Commits

Piotr Jessa  committed b01c89a

Moving with implmentation to mgr-test-12x

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  • Parent commits 075f8e2

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Files changed (29)

File resources/benchmarks/mgr-test12/in-1.properties

+# This is analysis of EDA performance on some koza test cases
+
+# Database connection information
+database = postgresql
+jdbc = jdbc:postgresql://localhost/mgr-test-12?user=dzess&password=qwerty
+
+# What experiments are to be done and with what class (use the typical run configuration provider)
+configuration = pl.put.gi.running.universal.RunnerConfigurationProvider
+
+# Map of experiments prototype_key = number_of_runs
+
+
+
+

File resources/benchmarks/mgr-test12/params/BOA_Perf_0.params

+# Key: 'Double_Regression_BOA_Perf_0'
+# Description: 'EDA Performance BOA optimal settings'
+# 
+# Exported: 
+# Mon Sep 17 19:26:08 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = pl.put.poznan.eda.SimpleEDABreeder
+breed.exchange-ratio = 1.0
+breed.sampler = pl.put.poznan.eda.boa.multinominal.ShortBOASampler
+breed.updater = pl.put.poznan.eda.boa.multinominal.ShortBOAUpdater
+breed.updater.quality = jbnc.measures.QualityMeasureLC
+breed.updater.search = jbnc.inducers.TANInducer
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza1.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = pl.put.poznan.eda.ModelSubpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.model = pl.put.poznan.eda.boa.multinominal.ShortBOAModel
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.00
+pop.subpop.0.species.pipe = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.0 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/BOA_Perf_1.params

+# Key: 'Double_Regression_BOA_Perf_1'
+# Description: 'EDA Performance BOA optimal settings'
+# 
+# Exported: 
+# Mon Sep 17 19:26:13 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = pl.put.poznan.eda.SimpleEDABreeder
+breed.exchange-ratio = 1.0
+breed.sampler = pl.put.poznan.eda.boa.multinominal.ShortBOASampler
+breed.updater = pl.put.poznan.eda.boa.multinominal.ShortBOAUpdater
+breed.updater.quality = jbnc.measures.QualityMeasureLC
+breed.updater.search = jbnc.inducers.TANInducer
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza2.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = pl.put.poznan.eda.ModelSubpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.model = pl.put.poznan.eda.boa.multinominal.ShortBOAModel
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.00
+pop.subpop.0.species.pipe = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.0 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/BOA_Perf_2.params

+# Key: 'Double_Regression_BOA_Perf_2'
+# Description: 'EDA Performance BOA optimal settings'
+# 
+# Exported: 
+# Mon Sep 17 19:26:18 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = pl.put.poznan.eda.SimpleEDABreeder
+breed.exchange-ratio = 1.0
+breed.sampler = pl.put.poznan.eda.boa.multinominal.ShortBOASampler
+breed.updater = pl.put.poznan.eda.boa.multinominal.ShortBOAUpdater
+breed.updater.quality = jbnc.measures.QualityMeasureLC
+breed.updater.search = jbnc.inducers.TANInducer
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza3.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = pl.put.poznan.eda.ModelSubpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.model = pl.put.poznan.eda.boa.multinominal.ShortBOAModel
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.00
+pop.subpop.0.species.pipe = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.0 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/Classic_Perf_0.params

