Optimizers (optimizers package)

To perform demographic inference optimization should be launched. There are different optimizers in GADMA: local search and global search algorithms.

Base Classes

Module gadma.optimizers.optimizer contains several base classes of optmizers.

Global optimizers

Module gadma.optimizers.global_optimizer contains base class for global optimizers.

Additional global optimizer could be implemented by creating new subclass of class gadma.optimizers.GlobalOptimizer and register it with function gadma.optimizers.register_global_optimizer().

Registered global optimizers

The following optimizers are registered:

ID	Description	Instance of
“Genetic_algorithm”	Genetic algorithm optimization	gadma.optimizers.GeneticAlgorithm
“GPyOpt_Bayesian_optimization”	Bayesian optimization (GPyOpt)	gadma.optimizers.GPyOptBayesianOptimizer
“SMAC_squirrel_optimization”	Bayesian optimization (SMAC squirrel)	gadma.optimizers.SMACSquirellOptimizer
“SMAC_BO_optimization”	Bayesian optimization (SMAC)	gadma.optimizers.SMACBayesianOptimizer
“SMAC_BO_combination”	Bayesian optimization ensemble	gadma.optimizers.SMACBOKernelCombination

Genetic algorithm

Bayesian optimization

Local optimizers

Module gadma.optimizers.local_optimizer contains classes for local serach optimizers.

Additional local optimizer could be implemented by creating new subclass of class gadma.optimizers.local_optimizer.LocalOptimizer and register it with function gadma.optimizers.local_optimizer.register_local_optimizer().

Registered local optimizers

The following optimizers are registered:

ID	Description	Instance of
None or “None”	None optimization is run	gadma.optimizers.NoneOptimizer
“L-BFGS-B”	L-BFGS-B from scipy	gadma.optimizers.ScipyConstrOptimizer
“L-BFGS-B_log”	L-BFGS-B from scipy with log transform of values	gadma.optimizers.ScipyConstrOptimizer
“BFGS”	Constrained BFGS from scipy	gadma.optimizers.ManuallyConstrOptimizer
“BFGS_log”	Constrained BFGS from scipy with log transform of values	gadma.optimizers.ManuallyConstrOptimizer
“Powell”	Constrained Powell’s method from scipy	gadma.optimizers.ManuallyConstrOptimizer
“Powell_log”	Constrained Powell’s method from scipy with log transform of values	gadma.optimizers.ManuallyConstrOptimizer
“Nelder-Mead”	Constrained Nelder-Mead method from scipy	gadma.optimizers.ManuallyConstrOptimizer
“Nelder-Mead_log”	Constrained Nelder-Mead method from scipy with log transform of values	gadma.optimizers.ManuallyConstrOptimizer

Combinations of optimizers

Module gadma.optimizers.combinations contains classes of optimizers that are combinations of other optimizers.

Optimizer result

Linear constrain