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Reading list

Machine Learning Basics for a Newbie
6 Steps of Machine learning Lifecycle Introduction to Predictive Modeling
Introduction to Exploratory Data Analysis & Data Insights Descriptive Statistics Inferential Statistics How to Understand Population Distributions?
Reading Data Files into Python Different Variable Datatypes
Probability for Data Science Basic Concepts of Probability Axioms of Probability Conditional Probability
Central Tendencies for Continuous Variables Spread of Data KDE plots for Continuous Variable Overview of Distribution for Continuous variables Normal Distribution Skewed Distribution Skeweness and Kurtosis Distribution for Continuous Variable
Central Tendencies for Categorical Variables Understanding Discrete Distributions Performing EDA on Categorical Variables
Dealing with Missing Values Understanding Outliers Identifying Outliers in Data Outlier Detection in Python Outliers Detection Using IQR, Z-score, LOF and DBSCAN
Sample and Population Central Limit Theorem Confidence Interval and Margin of Error
Bivariate Analysis Introduction
Covariance Pearson Correlation Spearman's Correlation & Kendall's Tau Correlation versus Causation Tabular and Graphical methods for Bivariate Analysis Performing Bivariate Analysis on Continuous-Continuous Variables
Tabular and Graphical methods for Continuous-Categorical Variables Introduction to Hypothesis Testing P-value Two sample Z-test T-test T-test vs Z-test Performing Bivariate Analysis on Continuous-Catagorical variables
Chi-Squares Test Bivariate Analysis on Categorical Categorical Variables
Multivariate Analysis A Comprehensive Guide to Data Exploration The Data Science behind IPL
Supervised Learning vs Unsupervised Learning Reinforcement Learning Generative and Descriminative Models Parametric and Non Parametric model
Machine Learning Pipeline Preparing Dataset Build a Benchmark Model: Regression Build a Benchmark Model: Classification
Evaluation Metrics for Machine Learning Everyone should know Confusion Matrix Accuracy Precision and Recall AUC-ROC Log Loss R2 and Adjusted R2
Dealing with Missing Values Replacing Missing Values Imputing Missing Values in Data Working with Categorical Variables Working with Outliers Preprocessing Data for Model Building
Understanding Cost Function Understanding Gradient Descent Math Behind Gradient Descent Assumptions of Linear Regression Implement Linear Regression from Scratch Train Linear Regression in Python Implementing Linear Regression in R Diagnosing Residual Plots in Linear Regression Models Generalized Linear Models Introduction to Logistic Regression Odds Ratio Implementing Logistic Regression from Scratch Introduction to Scikit-learn in Python Train Logistic Regression in python Multiclass using Logistic Regression How to use Multinomial and Ordinal Logistic Regression in R ? Challenges with Linear Regression Introduction to Regularisation Implementing Regularisation Ridge Regression Lasso Regression
Introduction to K Nearest Neighbours Determining the Right Value of K in KNN Implement KNN from Scratch Implement KNN in Python
Bias Variance Tradeoff Introduction to Overfitting and Underfitting Visualizing Overfitting and Underfitting Selecting the Right Model What is Validation? Hold-Out Validation Understanding K Fold Cross Validation
Introduction to Feature Selection Feature Selection Algorithms Missing Value Ratio Low Variance Filter High Correlation Filter Backward Feature Elimination Forward Feature Selection Implement Feature Selection in Python Implement Feature Selection in R
Introduction to Decision Tree Purity in Decision Tree Terminologies Related to Decision Tree How to Select Best Split Point in Decision Tree? Chi-Squares Information Gain Reduction in Variance Optimizing Performance of Decision Tree Train Decision Tree using Scikit Learn Pruning of Decision Trees
Introduction to Feature Engineering Feature Transformation Feature Scaling Feature Engineering Frequency Encoding Automated Feature Engineering: Feature Tools
Introduction to Naive Bayes Conditional Probability and Bayes Theorem Introduction to Bayesian Adjustment Rating: The Incredible Concept Behind Online Ratings! Working of Naive Bayes Math behind Naive Bayes Types of Naive Bayes Implementation of Naive Bayes
Understanding how to solve Multiclass and Multilabled Classification Problem Evaluation Metrics: Multi Class Classification
Introduction to Ensemble Techniques Basic Ensemble Techniques Implementing Basic Ensemble Techniques Finding Optimal Weights of Ensemble Learner using Neural Network Why Ensemble Models Work well?
Introduction to Stacking Implementing Stacking Variants of Stacking Implementing Variants of Stacking Introduction to Blending Bootstrap Sampling Introduction to Random Sampling Hyper-parameters of Random Forest Implementing Random Forest Out-of-Bag (OOB) Score in the Random Forest IPL Team Win Prediction Project Using Machine Learning Introduction to Boosting Gradient Boosting Algorithm Math behind GBM Implementing GBM in python Regularized Greedy Forests Extreme Gradient Boosting Implementing XGBM in python Tuning Hyperparameters of XGBoost in Python Implement XGBM in R/H2O Adaptive Boosting Implementing Adaptive Boosing LightGBM Implementing LightGBM in Python Catboost Implementing Catboost in Python
Different Hyperparameter Tuning methods Implementing Different Hyperparameter Tuning methods GridsearchCV RandomizedsearchCV Bayesian Optimization for Hyperparameter Tuning Hyperopt
Understanding SVM Algorithm SVM Kernels In-depth Intuition and Practical Implementation SVM Kernel Tricks Kernels and Hyperparameters in SVM Implementing SVM from Scratch in Python and R
Introduction to Principal Component Analysis Steps to Perform Principal Compound Analysis Computation of Covariance Matrix Finding Eigenvectors and Eigenvalues Implementing PCA in python Visualizing PCA A Brief Introduction to Linear Discriminant Analysis Introduction to Factor Analysis
Introduction to Clustering Applications of Clustering Evaluation Metrics for Clustering Understanding K-Means Implementation of K-Means in Python Implementation of K-Means in R Choosing Right Value for K Profiling Market Segments using K-Means Clustering Hierarchical Clustering Implementation of Hierarchial Clustering DBSCAN Defining Similarity between clusters Build Better and Accurate Clusters with Gaussian Mixture Models
Understand Basics of Recommendation Engine with Case Study
8 Ways to Improve Accuracy of Machine Learning Models
Introduction to Dask Working with CuML
Introduction to Machine Learning Interpretability Framework and Interpretable Models model Agnostic Methods for Interpretability Implementing Interpretable Model Understanding SHAP Out-of-Core ML Introduction to Interpretable Machine Learning Models Model Agnostic Methods for Interpretability Game Theory & Shapley Values
Introduction to Machine Learning Interpretability Framework and Interpretable Models model Agnostic Methods for Interpretability Implementing Interpretable Model Understanding SHAP Out-of-Core ML Introduction to Interpretable Machine Learning Models Model Agnostic Methods for Interpretability Game Theory & Shapley Values
Introduction to AutoML Implementation of MLBox Introduction to PyCaret TPOT Auto-Sklearn EvalML
Pickle and Joblib Introduction to Model Deployment
Deploying Machine Learning Model using Streamlit Deploying ML Models in Docker Deploy Using Streamlit Deploy on Heroku Deploy Using Netlify Introduction to Amazon Sagemaker Setting up Amazon SageMaker Using SageMaker Endpoint to Generate Inference Deploy on Microsoft Azure Cloud Introduction to Flask for Model Deploying ML model using Flask
Model Deployment in Android Model Deployment in Iphone

