cv_vim: Nonparametric Intrinsic Variable Importance Estimates and...

In bdwilliamson/npvi: Perform Inference on Algorithm-Agnostic Variable Importance

Nonparametric Intrinsic Variable Importance Estimates and Inference using Cross-fitting

Description

Compute estimates and confidence intervals using cross-fitting for nonparametric intrinsic variable importance based on the population-level contrast between the oracle predictiveness using the feature(s) of interest versus not.

Usage

cv_vim(
  Y = NULL,
  X = NULL,
  cross_fitted_f1 = NULL,
  cross_fitted_f2 = NULL,
  f1 = NULL,
  f2 = NULL,
  indx = 1,
  V = ifelse(is.null(cross_fitting_folds), 5, length(unique(cross_fitting_folds))),
  sample_splitting = TRUE,
  final_point_estimate = "split",
  sample_splitting_folds = NULL,
  cross_fitting_folds = NULL,
  stratified = FALSE,
  type = "r_squared",
  run_regression = TRUE,
  SL.library = c("SL.glmnet", "SL.xgboost", "SL.mean"),
  alpha = 0.05,
  delta = 0,
  scale = "identity",
  na.rm = FALSE,
  C = rep(1, length(Y)),
  Z = NULL,
  ipc_scale = "identity",
  ipc_weights = rep(1, length(Y)),
  ipc_est_type = "aipw",
  scale_est = TRUE,
  nuisance_estimators_full = NULL,
  nuisance_estimators_reduced = NULL,
  exposure_name = NULL,
  cross_fitted_se = TRUE,
  bootstrap = FALSE,
  b = 1000,
  boot_interval_type = "perc",
  clustered = FALSE,
  cluster_id = rep(NA, length(Y)),
  ...
)

