Index

A

absolute_error (Criterion attribute), [1] AdditiveDerivNoiser (class in simba_ml.simulation.derivative_noiser) (class in simba_ml.simulation.derivative_noiser.additive_deriv_noiser) AdditiveNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.additive_noiser) AdjustingMeanNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.adjusting_mean_noiser) alpha (BetaDistribution attribute), [1] apply_noisifier() (Constraint method), [1] (KeepSpeciesRange method), [1] (KeepSpeciesSum method), [1] (SpeciesValueTruncator method), [1] (SystemModel method), [1] (SystemModelInterface method)

apply_sparsifier() (Constraint method), [1] (KeepSpeciesRange method), [1] (KeepSpeciesSum method), [1] (SpeciesValueTruncator method), [1] (SystemModel method), [1] (SystemModelInterface method) ArchitectureParams (class in simba_ml.prediction.time_series.models.keras.keras_model) (class in simba_ml.prediction.time_series.models.pytorch_lightning.pytorch_lightning_model) AveragePredictor (class in simba_ml.prediction.time_series.models) (class in simba_ml.prediction.time_series.models.average_predictor) AveragePredictorConfig (class in simba_ml.prediction.time_series.models.average_predictor)

B

best (Splitter attribute), [1] beta (BetaDistribution attribute), [1]

BetaDistribution (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.beta_distribution)

C

ColumnNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.column_noiser) confirm_number_is_greater_or_equal_to_0() (in module simba_ml.error_handler) confirm_number_is_greater_than_0() (in module simba_ml.error_handler) confirm_number_is_in_interval() (in module simba_ml.error_handler) confirm_param_is_float() (in module simba_ml.error_handler) confirm_param_is_float_or_int() (in module simba_ml.error_handler) confirm_param_is_int() (in module simba_ml.error_handler) confirm_sequence_contains_only_floats_or_ints() (in module simba_ml.error_handler) confirm_sequence_is_not_empty() (in module simba_ml.error_handler) Constant (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.constant) ConstantKineticParameter (class in simba_ml.simulation.kinetic_parameters) (class in simba_ml.simulation.kinetic_parameters.constant_kinetic_parameter) ConstantSuffixRemover (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.constant_suffix_remover)

Constraint (class in simba_ml.simulation.constraints) (class in simba_ml.simulation.constraints.constraint) contained_in_output (Species attribute) ContinuousUniformDistribution (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.continuous_uniform_distribution) convert_dataframe_to_numpy() (in module simba_ml.prediction.preprocessing) create() (in module simba_ml.prediction.time_series.metrics.factory) (in module simba_ml.prediction.time_series.models.factory) (in module simba_ml.prediction.time_series.models.transfer_learning_factory) create_array_window() (in module simba_ml.prediction.time_series.data_loader.window_generator) create_dataset() (in module simba_ml.prediction.steady_state.data_loader.dataset_generator) create_window_dataset() (in module simba_ml.prediction.time_series.data_loader.window_generator) Criterion (class in simba_ml.prediction.time_series.models.sk_learn.decision_tree_regressor) (class in simba_ml.prediction.time_series.models.sk_learn.random_forest_regressor) criterion (DecisionTreeRegressorConfig attribute) (LinearRegressorConfig attribute) (RandomForestRegressorConfig attribute)

D

DataConfig (class in simba_ml.prediction.steady_state.config.steady_state_data_config) (class in simba_ml.prediction.time_series.config) (class in simba_ml.prediction.time_series.config.mixed_data_pipeline) (class in simba_ml.prediction.time_series.config.mixed_data_pipeline.mixed_data_config) (class in simba_ml.prediction.time_series.config.synthetic_data_pipeline) (class in simba_ml.prediction.time_series.config.synthetic_data_pipeline.synthetic_data_config) (class in simba_ml.prediction.time_series.config.transfer_learning_pipeline) (class in simba_ml.prediction.time_series.config.transfer_learning_pipeline.transfer_learning_data_config) DecisionTreeRegressorConfig (class in simba_ml.prediction.time_series.models.sk_learn.decision_tree_regressor) DecisionTreeRegressorModel (class in simba_ml.prediction.time_series.models.sk_learn) (class in simba_ml.prediction.time_series.models.sk_learn.decision_tree_regressor) denormalize_prediction_data() (Normalizer method) DenseNeuralNetwork (class in simba_ml.prediction.time_series.models.keras.dense_neural_network) (class in simba_ml.prediction.time_series.models.pytorch_lightning.dense_neural_network) DenseNeuralNetworkConfig (class in simba_ml.prediction.time_series.models.keras.dense_neural_network) (class in simba_ml.prediction.time_series.models.pytorch_lightning.dense_neural_network) deriv (Constraint property), [1] (KeepSpeciesRange property), [1] (KeepSpeciesSum property), [1] (SpeciesValueTruncator property), [1] (SystemModel property), [1] (SystemModelInterface property)

