialize the data loggers for the given run
IDataLogger navigatorDataLogger =
new FileDataLogger(string.Format("{0}\\{1} - Run{2} - NavigatorEvolution.csv", logFileDirectory,
experimentName,
runIdx));
IDataLogger navigatorGenomesLogger =
new FileDataLogger(string.Format("{0}\\{1} - Run{2} - NavigatorGenomes.csv", logFileDirectory,
experimentName,
runIdx));
IDataLogger mazeDataLogger =
new FileDataLogger(string.Format("{0}\\{1} - Run{2} - MazeEvolution.csv", logFileDirectory,
experimentName,
runIdx));
IDataLogger mazeGenomesLogger =
new FileDataLogger(string.Format("{0}\\{1} - Run{2} - MazeGenomes.csv", logFileDirectory,
experimentName,
runIdx));
// Initialize new experiment
experiment.Initialize(experimentName, xmlConfig.DocumentElement, navigatorDataLogger,
navigatorGenomesLogger, mazeDataLogger, mazeGenomesLogger);
_executionLogger.Info(string.Format("Initialized experiment {0}.", experiment.GetType()));
// If there were seed population files specified, read them in
if (Boolean.Parse(_executionConfiguration[ExecutionParameter.GeneratePopulation]) == false)
{
// TODO: Need to implement ability to load maze seed genomes
throw new NotImplementedException("Currently unable to read in serialized maze genomes.");
}
// Otherwise, generate the starting population
// Create a new agent genome factory
IGenomeFactory<NeatGenome> agentGenomeFactory = experiment.CreateAgentGenomeFactory();
// Create a new maze genome factory
IGenomeFactory<MazeGenome> mazeGenomeFactory = experiment.CreateMazeGenomeFactory();
// Generate the initial agent population
List<NeatGenome> agentGenomeList = agentGenomeFactory.CreateGenomeList(experiment.AgentInitializationGenomeCount,
0);
// Read in the seed population
List<MazeGenome> mazeGenomeList = ExperimentUtils.ReadSeedMazeGenomes(seedMazePath,
(MazeGenomeFactory) mazeGenomeFactory).Take(experiment.MazeSeedGenomeCount).ToList();
// Check for insufficient number of genomes in the seed maze file
if (mazeGenomeList.Count < experiment.MazeSeedGenomeCount)
{
throw new SharpNeatException(
string.Format(
"The maze genome input file contains only {0} genomes while the experiment configuration requires {1} genomes.",
mazeGenomeList.Count, experiment.MazeDefaultPopulationSize));
}
_executionLogger.Info(
string.Format("Loaded [{0}] navigator genomes and [{1}] seed maze genomes as initial populations.",
agentGenomeList.Count, mazeGenomeList.Count));
_executionLogger.Info("Kicking off Experiment initialization/execution");
// Kick off the experiment run
RunExperiment(agentGenomeFactory, mazeGenomeFactory, agentGenomeList, mazeGenomeList, experimentName,
experiment, numRuns, runIdx);
// Close the data loggers
navigatorDataLogger.Close();
navigatorGenomesLogger.Close();
mazeDataLogger.Close();
mazeGenomesLogger.Close();
}
}
/// <summary>
/// Reads the experiment logging configuration.
/// </summary>
/// <param name="xmlConfig">The reference to the XML configuration file.</param>
/// <param name="loggingType">The type of logging (evolution, evaluation, etc.).</param>
/// <param name="parentElementName">The name of the top-level logging configuration element.</param>
/// <returns>A constructed data logger.</returns>
public static IDataLogger ReadDataLogger(XmlElement xmlConfig, LoggingType loggingType, string parentElementName)
{
IDataLogger dataLogger = null;
XmlElement xmlLoggingConfig = null;
int cnt = 0;
// Get root of novelty configuration section
XmlNodeList nodeList = xmlConfig.GetElementsByTagName(parentElementName, "");
// Iterate through the list of logging configurations, finding one that matches the specified logging type
foreach (XmlElement curXmlLoggingConfig in nodeList)
{
if (loggingType ==
LoggingParameterUtils.ConvertStringToLoggingType(XmlUtils.TryGetValueAsString(curXmlLoggingConfig,
"Type")))
{
xmlLoggingConfig = curXmlLoggingConfig;
break;
}
}
// If no appropriate logger was found, just return null (meaning there won't be any logging for this type)
if (xmlLoggingConfig == null) return null;
// Get the logging destination
LoggingDestination loggingDestination =
LoggingParameterUtils.ConvertStringToLoggingDestination(
XmlUtils.TryGetValueAsString(xmlLoggingConfig,
"Destination"));
// Configure a file-based logger
if (LoggingDestination.File == loggingDestination)
{
// Read in the log file name
string logFileName = XmlUtils.TryGetValueAsString(xmlLoggingConfig, "LogFile");
// Instantiate the file data logger
dataLogger = new FileDataLogger(logFileName);
}
else if (LoggingDestination.Database == loggingDestination)
{
// Read in the experiment configuration and run number
string experimentConfigurationName = XmlUtils.TryGetValueAsString(xmlLoggingConfig,
"ExperimentConfigurationName");
if (LoggingType.Evolution == loggingType)
{
// Instantiate the evolution database data logger
dataLogger = new NoveltyExperimentEvaluationEntityDataLogger(experimentConfigurationName);
}
else if (LoggingType.Evaluation == loggingType)
{
// Instantiate the evaluation database data logger
dataLogger = new NoveltyExperimentOrganismStateEntityDataLogger(experimentConfigurationName);
}
}
return dataLogger;
}