+# Key: 'Double_Regression_Classic_Perf_0'
+# Description: 'Tree Based Regression, performance set of tests'
+# 
+# Exported: 
+# Mon Sep 17 19:27:26 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breed.reproduce.source.0 = ec.select.TournamentSelection
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = ec.simple.SimpleEvaluator
+eval.problem = pl.put.bi.problem.DoubleRegressionProblem
+eval.problem.data = pl.put.bi.data.DoubleData
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza1.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+gp.adf-stack.context = ec.gp.ADFContext
+gp.fs.0 = ec.gp.GPFunctionSet
+gp.fs.0.func.0 = pl.put.bi.functions.real.X0
+gp.fs.0.func.0.nc = nc0
+gp.fs.0.func.1 = pl.put.bi.functions.real.Zero
+gp.fs.0.func.1.nc = nc0
+gp.fs.0.func.10 = pl.put.bi.functions.real.ProtectedLog
+gp.fs.0.func.10.nc = nc1
+gp.fs.0.func.11 = pl.put.bi.functions.real.Add
+gp.fs.0.func.11.nc = nc2
+gp.fs.0.func.12 = pl.put.bi.functions.real.Sub
+gp.fs.0.func.12.nc = nc2
+gp.fs.0.func.13 = pl.put.bi.functions.real.Mul
+gp.fs.0.func.13.nc = nc2
+gp.fs.0.func.14 = pl.put.bi.functions.real.ProtectedDiv
+gp.fs.0.func.14.nc = nc2
+gp.fs.0.func.15 = pl.put.bi.functions.real.Power
+gp.fs.0.func.15.nc = nc2
+gp.fs.0.func.16 = pl.put.bi.functions.real.Max
+gp.fs.0.func.16.nc = nc2
+gp.fs.0.func.17 = pl.put.bi.functions.real.Min
+gp.fs.0.func.17.nc = nc2
+gp.fs.0.func.2 = pl.put.bi.functions.real.One
+gp.fs.0.func.2.nc = nc0
+gp.fs.0.func.3 = pl.put.bi.functions.real.Two
+gp.fs.0.func.3.nc = nc0
+gp.fs.0.func.4 = pl.put.bi.functions.real.Three
+gp.fs.0.func.4.nc = nc0
+gp.fs.0.func.5 = pl.put.bi.functions.real.Four
+gp.fs.0.func.5.nc = nc0
+gp.fs.0.func.6 = pl.put.bi.functions.real.Five
+gp.fs.0.func.6.nc = nc0
+gp.fs.0.func.7 = pl.put.bi.functions.real.Exp
+gp.fs.0.func.7.nc = nc1
+gp.fs.0.func.8 = pl.put.bi.functions.real.Cos
+gp.fs.0.func.8.nc = nc1
+gp.fs.0.func.9 = pl.put.bi.functions.real.Sin
+gp.fs.0.func.9.nc = nc1
+gp.fs.0.name = f0
+gp.fs.0.size = 18
+gp.fs.size = 1
+gp.koza.grow.max-depth = 5
+gp.koza.grow.min-depth = 5
+gp.koza.half.growp = 0.5
+gp.koza.half.max-depth = 6
+gp.koza.half.min-depth = 2
+gp.koza.mutate.build.0 = ec.gp.koza.GrowBuilder
+gp.koza.mutate.maxdepth = 17
+gp.koza.mutate.ns.0 = ec.gp.koza.KozaNodeSelector
+gp.koza.mutate.source.0 = ec.select.TournamentSelection
+gp.koza.mutate.tries = 1
+gp.koza.ns.nonterminals = 0.9
+gp.koza.ns.root = 0.0
+gp.koza.ns.terminals = 0.1
+gp.koza.xover.maxdepth = 17
+gp.koza.xover.ns.0 = ec.gp.koza.KozaNodeSelector
+gp.koza.xover.ns.1 = same
+gp.koza.xover.source.0 = ec.select.TournamentSelection
+gp.koza.xover.source.1 = same
+gp.koza.xover.tries = 1
+gp.nc.0 = ec.gp.GPNodeConstraints
+gp.nc.0.name = nc0
+gp.nc.0.returns = nil
+gp.nc.0.size = 0
+gp.nc.1 = ec.gp.GPNodeConstraints
+gp.nc.1.child.0 = nil
+gp.nc.1.name = nc1
+gp.nc.1.returns = nil
+gp.nc.1.size = 1
+gp.nc.2 = ec.gp.GPNodeConstraints
+gp.nc.2.child.0 = nil
+gp.nc.2.child.1 = nil
+gp.nc.2.name = nc2
+gp.nc.2.returns = nil
+gp.nc.2.size = 2
+gp.nc.3 = ec.gp.GPNodeConstraints
+gp.nc.3.child.0 = nil
+gp.nc.3.child.1 = nil
+gp.nc.3.child.2 = nil
+gp.nc.3.name = nc3
+gp.nc.3.returns = nil
+gp.nc.3.size = 3
+gp.nc.4 = ec.gp.GPNodeConstraints
+gp.nc.4.child.0 = nil
+gp.nc.4.child.1 = nil
+gp.nc.4.child.2 = nil
+gp.nc.4.child.3 = nil
+gp.nc.4.name = nc4
+gp.nc.4.returns = nil
+gp.nc.4.size = 4
+gp.nc.5 = ec.gp.GPNodeConstraints
+gp.nc.5.child.0 = nil
+gp.nc.5.child.1 = nil
+gp.nc.5.child.2 = nil
+gp.nc.5.child.3 = nil
+gp.nc.5.child.4 = nil
+gp.nc.5.name = nc5
+gp.nc.5.returns = nil
+gp.nc.5.size = 5
+gp.nc.6 = ec.gp.GPNodeConstraints
+gp.nc.6.child.0 = nil
+gp.nc.6.child.1 = nil
+gp.nc.6.child.2 = nil
+gp.nc.6.child.3 = nil
+gp.nc.6.child.4 = nil
+gp.nc.6.child.5 = nil
+gp.nc.6.name = nc6
+gp.nc.6.returns = nil
+gp.nc.6.size = 6
+gp.nc.size = 7
+gp.problem.stack = ec.gp.ADFStack
+gp.tc.0 = ec.gp.GPTreeConstraints
+gp.tc.0.fset = f0
+gp.tc.0.init = ec.gp.koza.HalfBuilder
+gp.tc.0.name = tc0
+gp.tc.0.returns = nil
+gp.tc.size = 1
+gp.type.a.0.name = nil
+gp.type.a.size = 1
+gp.type.s.size = 0
+init = ec.gp.GPInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 100
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.gp.GPSpecies
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.ind = ec.gp.GPIndividual
+pop.subpop.0.species.ind.numtrees = 1
+pop.subpop.0.species.ind.tree.0 = ec.gp.GPTree
+pop.subpop.0.species.ind.tree.0.tc = tc0
+pop.subpop.0.species.pipe = ec.breed.MultiBreedingPipeline
+pop.subpop.0.species.pipe.generate-max = false
+pop.subpop.0.species.pipe.num-sources = 2
+pop.subpop.0.species.pipe.source.0 = ec.gp.koza.CrossoverPipeline
+pop.subpop.0.species.pipe.source.0.prob = 0.9
+pop.subpop.0.species.pipe.source.1 = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.1.prob = 0.1
+pop.subpops = 1
+prefix = ec
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = ec.simple.SimpleEvolutionState