deriv() (in module simba_ml.example_problems.constant_function) (in module simba_ml.example_problems.salt_and_brine_tanks) (in module simba_ml.example_problems.sir) (in module simba_ml.example_problems.sird) (in module simba_ml.example_problems.trigonometry) DerivNoiser (class in simba_ml.simulation.derivative_noiser) (class in simba_ml.simulation.derivative_noiser.derivative_noiser) DictBasedKineticParameter (class in simba_ml.simulation.kinetic_parameters) (class in simba_ml.simulation.kinetic_parameters.dict_based_kinetic_parameter) distance (Weights attribute) distribution (AdditiveDerivNoiser attribute), [1] (AdditiveNoiser attribute), [1] Distribution (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.distribution) distribution (ConstantKineticParameter attribute), [1] (MultiplicativeDerivNoiser attribute), [1] (MultiplicativeNoiser attribute), [1] (Species attribute)

E

ElasticNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.elastic_noiser)

exponential (ElasticNoiser attribute), [1]

F

frac (ConstantSuffixRemover attribute), [1] (RandomSampleSparsifier attribute), [1] friedman_mse (Criterion attribute), [1]

function (FunctionBasedKineticParameter attribute), [1] FunctionBasedKineticParameter (class in simba_ml.simulation.kinetic_parameters) (class in simba_ml.simulation.kinetic_parameters.function_based_kinetic_parameter)

G

generate_csv() (TimeSeriesGenerator method), [1] generate_csvs() (TimeSeriesGenerator method), [1] generate_signal() (TimeSeriesGenerator method), [1] generate_signals() (PertubationGenerator method), [1] (SteadyStateGenerator method), [1] (TimeSeriesGenerator method), [1] generate_timepoints() (TimePointsGenerator method), [1] get_at_timestamp() (ConstantKineticParameter method), [1] (DictBasedKineticParameter method), [1] (FunctionBasedKineticParameter method), [1] (KineticParameter method), [1] get_clean_signal() (Constraint method), [1] (KeepSpeciesRange method), [1] (KeepSpeciesSum method), [1] (SpeciesValueTruncator method), [1] (SystemModel method), [1] (SystemModelInterface method) get_initial_values_from_hypercube_sampling() (Species method) get_model() (DecisionTreeRegressorModel method), [1] (DenseNeuralNetwork method), [1] (KerasModel method) (LinearRegressorModel method), [1] (NearestNeighborsRegressorModel method), [1] (PytorchLightningModel method) (RandomForestRegressorModel method), [1] (SkLearnModel method) (SVMRegressorModel method), [1]

get_random_array_from_distribution() (in module simba_ml.simulation.distributions) (in module simba_ml.simulation.distributions.helper_functions) get_random_value_from_distribution() (in module simba_ml.simulation.distributions) (in module simba_ml.simulation.distributions.helper_functions) get_random_values() (BetaDistribution method), [1] (Constant method), [1] (ContinuousUniformDistribution method), [1] (Distribution method), [1] (LogNormalDistribution method), [1] (NormalDistribution method), [1] (VectorDistribution method), [1] get_samples_from_hypercube() (BetaDistribution method), [1] (Constant method), [1] (ContinuousUniformDistribution method), [1] (Distribution method), [1] (LogNormalDistribution method), [1] (NormalDistribution method), [1] (VectorDistribution method), [1]

I

import_module() (in module simba_ml.prediction.plugin_loader) init() (WandbLogger method)

IntervalSparsifier (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.interval_sparsifier) invert (ElasticNoiser attribute), [1]

K

k (ElasticNoiser attribute), [1] KeepExtremeValuesSparsifier (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.keep_extreme_values_sparsifier) KeepSpeciesRange (class in simba_ml.simulation.constraints) (class in simba_ml.simulation.constraints.species_value_in_range) KeepSpeciesSum (class in simba_ml.simulation.constraints) (class in simba_ml.simulation.constraints.keep_species_sum) KerasModel (class in simba_ml.prediction.time_series.models.keras.keras_model) KerasModelConfig (class in simba_ml.prediction.time_series.models.keras.keras_model) Kernel (class in simba_ml.prediction.time_series.models.sk_learn.support_vector_machine_regressor)

kernel (SVMRegressorConfig attribute) kinetic_parameters (Constraint property), [1] (KeepSpeciesRange property), [1] (KeepSpeciesSum property), [1] (SpeciesValueTruncator property), [1] (SystemModel attribute), [1] (SystemModel property), [1] (SystemModelInterface property) KineticParameter (class in simba_ml.simulation.kinetic_parameters) (class in simba_ml.simulation.kinetic_parameters.kinetic_parameter)