An End-to-End Guide to Model Explainability

P
Priyanka Last Updated : 16 Oct, 2024
9 min read

This article was published as a part of the Data Science Blogathon.

In this article, we will learn about model explainability and the different ways to interpret a machine learning model.

What is Model Explainability?

Model explainability refers to the concept of being able to understand the machine learning model. For example – If a healthcare model is predicting whether a patient is suffering from a particular disease or not. The medical practitioners need to know what parameters the model is taking into account or if the model contains any bias. So, it is necessary that once the model is deployed in the real world. Then, the model developers can explain the model. 

Why is Model Explainability required?

  1. Being able to interpret a model increases trust in a machine learning model. This becomes all the more important in scenarios involving life-and-death situations like healthcare, law, credit lending, etc. For example – If a model is predicting cancer, the healthcare providers should be aware of the available variables.

  2. Once we understand a model, we can detect if there is any bias present in the model. For example – If a healthcare model has been trained on the American population, it might not be suitable for Asian people.

  3. Model Explainability becomes important while debugging a model during the development phase.

  4. Model Explainability is critical for getting models to vet by regulatory authorities like Food and Drug Administration (FDA), National Regulatory Authority, etc. It also helps to determine if the models are suitable to be deployed in real life.

How to develop Model Understanding?

Here we have two options at our disposal:

Option 1: Build models that are inherently interpretable – Glass Box Models.

For example – In a linear regression model of the form y = b0 + b1*x, we know that when x increases by 1% then y will increase by b1% keeping other factors constant.

