A Comprehensive Guide into SHAP (SHapley Additive exPlanations) Values

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A comprehensive guide into SHAP (SHapley Additive exPlanations) values

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In today’s fast-paced world, rapid technological advancements have made AI an essential and ubiquitous part of our daily lives. Central to these AI systems are sophisticated machine learning models that are crucial for making critical decisions across various domains. However, the increasing complexity of these models has made understanding their decision-making processes and predictions challenging and overwhelming, especially when the stakes are high. Picture yourself applying for a loan, only to have the model reject your application without any explanation – quite frustrating, right?

This is where SHAP values (SHapley Additive exPlanations) come to the rescue! In this comprehensive guide, we will delve into the depths of SHAP values and their significance in model interpretability. We’ll uncover the theoretical foundations of SHAP values, investigate various calculation methods such as KernelSHAP, TreeSHAP, and DeepSHAP, and examine their interpretation and visualization techniques. By the end of this article, you’ll grasp how SHAP values can be employed in real-world scenarios to render model decisions more transparent and equitable. So, strap in and prepare for a thrilling adventure into SHAP values and model interpretability!

Background on Model Interpretability

As the global landscape increasingly adopts machine learning (ML) and artificial intelligence (AI) across various sectors, the demand for model interpretability has reached unprecedented heights. With ML models’ growing complexity and capabilities, gaining insights into their inner workings and elucidating their predictions is becoming imperative. Often perceived as “black boxes,” ML models can be challenging to decipher, making it hard to discern the rationale behind a specific decision or prediction. This absence of interpretability poses significant concerns in numerous contexts, such as medical or financial sectors, where understanding the basis of a model’s diagnosis or decision is paramount.

Since the inception of AI in the 1960s, the ‘black box’ nature of models, especially neural networks, has been a concern for researchers. Rosenblatt’s perceptron (1958) was relatively interpretable due to its simplicity, but more complex models like multi-layer perceptrons emerged to tackle intricate problems, complicating understanding. During the 1960s and 1970s, researchers faced difficulties deciphering the inner workings of these networks, composed of multiple layers and numerous interconnected nodes, resulting in growing concerns about their opacity. This led to skepticism in trusting models with unclear decision-making processes. Concurrently, more interpretable AI approaches, such as rule-based systems and decision trees, emerged, providing greater transparency and becoming more appealing in contexts where interpretability was essential. The ‘black box’ debate and the pursuit of model interpretability persist as AI and machine learning advance. Researchers continuously develop innovative techniques to address these concerns and improve our understanding of these powerful yet enigmatic systems.

Interpretability is important for several reasons:

  • Trust: Transparent models foster trust among users and stakeholders, as they can comprehend the reasoning behind predictions.
  • Debugging: Interpretability allows for easier identification of errors and biases in the model.
  • Legal Compliance: Regulations like the European Union’s General Data Protection Regulation (GDPR) require AI systems to explain their decisions.
  • Ethical Considerations: As ML models affect real-world decisions, understanding their inner workings helps prevent potential harm or discrimination.
  • Scientific Understanding: Clear explanations promote the advancement of knowledge and facilitate collaboration among researchers.

Achieving interpretability in machine learning models is a complex task with several challenges, such as:

  • Model Complexity: As machine learning models, for example, large language models (LLMs) like OpenAI’s GPT series, become more sophisticated, their complexity increases, making it difficult to understand their decision-making processes. LLMs are based on deep learning architectures, such as the transformer, and consist of multiple layers with millions or even billions of parameters and non-linear transformations in their structure. These models’ sheer size and intricacy present a significant challenge to explainability, as comprehending the relationships between inputs and outputs and the decision-making processes becomes exceedingly difficult.
  • High-dimensional Data: Machine learning models frequently handle high-dimensional data consisting of many features or variables. Discerning relationships and dependencies among these features are challenging, as visualizing and comprehending high-dimensional data spaces is inherently difficult for humans. This limitation obstructs our understanding of the model’s inner workings and the extraction of valuable insights from its predictions. For instance, language models transform input words or tokens into continuous vector representations called embeddings. These high-dimensional embeddings encapsulate intricate semantic relationships between words, yet interpreting the connections between these embeddings and the model’s predictions remains a formidable task.
  • Confounding Variables: Interpretability is also challenged by confounding variables, which are factors that can influence the model’s predictions. These variables can create biases and false correlations, resulting in wrong or misleading interpretations. Separating the true relationships between features and outcomes from the effects of confounding variables is essential for interpretability, but this process can be complicated and difficult.
  • Data Quality and Integrity: Model interpretability in machine learning is heavily influenced by data quality and integrity. Insufficient data quality and integrity can lead to unpredictable and difficult-to-interpret predictions, as the model learns from flawed data. Noise in data and preprocessing transformations can impede interpretability by obscuring genuine patterns and altering feature relationships. Both factors emphasize data quality and integrity as essential challenges to overcome in enhancing machine learning model interpretability. Ensuring high-quality and trustworthy data is crucial for understanding a model’s predictions and addressing biases. This requires diligent data collection, processing, validation, ongoing monitoring, and maintenance using data cleaning and feature selection techniques.