L

LastValuePredictor (class in simba_ml.prediction.time_series.models) (class in simba_ml.prediction.time_series.models.last_value_predictor) LastValuePredictorConfig (class in simba_ml.prediction.time_series.models.last_value_predictor) LinearRegressorConfig (class in simba_ml.prediction.time_series.models.sk_learn.linear_regressor) LinearRegressorModel (class in simba_ml.prediction.time_series.models.sk_learn) (class in simba_ml.prediction.time_series.models.sk_learn.linear_regressor) list_of_train_validation_sets (MixedDataLoader property)

load_data() (MixedDataLoader method), [1] (SyntheticDataLoader method) (TransferLearningDataLoader method) load_plugins() (in module simba_ml.prediction.plugin_loader) LoggingConfig (class in simba_ml.prediction.logging.logging_config) LogNormalDistribution (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.lognormal_distribution)

M

main() (in module simba_ml.prediction.time_series.pipelines.mixed_data_pipeline) (in module simba_ml.prediction.time_series.pipelines.synthetic_data_pipeline) (in module simba_ml.prediction.time_series.pipelines.transfer_learning_pipeline) (in module simba_ml.start_prediction) max_value (ContinuousUniformDistribution attribute), [1] (Species attribute) MaxRetriesReachedError mean_absolute_error() (in module simba_ml.prediction.time_series.metrics.metrics) mean_absolute_error_matrix() (in module simba_ml.prediction.time_series.metrics.metrics) mean_absolute_percentage_error() (in module simba_ml.prediction.time_series.metrics.metrics) mean_absolute_percentage_error_matrix() (in module simba_ml.prediction.time_series.metrics.metrics) mean_squared_error() (in module simba_ml.prediction.time_series.metrics.metrics) mean_squared_error_matrix() (in module simba_ml.prediction.time_series.metrics.metrics) Metric (class in simba_ml.prediction.time_series.metrics.metrics) MetricNotFoundError min_value (ContinuousUniformDistribution attribute), [1] (Species attribute) mix_data() (in module simba_ml.prediction.preprocessing) MixedDataLoader (class in simba_ml.prediction.steady_state.data_loader.mixed_data_loader) (class in simba_ml.prediction.time_series.data_loader.mixed_data_loader) Model (class in simba_ml.prediction.time_series.models) (class in simba_ml.prediction.time_series.models.model) model_to_transfer_learning_model_with_pretraining() (in module simba_ml.prediction.time_series.models.model_to_transfer_learning_model) ModelConfig (class in simba_ml.prediction.time_series.models.model) ModelNotFoundError, [1] module simba_ml simba_ml.error_handler simba_ml.example_problems simba_ml.example_problems.constant_function simba_ml.example_problems.salt_and_brine_tanks simba_ml.example_problems.sir simba_ml.example_problems.sird simba_ml.example_problems.trigonometry simba_ml.prediction simba_ml.prediction.logging simba_ml.prediction.logging.logging_config simba_ml.prediction.logging.wandb_logger simba_ml.prediction.normalizer simba_ml.prediction.plugin_loader simba_ml.prediction.preprocessing simba_ml.prediction.steady_state simba_ml.prediction.steady_state.config simba_ml.prediction.steady_state.config.steady_state_data_config simba_ml.prediction.steady_state.data_loader simba_ml.prediction.steady_state.data_loader.dataset_generator simba_ml.prediction.steady_state.data_loader.mixed_data_loader simba_ml.prediction.steady_state.data_loader.splits simba_ml.prediction.time_series simba_ml.prediction.time_series.config simba_ml.prediction.time_series.config.mixed_data_pipeline simba_ml.prediction.time_series.config.mixed_data_pipeline.mixed_data_config simba_ml.prediction.time_series.config.mixed_data_pipeline.pipeline_config simba_ml.prediction.time_series.config.synthetic_data_pipeline simba_ml.prediction.time_series.config.synthetic_data_pipeline.pipeline_config simba_ml.prediction.time_series.config.synthetic_data_pipeline.synthetic_data_config simba_ml.prediction.time_series.config.time_series_config simba_ml.prediction.time_series.config.transfer_learning_pipeline simba_ml.prediction.time_series.config.transfer_learning_pipeline.transfer_learning_data_config simba_ml.prediction.time_series.config.transfer_learning_pipeline.transfer_learning_pipeline_config simba_ml.prediction.time_series.data_loader simba_ml.prediction.time_series.data_loader.mixed_data_loader simba_ml.prediction.time_series.data_loader.splits simba_ml.prediction.time_series.data_loader.synthetic_data_loader simba_ml.prediction.time_series.data_loader.transfer_learning_data_loader simba_ml.prediction.time_series.data_loader.window_generator