Index

_

__init__() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.model_compressor.ModelCompressor method), [1] (BNMPy.parameter_optimizer.OptimizationResult method) (BNMPy.parameter_optimizer.ParameterOptimizer method), [1] (BNMPy.PBN.ProbabilisticBN method) (BNMPy.result_evaluation.ResultEvaluator method) (BNMPy.simulation_evaluator.SimulationEvaluator method), [1] (BNMPy.steady_state.SteadyStateCalculator method)

A

all_boolean_combos() (in module BNMPy.build_bn_from_kg)

B

BN2PBN() (in module BNMPy.model_parser), [1] BNMPy.BMatrix module BNMPy.booleanNetwork module BNMPy.build_bn_from_kg module BNMPy.experiment_data module BNMPy.model_compressor module BNMPy.model_parser module BNMPy.parameter_optimizer module

BNMPy.PBN module BNMPy.result_evaluation module BNMPy.simulation_evaluator module BNMPy.steady_state module BNMPy.vis module BooleanNetwork (class in BNMPy.booleanNetwork) build_igraph() (in module BNMPy.vis) build_igraph_pbn() (in module BNMPy.vis) buildK() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

C

calculate_evaluation_metrics() (BNMPy.result_evaluation.ResultEvaluator method) check_inhibitor_wins_rule() (in module BNMPy.model_parser) cij_matrix (BNMPy.parameter_optimizer.OptimizationResult attribute) collapse_paths() (BNMPy.model_compressor.ModelCompressor method), [1] compress() (BNMPy.model_compressor.ModelCompressor method), [1] compress_model() (in module BNMPy.model_compressor), [1] compute_stationary_deterministic() (BNMPy.steady_state.SteadyStateCalculator method)

compute_stationary_mc() (BNMPy.steady_state.SteadyStateCalculator method) compute_stationary_tsmc() (BNMPy.steady_state.SteadyStateCalculator method) compute_steady_state() (BNMPy.steady_state.SteadyStateCalculator method) convergence_info (BNMPy.parameter_optimizer.OptimizationResult attribute) copy() (BNMPy.PBN.ProbabilisticBN method) create_matplotlib_extension_visualization() (in module BNMPy.vis) create_matplotlib_visualization() (in module BNMPy.vis)

E

evaluate_optimization_result() (in module BNMPy.result_evaluation), [1] evaluate_pbn() (in module BNMPy.result_evaluation), [1] ExperimentData (class in BNMPy.experiment_data), [1]

export_results_to_csv() (BNMPy.result_evaluation.ResultEvaluator method) extend_networks() (in module BNMPy.model_parser), [1] extract_experiment_nodes() (in module BNMPy.experiment_data) extract_logic_rules_from_network() (in module BNMPy.vis)

F

find_collapsible_paths() (BNMPy.model_compressor.ModelCompressor method), [1] find_direct_targets() (in module BNMPy.model_parser)

find_non_controllable_nodes() (BNMPy.model_compressor.ModelCompressor method), [1] find_non_observable_nodes() (BNMPy.model_compressor.ModelCompressor method), [1] fun (BNMPy.parameter_optimizer.OptimizationResult attribute)

G

generate_evaluation_report() (BNMPy.result_evaluation.ResultEvaluator method) generate_experiments() (in module BNMPy.experiment_data) get_cal_functions() (in module BNMPy.BMatrix) get_cal_upstream_genes() (in module BNMPy.BMatrix) get_calculating_scores() (in module BNMPy.BMatrix) get_compression_summary() (BNMPy.model_compressor.ModelCompressor method), [1] get_connectivity_matrix() (in module BNMPy.BMatrix) get_convergence_info() (BNMPy.steady_state.SteadyStateCalculator method) get_equations() (in module BNMPy.BMatrix) get_experiment_summary() (BNMPy.experiment_data.ExperimentData static method), [1] get_gene_dict() (in module BNMPy.BMatrix) get_knocking_genes() (in module BNMPy.BMatrix) get_mutation_dict() (in module BNMPy.BMatrix) get_optimized_pbn() (BNMPy.parameter_optimizer.ParameterOptimizer method), [1] get_parameter_bounds() (BNMPy.simulation_evaluator.SimulationEvaluator method), [1] get_pbn_rules_string() (BNMPy.parameter_optimizer.ParameterOptimizer method), [1]

get_truth_table() (in module BNMPy.BMatrix) get_upstream() (in module BNMPy.model_parser) get_upstream_genes() (in module BNMPy.BMatrix) getBias() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getDataFromFile() (in module BNMPy.booleanNetwork) getMaxConnectivity() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getMeanConnectivity() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getParametersFromFile() (in module BNMPy.booleanNetwork) getRandomInitialNodeValues() (in module BNMPy.booleanNetwork) getRandomParameters() (in module BNMPy.booleanNetwork) getRealization() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getTrajectory() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

