The most common machine learning task is to train a model which is able to predict an unknown outcome (response variable) based on a set of known input variables/features. When using such models for real life applications, it is often crucial to understand why a certain set of features lead to exactly that prediction. However, explaining predictions from complex, or seemingly simple, machine learning models is a practical and ethical question, as well as a legal issue. Can I trust the model? Is it biased? Can I explain it to others? We want to explain individual predictions from a complex machine learning model by learning simple, interpretable explanations.
Shapley values is the only prediction explanation framework with a solid theoretical foundation (Lundberg and Lee (2017)). Unless the true distribution of the features are known, and there are less than say 10-15 features, these Shapley values needs to be estimated/approximated. Popular methods like Shapley Sampling Values (Štrumbelj and Kononenko (2014)), SHAP/Kernel SHAP (Lundberg and Lee (2017)), and to some extent TreeSHAP (Lundberg, Erion, and Lee (2018)), assume that the features are independent when approximating the Shapley values for prediction explanation. This may lead to very inaccurate Shapley values, and consequently wrong interpretations of the predictions. Aas, Jullum, and Løland (2019) extends and improves the Kernel SHAP method of Lundberg and Lee (2017) to account for the dependence between the features, resulting in significantly more accurate approximations to the Shapley values. See the paper for details.
This package implements the methodology of Aas, Jullum, and Løland (2019).
The following methodology/features are currently implemented:
Future releases will include:
Note that both the features and the prediction must be numeric. The approach is constructed for continuous features. Discrete features may also work just fine with the empirical (conditional) distribution approach. Unlike SHAP and TreeSHAP, we decompose probability predictions directly to ease the interpretability, i.e. not via log odds transformations. The application programming interface (API) of
shapr is inspired by Pedersen and Benesty (2019).
To install the current stable release from CRAN, use
To install the current development version, use
If you would like to install all packages of the models we currently support, use
remotes::install_github("NorskRegnesentral/shapr", dependencies = TRUE)
If you would also like to build and view the vignette locally, use
remotes::install_github("NorskRegnesentral/shapr", dependencies = TRUE, build_vignettes = TRUE) vignette("understanding_shapr", "shapr")
You can always check out the latest version of the vignette here.
shapr supports computation of Shapley values with any predictive model which takes a set of numeric features and produces a numeric outcome.
The following example shows how a simple
xgboost model is trained using the Boston Housing Data, and how
shapr explains the individual predictions.
library(xgboost) library(shapr) data("Boston", package = "MASS") x_var <- c("lstat", "rm", "dis", "indus") y_var <- "medv" ind_x_test <- 1:6 x_train <- as.matrix(Boston[-ind_x_test, x_var]) y_train <- Boston[-ind_x_test, y_var] x_test <- as.matrix(Boston[ind_x_test, x_var]) # Looking at the dependence between the features cor(x_train) #> lstat rm dis indus #> lstat 1.0000000 -0.6108040 -0.4928126 0.5986263 #> rm -0.6108040 1.0000000 0.1999130 -0.3870571 #> dis -0.4928126 0.1999130 1.0000000 -0.7060903 #> indus 0.5986263 -0.3870571 -0.7060903 1.0000000 # Fitting a basic xgboost model to the training data model <- xgboost( data = x_train, label = y_train, nround = 20, verbose = FALSE ) # Prepare the data for explanation explainer <- shapr(x_train, model) # Specifying the phi_0, i.e. the expected prediction without any features p <- mean(y_train) # Computing the actual Shapley values with kernelSHAP accounting for feature dependence using # the empirical (conditional) distribution approach with bandwidth parameter sigma = 0.1 (default) explanation <- explain( x_test, approach = "empirical", explainer = explainer, prediction_zero = p ) # Printing the Shapley values for the test data. # For more information about the interpretation of the values in the table, see ?shapr::explain. print(explanation$dt) #> none lstat rm dis indus #> 1: 22.446 5.2632030 -1.2526613 0.2920444 4.5528644 #> 2: 22.446 0.1671901 -0.7088401 0.9689005 0.3786871 #> 3: 22.446 5.9888022 5.5450858 0.5660134 -1.4304351 #> 4: 22.446 8.2142204 0.7507572 0.1893366 1.8298304 #> 5: 22.446 0.5059898 5.6875103 0.8432238 2.2471150 #> 6: 22.446 1.9929673 -3.6001958 0.8601984 3.1510531 # Finally we plot the resulting explanations plot(explanation)
Please note that the ‘shapr’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Aas, Kjersti, Martin Jullum, and Anders Løland. 2019. “Explaining Individual Predictions When Features Are Dependent: More Accurate Approximations to Shapley Values.” arXiv Preprint arXiv:1903.10464.
Hurvich, Clifford M, Jeffrey S Simonoff, and Chih-Ling Tsai. 1998. “Smoothing Parameter Selection in Nonparametric Regression Using an Improved Akaike Information Criterion.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 60 (2): 271–93.
Lundberg, Scott M, Gabriel G Erion, and Su-In Lee. 2018. “Consistent Individualized Feature Attribution for Tree Ensembles.” arXiv Preprint arXiv:1802.03888.
Lundberg, Scott M, and Su-In Lee. 2017. “A Unified Approach to Interpreting Model Predictions.” In Advances in Neural Information Processing Systems, 4765–74.
Pedersen, Thomas Lin, and Michaël Benesty. 2019. Lime: Local Interpretable Model-Agnostic Explanations. https://CRAN.R-project.org/package=lime.
Redelmeier, Annabelle, Martin Jullum, and Kjersti Aas. 2020. “Explaining Predictive Models with Mixed Features Using Shapley Values and Conditional Inference Trees.” In International Cross-Domain Conference for Machine Learning and Knowledge Extraction, 117–37. Springer.
Štrumbelj, Erik, and Igor Kononenko. 2014. “Explaining Prediction Models and Individual Predictions with Feature Contributions.” Knowledge and Information Systems 41 (3): 647–65.