shap

Explain model predictions by attributing outcomes to input features with SHAP values.

4|1|Updated Jun 18, 2025
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill shap-holobiomicslab
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: shap
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/shap
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill shap-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Explain machine learning predictions by attributing outcomes to input features using SHAP values.

Core Features & Use Cases

  • SHAP-based explanations for model predictions across tree-based, deep, and linear models.
  • Global and local visualizations (beeswarm, waterfall, bar, scatter, heatmap) to diagnose and communicate model behavior.
  • Guidance for model debugging, fairness analysis, comparison, and production deployment of explanations.

Quick Start

Train or load a model, create an appropriate SHAP explainer, compute SHAP values for your data, and visualize the results.

Frequently Asked Questions about shap

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I explain machine learning predictions by attributing outcomes to input features?

SHAP values explain machine learning predictions by attributing outcomes to input features, quantifying each feature's contribution to a specific prediction. This allows you to understand and debug model behavior across tree-based, deep, and linear models.

Can I generate visualizations like beeswarm or waterfall charts to diagnose model behavior?

Yes, you can generate global and local visualizations including beeswarm, waterfall, bar, scatter, and heatmap charts to diagnose and communicate model behavior. These visualizations help identify feature importance and feature attribution patterns.

Does SHAP work with deep neural networks and tree-based models?

SHAP works with tree-based models, deep neural networks, and linear models by providing specific explainers: TreeExplainer, DeepExplainer, LinearExplainer, and KernelExplainer to compute accurate feature attribution values.

What is the best way to use SHAP for model debugging and fairness analysis?

The best way to use SHAP for model debugging and fairness analysis is to compute SHAP values across your dataset and use global visualizations like heatmaps and bar charts to identify biased feature attributions and diagnose anomalous model predictions.

How do I choose the right background data and baselines for SHAP explainers?

Choosing the right background data and baselines for SHAP explainers involves selecting representative background samples to serve as a reference distribution. This ensures accurate feature attribution calculations for your specific machine learning model and prediction context.

When should I not use SHAP values for model interpretation?

You should not use SHAP values for model interpretation when working with extremely large datasets where computing feature attributions becomes computationally prohibitive, or when you require real-time explanations without pre-computing background data distributions.