simba_ml.prediction.time_series.metrics simba_ml.prediction.time_series.metrics.factory simba_ml.prediction.time_series.metrics.metrics simba_ml.prediction.time_series.models simba_ml.prediction.time_series.models.average_predictor simba_ml.prediction.time_series.models.factory simba_ml.prediction.time_series.models.keras simba_ml.prediction.time_series.models.keras.dense_neural_network simba_ml.prediction.time_series.models.keras.keras_model simba_ml.prediction.time_series.models.last_value_predictor simba_ml.prediction.time_series.models.model simba_ml.prediction.time_series.models.model_to_transfer_learning_model simba_ml.prediction.time_series.models.pytorch_lightning simba_ml.prediction.time_series.models.pytorch_lightning.dense_neural_network simba_ml.prediction.time_series.models.pytorch_lightning.pytorch_lightning_model simba_ml.prediction.time_series.models.sk_learn simba_ml.prediction.time_series.models.sk_learn.decision_tree_regressor simba_ml.prediction.time_series.models.sk_learn.linear_regressor simba_ml.prediction.time_series.models.sk_learn.nearest_neighbors_regressor simba_ml.prediction.time_series.models.sk_learn.random_forest_regressor simba_ml.prediction.time_series.models.sk_learn.sk_learn_model simba_ml.prediction.time_series.models.sk_learn.support_vector_machine_regressor simba_ml.prediction.time_series.models.transfer_learning_factory simba_ml.prediction.time_series.models.transfer_learning_model simba_ml.prediction.time_series.pipelines simba_ml.prediction.time_series.pipelines.mixed_data_pipeline simba_ml.prediction.time_series.pipelines.synthetic_data_pipeline simba_ml.prediction.time_series.pipelines.transfer_learning_pipeline simba_ml.simulation simba_ml.simulation.constraints simba_ml.simulation.constraints.constraint simba_ml.simulation.constraints.keep_species_sum simba_ml.simulation.constraints.species_value_in_range simba_ml.simulation.constraints.species_value_truncator simba_ml.simulation.derivative_noiser simba_ml.simulation.derivative_noiser.additive_deriv_noiser simba_ml.simulation.derivative_noiser.derivative_noiser simba_ml.simulation.derivative_noiser.multi_deriv_noiser simba_ml.simulation.derivative_noiser.multiplicative_deriv_noiser simba_ml.simulation.derivative_noiser.no_deriv_noiser simba_ml.simulation.derivative_noiser.sequential_deriv_noiser simba_ml.simulation.distributions simba_ml.simulation.distributions.beta_distribution simba_ml.simulation.distributions.constant simba_ml.simulation.distributions.continuous_uniform_distribution simba_ml.simulation.distributions.distribution simba_ml.simulation.distributions.helper_functions simba_ml.simulation.distributions.lognormal_distribution simba_ml.simulation.distributions.normal_distribution simba_ml.simulation.distributions.vector_distribution simba_ml.simulation.generators simba_ml.simulation.generators.pertubation_generator simba_ml.simulation.generators.steady_state_generator simba_ml.simulation.generators.time_points_generator simba_ml.simulation.generators.time_series_generator simba_ml.simulation.kinetic_parameters simba_ml.simulation.kinetic_parameters.constant_kinetic_parameter simba_ml.simulation.kinetic_parameters.dict_based_kinetic_parameter simba_ml.simulation.kinetic_parameters.function_based_kinetic_parameter simba_ml.simulation.kinetic_parameters.kinetic_parameter simba_ml.simulation.noisers simba_ml.simulation.noisers.additive_noiser simba_ml.simulation.noisers.adjusting_mean_noiser simba_ml.simulation.noisers.column_noiser simba_ml.simulation.noisers.elastic_noiser simba_ml.simulation.noisers.multi_noiser simba_ml.simulation.noisers.multiplicative_noiser simba_ml.simulation.noisers.no_noiser simba_ml.simulation.noisers.noiser simba_ml.simulation.noisers.sequential_noiser simba_ml.simulation.sparsifier simba_ml.simulation.sparsifier.constant_suffix_remover simba_ml.simulation.sparsifier.interval_sparsifier simba_ml.simulation.sparsifier.keep_extreme_values_sparsifier simba_ml.simulation.sparsifier.no_sparsifier simba_ml.simulation.sparsifier.random_sample_sparsifier simba_ml.simulation.sparsifier.sequential_sparsifier simba_ml.simulation.sparsifier.sparsifier simba_ml.simulation.species simba_ml.simulation.system_model simba_ml.simulation.system_model.system_model simba_ml.simulation.system_model.system_model_interface simba_ml.start_prediction simba_ml.transformer simba_ml.transformer.config simba_ml.transformer.config.mixed_data_pipeline simba_ml.transformer.data_loader simba_ml.transformer.metrics simba_ml.transformer.models simba_ml.transformer.pipelines

