Generational algorithm with roulette wheel selection operator and unique operators and chromosome representation. More...

#include <AlgGEP.h>

Inheritance diagram for AlgGEP:

Public Member Functions
void	registerParameters (StateP state)
	Register algorithm's parameters (if any).
bool	initialize (StateP state)
	Initialize the algorithm, read parameters from the system, do a sanity check.
bool	advanceGeneration (StateP state, DemeP deme)
	Perform a single generation on a single deme.
void	invert (StateP state, const std::vector< IndividualP > &pool)
void	invertDc (StateP state, const std::vector< IndividualP > &pool)
void	transpose (StateP state, const std::vector< IndividualP > &pool)
void	transposeIS (StateP state, const std::vector< IndividualP > &pool)
void	transposeRIS (StateP state, const std::vector< IndividualP > &pool)
void	transposeGene (StateP state, const std::vector< IndividualP > &pool)
void	transposeDc (StateP state, const std::vector< IndividualP > &pool)
Public Member Functions inherited from Algorithm
std::string	getName ()
	Get algorithm name. Each algorithm is uniquely identified with its name.
virtual bool	isParallel ()
	Is algorithm parallel (false by default for all algorithms not inheriting ParallelAlgorithm class).
bool	isImplicitParallel ()
	Is algorithm run in implicit parallel mode (in development, see tutorial).
virtual bool	initializePopulation (StateP)
	Evaluate initial population (called by State::run before evolution starts).
virtual void	read ()
virtual bool	advanceGeneration (StateP state)
	Perform one generation of the algorithm on the whole population.
void	evaluate (IndividualP ind)
	Helper function: evaluate an individual.
uint	mutate (const std::vector< IndividualP > &pool)
	Helper function: send a vector of individuals to mutation.
uint	mutate (const IndividualP victim)
	Helper function: send a single individual to mutation.
void	replaceWith (IndividualP oldInd, IndividualP newInd)
	Helper function: replace an individual in current deme.
void	replaceWith (uint oldIndId, IndividualP newInd)
	Helper function: replace an individual at given position in current deme.
void	registerParallelParameters (StateP state)
	used only in parallel ECF
bool	initializeParallel (StateP state)
	used only in parallel ECF
virtual bool	advanceGeneration (StateP state)
	Parallel ECF: Perform one generation of the algorithm.
virtual void	bcastTermination (StateP state)
	Parallel ECF: broadcast termination to worker processes.
void	registerParallelParameters (StateP state)
	Parallel ECF: Register parameters for implicit parallel algorithm version.
bool	initializeParallel (StateP state)
	Parallel ECF: Initialize implicit parallel algorithm.
void	initializeImplicit (StateP state)
	Parallel ECF: Initialize implicit parallel mode.
bool	implicitParallelOperate (StateP state)
	Parallel ECF: Worker processes in implicit parallel algorithm.
void	evaluate (IndividualP ind)
	Parallel ECF: evaluate an individual.
void	implicitEvaluate (IndividualP ind)
	Parallel ECF: implicitly evaluate an individual (store for later evaluation in implicit parallel version).
uint	mutate (const IndividualP victim)
	Parallel ECF: immediately mutate an individual.
uint	mutate (const std::vector< IndividualP > &pool)
	Parallel ECF: mutate a vector of individuals.
uint	implicitMutate (IndividualP ind)
	Parallel ECF: implicitly mutate an individual (store for later mutation in implicit parallel version).
void	replaceWith (IndividualP oldInd, IndividualP newInd)
	Parallel ECF: replace an individual in a deme.
void	replaceWith (uint oldIndId, IndividualP newInd)
	Parallel ECF: replace an individual at given position in a deme.
bool	mate (IndividualP p1, IndividualP p2, IndividualP child)
	Helper function: crossover two individuals.
IndividualP	copy (IndividualP source)
	Helper function: make a copy of an individual.
bool	removeFrom (IndividualP victim, std::vector< IndividualP > &pool)
	Helper function: remove victim from pool of individual pointers.
bool	isMember (IndividualP single, std::vector< IndividualP > &pool)
	Helper function: check if individual is in the pool.