Option 2: Post-hoc explanation of pre-built models – Black Box Models

For example – In a deep learning model, the model developers are not aware of how the input variables have combined to produce a particular output.

 
Glass Box ModelsBlack Box Models 
  
SimpleComplex
InterpretableNot easily Interpretable
Low accuracyHigh accuracy
Examples – Linear Models, Decision TreeExamples – Random Forest, Deep Learning

Ways to interpret a Model

There are two ways to interpret the model – Global vs Local interpretation.
Global InterpretationLocal interpretation
This helps in understanding how a model makes decisions for the overall structureThis helps in understanding how the model makes decisions for a single instance
 Using global interpretation we can explain the complete behavior of the model Using local interpretation we can explain the individual predictions
Global interpretation help in understanding the suitability of the model for deploymentLocal interpretation helps in understanding the behavior of the model in the local neighborhood
Example – Predicting the risk of disease in patientsExample – Understanding why a specific person has a high risk of a disease

Local Interpretation

We will discuss the following methods of local interpretation:

  • LIME (Local Interpretable Model-agnostic Explanations)
  • SHAP (SHapley Additive exPlanations)

 

LIME (Local Interpretable Model-Agnostic Explanations)

LIME provides a local interpretation by modifying feature values of a single data sample and observing its impact on the output. It builds a surrogate model from the input (sample generation) and model predictions. An interpretable model can be used as a surrogate model. Because LIME is a model agnostic technique, therefore it can be used on any model.

Steps involved in LIME:

  1. It creates a permutation (fake) of the given data.
  2. It calculates the distance between permutations and the original observations. Also, we can specify the distance measured.
  3. Then, it makes predictions on the new data using some black-box models.
  4. It picks “m” features that describe the complex model. It is an outcome from the permuted data in the best possible way through the maximum likelihood approach. Here, we can decide the number of features i.e. the value of “m” we want to use.
  5. It picks the “m” features and fits a simple model to the permuted data with the similarity score as weights.
  6. The weights from the simple model are used to provide explanations for the complex model’s local behavior.

SHAP (SHapley Additive exPlanations)

SHAP shows the impact of each feature by interpreting the impact of a certain value compared to a baseline value. The baseline used for prediction is the average of all the predictions. SHAP values allow us to determine any prediction as a sum of the effects of each feature value.

The only disadvantage with SHAP is that the computing time is high. The Shapley values can be combined together and used to perform global interpretations also.

Global Interpretation

We will discuss the following methods of global interpretation:

  • PDP (Partial Dependency Plot)
  • ICE(Individual Conditional Expectation)

 

PDP (Partial Dependency Plot)

PDP explains the global behavior of a model by showing the relationship of the marginal effect of each of the predictors on the response variable.

It shows a relationship between the target variable and a feature variable. Such a relationship could be complex, monotonic, or even a simple linear one. The plot assumes that the feature of interest (whose partial dependence is being computed) is not highly correlated with the other features. If the features of the model are correlated, then PDP does not provide the correct interpretation. We cannot plot PDP for all complex classifiers like Neural Networks.

ICE (Individual Conditional Expectation)

ICE is an extension of PDP(global method) but they are more intuitive to understand as compared to PDP. Using ICE, we can explain heterogeneous relationships. While PDP supports two feature explanations using ICE we can explain only one feature at a time.

Thus, it provides a plot of the average predicted outcomes. These outcomes are for different values of a feature while keeping the values of other feature values are constant.

Hands-on learning model explainability methods

We will explore the different model interpretation methods using the famous “Pima Indians Diabetes Database”  to predict whether a patient has diabetes or not.

Dataset can be downloaded here.

Python Code:

import pandas as pd
import numpy as np
#import matplotlib.pyplot as plt
#import seaborn as sn
#from sklearn.model_selection import train_test_split

import warnings
warnings.filterwarnings('ignore')

diabetes_df = pd.read_csv( "diabetes.csv", index_col=[0] )

print(diabetes_df.head())
diabetes_df.info()

<class 'pandas.core.frame.DataFrame'>
Int64Index: 768 entries, 6 to 1
Data columns (total 8 columns):
 #   Column                    Non-Null Count  Dtype  
---  ------                    --------------  -----  
 0   Glucose                   768 non-null    int64  
 1   BloodPressure             768 non-null    int64  
 2   SkinThickness             768 non-null    int64  
 3   Insulin                   768 non-null    int64  
 4   BMI                       768 non-null    float64
 5   DiabetesPedigreeFunction  768 non-null    float64
 6   Age                       768 non-null    int64  
 7   Outcome                   768 non-null    int64  
dtypes: float64(2), int64(6)
memory usage: 54.0 KB