mu (LogNormalDistribution attribute), [1] (NormalDistribution attribute), [1] MultiDerivNoiser (class in simba_ml.simulation.derivative_noiser) (class in simba_ml.simulation.derivative_noiser.multi_deriv_noiser) MultiNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.multi_noiser) MultiplicativeDerivNoiser (class in simba_ml.simulation.derivative_noiser) (class in simba_ml.simulation.derivative_noiser.multiplicative_deriv_noiser) MultiplicativeNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.multiplicative_noiser)

N

n_neighbors (NearestNeighborsConfig attribute) name (AveragePredictor property), [1] (Constraint property), [1] (DecisionTreeRegressorConfig attribute) (DecisionTreeRegressorModel property), [1] (DenseNeuralNetwork property), [1] (KeepSpeciesRange property), [1] (KeepSpeciesSum property), [1] (KerasModel property) (LastValuePredictor property), [1] (LinearRegressorConfig attribute) (LinearRegressorModel property), [1] (Model property), [1] (NearestNeighborsConfig attribute) (NearestNeighborsRegressorModel property), [1] (PytorchLightningModel property) (RandomForestRegressorConfig attribute) (RandomForestRegressorModel property), [1] (SkLearnModel property) (Species attribute) (SpeciesValueTruncator property), [1] (SVMRegressorConfig attribute) (SVMRegressorModel property), [1] (SystemModel property), [1] (SystemModelInterface property) (TransferLearningModel property) NearestNeighborsConfig (class in simba_ml.prediction.time_series.models.sk_learn.nearest_neighbors_regressor) NearestNeighborsRegressorModel (class in simba_ml.prediction.time_series.models.sk_learn) (class in simba_ml.prediction.time_series.models.sk_learn.nearest_neighbors_regressor) NoDerivNoiser (class in simba_ml.simulation.derivative_noiser) (class in simba_ml.simulation.derivative_noiser.no_deriv_noiser) Noiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.noiser)

noiser (SystemModel attribute), [1] noisers (ColumnNoiser attribute), [1] (MultiDerivNoiser attribute), [1] (MultiNoiser attribute), [1] (SequentialDerivNoiser attribute), [1] (SequentialNoiser attribute), [1] (SequentialSparsifier attribute), [1] noisify() (AdditiveDerivNoiser method), [1] (AdditiveNoiser method), [1] (AdjustingMeanNoiser method), [1] (ColumnNoiser method), [1] (DerivNoiser method), [1] (ElasticNoiser method), [1] (MultiDerivNoiser method), [1] (MultiNoiser method), [1] (MultiplicativeDerivNoiser method), [1] (MultiplicativeNoiser method), [1] (NoDerivNoiser method), [1] (Noiser method), [1] (NoNoiser method), [1] (SequentialDerivNoiser method), [1] (SequentialNoiser method), [1] NoNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.no_noiser) NormalDistribution (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.normal_distribution) normalize_test_data() (Normalizer method) normalize_train_data() (Normalizer method) normalized_root_mean_squared_error() (in module simba_ml.prediction.time_series.metrics.metrics) Normalizer (class in simba_ml.prediction.normalizer) NoSparsifier (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.no_sparsifier) NotInitializedError

P

PertubationGenerator (class in simba_ml.simulation.generators) (class in simba_ml.simulation.generators.pertubation_generator) Pipeline (class in simba_ml.start_prediction) PipelineConfig (class in simba_ml.prediction.time_series.config) (class in simba_ml.prediction.time_series.config.mixed_data_pipeline) (class in simba_ml.prediction.time_series.config.mixed_data_pipeline.pipeline_config) (class in simba_ml.prediction.time_series.config.synthetic_data_pipeline) (class in simba_ml.prediction.time_series.config.synthetic_data_pipeline.pipeline_config) (class in simba_ml.prediction.time_series.config.transfer_learning_pipeline) (class in simba_ml.prediction.time_series.config.transfer_learning_pipeline.transfer_learning_pipeline_config) PluginInterface (class in simba_ml.prediction.plugin_loader) poisson (Criterion attribute), [1] predict() (AveragePredictor method), [1] (DecisionTreeRegressorModel method), [1] (DenseNeuralNetwork method), [1] (KerasModel method) (LastValuePredictor method), [1] (LinearRegressorModel method), [1] (Model method), [1] (NearestNeighborsRegressorModel method), [1] (PytorchLightningModel method) (RandomForestRegressorModel method), [1] (SkLearnModel method) (SVMRegressorModel method), [1] (TransferLearningModel method)

prepare_data() (MixedDataLoader method), [1] (SyntheticDataLoader method) (TransferLearningDataLoader method) prepare_samples() (ConstantKineticParameter method), [1] (DictBasedKineticParameter method), [1] (FunctionBasedKineticParameter method), [1] (KineticParameter method), [1] PytorchLightningModel (class in simba_ml.prediction.time_series.models.pytorch_lightning.pytorch_lightning_model) PytorchLightningModelConfig (class in simba_ml.prediction.time_series.models.pytorch_lightning.pytorch_lightning_model)

R

r_square() (in module simba_ml.prediction.time_series.metrics.metrics) r_square_matrix() (in module simba_ml.prediction.time_series.metrics.metrics) random (Splitter attribute), [1] RandomForestRegressorConfig (class in simba_ml.prediction.time_series.models.sk_learn.random_forest_regressor) RandomForestRegressorModel (class in simba_ml.prediction.time_series.models.sk_learn) (class in simba_ml.prediction.time_series.models.sk_learn.random_forest_regressor) RandomSampleSparsifier (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.random_sample_sparsifier)

read_dataframes_from_csvs() (in module simba_ml.prediction.preprocessing) register() (in module simba_ml.prediction.time_series.metrics.factory) (in module simba_ml.prediction.time_series.models.factory) (in module simba_ml.prediction.time_series.models.keras) (in module simba_ml.prediction.time_series.models.pytorch_lightning) (in module simba_ml.prediction.time_series.models.transfer_learning_factory) (PluginInterface static method) root_mean_squared_error() (in module simba_ml.prediction.time_series.metrics.metrics)

