API Reference

Core Modules

• BNMPy.BMatrix
  • get_equations()
  • get_gene_dict()
  • get_upstream_genes()
  • get_connectivity_matrix()
  • get_truth_table()
  • get_mutation_dict()
  • get_knocking_genes()
  • get_cal_upstream_genes()
  • get_cal_functions()
  • get_calculating_scores()
  • load_network_from_file()
  • load_network_from_string()
  • load_pbn_from_file()
  • load_pbn_from_string()
  • load_network()
  • rename_nodes()
• BNMPy.booleanNetwork
  • BooleanNetwork
  • getRandomParameters()
  • getRandomInitialNodeValues()
  • getDataFromFile()
  • getParametersFromFile()
• BNMPy.PBN
  • ProbabilisticBN
• BNMPy.steady_state
  • SteadyStateCalculator

Visualization

• BNMPy.vis
  • is_entire_rule_negated()
  • read_logic_rules()
  • extract_logic_rules_from_network()
  • build_igraph_pbn()
  • build_igraph()
  • create_matplotlib_visualization()
  • vis_network()
  • vis_compression()
  • vis_extension()
  • create_matplotlib_extension_visualization()

Knowledge Graph Integration

• BNMPy.build_bn_from_kg
  • all_boolean_combos()
  • load_signor_network()
  • merge_PBN_string()
• BNMPy.model_parser
  • simplify_expression()
  • parse_expression()
  • parse_equations()
  • get_upstream()
  • find_direct_targets()
  • check_inhibitor_wins_rule()
  • merge_networks()
  • BN2PBN()
  • extend_networks()
  • Example Usage
• BNMPy.phenotype_score
  • get_phenotypes()
  • proxpath()
  • phenotype_scores()

Optimization Modules

• BNMPy.parameter_optimizer
  • OptimizationResult
  • OptimizationError
  • ParameterOptimizer
  • Basic Usage
  • Value Normalization
  • Configuration
  • Results
  • Visualization
  • References
• BNMPy.simulation_evaluator
  • SimulationEvaluator
• BNMPy.experiment_data
  • ExperimentData
  • extract_experiment_nodes()
  • generate_experiments()
  • Data Format
• BNMPy.result_evaluation
  • get_pbn_rules_string()
  • ResultEvaluator
  • evaluate_optimization_result()
  • evaluate_pbn()
  • Basic Usage
  • Generated Plots
  • Output Files
  • See Also
• BNMPy.model_compressor
  • ModelCompressor
  • compress_model()
  • Features
  • Basic Usage
  • Step-by-Step Compression
  • Visualization