Arguments

Y	the outcome.
X	the covariates. If type = "average_value", then the exposure variable should be part of X, with its name provided in exposure_name.
cross_fitted_f1	the predicted values on validation data from a flexible estimation technique regressing Y on X in the training data. Provided as either (a) a vector, where each element is the predicted value when that observation is part of the validation fold; or (b) a list of length V, where each element in the list is a set of predictions on the corresponding validation data fold. If sample-splitting is requested, then these must be estimated specially; see Details. However, the resulting vector should be the same length as Y; if using a list, then the summed length of each element across the list should be the same length as Y (i.e., each observation is included in the predictions).
cross_fitted_f2	the predicted values on validation data from a flexible estimation technique regressing either (a) the fitted values in cross_fitted_f1, or (b) Y, on X withholding the columns in indx. Provided as either (a) a vector, where each element is the predicted value when that observation is part of the validation fold; or (b) a list of length V, where each element in the list is a set of predictions on the corresponding validation data fold. If sample-splitting is requested, then these must be estimated specially; see Details. However, the resulting vector should be the same length as Y; if using a list, then the summed length of each element across the list should be the same length as Y (i.e., each observation is included in the predictions).
f1	the fitted values from a flexible estimation technique regressing Y on X. If sample-splitting is requested, then these must be estimated specially; see Details. If cross_fitted_se = TRUE, then this argument is not used.
f2	the fitted values from a flexible estimation technique regressing either (a) f1 or (b) Y on X withholding the columns in indx. If sample-splitting is requested, then these must be estimated specially; see Details. If cross_fitted_se = TRUE, then this argument is not used.
indx	the indices of the covariate(s) to calculate variable importance for; defaults to 1.
V	the number of folds for cross-fitting, defaults to 5. If sample_splitting = TRUE, then a special type of V-fold cross-fitting is done. See Details for a more detailed explanation.
sample_splitting	should we use sample-splitting to estimate the full and reduced predictiveness? Defaults to TRUE, since inferences made using sample_splitting = FALSE will be invalid for variables with truly zero importance.
final_point_estimate	if sample splitting is used, should the final point estimates be based on only the sample-split folds used for inference ("split", the default), or should they instead be based on the full dataset ("full") or the average across the point estimates from each sample split ("average")? All three options result in valid point estimates – sample-splitting is only required for valid inference.
sample_splitting_folds	the folds used for sample-splitting; these identify the observations that should be used to evaluate predictiveness based on the full and reduced sets of covariates, respectively. Only used if run_regression = FALSE.
cross_fitting_folds	the folds for cross-fitting. Only used if run_regression = FALSE.
stratified	if run_regression = TRUE, then should the generated folds be stratified based on the outcome (helps to ensure class balance across cross-validation folds)
type	the type of importance to compute; defaults to r_squared, but other supported options are auc, accuracy, deviance, and anova.
run_regression	if outcome Y and covariates X are passed to vimp_accuracy, and run_regression is TRUE, then Super Learner will be used; otherwise, variable importance will be computed using the inputted fitted values.
SL.library	a character vector of learners to pass to SuperLearner, if f1 and f2 are Y and X, respectively. Defaults to SL.glmnet, SL.xgboost, and SL.mean.
alpha	the level to compute the confidence interval at. Defaults to 0.05, corresponding to a 95% confidence interval.
delta	the value of the \delta-null (i.e., testing if importance < \delta); defaults to 0.
scale	should CIs be computed on original ("identity") or another scale? (options are "log" and "logit")
na.rm	should we remove NAs in the outcome and fitted values in computation? (defaults to FALSE)
C	the indicator of coarsening (1 denotes observed, 0 denotes unobserved).
Z	either (i) NULL (the default, in which case the argument C above must be all ones), or (ii) a character vector specifying the variable(s) among Y and X that are thought to play a role in the coarsening mechanism. To specify the outcome, use "Y"; to specify covariates, use a character number corresponding to the desired position in X (e.g., "1").
ipc_scale	what scale should the inverse probability weight correction be applied on (if any)? Defaults to "identity". (other options are "log" and "logit")
ipc_weights	weights for the computed influence curve (i.e., inverse probability weights for coarsened-at-random settings). Assumed to be already inverted (i.e., ipc_weights = 1 / [estimated probability weights]).
ipc_est_type	the type of procedure used for coarsened-at-random settings; options are "ipw" (for inverse probability weighting) or "aipw" (for augmented inverse probability weighting). Only used if C is not all equal to 1.
scale_est	should the point estimate be scaled to be greater than or equal to 0? Defaults to TRUE.
nuisance_estimators_full	(only used if type = "average_value") a list of nuisance function estimators on the observed data (may be within a specified fold, for cross-fitted estimates). Specifically: an estimator of the optimal treatment rule; an estimator of the propensity score under the estimated optimal treatment rule; and an estimator of the outcome regression when treatment is assigned according to the estimated optimal rule.
nuisance_estimators_reduced	(only used if type = "average_value") a list of nuisance function estimators on the observed data (may be within a specified fold, for cross-fitted estimates). Specifically: an estimator of the optimal treatment rule; an estimator of the propensity score under the estimated optimal treatment rule; and an estimator of the outcome regression when treatment is assigned according to the estimated optimal rule.
exposure_name	(only used if type = "average_value") the name of the exposure of interest; binary, with 1 indicating presence of the exposure and 0 indicating absence of the exposure.
cross_fitted_se	should we use cross-fitting to estimate the standard errors (TRUE, the default) or not (FALSE)?
bootstrap	should bootstrap-based standard error estimates be computed? Defaults to FALSE (and currently may only be used if sample_splitting = FALSE).
b	the number of bootstrap replicates (only used if bootstrap = TRUE and sample_splitting = FALSE); defaults to 1000.
boot_interval_type	the type of bootstrap interval (one of "norm", "basic", "stud", "perc", or "bca", as in boot{boot.ci}) if requested. Defaults to "perc".
clustered	should the bootstrap resamples be performed on clusters rather than individual observations? Defaults to FALSE.
cluster_id	vector of the same length as Y giving the cluster IDs used for the clustered bootstrap, if clustered is TRUE.
...	other arguments to the estimation tool, see "See also".

Details

We define the population variable importance measure (VIM) for the group of features (or single feature) s with respect to the predictiveness measure V by

\psi_{0,s} := V(f_0, P_0) - V(f_{0,s}, P_0),

where f_0 is the population predictiveness maximizing function, f_{0,s} is the population predictiveness maximizing function that is only allowed to access the features with index not in s, and P_0 is the true data-generating distribution.

Cross-fitted VIM estimates are computed differently if sample-splitting is requested versus if it is not. We recommend using sample-splitting in most cases, since only in this case will inferences be valid if the variable(s) of interest have truly zero population importance. The purpose of cross-fitting is to estimate f_0 and f_{0,s} on independent data from estimating P_0; this can result in improved performance, especially when using flexible learning algorithms. The purpose of sample-splitting is to estimate f_0 and f_{0,s} on independent data; this allows valid inference under the null hypothesis of zero importance.

Without sample-splitting, cross-fitted VIM estimates are obtained by first splitting the data into K folds; then using each fold in turn as a hold-out set, constructing estimators f_{n,k} and f_{n,k,s} of f_0 and f_{0,s}, respectively on the training data and estimator P_{n,k} of P_0 using the test data; and finally, computing

\psi_{n,s} := K^{(-1)}\sum_{k=1}^K \{V(f_{n,k},P_{n,k}) - V(f_{n,k,s}, P_{n,k})\}.

With sample-splitting, cross-fitted VIM estimates are obtained by first splitting the data into 2K folds. These folds are further divided into 2 groups of folds. Then, for each fold k in the first group, estimator f_{n,k} of f_0 is constructed using all data besides the kth fold in the group (i.e., (2K - 1)/(2K) of the data) and estimator P_{n,k} of P_0 is constructed using the held-out data (i.e., 1/2K of the data); then, computing

v_{n,k} = V(f_{n,k},P_{n,k}).

