permshap: Permutation SHAP

In kernelshap: Kernel SHAP

Permutation SHAP

Description

Exact permutation SHAP algorithm with respect to a background dataset, see Strumbelj and Kononenko. The function works for up to 14 features. For eight or more features, we recomment to switch to kernelshap().

Usage

permshap(object, ...)

## Default S3 method:
permshap(
  object,
  X,
  bg_X = NULL,
  pred_fun = stats::predict,
  feature_names = colnames(X),
  bg_w = NULL,
  bg_n = 200L,
  parallel = FALSE,
  parallel_args = NULL,
  verbose = TRUE,
  ...
)

## S3 method for class 'ranger'
permshap(
  object,
  X,
  bg_X = NULL,
  pred_fun = NULL,
  feature_names = colnames(X),
  bg_w = NULL,
  bg_n = 200L,
  parallel = FALSE,
  parallel_args = NULL,
  verbose = TRUE,
  survival = c("chf", "prob"),
  ...
)

Arguments

object	Fitted model object.
...	Additional arguments passed to pred_fun(object, X, ...).
X	(n \times p) matrix or data.frame with rows to be explained. The columns should only represent model features, not the response (but see feature_names on how to overrule this).
bg_X	Background data used to integrate out "switched off" features, often a subset of the training data (typically 50 to 500 rows). In cases with a natural "off" value (like MNIST digits), this can also be a single row with all values set to the off value. If no bg_X is passed (the default) and if X is sufficiently large, a random sample of bg_n rows from X serves as background data.
pred_fun	Prediction function of the form ⁠function(object, X, ...)⁠, providing K \ge 1 predictions per row. Its first argument represents the model object, its second argument a data structure like X. Additional (named) arguments are passed via .... The default, stats::predict(), will work in most cases.
feature_names	Optional vector of column names in X used to calculate SHAP values. By default, this equals colnames(X). Not supported if X is a matrix.
bg_w	Optional vector of case weights for each row of bg_X. If bg_X = NULL, must be of same length as X. Set to NULL for no weights.
bg_n	If bg_X = NULL: Size of background data to be sampled from X.
parallel	If TRUE, use parallel foreach::foreach() to loop over rows to be explained. Must register backend beforehand, e.g., via 'doFuture' package, see README for an example. Parallelization automatically disables the progress bar.
parallel_args	Named list of arguments passed to foreach::foreach(). Ideally, this is NULL (default). Only relevant if parallel = TRUE. Example on Windows: if object is a GAM fitted with package 'mgcv', then one might need to set parallel_args = list(.packages = "mgcv").
verbose	Set to FALSE to suppress messages and the progress bar.
survival	Should cumulative hazards ("chf", default) or survival probabilities ("prob") per time be predicted? Only in ranger() survival models.

Value

An object of class "kernelshap" with the following components:

• S: (n \times p) matrix with SHAP values or, if the model output has dimension K > 1, a list of K such matrices.

• X: Same as input argument X.

• baseline: Vector of length K representing the average prediction on the background data.

• bg_X: The background data.

• bg_w: The background case weights.

• m_exact: Integer providing the effective number of exact on-off vectors used.

• exact: Logical flag indicating whether calculations are exact or not (currently TRUE).

• txt: Summary text.

• predictions: (n \times K) matrix with predictions of X.

• algorithm: "permshap".

Methods (by class)

• permshap(default): Default permutation SHAP method.

• permshap(ranger): Permutation SHAP method for "ranger" models, see Readme for an example.

References

1. Erik Strumbelj and Igor Kononenko. Explaining prediction models and individual predictions with feature contributions. Knowledge and Information Systems 41, 2014.

Examples

# MODEL ONE: Linear regression
fit <- lm(Sepal.Length ~ ., data = iris)

# Select rows to explain (only feature columns)
X_explain <- iris[-1]

# Calculate SHAP values
s <- permshap(fit, X_explain)
s

# MODEL TWO: Multi-response linear regression
fit <- lm(as.matrix(iris[, 1:2]) ~ Petal.Length + Petal.Width + Species, data = iris)
s <- permshap(fit, iris[3:5])
s

# Note 1: Feature columns can also be selected 'feature_names'
# Note 2: Especially when X is small, pass a sufficiently large background data bg_X
s <- permshap(
  fit,
  iris[1:4, ],
  bg_X = iris,
  feature_names = c("Petal.Length", "Petal.Width", "Species")
)
s

kernelshap documentation built on Sept. 11, 2024, 9:35 p.m.