Clonal Selection Algorithm (see e.g. http://en.wikipedia.org/wiki/Clonal_Selection_Algorithm). More...

#include <AlgClonalg.h>

Inheritance diagram for Clonalg:

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.
bool	markAntibodies (DemeP deme)
	mark antibodies so the alg can know which clone belongs to which parent Antibody
bool	cloningPhase (StateP state, DemeP deme, std::vector< IndividualP > &clones)
bool	hypermutationPhase (StateP state, DemeP deme, std::vector< IndividualP > &clones)
bool	selectionPhase (StateP state, DemeP deme, std::vector< IndividualP > &clones)
bool	birthPhase (StateP state, DemeP deme, std::vector< IndividualP > &clones)
bool	replacePopulation (StateP state, DemeP deme, std::vector< IndividualP > &clones)
	replace population with the contents of clones vector
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.

Static Protected Member Functions
static bool	sortPopulationByFitness (IndividualP ab1, IndividualP ab2)
	sort vector of antibodies in regards to their fitness
static bool	sortPopulationByParentAndFitness (IndividualP ab1, IndividualP ab2)
	sort vector of antibodies first by their antibody parents and then by their fitness

Protected Attributes
double	ubound
double	lbound
uint	dimension
bool	areGenotypesAdded_
uint	n
	number of antibodies cloned every generation
double	beta
	parameter which determines the number of clones for every antibody
double	c
	mutation parameter
double	d
	fraction of population regenerated every generation
std::string	cloningVersion
	specifies whether to use static or proportional cloning
std::string	selectionScheme
	specifies which selection scheme to use CLONALG1 or CLONALG2
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

Clonal Selection Algorithm (see e.g. http://en.wikipedia.org/wiki/Clonal_Selection_Algorithm).

This CLONALG implements:

cloning Versions:
- static cloning : n of the best antibodies are cloned beta*populationSize times
- proportional cloning: number of clones per antibody is proportional to that ab's fitness
inversely proportional hypermutation : better antibodies are mutated less
selectionSchemes:
- CLONALG1 - at new generation each antibody will be substituded by the best individual of its set of beta*population clones
- CLONALG2 - new generation will be formed by the best (1-d)*populationSize clones ( or all if the number of clones is less than that )
birthPhase: where d * populationSize of new antibodies are randomly created and added to the population for diversification

CLONALG algorithm accepts only a single FloatingPoint genotype. Additionally, if chosen, selectionScheme CLONALG1 adds a FloatingPoint genotype (parentAntibody) to mark which clone came from which antibodies.

Definition at line 24 of file AlgClonalg.h.

Constructor & Destructor Documentation

◆ Clonalg()

Clonalg::Clonalg ( )

Definition at line 7 of file AlgClonalg.cpp.

Member Function Documentation

◆ advanceGeneration()

bool Clonalg::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 125 of file AlgClonalg.cpp.

◆ birthPhase()

bool Clonalg::birthPhase	(	StateP	state,
		DemeP	deme,
		std::vector< IndividualP > &	clones )

Definition at line 275 of file AlgClonalg.cpp.

◆ cloningPhase()

bool Clonalg::cloningPhase	(	StateP	state,
		DemeP	deme,
		std::vector< IndividualP > &	clones )

Definition at line 152 of file AlgClonalg.cpp.

◆ hypermutationPhase()

bool Clonalg::hypermutationPhase	(	StateP	state,
		DemeP	deme,
		std::vector< IndividualP > &	clones )

Definition at line 188 of file AlgClonalg.cpp.

◆ initialize()

bool Clonalg::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 33 of file AlgClonalg.cpp.

◆ markAntibodies()

bool Clonalg::markAntibodies ( DemeP deme )

mark antibodies so the alg can know which clone belongs to which parent Antibody

Definition at line 141 of file AlgClonalg.cpp.

◆ registerParameters()

void Clonalg::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 16 of file AlgClonalg.cpp.

◆ replacePopulation()

bool Clonalg::replacePopulation	(	StateP	state,
		DemeP	deme,
		std::vector< IndividualP > &	clones )

replace population with the contents of clones vector

Definition at line 296 of file AlgClonalg.cpp.

◆ selectionPhase()

bool Clonalg::selectionPhase	(	StateP	state,
		DemeP	deme,
		std::vector< IndividualP > &	clones )

Definition at line 244 of file AlgClonalg.cpp.

◆ sortPopulationByFitness()

bool Clonalg::sortPopulationByFitness	(	IndividualP	ab1,
		IndividualP	ab2 )

inlinestaticprotected

sort vector of antibodies in regards to their fitness

Definition at line 41 of file AlgClonalg.h.

◆ sortPopulationByParentAndFitness()

bool Clonalg::sortPopulationByParentAndFitness	(	IndividualP	ab1,
		IndividualP	ab2 )

inlinestaticprotected

sort vector of antibodies first by their antibody parents and then by their fitness

Definition at line 44 of file AlgClonalg.h.

Member Data Documentation

◆ areGenotypesAdded_

bool Clonalg::areGenotypesAdded_

protected

Definition at line 31 of file AlgClonalg.h.

◆ beta

double Clonalg::beta

protected

parameter which determines the number of clones for every antibody

Definition at line 34 of file AlgClonalg.h.

◆ c

double Clonalg::c

protected

mutation parameter

Definition at line 35 of file AlgClonalg.h.

◆ cloningVersion

std::string Clonalg::cloningVersion

protected

specifies whether to use static or proportional cloning

Definition at line 37 of file AlgClonalg.h.

◆ d

double Clonalg::d

protected

fraction of population regenerated every generation

Definition at line 36 of file AlgClonalg.h.

◆ dimension

uint Clonalg::dimension

protected

Definition at line 30 of file AlgClonalg.h.

◆ lbound

double Clonalg::lbound

protected

Definition at line 29 of file AlgClonalg.h.

◆ n

uint Clonalg::n

protected

number of antibodies cloned every generation

Definition at line 33 of file AlgClonalg.h.

◆ selectionScheme

std::string Clonalg::selectionScheme

protected

specifies which selection scheme to use CLONALG1 or CLONALG2

Definition at line 38 of file AlgClonalg.h.

◆ ubound

double Clonalg::ubound

protected

Definition at line 28 of file AlgClonalg.h.

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

D:/Projekt/ECF/ECF_master/ECF/AlgClonalg.h
D:/Projekt/ECF/ECF_master/ECF/AlgClonalg.cpp

Public Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Clonalg()

Member Function Documentation

◆ advanceGeneration()

◆ birthPhase()

◆ cloningPhase()

◆ hypermutationPhase()

◆ initialize()

◆ markAntibodies()

◆ registerParameters()

◆ replacePopulation()

◆ selectionPhase()

◆ sortPopulationByFitness()

◆ sortPopulationByParentAndFitness()

Member Data Documentation

◆ areGenotypesAdded_

◆ beta

◆ c

◆ cloningVersion

◆ d

◆ dimension

◆ lbound

◆ n

◆ selectionScheme

◆ ubound