Over time, researchers have devised various techniques to enhance interpretability, including:

  1. Inherently Interpretable Models: Models such as linear regression, decision trees, and rule-based systems prioritize interpretability by design.
  2. Model-Agnostic Methods: LIME (Local Interpretable Model-agnostic Explanations) and SHAP (SHapley Additive exPlanations) are techniques that simplify the understanding of any machine learning model. They do this by focusing on specific parts or local areas of the model’s decision-making process, making it easier to see how the model arrives at its predictions.
  3. Visualization Techniques: Tools like t-SNE (t-Distributed Stochastic Neighbor Embedding) and UMAP (Uniform Manifold Approximation and Projection) facilitate the visualization of high-dimensional data, shedding light on model behavior.

Ethics and regulation play crucial roles in ensuring responsible AI as ML models gain prominence. Guidelines such as the GDPR mandate clear explanations of AI systems’ decisions, and various AI ethics frameworks emphasize transparency and accountability to avert potential harm or discrimination.

Overview of SHAP Values and their Significance in Model Interpretability

One key approach to enhancing model interpretability is the use of SHAP (SHapley Additive exPlanations), a powerful method for attributing the contribution of each feature to a model’s prediction for a specific instance. Introduced by Lundberg and Lee in 2017, SHAP values are rooted in cooperative game theory (which is concerned with how groups of individuals can work together to achieve a common goal) and inspired by the work of Nobel laureate Lloyd Shapley.

The Shapley value, derived from Lloyd Shapley’s work in cooperative game theory, offers a unique and fair means of allocating payoffs among players. The Shapley value calculation involves averaging the marginal contributions of each player (or feature) across all potential permutations of players. This involves assessing every possible combination of features and determining the impact each feature has on the model’s prediction when included in these combinations. By averaging these contributions across all possible feature arrangements, we can achieve a balanced and interpretable evaluation of each feature’s importance in the model’s prediction.

SHAP is a technique that aids in understanding how individual features affect a model’s output. In short, SHAP values estimate the significance of each feature within a model. These values provide a consistent and interpretable method for comprehending the predictions made by any ML model. The core concept behind SHAP values is to allocate a specific value to each input feature, representing its contribution to a particular prediction.

This process ensures that SHAP values follow three essential properties:

  • Efficiency: The sum of all SHAP values, for instance, shows the combined effect of its features on the model’s prediction. By quantifying how each feature moves the prediction away from the average, SHAP values help explain the model’s output. For instance, if the average prediction is 50 and the model’s prediction is 60, the difference is 10. The sum of all SHAP values for the features should equal 10, representing each feature’s contribution to the difference. By adding up all SHAP values, we can account for the entire influence of the features on the prediction.
  • Symmetry: If two features contribute equally to a prediction, they will have the same SHAP values. This ensures fairness in attributing importance to features.
  • Additivity: SHAP values can be added to show the joint contribution of several features to a prediction. This helps understand the combined effect of multiple features on the model’s output.

SHAP values offer significant advantages in enhancing model interpretability:

  • Model Agnosticism: SHAP values can be applied to any ML model, including black-box models like deep neural networks, gradient-boosted trees, and support vector machines, allowing practitioners to choose accurate models without sacrificing interpretability. However, calculating SHAP values for large language models (LLMs) like OpenAI’s GPT series is theoretically possible but computationally challenging due to their scale and complexity. Despite these challenges, recent research explores the applicability of SHAP and similar methods to natural language processing tasks.
  • Local Explanations: SHAP values provide instance-specific explanations, helping stakeholders understand the factors behind individual predictions. This is especially valuable when understanding single decisions such as loan approvals or medical diagnoses.
  • Global Insights: Aggregating SHAP values across numerous instances enables researchers and practitioners to comprehensively understand a model’s behavior and pinpoint key features that drive predictions. This valuable information can be harnessed to fine-tune the model and address potential biases.
  • Fairness and Accountability: SHAP values help identify and quantify potential biases or unfair treatment within a dataset, enabling practitioners to take steps to mitigate them and ensure fairness and accountability in their ML models.