Encode the Categorical Variable

X_features = list( diabetes_df.columns )

X_features.remove( "Outcome" )

Split the Dataset

from sklearn.model_selection import train_test_split

X_train, X_test, \
y_train, y_test = train_test_split( diabetes_df[X_features],
                                    diabetes_df.Outcome,
                                    test_size = 0.3,
                                    random_state = 100 )

X_train.shape

(537, 7)
X_test.shape

(231, 7)

Build a RandomForest Model

from sklearn.ensemble import RandomForestClassifier

rf_clf = RandomForestClassifier( n_estimators = 100,
                                 max_features = 0.2,
                                 max_depth = 10,
                                 max_samples = 0.5)

rf_clf.fit(X_train, y_train)

RandomForestClassifier(max_depth=10, max_features=0.2, max_samples=0.5)
y_pred_prob = rf_clf.predict_proba( X_test )[:,1]
y_pred = rf_clf.predict( X_test )

Understanding the Model using ELI5

  • Install ELI5
code
pip install eli5
!pip install eli5

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import eli5.sklearn

eli5.explain_weights( 
    rf_clf, 
    feature_names = X_features )
WeightFeature
0.2326 ± 0.1904Glucose
0.1686 ± 0.1484BMI
0.1480 ± 0.1107Diabetes Pedigree Function
0.1445 ± 0.1298Age
0.1214 ± 0.0904Blood Pressure
0.1004 ± 0.0842Skin Thickness
0.0844 ± 0.0768Insulin

Explaining the weights for a Non-diabetes

X_test.iloc[0]

Glucose                     79.000
BloodPressure               60.000
Skin Thickness              42.000
Insulin                     48.000
BMI                         43.500
Diabetes Pedigree Function  0.678
Age                         23.000
Name: 1, dtype: float64
y_test.iloc[0]

0
eli5.explain_prediction( rf_clf,
                         X_test.iloc[0],
                         target_names = ['Non-diabetes', 'Diabetes'] )

y=Non-diabetes (probability 0.869) top features

Contribution?Feature
+0.656<BIAS>
+0.162Glucose
+0.106Insulin
+0.081Age
+0.047Blood Pressure
-0.049Diabetes Pedigree Function
-0.066Skin Thickness
-0.067BMI

Explaining the weights for a Non-diabetes

X_test.iloc[4]

Glucose                     123.000
Blood Pressure               70.000
Skin Thickness               44.000
Insulin                      94.000
BMI                          33.100
Diabetes Pedigree Function   0.374
Age                          40.000
Name: 9, dtype: float64
y_test.iloc[4]

0
eli5.explain_prediction( rf_clf,
                         X_test.iloc[4],
                         target_names = ['Non-diabetes', 'Diabetes'] )

y=Non-diabetes (probability 0.524) top features

Contribution?Feature
+0.656<BIAS>
+0.072Insulin
+0.013Diabetes Pedigree Function
+0.002Glucose
-0.011Blood Pressure
-0.017BMI
-0.067Skin Thickness
-0.125Age

Partial Dependence Plots (PDPs)

from sklearn.inspection import PartialDependenceDisplay

Effect of Insulin on Diabetes

fig, ax = plt.subplots(figsize=(12, 6))
ax.set_title("Partial Dependency Plot")
PartialDependenceDisplay.from_estimator(rf_clf,
                                        X_test,
                                        features = ['Insulin'],
                                        feature_names = X_features,
                                        ax = ax);

Effect of Glucose on Diabetes

fig, ax = plt.subplots(figsize=(12, 6))
ax.set_title("Partial Dependency Plot")
PartialDependenceDisplay.from_estimator(rf_clf,
                                        X_test,
                                        features = ['Glucose'],
                                        feature_names = X_features,
                                        ax = ax)

<sklearn.inspection._plot.partial_dependence.PartialDependenceDisplay at 0x7f1e39141e10>

LIME – Local Interpretation of Model Explanation

!pip install lime

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import lime
import lime.lime_tabular

explainer = (lime
             .lime_tabular
             .LimeTabularExplainer(training_data = X_train.to_numpy(), 
                                   training_labels = y_train,                                   
                                   feature_names = X_features, 
                                   class_names = ['Non-diabetes','Diabetes'],
                                   kernel_width=3,
                                   verbose = True ))

Explaining a case of Non-Diabetes

X_test.iloc[0]