Protected Attributes
double	crxRate_
	crossover rate
double	selPressure_
	selection pressure
double	invRate_
	inversion rate
double	invDcRate_
	Constant domain inversion rate.
double	invMaxLength_
	inversion maximum sequence length
double	transISRate_
	IS transposition rate.
double	transRISRate_
	RIS transposition rate.
double	transGeneRate_
	gene transposition rate
double	transDcRate_
	constant domain transposition rate
double	transMaxLength_
	maximum sequence transposition length
SelRandomOpP	selRandomOp
SelBestOpP	selBestOp
SelFitnessProportionalOpP	selFitPropOp
Protected Attributes inherited from Algorithm
DemeP	activeDeme_
std::string	name_
	algorithm name
bool	bImplicitParallel_
	implicit parallel flag
std::vector< SelectionOperatorP >	selectionOp
	sel. operators used by algorithm
std::vector< IndividualP >	requests_
std::vector< IndividualP >	stored_
	individual vectors for implicit evaluation
std::vector< uint >	requestIds_
	individual indexes for implicit evaluation
std::vector< IndividualP >	demeCopy_
std::vector< IndividualP >	myJob_
	worker's individual vector
CommunicatorP	comm_
uint	jobSize_
uint	totalEvaluations_
uint	wastedEvaluations_
bool	bImplicitEvaluation_
	implicit evaluation flag
bool	bImplicitMutation_
	implicit mutation flag
bool	bSynchronized_
	is implicit paralelization synchronous
SelectionOperatorP	selBestOp
std::vector< IndividualP >	requestsMut_
std::vector< IndividualP >	receivedMut_
	individual vectors for implicit mutation
std::vector< uint >	requestMutIds_
	individual indexes for implicit mutation
IndividualP	currentBest_
std::vector< IndividualP >	storedInds_
std::vector< std::vector< IndividualP > >	sentInds_
	individuals sent for evaluation
std::vector< bool >	isConsistent_
	is individual (genotype-fitness pair) consistent

Additional Inherited Members
Public Attributes inherited from Algorithm
CrossoverP	crossover_
	sptr to container of crossover operators (set by the system)
MutationP	mutation_
	sptr to container of mutation operators (set by the system)
EvaluateOpP	evalOp_
	sptr to evaluation operator (set by the system)
StateP	state_
Protected Member Functions inherited from Algorithm
bool	registerParameter (StateP state, std::string name, voidP value, enum ECF::type T, std::string description="")
	Helper function: register a single parameter with the system.
voidP	getParameterValue (StateP state, std::string name)
	Helper function: get parameter value from the system.
void	storeIndividual (IndividualP)
	stores the individual (if it is consistent), resets consistency flag
void	storeGenotypes (std::vector< IndividualP > &)
	adds genotypes of individuals to 'sent' repository
void	setConsistency (IndividualP)
	denotes current individual as consistent
void	restoreIndividuals (std::vector< uint >)
	restores individuals whose fitness is received
void	restorePopulation ()
	restores inconsistent individuals to last consistent state

Detailed Description

Generational algorithm with roulette wheel selection operator and unique operators and chromosome representation.

This algorithm requires one GEPChromosome genotype.

The algorithm flow:

single generation {
select individuals to form the new generation (fitness proportional selection operator);
create new generation (make copies);
noCrx = (deme size) * <crxRate_> / 2;
repeat(<noCrx> times) {
randomly select two parents;
perform crossover, _replace_ parents with their children;
}
perform mutation on new generation;
perform transposition on new generation;
perform inversion on new generation
}

Definition at line 35 of file AlgGEP.h.

Constructor & Destructor Documentation

◆ AlgGEP()

AlgGEP::AlgGEP ( )

Definition at line 4 of file AlgGEP.cpp.

Member Function Documentation

◆ advanceGeneration()

bool AlgGEP::advanceGeneration	(	StateP	state,
		DemeP	deme )

virtual

Perform a single generation on a single deme.

Must be implemented by a specific algorithm class

Implements Algorithm.

Definition at line 74 of file AlgGEP.cpp.