Similarly, for each fold k in the second group, estimator f_{n,k,s} of f_{0,s} is constructed using all data besides the kth fold in the group (i.e., (2K - 1)/(2K) of the data) and estimator P_{n,k} of P_0 is constructed using the held-out data (i.e., 1/2K of the data); then, computing

v_{n,k,s} = V(f_{n,k,s},P_{n,k}).

Finally,

\psi_{n,s} := K^{(-1)}\sum_{k=1}^K \{v_{n,k} - v_{n,k,s}\}.

See the paper by Williamson, Gilbert, Simon, and Carone for more details on the mathematics behind the cv_vim function, and the validity of the confidence intervals.

In the interest of transparency, we return most of the calculations within the vim object. This results in a list including:

s

the column(s) to calculate variable importance for

SL.library

the library of learners passed to SuperLearner

full_fit

the fitted values of the chosen method fit to the full data (a list, for train and test data)

red_fit

the fitted values of the chosen method fit to the reduced data (a list, for train and test data)

est

the estimated variable importance

naive

the naive estimator of variable importance

eif

the estimated efficient influence function

eif_full

the estimated efficient influence function for the full regression

eif_reduced

the estimated efficient influence function for the reduced regression

se

the standard error for the estimated variable importance

ci

the (1-\alpha) \times 100% confidence interval for the variable importance estimate

test

a decision to either reject (TRUE) or not reject (FALSE) the null hypothesis, based on a conservative test

p_value

a p-value based on the same test as test

full_mod

the object returned by the estimation procedure for the full data regression (if applicable)

red_mod

the object returned by the estimation procedure for the reduced data regression (if applicable)

alpha

the level, for confidence interval calculation

sample_splitting_folds

the folds used for hypothesis testing

cross_fitting_folds

the folds used for cross-fitting

y

the outcome

ipc_weights

the weights

cluster_id

the cluster IDs

mat

a tibble with the estimate, SE, CI, hypothesis testing decision, and p-value

Value

An object of class vim. See Details for more information.

See Also

SuperLearner for specific usage of the SuperLearner function and package.

Examples

n <- 100
p <- 2
# generate the data
x <- data.frame(replicate(p, stats::runif(n, -5, 5)))

# apply the function to the x's
smooth <- (x[,1]/5)^2*(x[,1]+7)/5 + (x[,2]/3)^2

# generate Y ~ Normal (smooth, 1)
y <- as.matrix(smooth + stats::rnorm(n, 0, 1))

# set up a library for SuperLearner; note simple library for speed
library("SuperLearner")
learners <- c("SL.glm")

# -----------------------------------------
# using Super Learner (with a small number of folds, for illustration only)
# -----------------------------------------
set.seed(4747)
est <- cv_vim(Y = y, X = x, indx = 2, V = 2,
type = "r_squared", run_regression = TRUE,
SL.library = learners, cvControl = list(V = 2), alpha = 0.05)

# ------------------------------------------
# doing things by hand, and plugging them in
# (with a small number of folds, for illustration only)
# ------------------------------------------
# set up the folds
indx <- 2
V <- 2
Y <- matrix(y)
set.seed(4747)
# Note that the CV.SuperLearner should be run with an outer layer
# of 2*V folds (for V-fold cross-fitted importance)
full_cv_fit <- suppressWarnings(SuperLearner::CV.SuperLearner(
Y = Y, X = x, SL.library = learners, cvControl = list(V = 2 * V),
innerCvControl = list(list(V = V))
))
full_cv_preds <- full_cv_fit$SL.predict
# use the same cross-fitting folds for reduced
reduced_cv_fit <- suppressWarnings(SuperLearner::CV.SuperLearner(
    Y = Y, X = x[, -indx, drop = FALSE], SL.library = learners,
    cvControl = SuperLearner::SuperLearner.CV.control(
        V = 2 * V, validRows = full_cv_fit$folds
    ),
    innerCvControl = list(list(V = V))
))
reduced_cv_preds <- reduced_cv_fit$SL.predict
# for hypothesis testing
cross_fitting_folds <- get_cv_sl_folds(full_cv_fit$folds)
set.seed(1234)
sample_splitting_folds <- make_folds(unique(cross_fitting_folds), V = 2)
set.seed(5678)
est <- cv_vim(Y = y, cross_fitted_f1 = full_cv_preds,
cross_fitted_f2 = reduced_cv_preds, indx = 2, delta = 0, V = V, type = "r_squared",
cross_fitting_folds = cross_fitting_folds,
sample_splitting_folds = sample_splitting_folds,
run_regression = FALSE, alpha = 0.05, na.rm = TRUE)

bdwilliamson/npvi documentation built on Feb. 1, 2024, 10:46 p.m.