File resources/benchmarks/mgr-test12/params/Classic_Perf_1.params

+# Key: 'Double_Regression_Classic_Perf_1'
+# Description: 'Tree Based Regression, performance set of tests'
+# 
+# Exported: 
+# Mon Sep 17 19:27:31 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breed.reproduce.source.0 = ec.select.TournamentSelection
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = ec.simple.SimpleEvaluator
+eval.problem = pl.put.bi.problem.DoubleRegressionProblem
+eval.problem.data = pl.put.bi.data.DoubleData
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza2.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+gp.adf-stack.context = ec.gp.ADFContext
+gp.fs.0 = ec.gp.GPFunctionSet
+gp.fs.0.func.0 = pl.put.bi.functions.real.X0
+gp.fs.0.func.0.nc = nc0
+gp.fs.0.func.1 = pl.put.bi.functions.real.Zero
+gp.fs.0.func.1.nc = nc0
+gp.fs.0.func.10 = pl.put.bi.functions.real.ProtectedLog
+gp.fs.0.func.10.nc = nc1
+gp.fs.0.func.11 = pl.put.bi.functions.real.Add
+gp.fs.0.func.11.nc = nc2
+gp.fs.0.func.12 = pl.put.bi.functions.real.Sub
+gp.fs.0.func.12.nc = nc2
+gp.fs.0.func.13 = pl.put.bi.functions.real.Mul
+gp.fs.0.func.13.nc = nc2
+gp.fs.0.func.14 = pl.put.bi.functions.real.ProtectedDiv
+gp.fs.0.func.14.nc = nc2
+gp.fs.0.func.15 = pl.put.bi.functions.real.Power
+gp.fs.0.func.15.nc = nc2
+gp.fs.0.func.16 = pl.put.bi.functions.real.Max
+gp.fs.0.func.16.nc = nc2
+gp.fs.0.func.17 = pl.put.bi.functions.real.Min
+gp.fs.0.func.17.nc = nc2
+gp.fs.0.func.2 = pl.put.bi.functions.real.One
+gp.fs.0.func.2.nc = nc0
+gp.fs.0.func.3 = pl.put.bi.functions.real.Two
+gp.fs.0.func.3.nc = nc0
+gp.fs.0.func.4 = pl.put.bi.functions.real.Three
+gp.fs.0.func.4.nc = nc0
+gp.fs.0.func.5 = pl.put.bi.functions.real.Four
+gp.fs.0.func.5.nc = nc0
+gp.fs.0.func.6 = pl.put.bi.functions.real.Five
+gp.fs.0.func.6.nc = nc0
+gp.fs.0.func.7 = pl.put.bi.functions.real.Exp
+gp.fs.0.func.7.nc = nc1
+gp.fs.0.func.8 = pl.put.bi.functions.real.Cos
+gp.fs.0.func.8.nc = nc1
+gp.fs.0.func.9 = pl.put.bi.functions.real.Sin
+gp.fs.0.func.9.nc = nc1
+gp.fs.0.name = f0
+gp.fs.0.size = 18
+gp.fs.size = 1
+gp.koza.grow.max-depth = 5
+gp.koza.grow.min-depth = 5
+gp.koza.half.growp = 0.5
+gp.koza.half.max-depth = 6
+gp.koza.half.min-depth = 2
+gp.koza.mutate.build.0 = ec.gp.koza.GrowBuilder
+gp.koza.mutate.maxdepth = 17
+gp.koza.mutate.ns.0 = ec.gp.koza.KozaNodeSelector
+gp.koza.mutate.source.0 = ec.select.TournamentSelection
+gp.koza.mutate.tries = 1
+gp.koza.ns.nonterminals = 0.9
+gp.koza.ns.root = 0.0
+gp.koza.ns.terminals = 0.1
+gp.koza.xover.maxdepth = 17
+gp.koza.xover.ns.0 = ec.gp.koza.KozaNodeSelector
+gp.koza.xover.ns.1 = same
+gp.koza.xover.source.0 = ec.select.TournamentSelection
+gp.koza.xover.source.1 = same
+gp.koza.xover.tries = 1
+gp.nc.0 = ec.gp.GPNodeConstraints
+gp.nc.0.name = nc0
+gp.nc.0.returns = nil
+gp.nc.0.size = 0
+gp.nc.1 = ec.gp.GPNodeConstraints
+gp.nc.1.child.0 = nil
+gp.nc.1.name = nc1
+gp.nc.1.returns = nil
+gp.nc.1.size = 1
+gp.nc.2 = ec.gp.GPNodeConstraints
+gp.nc.2.child.0 = nil
+gp.nc.2.child.1 = nil
+gp.nc.2.name = nc2
+gp.nc.2.returns = nil
+gp.nc.2.size = 2
+gp.nc.3 = ec.gp.GPNodeConstraints
+gp.nc.3.child.0 = nil
+gp.nc.3.child.1 = nil
+gp.nc.3.child.2 = nil
+gp.nc.3.name = nc3
+gp.nc.3.returns = nil
+gp.nc.3.size = 3
+gp.nc.4 = ec.gp.GPNodeConstraints
+gp.nc.4.child.0 = nil
+gp.nc.4.child.1 = nil
+gp.nc.4.child.2 = nil
+gp.nc.4.child.3 = nil
+gp.nc.4.name = nc4
+gp.nc.4.returns = nil
+gp.nc.4.size = 4
+gp.nc.5 = ec.gp.GPNodeConstraints
+gp.nc.5.child.0 = nil
+gp.nc.5.child.1 = nil
+gp.nc.5.child.2 = nil
+gp.nc.5.child.3 = nil
+gp.nc.5.child.4 = nil
+gp.nc.5.name = nc5
+gp.nc.5.returns = nil
+gp.nc.5.size = 5
+gp.nc.6 = ec.gp.GPNodeConstraints
+gp.nc.6.child.0 = nil
+gp.nc.6.child.1 = nil
+gp.nc.6.child.2 = nil
+gp.nc.6.child.3 = nil
+gp.nc.6.child.4 = nil
+gp.nc.6.child.5 = nil
+gp.nc.6.name = nc6
+gp.nc.6.returns = nil
+gp.nc.6.size = 6
+gp.nc.size = 7
+gp.problem.stack = ec.gp.ADFStack
+gp.tc.0 = ec.gp.GPTreeConstraints
+gp.tc.0.fset = f0
+gp.tc.0.init = ec.gp.koza.HalfBuilder
+gp.tc.0.name = tc0
+gp.tc.0.returns = nil
+gp.tc.size = 1
+gp.type.a.0.name = nil
+gp.type.a.size = 1
+gp.type.s.size = 0
+init = ec.gp.GPInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 100
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.gp.GPSpecies
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.ind = ec.gp.GPIndividual
+pop.subpop.0.species.ind.numtrees = 1
+pop.subpop.0.species.ind.tree.0 = ec.gp.GPTree
+pop.subpop.0.species.ind.tree.0.tc = tc0
+pop.subpop.0.species.pipe = ec.breed.MultiBreedingPipeline
+pop.subpop.0.species.pipe.generate-max = false
+pop.subpop.0.species.pipe.num-sources = 2
+pop.subpop.0.species.pipe.source.0 = ec.gp.koza.CrossoverPipeline
+pop.subpop.0.species.pipe.source.0.prob = 0.9
+pop.subpop.0.species.pipe.source.1 = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.1.prob = 0.1
+pop.subpops = 1
+prefix = ec
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = ec.simple.SimpleEvolutionState

