ShapSAFE

The largest open-source medical AI skills library for OpenClaw🦞.

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
name: shap
description: Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
---

# SHAP (SHapley Additive exPlanations)

## Overview

SHAP is a unified approach to explain machine learning model outputs using Shapley values from cooperative game theory. This skill provides comprehensive guidance for:

- Computing SHAP values for any model type
- Creating visualizations to understand feature importance
- Debugging and validating model behavior
- Analyzing fairness and bias
- Implementing explainable AI in production

SHAP works with all model types: tree-based models (XGBoost, LightGBM, CatBoost, Random Forest), deep learning models (TensorFlow, PyTorch, Keras), linear models, and black-box models.

## When to Use This Skill

**Trigger this skill when users ask about**:
- "Explain which features are most important in my model"
- "Generate SHAP plots" (waterfall, beeswarm, bar, scatter, force, heatmap, etc.)
- "Why did my model make this prediction?"
- "Calculate SHAP values for my model"
- "Visualize feature importance using SHAP"
- "Debug my model's behavior" or "validate my model"
- "Check my model for bias" or "analyze fairness"
- "Compare feature importance across models"
- "Implement explainable AI" or "add explanations to my model"
- "Understand feature interactions"
- "Create model interpretation dashboard"

## Quick Start Guide

### Step 1: Select the Right Explainer

**Decision Tree**:

1. **Tree-based model?** (XGBoost, LightGBM, CatBoost, Random Forest, Gradient Boosting)
   - Use `shap.TreeExplainer` (fast, exact)

2. **Deep neural network?** (TensorFlow, PyTorch, Keras, CNNs, RNNs, Transformers)
   - Use `shap.DeepExplainer` or `shap.GradientExplainer`

3. **Linear model?** (Linear/Logistic Regression, GLMs)
   - Use `shap.LinearExplainer` (extremely fast)

4. **Any other model?** (SVMs, custom functions, black-box models)
   - Use `shap.KernelExplainer` (model-agnostic but slower)

5. **Unsure?**
   - Use `shap.Explainer` (automatically selects best algorithm)

**See `references/explainers.md` for detailed information on all explainer types.**

### Step 2: Compute SHAP Values

```python
import shap

# Example with tree-based model (XGBoost)
import xgboost as xgb

# Train model
model = xgb.XGBClassifier().fit(X_train, y_train)

# Create explainer
explainer = shap.TreeExplainer(model)

# Compute SHAP values
shap_values = explainer(X_test)

# The shap_values object contains:
# - values: SHAP values (feature attributions)
# - base_values: Expected model output (baseline)
# - data: Original feature values
```

### Step 3: Visualize Results

**For Global Understanding** (entire dataset):
```python
# Beeswarm plot - shows feature importance with value distributions
shap.plots.beeswarm(shap_values, max_display=15)

# Bar plot - clean summary of feature importance
shap.plots.bar(shap_values)
```

**For Individual Predictions**:
```python
# Waterfall plot - detailed breakdown of single prediction
shap.plots.waterfall(shap_values[0])

# Force plot - additive force visualization
shap.plots.force(shap_values[0])
```

**For Feature Relationships**:
```python
# Scatter plot - feature-prediction relationship
shap.plots.scatter(shap_values[:, "Feature_Name"])

# Colored by another feature to show interactions
shap.plots.scatter(shap_values[:, "Age"], color=shap_values[:, "Education"])
```

**See `references/plots.md` for comprehensive guide on all plot types.**

## Core Workflows

This skill supports several common workflows. Choose the workflow that matches the current task.

### Workflow 1: Basic Model Explanation

**Goal**: Understand what drives model predictions

**Steps**:
1. Train model and create appropriate explainer
2. Compute SHAP values for test set
3. Generate global importance plots (beeswarm or bar)
4. Examine top feature relationships (scatter plots)
5. Explain specific predictions (waterfall plots)

**Example**:
```python
# Step 1-2: Setup
explainer = shap.TreeExplainer(model)
shap_values = explainer(X_test)

# Step 3: Global importance
shap.plots.beeswarm(shap_values)

# Step 4: Feature relationships
shap.plots.scatter(shap_values[:, "Most_Important_Feature"])

# Step 5: Individual explanation
shap.plots.waterfall(shap_values[0])
```

### Workflow 2: Model Debugging

**Goal**: Identify and fix model issues

**Steps**:
1. Compute SHAP values
2. Identify prediction errors
3. Explain misclassified samples
4. Check for unexpected feature importance (data leakage)
5. Validate feature relationships make sense
6. Check feature interactions

**See `references/workflows.md` for detailed debugging workflow.**

### Workflow 3: Feature Engineering

**Goal**: Use SHAP insights to improve features

**Steps**:
1. Compute SHAP values for baseline model
2. Identify nonlinear relationships (candidates for transformation)
3. Identify feature interactions (candidates for interaction terms)
4. Engineer new features
5. Retrain and compare SHAP values
6. Validate improvements

**See `references/workflows.md` for detailed feature engineering workflow.**

### Workflow 4: Model Comparison

**Goal**: Compare multiple models to select best interpretable option

**Steps**:
1. Train multiple models
2. Compute SHAP values for each
3. Compare global feature importance
4. Check consistency of feature rankings
5. Analyze specific predictions across models
6. Select based on accuracy, interpretability, and consistency

**See `references/workflows.md` for detailed model comparison workflow.**

### Workflow 5: Fairness and Bias Analysis

**Goal**: Detect and analyz

SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.

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