S

sample_species_start_values_from_hypercube() (SystemModel method), [1] sample_start_values_from_hypercube() (Constraint method), [1] (KeepSpeciesRange method), [1] (KeepSpeciesSum method), [1] (SpeciesValueTruncator method), [1] (SystemModel method), [1] (SystemModelInterface method) samples (ConstantKineticParameter attribute), [1] save_signal() (TimeSeriesGenerator method), [1] SequentialDerivNoiser (class in simba_ml.simulation.derivative_noiser) (class in simba_ml.simulation.derivative_noiser.sequential_deriv_noiser) SequentialNoiser (class in simba_ml.simulation.noisers) (class in simba_ml.simulation.noisers.sequential_noiser) SequentialSparsifier (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.sequential_sparsifier) set_for_run() (ConstantKineticParameter method), [1] sigma (LogNormalDistribution attribute), [1] (NormalDistribution attribute), [1] simba_ml module simba_ml.error_handler module simba_ml.example_problems module simba_ml.example_problems.constant_function module simba_ml.example_problems.salt_and_brine_tanks module simba_ml.example_problems.sir module simba_ml.example_problems.sird module simba_ml.example_problems.trigonometry module simba_ml.prediction module simba_ml.prediction.logging module simba_ml.prediction.logging.logging_config module simba_ml.prediction.logging.wandb_logger module simba_ml.prediction.normalizer module simba_ml.prediction.plugin_loader module simba_ml.prediction.preprocessing module simba_ml.prediction.steady_state module simba_ml.prediction.steady_state.config module simba_ml.prediction.steady_state.config.steady_state_data_config module simba_ml.prediction.steady_state.data_loader module simba_ml.prediction.steady_state.data_loader.dataset_generator module simba_ml.prediction.steady_state.data_loader.mixed_data_loader module simba_ml.prediction.steady_state.data_loader.splits module simba_ml.prediction.time_series module simba_ml.prediction.time_series.config module simba_ml.prediction.time_series.config.mixed_data_pipeline module simba_ml.prediction.time_series.config.mixed_data_pipeline.mixed_data_config module simba_ml.prediction.time_series.config.mixed_data_pipeline.pipeline_config module simba_ml.prediction.time_series.config.synthetic_data_pipeline module simba_ml.prediction.time_series.config.synthetic_data_pipeline.pipeline_config module simba_ml.prediction.time_series.config.synthetic_data_pipeline.synthetic_data_config module simba_ml.prediction.time_series.config.time_series_config module simba_ml.prediction.time_series.config.transfer_learning_pipeline module simba_ml.prediction.time_series.config.transfer_learning_pipeline.transfer_learning_data_config module simba_ml.prediction.time_series.config.transfer_learning_pipeline.transfer_learning_pipeline_config module simba_ml.prediction.time_series.data_loader module simba_ml.prediction.time_series.data_loader.mixed_data_loader module simba_ml.prediction.time_series.data_loader.splits module simba_ml.prediction.time_series.data_loader.synthetic_data_loader module simba_ml.prediction.time_series.data_loader.transfer_learning_data_loader module simba_ml.prediction.time_series.data_loader.window_generator module simba_ml.prediction.time_series.metrics module simba_ml.prediction.time_series.metrics.factory module simba_ml.prediction.time_series.metrics.metrics module simba_ml.prediction.time_series.models module simba_ml.prediction.time_series.models.average_predictor module simba_ml.prediction.time_series.models.factory module simba_ml.prediction.time_series.models.keras module simba_ml.prediction.time_series.models.keras.dense_neural_network module simba_ml.prediction.time_series.models.keras.keras_model module simba_ml.prediction.time_series.models.last_value_predictor module simba_ml.prediction.time_series.models.model module simba_ml.prediction.time_series.models.model_to_transfer_learning_model module simba_ml.prediction.time_series.models.pytorch_lightning module simba_ml.prediction.time_series.models.pytorch_lightning.dense_neural_network module simba_ml.prediction.time_series.models.pytorch_lightning.pytorch_lightning_model module simba_ml.prediction.time_series.models.sk_learn module simba_ml.prediction.time_series.models.sk_learn.decision_tree_regressor module simba_ml.prediction.time_series.models.sk_learn.linear_regressor module simba_ml.prediction.time_series.models.sk_learn.nearest_neighbors_regressor module simba_ml.prediction.time_series.models.sk_learn.random_forest_regressor module simba_ml.prediction.time_series.models.sk_learn.sk_learn_model module simba_ml.prediction.time_series.models.sk_learn.support_vector_machine_regressor module simba_ml.prediction.time_series.models.transfer_learning_factory module simba_ml.prediction.time_series.models.transfer_learning_model module simba_ml.prediction.time_series.pipelines module simba_ml.prediction.time_series.pipelines.mixed_data_pipeline module simba_ml.prediction.time_series.pipelines.synthetic_data_pipeline module simba_ml.prediction.time_series.pipelines.transfer_learning_pipeline module simba_ml.simulation module simba_ml.simulation.constraints module