SHAP Calculation

Different algorithms have been developed to calculate SHAP values for various model types, with the most notable methods being KernelSHAP, TreeSHAP, and DeepSHAP.

  • KernelSHAP: KernelSHAP is a model-agnostic method for computing SHAP values applicable to any model. It employs a weighted linear regression technique to approximate Shapley values for each feature. However, this method can be computationally expensive, particularly with many features. KernelSHAP generates the original data’s perturbations, or “shadows,” using a kernel to approximate the feature value distribution. The model predicts the output for each perturbation, and the differences between predicted and original outputs help compute each feature’s SHAP value. This approach is advantageous because it can handle high-dimensional datasets and is compatible with any model type, offering flexibility and power for enhancing model interpretability. The algorithm uses linear regression to approximate the relationship between input features and model output, where the linear model’s coefficients represent the SHAP values. KernelSHAP creates perturbed samples by removing some features and replacing them with expected values. This new dataset trains a linear regression model to fit the model’s output, and the resulting coefficients serve as SHAP values, indicating feature importance for a specific instance.
  • TreeSHAP: TreeSHAP is a powerful method for computing SHAP values designed explicitly for tree-based models, including decision trees, random forests, and gradient-boosted trees. This algorithm takes advantage of the tree structure to efficiently calculate SHAP values. By breaking down a model’s decision process into a series of smaller decisions associated with specific features, TreeSHAP can handle non-linear and non-additive interactions between features often present in these models. Additionally, TreeSHAP reduces the computational complexity of calculating SHAP values by leveraging the tree structure, making it efficient and scalable for large datasets and complex tree-based models. Overall, TreeSHAP is a useful tool for improving model interpretability and transparency in tree-based ML models.
  • DeepSHAP: DeepSHAP is a technique used to calculate SHAP values for deep neural networks to improve model interpretability. It combines the DeepLIFT method with the SHAP framework, which assigns importance scores to input features. This approach allows DeepSHAP to handle the complex, non-linear interactions between features often found in deep neural networks. By propagating SHAP values from the output layer back to the input layer, DeepSHAP offers a clear and intuitive understanding of each feature’s contribution to the model’s output. It adapts the SHAP concept for deep learning models by recursively calculating SHAP values for each neuron, starting from the output layer and considering the neuron’s activation function and contribution to the model’s output. Ultimately, DeepSHAP provides interpretable explanations for complex deep learning models while maintaining the consistency and fairness properties of SHAP values.
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Interpreting SHAP Values for Enhanced Model Understanding

Global Interpretation

Global interpretation involves aggregating SHAP values across multiple instances to understand the overall behavior of a machine learning model and identify the most important features driving its predictions. This can be done by calculating the mean SHAP value for each feature. Mean SHAP values can be used to rank features by their importance and improve the accuracy and reliability of a model. Global interpretation is valuable for refining models, addressing potential biases, and prioritizing features for further analysis.

Local Interpretation

Local interpretation focuses on understanding the factors driving individual predictions using SHAP values, which provide instance-specific explanations. This is useful when understanding single decisions is critical, such as loan approvals, medical diagnoses, or fraud detection. Local interpretation involves calculating the SHAP values for each feature for a specific instance to gain insight into which features were most important for that decision and why the model made that particular decision. This can help identify potential biases or errors in the model and improve its fairness and transparency. Local interpretation is valuable for understanding the behavior of a model in specific instances and improving model interpretability.


Several visualization techniques are available for interpreting SHAP values, which can aid in understanding the impact of features on model predictions. We will discuss these visualization techniques under two categories: global and local interpretation visualizations. To implement these visualizations, we will build a model to interpret the impact of its features on the model using a default probability prediction use case. The dataset contains information on customers who have taken out loans and whether they have defaulted on their payments. The task is to predict whether a loan applicant is likely to default on their loan payments.

