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integrate feature importance analysis into comparing (goeckslab#21)
* init feature_importance * integrate result into comparing result * changed the title of plots * changed for flask8 * resolved bugs and added tests for best_model.csv * updated the test file * clear for lint
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| Original file line number | Diff line number | Diff line change |
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@@ -6,4 +6,6 @@ env | |
| *.pkl | ||
| *.ipynb | ||
| __pycache__ | ||
| .DS_Store | ||
| .DS_Store | ||
| tool_test_output.html | ||
| tool_test_output.json | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| import base64 | ||
| import logging | ||
| import os | ||
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| import matplotlib.pyplot as plt | ||
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| import pandas as pd | ||
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| from pycaret.classification import ClassificationExperiment | ||
| from pycaret.regression import RegressionExperiment | ||
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| logging.basicConfig(level=logging.DEBUG) | ||
| LOG = logging.getLogger(__name__) | ||
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| class FeatureImportanceAnalyzer: | ||
| def __init__( | ||
| self, | ||
| task_type, | ||
| output_dir, | ||
| data_path=None, | ||
| data=None, | ||
| target_col=None): | ||
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||
| if data is not None: | ||
| self.data = data | ||
| LOG.info("Data loaded from memory") | ||
| else: | ||
| self.target_col = target_col | ||
| self.data = pd.read_csv(data_path, sep=None, engine='python') | ||
| self.data.columns = self.data.columns.str.replace('.', '_') | ||
| self.data = self.data.fillna(self.data.median(numeric_only=True)) | ||
| self.task_type = task_type | ||
| self.target = self.data.columns[int(target_col) - 1] | ||
| self.exp = ClassificationExperiment() \ | ||
| if task_type == 'classification' \ | ||
| else RegressionExperiment() | ||
| self.plots = {} | ||
| self.output_dir = output_dir | ||
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| def setup_pycaret(self): | ||
| LOG.info("Initializing PyCaret") | ||
| setup_params = { | ||
| 'target': self.target, | ||
| 'session_id': 123, | ||
| 'html': True, | ||
| 'log_experiment': False, | ||
| 'system_log': False | ||
| } | ||
| LOG.info(self.task_type) | ||
| LOG.info(self.exp) | ||
| self.exp.setup(self.data, **setup_params) | ||
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| def save_coefficients(self): | ||
| model = self.exp.create_model('lr') | ||
| coef_df = pd.DataFrame({ | ||
| 'Feature': self.data.columns.drop(self.target), | ||
| 'Coefficient': model.coef_[0] | ||
| }) | ||
| coef_html = coef_df.to_html(index=False) | ||
| return coef_html | ||
|
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| def save_tree_importance(self): | ||
| model = self.exp.create_model('rf') | ||
| importances = model.feature_importances_ | ||
| feature_importances = pd.DataFrame({ | ||
| 'Feature': self.data.columns.drop(self.target), | ||
| 'Importance': importances | ||
| }).sort_values(by='Importance', ascending=False) | ||
| plt.figure(figsize=(10, 6)) | ||
| plt.barh( | ||
| feature_importances['Feature'], | ||
| feature_importances['Importance']) | ||
| plt.xlabel('Importance') | ||
| plt.title('Feature Importance (Random Forest)') | ||
| plot_path = os.path.join( | ||
| self.output_dir, | ||
| 'tree_importance.png') | ||
| plt.savefig(plot_path) | ||
| plt.close() | ||
| self.plots['tree_importance'] = plot_path | ||
|
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| def save_shap_values(self): | ||
| model = self.exp.create_model('lightgbm') | ||
| import shap | ||
| explainer = shap.Explainer(model) | ||
| shap_values = explainer.shap_values( | ||
| self.data.drop(columns=[self.target])) | ||
| shap.summary_plot(shap_values, self.data.drop( | ||
| columns=[self.target]), show=False) | ||
| plt.title('Shap (LightGBM)') | ||
| plot_path = os.path.join( | ||
| self.output_dir, 'shap_summary.png') | ||
| plt.savefig(plot_path) | ||
| plt.close() | ||
| self.plots['shap_summary'] = plot_path | ||
|
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| def generate_feature_importance(self): | ||
| coef_html = self.save_coefficients() | ||
| self.save_tree_importance() | ||
| self.save_shap_values() | ||
| return coef_html | ||
|
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| def encode_image_to_base64(self, img_path): | ||
| with open(img_path, 'rb') as img_file: | ||
| return base64.b64encode(img_file.read()).decode('utf-8') | ||
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| def generate_html_report(self, coef_html): | ||
| LOG.info("Generating HTML report") | ||
|
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| # Read and encode plot images | ||
| plots_html = "" | ||
| for plot_name, plot_path in self.plots.items(): | ||
| encoded_image = self.encode_image_to_base64(plot_path) | ||
| plots_html += f""" | ||
| <div class="plot" id="{plot_name}"> | ||
| <h2>Feature importance analysis from a | ||
| trained Random Forest</h2> | ||
| <h3>{'Use gini impurity for' | ||
| 'calculating feature importance for classification' | ||
| 'and Variance Reduction for regression' | ||
| if plot_name == 'tree_importance' | ||
| else 'SHAP Summary from a trained lightgbm'}</h3> | ||
| <img src="data:image/png;base64, | ||
| {encoded_image}" alt="{plot_name}"> | ||
| </div> | ||
| """ | ||
|
|
||
| # Generate HTML content with tabs | ||
| html_content = f""" | ||
| <h1>PyCaret Feature Importance Report</h1> | ||
| <div id="coefficients" class="tabcontent"> | ||
| <h2>Coefficients (based on a trained | ||
| {'Logistic Regression' | ||
| if self.task_type == 'classification' | ||
| else 'Linear Regression'} Model)</h2> | ||
| <div>{coef_html}</div> | ||
| </div> | ||
| {plots_html} | ||
| """ | ||
|
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| return html_content | ||
|
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| def run(self): | ||
| LOG.info("Running feature importance analysis") | ||
| self.setup_pycaret() | ||
| coef_html = self.generate_feature_importance() | ||
| html_content = self.generate_html_report(coef_html) | ||
| LOG.info("Feature importance analysis completed") | ||
| return html_content | ||
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| if __name__ == "__main__": | ||
| import argparse | ||
| parser = argparse.ArgumentParser(description="Feature Importance Analysis") | ||
| parser.add_argument( | ||
| "--data_path", type=str, help="Path to the dataset") | ||
| parser.add_argument( | ||
| "--target_col", type=int, | ||
| help="Index of the target column (1-based)") | ||
| parser.add_argument( | ||
| "--task_type", type=str, | ||
| choices=["classification", "regression"], | ||
| help="Task type: classification or regression") | ||
| parser.add_argument( | ||
| "--output_dir", | ||
| type=str, | ||
| help="Directory to save the outputs") | ||
| args = parser.parse_args() | ||
|
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| analyzer = FeatureImportanceAnalyzer( | ||
| args.data_path, args.target_col, | ||
| args.task_type, args.output_dir) | ||
| analyzer.run() |
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