BNMPy.result_evaluation¶

The result_evaluation module provides tools for evaluating optimization results.

BNMPy.result_evaluation.get_pbn_rules_string(pbn) → str[source]¶: Format the final PBN into a readable string.

class BNMPy.result_evaluation.ResultEvaluator(optimizer_result, parameter_optimizer)[source]¶

Bases: object

Evaluate optimization results by comparing simulation output with experimental data.

This provides tools to assess the quality of optimized models by: 1. Simulating the optimized model on experimental conditions 2. Comparing simulation results with experimental measurements 3. Calculating correlation and other statistical metrics 4. Generating visualization plots

Methods

`calculate_evaluation_metrics`()	Calculate evaluation metrics comparing simulation results with experimental data.
`export_results_to_csv`(save_path)	Export detailed results to CSV for further analysis.
`generate_evaluation_report`([save_path, ...])	Generate a comprehensive evaluation report.
`plot_prediction_vs_experimental`([save_path, ...])	Create a scatter plot comparing predicted vs experimental values.
`plot_residuals`([save_path, ...])	Create residual plots to assess model fit quality.
`simulate_optimized_model`()	Simulate the optimized model on all experimental conditions.

__init__(optimizer_result, parameter_optimizer)[source]¶: Initialize the result evaluator.

simulate_optimized_model() → Dict[source]¶: Simulate the optimized model on all experimental conditions.

calculate_evaluation_metrics() → Dict[source]¶: Calculate evaluation metrics comparing simulation results with experimental data.

plot_prediction_vs_experimental(save_path: str | None = None, show_confidence_interval: bool = False, show_experiment_ids: bool = False, figsize: Tuple[int, int] = (8, 6)) → Figure[source]¶: Create a scatter plot comparing predicted vs experimental values.

plot_residuals(save_path: str | None = None, show_experiment_ids: bool = False, figsize: Tuple[int, int] = (9, 4)) → Figure[source]¶: Create residual plots to assess model fit quality.

generate_evaluation_report(save_path: str | None = None, include_config: bool = True) → str[source]¶: Generate a comprehensive evaluation report.

export_results_to_csv(save_path: str)[source]¶: Export detailed results to CSV for further analysis.

BNMPy.result_evaluation.evaluate_optimization_result(optimizer_result, parameter_optimizer, output_dir: str = '.', plot_residuals: bool = True, save: bool = True, detailed: bool = False, figsize: Tuple[int, int] = (8, 6), show_confidence_interval: bool = False) → ResultEvaluator[source]¶

Convenience function to perform a complete evaluation of optimization results.

This function generates and saves the following files in output_dir: - prediction_vs_experimental.png: Scatter plot of predicted vs experimental values - residual_analysis.png: Residual plots (if plot_residuals=True) - evaluation_report.txt: Text report with metrics and optimization config - detailed_results.csv: CSV file with all data points - pbn.txt: Optimized PBN model in text format

BNMPy.result_evaluation.evaluate_pbn(pbn, experiments, output_dir: str = '.', plot_residuals: bool = True, save: bool = True, detailed: bool = True, config: dict | None = None, Measured_formula: str | None = None, normalize: bool = False, figsize: Tuple[int, int] = (8, 6), show_confidence_interval: bool = False)[source]¶

Evaluate a PBN directly against experiment data (list or CSV).

This function generates and saves the following files in output_dir: - prediction_vs_experimental.png: Scatter plot of predicted vs experimental values - residual_analysis.png: Residual plots (if plot_residuals=True) - evaluation_report.txt: Text report with metrics - detailed_results.csv: CSV file with all data points - pbn.txt: PBN model in text format

Basic Usage¶

Evaluating Optimization Results¶

import BNMPy

# Run optimization
optimizer = BNMPy.ParameterOptimizer(pbn, "experiments.csv")
result = optimizer.optimize(method='differential_evolution')

# Evaluate results with plots and report
evaluator = BNMPy.evaluate_optimization_result(
    result,
    optimizer,
    output_dir="evaluation_results",
    plot_residuals=True,
    save=True,
    detailed=True,
    figsize=(8, 6)
)

Evaluating a PBN¶

import BNMPy

# Evaluate an existing PBN
pbn = BNMPy.load_pbn_from_file("network.txt")
exp_data = BNMPy.ExperimentData("experiments.csv")

results = BNMPy.evaluate_pbn(
    pbn,
    exp_data,
    output_dir="pbn_evaluation",
    config={'steady_state': {'method': 'monte_carlo'}}
)

print(f"MSE: {results['mse']:.4f}")
print(f"Correlation: {results['correlation']:.3f}")

Generated Plots¶

The evaluation functions generate several plots to assess model quality:

1. Prediction vs Experimental Plot¶

prediction_vs_experimental.png

Scatter plot comparing predicted vs experimental values:

X-axis: Experimental values from CSV file
Y-axis: Predicted values from the model
Perfect prediction line: Red dashed line (y=x)
Regression line: Green line showing linear relationship
Confidence interval: Light green shaded area (95% confidence)
Statistics: Correlation coefficient (r), p-value, and MSE

2. Residuals Plot¶

residuals.png

Shows distribution of prediction errors:

Left panel: Residuals vs Predicted values
- Residuals = Predicted - Experimental
- Horizontal red line at y=0
Right panel: Histogram of residuals
- Distribution of prediction errors
- Shows mean and standard deviation

3. Optimization History Plot¶

optimization_history.png

Shows MSE progression during optimization:

X-axis: Optimization iterations
Y-axis: Mean Squared Error (MSE)
Line: MSE values over iterations
Stagnation periods: Highlighted if enabled

Output Files¶

When save=True, the function generates:

detailed_results.csv: Per-experiment predictions and errors
evaluation_report.txt: Summary statistics and model performance
prediction_vs_experimental.png: Prediction quality plot
residuals.png: Residual analysis (if plot_residuals=True)

Example Output Structure¶

evaluation_results/
├── detailed_results.csv
├── evaluation_report.txt
├── prediction_vs_experimental.png
└── residuals.png

Evaluation Report¶

Text file with summary statistics:

Optimization Evaluation Report
==============================

Final MSE: 0.0123
Correlation: 0.89
P-value: 1.2e-15
RMSE: 0.111
MAE: 0.089

Number of experiments: 10
Number of measurements: 40

Optimization converged successfully
Iterations: 245
Function evaluations: 3675