Glucose                     79.000
BloodPressure               60.000
SkinThickness               42.000
Insulin                     48.000
BMI                         43.500
DiabetesPedigreeFunction     0.678
Age                         23.000
Name: 1, dtype: float64
exp = explainer.explain_instance( X_test.iloc[0].to_numpy(), 
                                  rf_clf.predict_proba )

Intercept 0.3836565649244127
Prediction_local [0.32668078]
Right: 0.13058823529411764

exp.show_in_notebook(show_table=True, show_all=False)

Explaining a case of Diabetes

exp = explainer.explain_instance( X_test.iloc[4].to_numpy(), 
                                  rf_clf.predict_proba )

Intercept 0.3299430371346654
Prediction_local [0.45386335]
Right: 0.47641411034143033

exp.show_in_notebook(show_table=True, show_all=False)

Using Shapley Values

  • Install SHAP


pip install shap

!pip install shap

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import shap

Explaining a case of Non-diabetes

row_to_show = 1
data_for_prediction = X_test.iloc[row_to_show]
data_for_prediction_array = data_for_prediction.values.reshape(1, -1)
rf_clf.predict_proba(data_for_prediction_array)

array([[0.90805083, 0.09194917]])
explainer = shap.TreeExplainer(rf_clf)

shap_values = explainer.shap_values(data_for_prediction_array)

shap.initjs()
shap.force_plot( explainer.expected_value[1], 
                 shap_values[1], 
                 data_for_prediction,
                 figsize=(20, 2) )

Visualization omitted, Javascript library not loaded! 

Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). The Javascript has been stripped for security, if you notice the notebook on GitHub. When you use JupyterLab, this error will occur because it is a JupyterLab extension that has not yet been written.

Explaining a case of Diabetes

row_to_show = 4
data_for_prediction = X_test.iloc[row_to_show]
data_for_prediction_array = data_for_prediction.values.reshape(1, -1)
rf_clf.predict_proba(data_for_prediction_array)

shap_values = explainer.shap_values(data_for_prediction_array)

shap.initjs()
shap.force_plot( explainer.expected_value[1], 
                 shap_values[1], 
                 data_for_prediction,
                 figsize=(20, 2) )

Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). The GitHub notebook shows that the Javascript has been stripped for security. If you notice this error in JupyterLab. It is there because a JupyterLab extension has not yet been written.

Global Explanation of SHAP

explainer = shap.TreeExplainer( rf_clf )

shap_values = explainer.shap_values( X_train )

shap.summary_plot( shap_values[1], X_train, plot_type = 'dot' )

explainer.expected_value

array([0.65552239, 0.34447761])
shap.initjs()
shap.force_plot( explainer.expected_value[1], 
                 shap_values[1], 
                 X_train )

Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). The notebook is available on GitHub where the Javascript has been stripped for security. If you happen to use JupyterLab. Then, this error is because a JupyterLab extension has not yet been written.

Individual Conditional Expectations (ICE)

import matplotlib.pyplot as plt

from sklearn.inspection import PartialDependenceDisplay

fig, ax = plt.subplots(figsize=(12, 8))
ax.set_title("Individual Conditional Expectations")

display = PartialDependenceDisplay.from_estimator(
    rf_clf,
    X_train,
    features=["Age"],
    kind="individual",
    subsample=100,
    n_jobs=3,
    grid_resolution=20,
    random_state=0,
    ice_lines_kw={"color": "tab:blue", "alpha": 0.5, "linewidth": 0.5},
    ax = ax
)

fig, ax = plt.subplots(figsize=(12, 8))
ax.set_title("Individual Conditional Expectations")

display = PartialDependenceDisplay.from_estimator(
    rf_clf,
    X_train,
    features=["Age"],
    kind="both",
    subsample=100,
    n_jobs=3,
    grid_resolution=20,
    random_state=0,
    ice_lines_kw={"color": "tab:blue", "alpha": 0.5, "linewidth": 0.5},
    pd_line_kw={"color": "tab:orange", "linestyle": "--"},
    ax = ax
)
Model Explainability

For full code visit Github

Conclusion

Machine learning models are often seen as black-box models. However, in this article, we have seen how we can explain such models and why it is important to do so. Further, we have discussed ways to interpret and explain a model. Explainable AI (XAI) is emerging and we would possibly be able to automate the interpretation of ML models in the near future.

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Priyanka

Priyanka Dalmia is pursuing MBA from IIM Bangalore. She likes to write about Product Management, Machine Learning & Quantitative finance. Follow her on Twitter @Quant_Dalmia

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