File resources/benchmarks/mgr-test12/params/Classic_Perf_2.params

+# Key: 'Double_Regression_Classic_Perf_2'
+# Description: 'Tree Based Regression, performance set of tests'
+# 
+# Exported: 
+# Mon Sep 17 19:27:42 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breed.reproduce.source.0 = ec.select.TournamentSelection
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = ec.simple.SimpleEvaluator
+eval.problem = pl.put.bi.problem.DoubleRegressionProblem
+eval.problem.data = pl.put.bi.data.DoubleData
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza3.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+gp.adf-stack.context = ec.gp.ADFContext
+gp.fs.0 = ec.gp.GPFunctionSet
+gp.fs.0.func.0 = pl.put.bi.functions.real.X0
+gp.fs.0.func.0.nc = nc0
+gp.fs.0.func.1 = pl.put.bi.functions.real.Zero
+gp.fs.0.func.1.nc = nc0
+gp.fs.0.func.10 = pl.put.bi.functions.real.ProtectedLog
+gp.fs.0.func.10.nc = nc1
+gp.fs.0.func.11 = pl.put.bi.functions.real.Add
+gp.fs.0.func.11.nc = nc2
+gp.fs.0.func.12 = pl.put.bi.functions.real.Sub
+gp.fs.0.func.12.nc = nc2
+gp.fs.0.func.13 = pl.put.bi.functions.real.Mul
+gp.fs.0.func.13.nc = nc2
+gp.fs.0.func.14 = pl.put.bi.functions.real.ProtectedDiv
+gp.fs.0.func.14.nc = nc2
+gp.fs.0.func.15 = pl.put.bi.functions.real.Power
+gp.fs.0.func.15.nc = nc2
+gp.fs.0.func.16 = pl.put.bi.functions.real.Max
+gp.fs.0.func.16.nc = nc2
+gp.fs.0.func.17 = pl.put.bi.functions.real.Min
+gp.fs.0.func.17.nc = nc2
+gp.fs.0.func.2 = pl.put.bi.functions.real.One
+gp.fs.0.func.2.nc = nc0
+gp.fs.0.func.3 = pl.put.bi.functions.real.Two
+gp.fs.0.func.3.nc = nc0
+gp.fs.0.func.4 = pl.put.bi.functions.real.Three
+gp.fs.0.func.4.nc = nc0
+gp.fs.0.func.5 = pl.put.bi.functions.real.Four
+gp.fs.0.func.5.nc = nc0
+gp.fs.0.func.6 = pl.put.bi.functions.real.Five
+gp.fs.0.func.6.nc = nc0
+gp.fs.0.func.7 = pl.put.bi.functions.real.Exp
+gp.fs.0.func.7.nc = nc1
+gp.fs.0.func.8 = pl.put.bi.functions.real.Cos
+gp.fs.0.func.8.nc = nc1
+gp.fs.0.func.9 = pl.put.bi.functions.real.Sin
+gp.fs.0.func.9.nc = nc1
+gp.fs.0.name = f0
+gp.fs.0.size = 18
+gp.fs.size = 1
+gp.koza.grow.max-depth = 5
+gp.koza.grow.min-depth = 5
+gp.koza.half.growp = 0.5
+gp.koza.half.max-depth = 6
+gp.koza.half.min-depth = 2
+gp.koza.mutate.build.0 = ec.gp.koza.GrowBuilder
+gp.koza.mutate.maxdepth = 17
+gp.koza.mutate.ns.0 = ec.gp.koza.KozaNodeSelector
+gp.koza.mutate.source.0 = ec.select.TournamentSelection
+gp.koza.mutate.tries = 1
+gp.koza.ns.nonterminals = 0.9
+gp.koza.ns.root = 0.0
+gp.koza.ns.terminals = 0.1
+gp.koza.xover.maxdepth = 17
+gp.koza.xover.ns.0 = ec.gp.koza.KozaNodeSelector
+gp.koza.xover.ns.1 = same
+gp.koza.xover.source.0 = ec.select.TournamentSelection
+gp.koza.xover.source.1 = same
+gp.koza.xover.tries = 1
+gp.nc.0 = ec.gp.GPNodeConstraints
+gp.nc.0.name = nc0
+gp.nc.0.returns = nil
+gp.nc.0.size = 0
+gp.nc.1 = ec.gp.GPNodeConstraints
+gp.nc.1.child.0 = nil
+gp.nc.1.name = nc1
+gp.nc.1.returns = nil
+gp.nc.1.size = 1
+gp.nc.2 = ec.gp.GPNodeConstraints
+gp.nc.2.child.0 = nil
+gp.nc.2.child.1 = nil
+gp.nc.2.name = nc2
+gp.nc.2.returns = nil
+gp.nc.2.size = 2
+gp.nc.3 = ec.gp.GPNodeConstraints
+gp.nc.3.child.0 = nil
+gp.nc.3.child.1 = nil
+gp.nc.3.child.2 = nil
+gp.nc.3.name = nc3
+gp.nc.3.returns = nil
+gp.nc.3.size = 3
+gp.nc.4 = ec.gp.GPNodeConstraints
+gp.nc.4.child.0 = nil
+gp.nc.4.child.1 = nil
+gp.nc.4.child.2 = nil
+gp.nc.4.child.3 = nil
+gp.nc.4.name = nc4
+gp.nc.4.returns = nil
+gp.nc.4.size = 4
+gp.nc.5 = ec.gp.GPNodeConstraints
+gp.nc.5.child.0 = nil
+gp.nc.5.child.1 = nil
+gp.nc.5.child.2 = nil
+gp.nc.5.child.3 = nil
+gp.nc.5.child.4 = nil
+gp.nc.5.name = nc5
+gp.nc.5.returns = nil
+gp.nc.5.size = 5
+gp.nc.6 = ec.gp.GPNodeConstraints
+gp.nc.6.child.0 = nil
+gp.nc.6.child.1 = nil
+gp.nc.6.child.2 = nil
+gp.nc.6.child.3 = nil
+gp.nc.6.child.4 = nil
+gp.nc.6.child.5 = nil
+gp.nc.6.name = nc6
+gp.nc.6.returns = nil
+gp.nc.6.size = 6
+gp.nc.size = 7
+gp.problem.stack = ec.gp.ADFStack
+gp.tc.0 = ec.gp.GPTreeConstraints
+gp.tc.0.fset = f0
+gp.tc.0.init = ec.gp.koza.HalfBuilder
+gp.tc.0.name = tc0
+gp.tc.0.returns = nil
+gp.tc.size = 1
+gp.type.a.0.name = nil
+gp.type.a.size = 1
+gp.type.s.size = 0
+init = ec.gp.GPInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 100
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.gp.GPSpecies
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.ind = ec.gp.GPIndividual
+pop.subpop.0.species.ind.numtrees = 1
+pop.subpop.0.species.ind.tree.0 = ec.gp.GPTree
+pop.subpop.0.species.ind.tree.0.tc = tc0
+pop.subpop.0.species.pipe = ec.breed.MultiBreedingPipeline
+pop.subpop.0.species.pipe.generate-max = false
+pop.subpop.0.species.pipe.num-sources = 2
+pop.subpop.0.species.pipe.source.0 = ec.gp.koza.CrossoverPipeline
+pop.subpop.0.species.pipe.source.0.prob = 0.9
+pop.subpop.0.species.pipe.source.1 = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.1.prob = 0.1
+pop.subpops = 1
+prefix = ec
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = ec.simple.SimpleEvolutionState

