Divide By Mean

class DivideByMean(filter=<function DivideByMean.<lambda>>)[source]

Bases: stk.ea.fitness_normalizers.fitness_normalizer.FitnessNormalizer

Divides fitness values by the population mean.

While this function can be used if the fitness value of each Molecule in the population is a single number, it is most useful when the fitness value is a tuple of numbers. In this case, it is necessary to somehow combine the numbers so that a single fitness value is produced. For example, take a fitness value which is the vector holding the properties [energy, diameter, num_atoms]. For a given molecule these numbers may be something like [200,000, 12, 140]. If we were to sum these numbers, the energy term would dominate the final fitness value. In order to combine these numbers we can divide them by the population averages. For example, if the average energy of molecules in the population is 300,000 the average diameter is 10 and the average number of atoms is 70 then the fitness vector would be scaled to [0.5, 1.2, 2]. These numbers are now of a similar magnitude and can be summed to give a reasonable value. After division , each value represents how much better than the population average each property value is. In essence we have removed the units from each parameter.

Examples

Selectively Normalizing Fitness Values

Sometimes you do not want to normalize all the values in a population together. For example, if a failed fitness value calculation resulted in some records having a fitness value of None, you would want to ignore these records from the normalization

import stk
import numpy as np

building_block = stk.BuildingBlock(
    smiles='BrCCBr',
    functional_groups=[stk.BromoFactory()],
)

population = (
    stk.MoleculeRecord(
        topology_graph=stk.polymer.Linear(
            building_blocks=(building_block, ),
            repeating_unit='A',
            num_repeating_units=2,
        ),
    ).with_fitness_value(
        fitness_value=(1., 2., 3.),
        normalized=False,
    ),
    # This will have a fitness value of None.
    stk.MoleculeRecord(
        topology_graph=stk.polymer.Linear(
            building_blocks=(building_block, ),
            repeating_unit='A',
            num_repeating_units=2,
        ),
    ),
)

mean_scaler = stk.DivideByMean(
    # Only normalize values which are not None.
    filter=lambda population, record:
        record.get_fitness_value() is not None
)
# Calling mean_scaler.normalize() will return a new
# population holding the molecule records with normalized
# fitness values.
normalized_population = tuple(mean_scaler.normalize(
    population=population,
))
normalized_record1, normalized_record2 = normalized_population
assert np.all(np.equal(
    normalized_record1.get_fitness_value(),
    (1, 1, 1),
))

Methods

normalize(population)

Normalize the fitness values in population.

__init__(filter=<function DivideByMean.<lambda>>)[source]

Initialize a DivideByMean instance.

Parameters

filter (callable, optional) – Takes two parameters, first is a tuple of MoleculeRecord instances, and the second is a MoleculeRecord. The callable returns True or False. Only molecules which return True will have fitness values normalized. By default, all molecules will have fitness values normalized. The instance passed to the population argument of normalize() is passed as the first argument, while the second argument will be passed every MoleculeRecord in it, one at a time.

normalize(population)[source]

Normalize the fitness values in population.

Parameters

population (tuple of MoleculeRecord) – The molecules which need to have their fitness values normalized.

Yields

MoleculeRecord – A record with a normalized fitness value.