GPTomics/bio-machine-learning-prediction-explanation

Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scikit-learn 1.4+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Model Interpretation for Omics Classifiers

"Which genes drive my classifier's predictions?" -> Compute per-feature attribution scores using SHAP values or LIME to explain which genes or features contribute most to model decisions.

• Python: shap.TreeExplainer(model).shap_values(X), lime.lime_tabular.LimeTabularExplainer()

SHAP TreeExplainer

Goal: Compute exact SHAP values for tree-based models to quantify each feature's contribution to predictions.

Approach: Use TreeExplainer for polynomial-time exact Shapley value computation on Random Forest or boosted tree models.

import shap
from sklearn.ensemble import RandomForestClassifier

model = RandomForestClassifier(n_estimators=100, random_state=42)
model.fit(X_train, y_train)

explainer = shap.TreeExplainer(model)
# CORRECT (v0.47+): Call explainer directly, NOT .shap_values()
shap_values = explainer(X_test)

# shap_values is an Explanation object
# .values has shape (n_samples, n_features) for binary
# .base_values has expected value
print(f'SHAP values shape: {shap_values.values.shape}')

Summary Plot (Global Feature Importance)

import shap
import matplotlib.pyplot as plt

# Beeswarm plot: shows impact direction and magnitude
shap.plots.beeswarm(shap_values, max_display=20, show=False)
plt.tight_layout()
plt.savefig('shap_summary.png', dpi=150, bbox_inches='tight')
plt.close()

# Bar plot: mean absolute SHAP values
shap.plots.bar(shap_values, max_display=20, show=False)
plt.savefig('shap_bar.png', dpi=150, bbox_inches='tight')

Force Plot (Individual Prediction)

# Explain single prediction
sample_idx = 0
shap.plots.force(shap_values[sample_idx], matplotlib=True, show=False)
plt.savefig('shap_force_single.png', dpi=150, bbox_inches='tight')

# Waterfall plot (cleaner alternative)
shap.plots.waterfall(shap_values[sample_idx], max_display=15, show=False)
plt.savefig('shap_waterfall.png', dpi=150, bbox_inches='tight')

SHAP for XGBoost

from xgboost import XGBClassifier
import shap

xgb = XGBClassifier(n_estimators=100, random_state=42, eval_metric='logloss')
xgb.fit(X_train, y_train)

explainer = shap.TreeExplainer(xgb)
shap_values = explainer(X_test)

# For XGBoost, shap_values contains log-odds contributions
shap.plots.beeswarm(shap_values, max_display=20)

LIME (Local Interpretable Model-agnostic Explanations)

from lime.lime_tabular import LimeTabularExplainer
import numpy as np

explainer = LimeTabularExplainer(
    X_train.values,
    feature_names=X_train.columns.tolist(),
    class_names=['control', 'disease'],
    mode='classification'
)

# Explain single instance
sample_idx = 0
exp = explainer.explain_instance(
    X_test.iloc[sample_idx].values,
    model.predict_proba,
    num_features=20
)

exp.save_to_file('lime_explanation.html')
# Or get as list: exp.as_list()

Extract Top Features from SHAP

import pandas as pd
import numpy as np

# Mean absolute SHAP value per feature
mean_shap = np.abs(shap_values.values).mean(axis=0)
feature_importance = pd.DataFrame({
    'feature': X_test.columns,
    'mean_shap': mean_shap
}).sort_values('mean_shap', ascending=False)

top_features = feature_importance.head(20)
top_features.to_csv('shap_top_features.csv', index=False)

Dependence Plot (Feature Interactions)

# Shows how SHAP value varies with feature value
# Automatically colors by interacting feature
shap.plots.scatter(shap_values[:, 'GENE1'], color=shap_values, show=False)
plt.savefig('shap_dependence.png', dpi=150, bbox_inches='tight')

Multi-class SHAP

explainer = shap.TreeExplainer(model)
shap_values = explainer(X_test)

# For multi-class, shap_values.values has shape (n_samples, n_features, n_classes)
# Access class-specific values:
class_idx = 1
shap.plots.beeswarm(shap_values[:, :, class_idx], max_display=20)

Related Skills

• machine-learning/omics-classifiers - Train models to interpret
• machine-learning/biomarker-discovery - Compare with selection-based importance
• data-visualization/heatmaps-clustering - Visualize SHAP values as heatmap