I

initializeOutput() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

K

knockdown() (BNMPy.PBN.ProbabilisticBN method)

knockout() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

L

load_from_csv() (BNMPy.experiment_data.ExperimentData static method), [1] load_network_from_file() (in module BNMPy.BMatrix) load_network_from_string() (in module BNMPy.BMatrix)

load_pbn_from_file() (in module BNMPy.BMatrix) load_pbn_from_string() (in module BNMPy.BMatrix) load_signor_network() (in module BNMPy.build_bn_from_kg)

M

merge_networks() (in module BNMPy.model_parser), [1] merge_PBN_string() (in module BNMPy.build_bn_from_kg) message (BNMPy.parameter_optimizer.OptimizationResult attribute) method (BNMPy.parameter_optimizer.OptimizationResult attribute) ModelCompressor (class in BNMPy.model_compressor), [1] module BNMPy.BMatrix BNMPy.booleanNetwork BNMPy.build_bn_from_kg BNMPy.experiment_data BNMPy.model_compressor BNMPy.model_parser BNMPy.parameter_optimizer BNMPy.PBN BNMPy.result_evaluation BNMPy.simulation_evaluator BNMPy.steady_state BNMPy.vis

N

nfev (BNMPy.parameter_optimizer.OptimizationResult attribute)

nit (BNMPy.parameter_optimizer.OptimizationResult attribute)

O

objective_function() (BNMPy.simulation_evaluator.SimulationEvaluator method), [1] OptimizationError

OptimizationResult (class in BNMPy.parameter_optimizer) optimize() (BNMPy.parameter_optimizer.ParameterOptimizer method), [1]

P

ParameterOptimizer (class in BNMPy.parameter_optimizer), [1] parse_equations() (in module BNMPy.model_parser) parse_expression() (in module BNMPy.model_parser)

plot_optimization_history() (BNMPy.parameter_optimizer.ParameterOptimizer method), [1] plot_prediction_vs_experimental() (BNMPy.result_evaluation.ResultEvaluator method) plot_residuals() (BNMPy.result_evaluation.ResultEvaluator method) ProbabilisticBN (class in BNMPy.PBN)

R

read_logic_rules() (in module BNMPy.vis) remove_nodes() (BNMPy.model_compressor.ModelCompressor method), [1]

rename_nodes() (in module BNMPy.BMatrix) reset_network_conditions() (BNMPy.steady_state.SteadyStateCalculator method) ResultEvaluator (class in BNMPy.result_evaluation)

S

set_experimental_conditions() (BNMPy.steady_state.SteadyStateCalculator method) setInitialValue() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) setInitialValues() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) simplify_expression() (in module BNMPy.model_parser)

simulate_optimized_model() (BNMPy.result_evaluation.ResultEvaluator method) SimulationEvaluator (class in BNMPy.simulation_evaluator), [1] stateToWrite() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) SteadyStateCalculator (class in BNMPy.steady_state) success (BNMPy.parameter_optimizer.OptimizationResult attribute)

T

test_steady_states() (BNMPy.parameter_optimizer.ParameterOptimizer method), [1]

toGraph() (BNMPy.booleanNetwork.BooleanNetwork method)

U

undoKnockouts() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) update() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) update_cumulative_probabilities() (BNMPy.PBN.ProbabilisticBN method)

update_noise() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) update_one() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) updateUntilAttractorIsReached() (BNMPy.booleanNetwork.BooleanNetwork method)

V

validate_experiments() (BNMPy.experiment_data.ExperimentData static method), [1] vis_compression() (in module BNMPy.vis)

vis_extension() (in module BNMPy.vis) vis_network() (in module BNMPy.vis) visualize_compression() (BNMPy.model_compressor.ModelCompressor method), [1]

W

writeNetworkHistory() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

X

x (BNMPy.parameter_optimizer.OptimizationResult attribute)