genui.generators.extensions.genuidrugex.genuimodels package

Submodules

genui.generators.extensions.genuidrugex.genuimodels.algorithms module

algorithms

Created by: Martin Sicho On: 1/26/20, 5:43 PM

class genui.generators.extensions.genuidrugex.genuimodels.algorithms.DrugExAgent(builder, callback=None)

Bases: DrugExAlgorithm

fit(X=None, y=None)

name = 'DrugExAgent'

parameters = {'batchSize': {'defaultValue': 512, 'type': 'integer'}, 'beta': {'defaultValue': 0.1, 'type': 'float'}, 'epsilon': {'defaultValue': 0.01, 'type': 'float'}, 'nEpochs': {'defaultValue': 60, 'type': 'integer'}}

class genui.generators.extensions.genuidrugex.genuimodels.algorithms.DrugExAlgorithm(builder, callback=None)

Bases: Algorithm, ABC

getDeserializer()

classmethod getFileFormats(attach_to=None)

classmethod getModes()

getSerializer()

property model

predict(X)

sample(n_samples, from_inputs=None)

class genui.generators.extensions.genuidrugex.genuimodels.algorithms.DrugExNetwork(builder, callback=None)

Bases: DrugExAlgorithm

fit(X, y=None)

name = 'DrugExNetwork'

parameters = {'batchSize': {'defaultValue': 512, 'type': 'integer'}, 'nEpochs': {'defaultValue': 60, 'type': 'integer'}}

genui.generators.extensions.genuidrugex.genuimodels.builders module

builders

Created by: Martin Sicho On: 1/26/20, 6:27 PM

class genui.generators.extensions.genuidrugex.genuimodels.builders.DrugExAgentBuilder(instance: DrugExAgent, progress=None, noMonitor=False)

Bases: DrugExBuilder

getX()

sample(n_samples, from_inputs=None)

class genui.generators.extensions.genuidrugex.genuimodels.builders.DrugExBuilder(instance, progress, *args, **kwargs)

Bases: ProgressMixIn, ModelBuilder, ABC

property corePackage

getY()

abstract sample(n_samples, from_inputs=None)

class genui.generators.extensions.genuidrugex.genuimodels.builders.DrugExNetBuilder(instance: DrugExNet, initial: Optional[DrugExNet] = None, progress=None, noMonitor=False)

Bases: DrugExBuilder

build() → Model

getX(update=True)

sample(n_samples, from_inputs=None)

genui.generators.extensions.genuidrugex.genuimodels.metrics module

metrics

Created by: Martin Sicho On: 27-01-20, 11:08

class genui.generators.extensions.genuidrugex.genuimodels.metrics.DrugExLoss(builder)

Bases: ValidationMetric

description = 'Value of the DrugEx loss function.'

modes = ['generator']

name = 'DrExLoss'

class genui.generators.extensions.genuidrugex.genuimodels.metrics.MeanDrExDesirability(builder)

Bases: ValidationMetric

algorithms = [<class 'genui.generators.extensions.genuidrugex.genuimodels.algorithms.DrugExAgent'>]

description = 'Ratio of the desired molecules generated in the set.'

modes = ['generator']

name = 'DrExDesire'

class genui.generators.extensions.genuidrugex.genuimodels.metrics.SMILESErrorRate(builder)

Bases: ValidationMetric

description = 'Percentage of invalid smiles in the generated structures.'

modes = ['generator']

name = 'SMILES_ER'

class genui.generators.extensions.genuidrugex.genuimodels.metrics.SMILESUniqueRate(builder)

Bases: ValidationMetric

algorithms = [<class 'genui.generators.extensions.genuidrugex.genuimodels.algorithms.DrugExAgent'>]

description = 'Percentage of valid unique smiles that scored above the decision threshold in the predicted activity values.'

modes = ['generator']

name = 'SMILES_UQR'

genui.generators.extensions.genuidrugex.genuimodels.monitors module

monitors

Created by: Martin Sicho On: 30-01-20, 15:05

class genui.generators.extensions.genuidrugex.genuimodels.monitors.DrugExMonitor(model_instance, progress_callback)

Bases: DictMonitor

close()

Close this monitor. Training has finished.

saveEpochData(df)

saveModel(model)

Save the state dictionary of the Model instance currently being trained or serialize the model any other way.

Args:

model: a DrugEx Model

saveMolecules(df)

savePerformance(metric, value, isValidation, note='')

Module contents

__init__.py

Created by: Martin Sicho On: 1/26/20, 5:41 PM