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.