Global Interpretation Visualizations:

  • SHAP Summary plot: A summary plot offers a comprehensive view of the most influential features in a model. It ranks features based on their effect on the model’s predictions, with the x-axis representing the SHAP value – a measure that quantifies a feature’s influence on a specific prediction. The y-axis displays the features, while the plot also demonstrates the distribution of SHAP values for each feature, and the color represents the value of the feature from low to high. This aids in determining the features with the greatest impact on model predictions. Each dot signifies the SHAP value of a particular feature for a given data point, allowing for the identification of the most critical features, the nature of their influence on model outputs (positive or negative), and the extent of their contribution. This can be implemented as follows:
    # Assuming the model has already been built using the XGboost Classifier
    # Calculate SHAP values
    explainer = shap.TreeExplainer(model)
    shap_values = explainer(X_test)
    # Summary plot
    shap.summary_plot(shap_values, X_test)

    SHAP Summary plot

  • Bar Plot: The SHAP bar plot offers an alternative way to visualize global feature importance. It presents each feature’s average absolute SHAP values as bars in a chart format. Taller bars signify the greater importance of the feature to the model. This plot delivers a clear and straightforward representation of global feature importance. A bar plot effectively illustrates the contribution of individual features to a single prediction, with bars reflecting the magnitude and direction of their impact. Positive values denote a positive influence on the prediction, while negative values suggest a negative influence. With the already calculated SHAP values we can implement this as follows:
    # Feature importance

    Bar Plot

  • SHAP Force Plot: The force plot offers an in-depth perspective of SHAP values for individual instances. It displays the base value (expected model output) and demonstrates how each feature’s influence pushes the model’s prediction above or below this base value. The plot aids in comprehending the contributions of each feature to the model’s output for a specific instance while emphasizing positive and negative impacts. A force plot serves as an enhanced version of a bar plot, illustrating how each feature contributes to a prediction and how their contributions vary with the changing values of the features. The plot commences with a baseline value, representing the model’s average prediction. It then exhibits how the SHAP values of each feature contribute to the prediction and how the prediction evolves as features are added or removed. The force plot can be implemented as follows:
    # Force plot
    instance_index = 0

    SHAP Force Plot

  • SHAP Waterfall Plot: The SHAP Waterfall Plot is a useful visualization tool that displays the additive contributions of features to a model’s prediction for a specific instance. Compared to the decision plot, the waterfall plot presents the contributions as a bar chart, making it easier to identify each feature’s positive and negative impact. This type of force plot depicts how the SHAP values of each feature combine to produce the final prediction. The plot begins with a baseline value and then shows how each feature contributes to the overall prediction. This visualization makes it possible to identify the features that impact the model’s predictions most. The waterfall plot can be implemented as follows:
    # Waterfall plot

    SHAP Waterfall Plot

Use Case and Applications

SHAP has various use cases and applications, including:

  • Feature Importance: SHAP can help determine the importance of features in a model. Analyzing the SHAP values for each feature can identify which features have the most significant impact on the model’s predictions.
  • Model Debugging: SHAP can detect issues with a model, such as bias or overfitting. By analyzing the SHAP values for each feature, we can identify which features are causing the model to produce inaccurate predictions.
  • Model Comparison: SHAP can compare the performance of different models. Analyzing the SHAP values for each model can determine which model produces more accurate predictions and which features contribute the most to the differences in performance.
  • Explainable AI: SHAP can provide explanations for model predictions. Analyzing the SHAP values for each feature can offer a user-friendly explanation of how the model arrived at its prediction.
  • Data Exploration: SHAP can explore a dataset and identify relationships between features. Analyzing the SHAP values for each feature can identify which features relate to each other and which are most important for making accurate predictions.

Limitation and Challenges

SHAP is a useful technique for interpreting machine learning models, but there are some limitations and challenges to consider.

These include:

  1. Limited Support for Categorical Features: SHAP has limited support for categorical features, which can limit its ability to provide meaningful explanations for models that rely heavily on such features.
  2. Lack of a Unified Approach for Handling Time Series Data: SHAP does not have a unified approach for handling time series data, making it difficult to use for interpret models that use such data.
  3. Challenges with High-Dimensional Data: SHAP can become computationally infeasible when dealing with high-dimensional data, limiting its ability to provide accurate and timely explanations for complex models with many features.
  4. Computationally Intensive: SHAP calculations can be computationally intensive, making it challenging to use in real-time applications.
  5. Interpretability vs. Accuracy Trade-Off: While SHAP provides local interpretability, it comes at the cost of global accuracy. The SHAP values provide an approximate explanation of how each feature contributes to the output, but they may not capture the full complexity of the model.
  6. Dependence on the Choice of Background Dataset: The background dataset’s choice can significantly impact the SHAP values, potentially leading to biased or incorrect explanations.
  7. Interpretability: The explanations provided by SHAP can still be difficult for non-experts to understand, limiting its use in certain applications.


SHAP has numerous use cases and applications, including feature importance, model debugging, model comparison, explainable AI, and data exploration. However, it is important to consider the limitations and challenges associated with SHAP when applying it to real-world problems. With a deep understanding of SHAP values, we can develop more accurate and transparent ML models.

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