File resources/benchmarks/mgr-test12/params/Push_Perf_0.params

+# Key: 'Double_Regression_Psh_Perf_0'
+# Description: 'EDA performance testing - control group'
+# 
+# Exported: 
+# Mon Sep 17 19:27:56 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza1.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-prob = 1.0
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.0
+pop.subpop.0.species.pipe = ec.vector.breed.VectorMutationPipeline
+pop.subpop.0.species.pipe.source.0 = ec.vector.breed.VectorCrossoverPipeline
+pop.subpop.0.species.pipe.source.0.source.0 = ec.select.TournamentSelection
+pop.subpop.0.species.pipe.source.0.source.1 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/Push_Perf_1.params

+# Key: 'Double_Regression_Psh_Perf_1'
+# Description: 'EDA performance testing - control group'
+# 
+# Exported: 
+# Mon Sep 17 19:28:02 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza2.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-prob = 1.0
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.0
+pop.subpop.0.species.pipe = ec.vector.breed.VectorMutationPipeline
+pop.subpop.0.species.pipe.source.0 = ec.vector.breed.VectorCrossoverPipeline
+pop.subpop.0.species.pipe.source.0.source.0 = ec.select.TournamentSelection
+pop.subpop.0.species.pipe.source.0.source.1 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/Push_Perf_2.params

+# Key: 'Double_Regression_Psh_Perf_2'
+# Description: 'EDA performance testing - control group'
+# 
+# Exported: 
+# Mon Sep 17 19:28:08 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza3.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-prob = 1.0
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.0
+pop.subpop.0.species.pipe = ec.vector.breed.VectorMutationPipeline
+pop.subpop.0.species.pipe.source.0 = ec.vector.breed.VectorCrossoverPipeline
+pop.subpop.0.species.pipe.source.0.source.0 = ec.select.TournamentSelection
+pop.subpop.0.species.pipe.source.0.source.1 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/Push_Pure_Perf_0.params

+# Key: 'Double_Regression_Psh_Pure_Perf_0'
+# Description: 'Performance of eda - control gropu experiment'
+# 
+# Exported: 
+# Mon Sep 17 19:26:55 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breed.reproduce.source.0 = ec.select.TournamentSelection
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.regression.psh.ClassicDoublePshRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza1.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.size = 200
+pop.subpop.0.species = org.ecj.psh.PshSpecies
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.ind = org.ecj.psh.PshIndividual
+pop.subpop.0.species.pipe = ec.breed.MultiBreedingPipeline
+pop.subpop.0.species.pipe.generate-max = false
+pop.subpop.0.species.pipe.num-sources = 4
+pop.subpop.0.species.pipe.source.0 = org.ecj.psh.breed.PshCrossover
+pop.subpop.0.species.pipe.source.0.prob = 0.70
+pop.subpop.0.species.pipe.source.1 = org.ecj.psh.breed.PshMutation
+pop.subpop.0.species.pipe.source.1.prob = 0.20
+pop.subpop.0.species.pipe.source.2 = org.ecj.psh.breed.PshSimplification
+pop.subpop.0.species.pipe.source.2.prob = 0.05
+pop.subpop.0.species.pipe.source.3 = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.3.prob = 0.05
+pop.subpops = 1
+prefix = psh
+psh.breed.one-point-xover.source.0 = ec.select.TournamentSelection
+psh.breed.one-point-xover.source.1 = same
+psh.breed.one-point-xover.toss = true
+psh.breed.psh-mutate.fair-mutation-range = 0.50
+psh.breed.psh-mutate.source.0 = ec.select.TournamentSelection
+psh.breed.psh-mutate.use-fair = true
+psh.breed.psh-simplify.flatten-prob = 0.20
+psh.breed.psh-simplify.source.0 = ec.select.TournamentSelection
+psh.breed.psh-simplify.steps = 20
+psh.breed.psh-xover.source.0 = ec.select.TournamentSelection
+psh.breed.psh-xover.source.1 = same
+psh.breed.psh-xover.toss = true
+psh.breed.two-point-xover.source.0 = ec.select.TournamentSelection
+psh.breed.two-point-xover.source.1 = same
+psh.breed.two-point-xover.toss = true
+psh.ideal-threshold = 0.1
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 100
+psh.interpreter.generate-flat = true
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/pure-instructions.txt
+psh.interpreter.max-points-in-program = 50
+psh.interpreter.max-random-code-size = 30
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 1.00
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = org.ecj.psh.PshShortStatistics
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/Push_Pure_Perf_1.params