simba_ml.simulation.constraints.constraint module simba_ml.simulation.constraints.keep_species_sum module simba_ml.simulation.constraints.species_value_in_range module simba_ml.simulation.constraints.species_value_truncator module simba_ml.simulation.derivative_noiser module simba_ml.simulation.derivative_noiser.additive_deriv_noiser module simba_ml.simulation.derivative_noiser.derivative_noiser module simba_ml.simulation.derivative_noiser.multi_deriv_noiser module simba_ml.simulation.derivative_noiser.multiplicative_deriv_noiser module simba_ml.simulation.derivative_noiser.no_deriv_noiser module simba_ml.simulation.derivative_noiser.sequential_deriv_noiser module simba_ml.simulation.distributions module simba_ml.simulation.distributions.beta_distribution module simba_ml.simulation.distributions.constant module simba_ml.simulation.distributions.continuous_uniform_distribution module simba_ml.simulation.distributions.distribution module simba_ml.simulation.distributions.helper_functions module simba_ml.simulation.distributions.lognormal_distribution module simba_ml.simulation.distributions.normal_distribution module simba_ml.simulation.distributions.vector_distribution module simba_ml.simulation.generators module simba_ml.simulation.generators.pertubation_generator module simba_ml.simulation.generators.steady_state_generator module simba_ml.simulation.generators.time_points_generator module simba_ml.simulation.generators.time_series_generator module simba_ml.simulation.kinetic_parameters module simba_ml.simulation.kinetic_parameters.constant_kinetic_parameter module simba_ml.simulation.kinetic_parameters.dict_based_kinetic_parameter module simba_ml.simulation.kinetic_parameters.function_based_kinetic_parameter module simba_ml.simulation.kinetic_parameters.kinetic_parameter module simba_ml.simulation.noisers module simba_ml.simulation.noisers.additive_noiser module simba_ml.simulation.noisers.adjusting_mean_noiser module simba_ml.simulation.noisers.column_noiser module simba_ml.simulation.noisers.elastic_noiser module simba_ml.simulation.noisers.multi_noiser module simba_ml.simulation.noisers.multiplicative_noiser module simba_ml.simulation.noisers.no_noiser module simba_ml.simulation.noisers.noiser module simba_ml.simulation.noisers.sequential_noiser module simba_ml.simulation.sparsifier module simba_ml.simulation.sparsifier.constant_suffix_remover module simba_ml.simulation.sparsifier.interval_sparsifier module simba_ml.simulation.sparsifier.keep_extreme_values_sparsifier module simba_ml.simulation.sparsifier.no_sparsifier module simba_ml.simulation.sparsifier.random_sample_sparsifier module simba_ml.simulation.sparsifier.sequential_sparsifier module simba_ml.simulation.sparsifier.sparsifier module simba_ml.simulation.species module simba_ml.simulation.system_model module simba_ml.simulation.system_model.system_model module simba_ml.simulation.system_model.system_model_interface module simba_ml.start_prediction module simba_ml.transformer module simba_ml.transformer.config module simba_ml.transformer.config.mixed_data_pipeline module simba_ml.transformer.data_loader module simba_ml.transformer.metrics module simba_ml.transformer.models module simba_ml.transformer.pipelines module SkLearnModel (class in simba_ml.prediction.time_series.models.sk_learn.sk_learn_model) SkLearnModelConfig (class in simba_ml.prediction.time_series.models.sk_learn.sk_learn_model) solver_method (SystemModel attribute), [1] Sparsifier (class in simba_ml.simulation.sparsifier) (class in simba_ml.simulation.sparsifier.sparsifier) sparsifier (SystemModel attribute), [1] sparsify() (ConstantSuffixRemover method), [1] (IntervalSparsifier method), [1] (KeepExtremeValuesSparsifier method), [1] (NoSparsifier method), [1] (RandomSampleSparsifier method), [1] (SequentialSparsifier method), [1] (Sparsifier method), [1] Species (class in simba_ml.simulation.species) specieses (Constraint property), [1] (KeepSpeciesRange property), [1] (KeepSpeciesSum property), [1] (SpeciesValueTruncator property), [1] (SystemModel property), [1] (SystemModelInterface property) SpeciesValueTruncator (class in simba_ml.simulation.constraints) (class in simba_ml.simulation.constraints.species_value_truncator) split_features_and_labels() (in module simba_ml.prediction.steady_state.data_loader.dataset_generator) Splitter (class in simba_ml.prediction.time_series.models.sk_learn.decision_tree_regressor) (class in simba_ml.prediction.time_series.models.sk_learn.random_forest_regressor) splitter (DecisionTreeRegressorConfig attribute) (LinearRegressorConfig attribute) (RandomForestRegressorConfig attribute) squared_error (Criterion attribute), [1] SteadyStateGenerator (class in simba_ml.simulation.generators) (class in simba_ml.simulation.generators.steady_state_generator) SVMRegressorConfig (class in simba_ml.prediction.time_series.models.sk_learn.support_vector_machine_regressor) SVMRegressorModel (class in simba_ml.prediction.time_series.models.sk_learn) (class in simba_ml.prediction.time_series.models.sk_learn.support_vector_machine_regressor) SyntheticDataLoader (class in simba_ml.prediction.time_series.data_loader.synthetic_data_loader) SystemModel (class in simba_ml.simulation.system_model) (class in simba_ml.simulation.system_model.system_model) SystemModelInterface (class in simba_ml.simulation.system_model.system_model_interface)