◆ initialize()

bool AlgGEP::initialize ( StateP state )

virtual

Initialize the algorithm, read parameters from the system, do a sanity check.

Called by the system before the algorithm starts (Algorithm::advanceGeneration)

Reimplemented from Algorithm.

Definition at line 27 of file AlgGEP.cpp.

◆ invert()

void AlgGEP::invert	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 143 of file AlgGEP.cpp.

◆ invertDc()

void AlgGEP::invertDc	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 191 of file AlgGEP.cpp.

◆ registerParameters()

void AlgGEP::registerParameters ( StateP state )

virtual

Register algorithm's parameters (if any).

Called by the system before algorithm initialization (Algorithm::initialize)

Reimplemented from Algorithm.

Definition at line 12 of file AlgGEP.cpp.

◆ transpose()

void AlgGEP::transpose	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 246 of file AlgGEP.cpp.

◆ transposeDc()

void AlgGEP::transposeDc	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 417 of file AlgGEP.cpp.

◆ transposeGene()

void AlgGEP::transposeGene	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 376 of file AlgGEP.cpp.

◆ transposeIS()

void AlgGEP::transposeIS	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 255 of file AlgGEP.cpp.

◆ transposeRIS()

void AlgGEP::transposeRIS	(	StateP	state,
		const std::vector< IndividualP > &	pool )

Definition at line 312 of file AlgGEP.cpp.

Member Data Documentation

◆ crxRate_

double AlgGEP::crxRate_

protected

crossover rate

Definition at line 50 of file AlgGEP.h.

◆ invDcRate_

double AlgGEP::invDcRate_

protected

Constant domain inversion rate.

Definition at line 53 of file AlgGEP.h.

◆ invMaxLength_

double AlgGEP::invMaxLength_

protected

inversion maximum sequence length

Definition at line 54 of file AlgGEP.h.

◆ invRate_

double AlgGEP::invRate_

protected

inversion rate

Definition at line 52 of file AlgGEP.h.

◆ selBestOp

SelBestOpP AlgGEP::selBestOp

protected

Definition at line 62 of file AlgGEP.h.

◆ selFitPropOp

SelFitnessProportionalOpP AlgGEP::selFitPropOp

protected

Definition at line 63 of file AlgGEP.h.

◆ selPressure_

double AlgGEP::selPressure_

protected

selection pressure

Definition at line 51 of file AlgGEP.h.

◆ selRandomOp

SelRandomOpP AlgGEP::selRandomOp

protected

Definition at line 61 of file AlgGEP.h.

◆ transDcRate_

double AlgGEP::transDcRate_

protected

constant domain transposition rate

Definition at line 58 of file AlgGEP.h.

◆ transGeneRate_

double AlgGEP::transGeneRate_

protected

gene transposition rate

Definition at line 57 of file AlgGEP.h.

◆ transISRate_

double AlgGEP::transISRate_

protected

IS transposition rate.

Definition at line 55 of file AlgGEP.h.

◆ transMaxLength_

double AlgGEP::transMaxLength_

protected

maximum sequence transposition length

Definition at line 59 of file AlgGEP.h.

◆ transRISRate_

double AlgGEP::transRISRate_

protected

RIS transposition rate.

Definition at line 56 of file AlgGEP.h.

The documentation for this class was generated from the following files:

D:/Projekt/ECF/ECF_master/ECF/gep/AlgGEP.h
D:/Projekt/ECF/ECF_master/ECF/gep/AlgGEP.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AlgGEP()

Member Function Documentation

◆ advanceGeneration()

◆ initialize()

◆ invert()

◆ invertDc()

◆ registerParameters()

◆ transpose()

◆ transposeDc()

◆ transposeGene()

◆ transposeIS()

◆ transposeRIS()

Member Data Documentation

◆ crxRate_

◆ invDcRate_

◆ invMaxLength_

◆ invRate_

◆ selBestOp

◆ selFitPropOp

◆ selPressure_

◆ selRandomOp

◆ transDcRate_

◆ transGeneRate_

◆ transISRate_

◆ transMaxLength_

◆ transRISRate_