+# Key: 'Double_Regression_Psh_Pure_Perf_1'
+# Description: 'Performance of eda - control gropu experiment'
+# 
+# Exported: 
+# Mon Sep 17 19:27:01 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breed.reproduce.source.0 = ec.select.TournamentSelection
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.regression.psh.ClassicDoublePshRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza2.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.size = 200
+pop.subpop.0.species = org.ecj.psh.PshSpecies
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.ind = org.ecj.psh.PshIndividual
+pop.subpop.0.species.pipe = ec.breed.MultiBreedingPipeline
+pop.subpop.0.species.pipe.generate-max = false
+pop.subpop.0.species.pipe.num-sources = 4
+pop.subpop.0.species.pipe.source.0 = org.ecj.psh.breed.PshCrossover
+pop.subpop.0.species.pipe.source.0.prob = 0.70
+pop.subpop.0.species.pipe.source.1 = org.ecj.psh.breed.PshMutation
+pop.subpop.0.species.pipe.source.1.prob = 0.20
+pop.subpop.0.species.pipe.source.2 = org.ecj.psh.breed.PshSimplification
+pop.subpop.0.species.pipe.source.2.prob = 0.05
+pop.subpop.0.species.pipe.source.3 = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.3.prob = 0.05
+pop.subpops = 1
+prefix = psh
+psh.breed.one-point-xover.source.0 = ec.select.TournamentSelection
+psh.breed.one-point-xover.source.1 = same
+psh.breed.one-point-xover.toss = true
+psh.breed.psh-mutate.fair-mutation-range = 0.50
+psh.breed.psh-mutate.source.0 = ec.select.TournamentSelection
+psh.breed.psh-mutate.use-fair = true
+psh.breed.psh-simplify.flatten-prob = 0.20
+psh.breed.psh-simplify.source.0 = ec.select.TournamentSelection
+psh.breed.psh-simplify.steps = 20
+psh.breed.psh-xover.source.0 = ec.select.TournamentSelection
+psh.breed.psh-xover.source.1 = same
+psh.breed.psh-xover.toss = true
+psh.breed.two-point-xover.source.0 = ec.select.TournamentSelection
+psh.breed.two-point-xover.source.1 = same
+psh.breed.two-point-xover.toss = true
+psh.ideal-threshold = 0.1
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 100
+psh.interpreter.generate-flat = true
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/pure-instructions.txt
+psh.interpreter.max-points-in-program = 50
+psh.interpreter.max-random-code-size = 30
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 1.00
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = org.ecj.psh.PshShortStatistics
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/Push_Pure_Perf_2.params

+# Key: 'Double_Regression_Psh_Pure_Perf_2'
+# Description: 'Performance of eda - control gropu experiment'
+# 
+# Exported: 
+# Mon Sep 17 19:27:06 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = ec.simple.SimpleBreeder
+breed.reproduce.source.0 = ec.select.TournamentSelection
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.regression.psh.ClassicDoublePshRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza3.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = ec.Subpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.size = 200
+pop.subpop.0.species = org.ecj.psh.PshSpecies
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.ind = org.ecj.psh.PshIndividual
+pop.subpop.0.species.pipe = ec.breed.MultiBreedingPipeline
+pop.subpop.0.species.pipe.generate-max = false
+pop.subpop.0.species.pipe.num-sources = 4
+pop.subpop.0.species.pipe.source.0 = org.ecj.psh.breed.PshCrossover
+pop.subpop.0.species.pipe.source.0.prob = 0.70
+pop.subpop.0.species.pipe.source.1 = org.ecj.psh.breed.PshMutation
+pop.subpop.0.species.pipe.source.1.prob = 0.20
+pop.subpop.0.species.pipe.source.2 = org.ecj.psh.breed.PshSimplification
+pop.subpop.0.species.pipe.source.2.prob = 0.05
+pop.subpop.0.species.pipe.source.3 = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.3.prob = 0.05
+pop.subpops = 1
+prefix = psh
+psh.breed.one-point-xover.source.0 = ec.select.TournamentSelection
+psh.breed.one-point-xover.source.1 = same
+psh.breed.one-point-xover.toss = true
+psh.breed.psh-mutate.fair-mutation-range = 0.50
+psh.breed.psh-mutate.source.0 = ec.select.TournamentSelection
+psh.breed.psh-mutate.use-fair = true
+psh.breed.psh-simplify.flatten-prob = 0.20
+psh.breed.psh-simplify.source.0 = ec.select.TournamentSelection
+psh.breed.psh-simplify.steps = 20
+psh.breed.psh-xover.source.0 = ec.select.TournamentSelection
+psh.breed.psh-xover.source.1 = same
+psh.breed.psh-xover.toss = true
+psh.breed.two-point-xover.source.0 = ec.select.TournamentSelection
+psh.breed.two-point-xover.source.1 = same
+psh.breed.two-point-xover.toss = true
+psh.ideal-threshold = 0.1
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 100
+psh.interpreter.generate-flat = true
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/pure-instructions.txt
+psh.interpreter.max-points-in-program = 50
+psh.interpreter.max-random-code-size = 30
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 1.00
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = org.ecj.psh.PshShortStatistics
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/UMDA_Perf_0.params

+# Key: 'Double_Regression_UMDA_Perf_0'
+# Description: 'UMDA performance - optimal settings'
+# 
+# Exported: 
+# Mon Sep 17 19:26:31 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = pl.put.poznan.eda.SimpleEDABreeder
+breed.exchange-ratio = 1.0
+breed.sampler = pl.put.poznan.eda.umda.DenseUMDASampler
+breed.updater = pl.put.poznan.eda.umda.DenseUMDAUpdater
+breed.updater.weight = 0.1
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza1.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = pl.put.poznan.eda.ModelSubpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.model = pl.put.poznan.eda.umda.DenseUMDAModel
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.00
+pop.subpop.0.species.pipe = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.0 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/UMDA_Perf_1.params