T

test_input() (in module simba_ml.prediction.time_series.metrics.metrics) TimePointsGenerator (class in simba_ml.simulation.generators) (class in simba_ml.simulation.generators.time_points_generator) TimeSeriesConfig (class in simba_ml.prediction.time_series.config.time_series_config) TimeSeriesGenerator (class in simba_ml.simulation.generators) (class in simba_ml.simulation.generators.time_series_generator) timestamps (SystemModel attribute), [1] train (SyntheticDataLoader property) train() (AveragePredictor method), [1] (DecisionTreeRegressorModel method), [1] (DenseNeuralNetwork method), [1] (KerasModel method) (LastValuePredictor method), [1] (LinearRegressorModel method), [1] (Model method), [1] (NearestNeighborsRegressorModel method), [1] (PytorchLightningModel method) (RandomForestRegressorModel method), [1] (SkLearnModel method) (SVMRegressorModel method), [1] (TransferLearningModel method)

train_observed (TransferLearningDataLoader property) train_sets (MixedDataLoader property) train_synthetic (TransferLearningDataLoader property) train_test_split() (in module simba_ml.prediction.steady_state.data_loader.splits) (in module simba_ml.prediction.time_series.data_loader.splits) train_test_split_horizontal() (in module simba_ml.prediction.time_series.data_loader.splits) train_test_split_vertical() (in module simba_ml.prediction.time_series.data_loader.splits) train_validation_sets (MixedDataLoader attribute), [1] (SyntheticDataLoader attribute) (TransferLearningDataLoader attribute) train_validation_split() (in module simba_ml.prediction.steady_state.data_loader.splits) TrainingParams (class in simba_ml.prediction.time_series.models.keras.keras_model) (class in simba_ml.prediction.time_series.models.pytorch_lightning.pytorch_lightning_model) TransferLearningDataLoader (class in simba_ml.prediction.time_series.data_loader.transfer_learning_data_loader) TransferLearningModel (class in simba_ml.prediction.time_series.models.transfer_learning_model)

U

uniform (Weights attribute) unregister() (in module simba_ml.prediction.time_series.metrics.factory) (in module simba_ml.prediction.time_series.models.factory) (in module simba_ml.prediction.time_series.models.transfer_learning_factory)

V

validate_prediction_input() (AveragePredictor method), [1] (DecisionTreeRegressorModel method), [1] (DenseNeuralNetwork method), [1] (KerasModel method) (LastValuePredictor method), [1] (LinearRegressorModel method), [1] (Model method), [1] (NearestNeighborsRegressorModel method), [1] (PytorchLightningModel method) (RandomForestRegressorModel method), [1] (SkLearnModel method) (SVMRegressorModel method), [1] (TransferLearningModel method)

value (Constant attribute), [1] values (DictBasedKineticParameter attribute), [1] (VectorDistribution attribute), [1] VectorDistribution (class in simba_ml.simulation.distributions) (class in simba_ml.simulation.distributions.vector_distribution)

W

WandbLogger (class in simba_ml.prediction.logging.wandb_logger) weight (AdjustingMeanNoiser attribute), [1] Weights (class in simba_ml.prediction.time_series.models.sk_learn.nearest_neighbors_regressor) weights (NearestNeighborsConfig attribute)

with_traceback() (MaxRetriesReachedError method) (MetricNotFoundError method) (ModelNotFoundError method), [1] (NotInitializedError method) (ZeroNotSetError method)

X

X_test (MixedDataLoader attribute), [1] (MixedDataLoader property), [1] (SyntheticDataLoader attribute) (SyntheticDataLoader property) (TransferLearningDataLoader attribute) (TransferLearningDataLoader property)

Y

y_test (MixedDataLoader attribute), [1] (MixedDataLoader property), [1] (SyntheticDataLoader attribute) (SyntheticDataLoader property) (TransferLearningDataLoader attribute) (TransferLearningDataLoader property)

Z

ZeroNotSetError