Index

_

__init__() (KGBN.booleanNetwork.BooleanNetwork method) (KGBN.model_compressor.ModelCompressor method) (KGBN.parameter_optimizer.OptimizationResult method) (KGBN.parameter_optimizer.ParameterOptimizer method) (KGBN.PBN.ProbabilisticBN method) (KGBN.result_evaluation.ResultEvaluator method) (KGBN.simulation_evaluator.SimulationEvaluator method) (KGBN.steady_state.SteadyStateCalculator method)

A

all_boolean_combos() (in module KGBN.KG_BN)

B

BN2PBN() (in module KGBN.model_parser) BooleanNetwork (class in KGBN.booleanNetwork) build_igraph() (in module KGBN.vis)

build_igraph_pbn() (in module KGBN.vis) buildK() (KGBN.booleanNetwork.BooleanNetwork method) (KGBN.PBN.ProbabilisticBN method)

C

calculate_evaluation_metrics() (KGBN.result_evaluation.ResultEvaluator method) check_inhibitor_wins_rule() (in module KGBN.model_parser) cij_matrix (KGBN.parameter_optimizer.OptimizationResult attribute) collapse_paths() (KGBN.model_compressor.ModelCompressor method) compress() (KGBN.model_compressor.ModelCompressor method) compress_model() (in module KGBN.model_compressor) compute_stationary_deterministic() (KGBN.steady_state.SteadyStateCalculator method)

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

E

evaluate_optimization_result() (in module KGBN.result_evaluation) evaluate_pbn() (in module KGBN.result_evaluation) ExperimentData (class in KGBN.experiment_data)

export_results_to_csv() (KGBN.result_evaluation.ResultEvaluator method) extend_networks() (in module KGBN.model_parser) extract_experiment_nodes() (in module KGBN.experiment_data) extract_logic_rules_from_network() (in module KGBN.vis)

F

find_collapsible_paths() (KGBN.model_compressor.ModelCompressor method) find_direct_targets() (in module KGBN.model_parser)

find_non_controllable_nodes() (KGBN.model_compressor.ModelCompressor method) find_non_observable_nodes() (KGBN.model_compressor.ModelCompressor method) fun (KGBN.parameter_optimizer.OptimizationResult attribute)

G

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

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

I

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

is_entire_rule_negated() (in module KGBN.vis)

K

KGBN.BMatrix module KGBN.booleanNetwork module KGBN.experiment_data module KGBN.KG_BN module KGBN.model_compressor module KGBN.model_parser module KGBN.parameter_optimizer module

KGBN.PBN module KGBN.phenotype_score module KGBN.result_evaluation module KGBN.simulation_evaluator module KGBN.steady_state module KGBN.vis module knockdown() (KGBN.PBN.ProbabilisticBN method) knockout() (KGBN.booleanNetwork.BooleanNetwork method) (KGBN.PBN.ProbabilisticBN method)

L

load_from_csv() (KGBN.experiment_data.ExperimentData static method) load_network() (in module KGBN.BMatrix) load_network_from_file() (in module KGBN.BMatrix)

load_network_from_string() (in module KGBN.BMatrix) load_pbn_from_file() (in module KGBN.BMatrix) load_pbn_from_string() (in module KGBN.BMatrix) load_signor_network() (in module KGBN.KG_BN)

M

merge_networks() (in module KGBN.model_parser) merge_PBN_string() (in module KGBN.KG_BN) message (KGBN.parameter_optimizer.OptimizationResult attribute) method (KGBN.parameter_optimizer.OptimizationResult attribute) ModelCompressor (class in KGBN.model_compressor) module KGBN.BMatrix KGBN.booleanNetwork KGBN.experiment_data KGBN.KG_BN KGBN.model_compressor KGBN.model_parser KGBN.parameter_optimizer KGBN.PBN KGBN.phenotype_score KGBN.result_evaluation KGBN.simulation_evaluator KGBN.steady_state KGBN.vis

N

nfev (KGBN.parameter_optimizer.OptimizationResult attribute)

nit (KGBN.parameter_optimizer.OptimizationResult attribute)

O

objective_function() (KGBN.simulation_evaluator.SimulationEvaluator method) OptimizationError

OptimizationResult (class in KGBN.parameter_optimizer) optimize() (KGBN.parameter_optimizer.ParameterOptimizer method)

P

ParameterOptimizer (class in KGBN.parameter_optimizer) parse_equations() (in module KGBN.model_parser) parse_expression() (in module KGBN.model_parser) phenotype_scores() (in module KGBN.phenotype_score)

plot_optimization_history() (KGBN.parameter_optimizer.ParameterOptimizer method) plot_prediction_vs_experimental() (KGBN.result_evaluation.ResultEvaluator method) plot_residuals() (KGBN.result_evaluation.ResultEvaluator method) ProbabilisticBN (class in KGBN.PBN) proxpath() (in module KGBN.phenotype_score)

R

read_logic_rules() (in module KGBN.vis) remove_nodes() (KGBN.model_compressor.ModelCompressor method)

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

S

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

simulate_optimized_model() (KGBN.result_evaluation.ResultEvaluator method) SimulationEvaluator (class in KGBN.simulation_evaluator) stateToWrite() (KGBN.booleanNetwork.BooleanNetwork method) (KGBN.PBN.ProbabilisticBN method) SteadyStateCalculator (class in KGBN.steady_state) success (KGBN.parameter_optimizer.OptimizationResult attribute)

T

test_steady_states() (KGBN.parameter_optimizer.ParameterOptimizer method)

toGraph() (KGBN.booleanNetwork.BooleanNetwork method)

U

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

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

V

validate_experiments() (KGBN.experiment_data.ExperimentData static method) vis_compression() (in module KGBN.vis)

vis_extension() (in module KGBN.vis) vis_network() (in module KGBN.vis) visualize_compression() (KGBN.model_compressor.ModelCompressor method)

W

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

X

x (KGBN.parameter_optimizer.OptimizationResult attribute)