+# Key: 'Double_Regression_UMDA_Perf_1'
+# Description: 'UMDA performance - optimal settings'
+# 
+# Exported: 
+# Mon Sep 17 19:26:36 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = pl.put.poznan.eda.SimpleEDABreeder
+breed.exchange-ratio = 1.0
+breed.sampler = pl.put.poznan.eda.umda.DenseUMDASampler
+breed.updater = pl.put.poznan.eda.umda.DenseUMDAUpdater
+breed.updater.weight = 0.1
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza2.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = pl.put.poznan.eda.ModelSubpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.model = pl.put.poznan.eda.umda.DenseUMDAModel
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.00
+pop.subpop.0.species.pipe = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.0 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File resources/benchmarks/mgr-test12/params/UMDA_Perf_2.params

+# Key: 'Double_Regression_UMDA_Perf_2'
+# Description: 'UMDA performance - optimal settings'
+# 
+# Exported: 
+# Mon Sep 17 19:26:41 CEST 2012
+# pl.put.gi.exporters.FlatFileParametersExporter
+# 
+breed = pl.put.poznan.eda.SimpleEDABreeder
+breed.exchange-ratio = 1.0
+breed.sampler = pl.put.poznan.eda.umda.DenseUMDASampler
+breed.updater = pl.put.poznan.eda.umda.DenseUMDAUpdater
+breed.updater.weight = 0.1
+breedthreads = 1
+checkpoint = false
+checkpoint-modulo = 1
+eval = org.ecj.psh.PshEvaluator
+eval.problem = pl.put.ri.problem.DoubleRegressionProblem
+eval.problem.test-cases-file = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/cases/koza3.txt
+evalthreads = 1
+exch = ec.simple.SimpleExchanger
+finish = ec.simple.SimpleFinisher
+generations = 200
+init = ec.simple.SimpleInitializer
+pop = ec.Population
+pop.subpop.0 = pl.put.poznan.eda.ModelSubpopulation
+pop.subpop.0.duplicate-retries = 0
+pop.subpop.0.model = pl.put.poznan.eda.umda.DenseUMDAModel
+pop.subpop.0.size = 200
+pop.subpop.0.species = ec.vector.IntegerVectorSpecies
+pop.subpop.0.species.crossover-type = one
+pop.subpop.0.species.fitness = ec.gp.koza.KozaFitness
+pop.subpop.0.species.genome-size = 20
+pop.subpop.0.species.ind = ec.vector.ShortVectorIndividual
+pop.subpop.0.species.max-gene = 10
+pop.subpop.0.species.min-gene = 0
+pop.subpop.0.species.mutation-prob = 0.00
+pop.subpop.0.species.pipe = ec.breed.ReproductionPipeline
+pop.subpop.0.species.pipe.source.0 = ec.select.TournamentSelection
+pop.subpops = 1
+prefix = ec
+psh.interpreter = org.spiderland.Psh.Interpreter
+psh.interpreter.execution-limit = 80
+psh.interpreter.generate-flat = false
+psh.interpreter.instruction-list = /home/dzess/MGR/workspace/gray-ibis/src/test/resources/psh/float-instructions-3.txt
+psh.interpreter.max-points-in-program = 40
+psh.interpreter.max-random-code-size = 40
+psh.interpreter.max-random-float = 10.0
+psh.interpreter.max-random-integer = 10
+psh.interpreter.min-random-float = -10.0
+psh.interpreter.min-random-integer = -10
+psh.interpreter.push-frame-mode = false
+psh.interpreter.random-float-res = 0.01
+psh.interpreter.random-integer-res = 1
+quit-on-run-complete = true
+seed.0 = time
+select.tournament.size = 7
+stat = ec.simple.SimpleStatistics
+stat.file = $out.stat
+state = org.ecj.psh.PshEvolutionState

File rproject/cases.r

 }
 
 gi.dump <- function(dataset,name){
-  fileName <-  paste(name,".txt",separator="")
-  write.table(dataset,file = fileName ,row.names = FALSE, col.names = FALSE)
+  write.table(dataset,file = name ,row.names = FALSE, col.names = FALSE)
 }
 
 gi.plot <- function(dataset){

File rproject/koza1

+-1 0
+-0.9 -0.1629
+-0.8 -0.2624
+-0.7 -0.3129
+-0.6 -0.3264
+-0.5 -0.3125
+-0.4 -0.2784
+-0.3 -0.2289
+-0.2 -0.1664
+-0.1 -0.0909
+0 0
+0.1 0.1111
+0.2 0.2496
+0.3 0.4251
+0.4 0.6496
+0.5 0.9375
+0.6 1.3056
+0.7 1.7731
+0.8 2.3616
+0.9 3.0951
+1 4

File rproject/koza2

+-1 0
+-0.9 -0.0324899999999999
+-0.8 -0.10368
+-0.7 -0.18207
+-0.6 -0.24576
+-0.5 -0.28125
+-0.4 -0.28224
+-0.3 -0.24843
+-0.2 -0.18432
+-0.1 -0.09801
+0 0
+0.1 0.0980100000000001
+0.2 0.18432
+0.3 0.24843
+0.4 0.28224
+0.5 0.28125
+0.6 0.24576
+0.7 0.18207
+0.8 0.10368
+0.9 0.0324899999999999
+1 0

File rproject/koza3

+-1 0
+-0.9 0.0292410000000001
+-0.8 0.0829440000000001
+-0.7 0.127449
+-0.6 0.147456
+-0.5 0.140625
+-0.4 0.112896
+-0.3 0.074529
+-0.2 0.036864
+-0.1 0.009801
+0 0
+0.1 0.00980100000000002
+0.2 0.0368640000000001
+0.3 0.074529
+0.4 0.112896
+0.5 0.140625
+0.6 0.147456
+0.7 0.127449
+0.8 0.0829440000000001
+0.9 0.0292410000000001
+1 0

File src/main/scala/pl/put/regression/RegressionProblem.scala

 /**
  * Base class for regression problems. Responsible for iterating through test cases,
  * loading them, applying metrics to the result and so on...
+ * 
+ * TODO: the applied metric should be changeable, the precision levels should also be changeable.
  */
 abstract trait RegressionProblem {
 
             val error = if (y != y) {
                 penalty
             } else {
-                (y - output) * (y - output)
+                // NOTE: this code as a metric should be done as injectable one !
+                math.abs(y - output)
             }
 
             // in case of integer problem there is no need to be thinking about precision 
-            //if (error <= precision * math.abs(y)) {
             if (error <= 0.01) {
                 sumHits += 1
             } else {

File src/main/scala/pl/put/regression/psh/ClassicDoublePshRegressionProblem.scala

 import pl.put.regression.RegressionProblem
 import org.ecj.psh.PshProblem
 
-
 /**
  * Concrete class implementing symbolic regression problem with PushGP. Based on
  * work by Tomasz Kamiński from ecj-psh.
     protected var interpreter: Interpreter = null
     protected var program: Program = null
 
+    val P_REPEATINTSTACK = "repeat-stack"
+    private var repeatsInStack = 10
+
     override def setup(state: EvolutionState, base: Parameter) = {
         super.setup(state, base)
 
         // use the method defined in regression problem to load the test cases
         loadTestCases(state, base)
+        
+        repeatsInStack = state.parameters.getIntWithDefault(base.push(P_REPEATINTSTACK), null, 1);
 
         // safe check
         state.output.exitIfErrors()
 
         interpreter.ClearStacks()
 
-        for (value <- testCase.variables) {
-            // pushing input value to float stack
-            interpreter.floatStack().push(value.toFloat)
+        for (i <- 0 until repeatsInStack) {
+            for (value <- testCase.variables) {
+                // pushing input value to float stack
+                interpreter.floatStack().push(value.toFloat)
+            }
         }
 
         // setting input value to input stack

File src/main/scala/pl/put/regression/psh/ClassicIntegerPshRegressionProblem.scala

 
 /**
  * Concrete class implementing the symbolic regression problem with PushGP. Based on
- * work by Tomasz Kamiński from ecj-psh. 
- * 
- * Works on the integer domain. 
+ * work by Tomasz Kamiński from ecj-psh.
+ *
+ * Works on the integer domain.
  */
 class ClassicIntegerPshRegressionProblem extends PshProblem with RegressionProblem {
-    
+
     // there protected values are used by inherited classes
     protected var interpreter: Interpreter = null
     protected var program: Program = null
 
+    val P_REPEATINTSTACK = "repeat-stack"
+    private var repeatsInStack = 10
+
     override def setup(state: EvolutionState, base: Parameter) = {
         super.setup(state, base)
 
         // use the method defined in regression problem to load the test cases
         loadTestCases(state, base)
 
+        repeatsInStack = state.parameters.getIntWithDefault(base.push(P_REPEATINTSTACK), null, 1);
+
         // safe check
         state.output.exitIfErrors()
     }
 
         interpreter.ClearStacks()
 
-        for (value <- testCase.variables) {
-            // pushing input value to float stack
-            interpreter.intStack().push(value.toInt)
+        // pushing input value to float stack
+        for (i <- 0 until repeatsInStack) {
+            for (value <- testCase.variables) {
+
+                interpreter.intStack().push(value.toInt)
+            }
         }
 
         // setting input value to input stack

File src/main/scala/pl/put/ri/problem/DoubleRegressionProblem.scala

 
         interpreter.ClearStacks()
 
-        for (value <- testCase.variables) {
-            // pushing input value to float stack
-            interpreter.floatStack().push(value.toFloat)
+        // pushing input value to float stack, this many times as 
+        // parameters repeat in stack specifies
+        for (i <- 0 until repeatInStack) {
+            for (value <- testCase.variables) {
+                interpreter.floatStack().push(value.toFloat)
+            }
         }
 
         // setting input value to input stack

File src/main/scala/pl/put/ri/problem/IntRegressionProblem.scala

         val input = testCase.variables(0).toInt
 
         // pushing input value to int stack
-        for (value <- testCase.variables) {
-            // pushing input value to float stack
-            interpreter.intStack().push(value.toInt)
+        for (i <- 0 until repeatInStack) {
+            for (value <- testCase.variables) {
+                interpreter.intStack().push(value.toInt)
+            }
         }
 
         // setting input value to input stack

File src/main/scala/pl/put/ri/problem/PshRegressionProblem.scala

     with SimpleProblemForm with RegressionProblem {
 
     // TODO: some options need to be injected via setup method
-    val P_REPEATINTSTACK = "repeat-int-stack"
+    val P_REPEATINTSTACK = "repeat-stack"
     val P_MAPPER = "mapper"
 
     private var mapper: ICodeMapper = null
 
     // there protected values are used by inherited classes
-    protected var repeatIntStack: Int = -1
+    protected var repeatInStack: Int = 10
+    
     protected var interpreter: Interpreter = null
     protected var program: Program = null
 
 
         // read code mapper 
         mapper = new FlatCodeMapper()
-        repeatIntStack = state.parameters.getIntWithDefault(base.push(P_REPEATINTSTACK), null, 1);
+        repeatInStack = state.parameters.getIntWithDefault(base.push(P_REPEATINTSTACK), null, 1);
 
         // safe check
         state.output.exitIfErrors()

File src/test/resources/cases2/koza1

+-1 0 
+-0.9 -0.1629
+-0.8 -0.2624
+-0.7 -0.3129
+-0.6 -0.3264
+-0.5 -0.3125
+-0.4 -0.2784
+-0.3 -0.2289
+-0.2 -0.1664
+-0.1 -0.0909
+0.1 0.1111
+0.2 0.2496
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