cv_nb_grpreg {SSGL}

Cross-validation for Group-Regularized Negative Binomial Regression

Description

This function implements K-fold cross-validation for group-regularized negative binomial regression with a known size parameter \alpha and the log link. The cross-validation error (CVE) and cross-validation standard error (CVSE) are computed using the deviance for negative binomial regression.

For a description of group-regularized negative binomial regression, see the description for the nb_grpreg function. Our implementation is based on the least squares approximation approach of Wang and Leng (2007), and hence, the function does not allow the total number of covariates p to be greater than \frac{K-1}{K} \times sample size, where K is the number of folds.

Note that the nb_grpreg function also returns the generalized information criterion (GIC) of Fan and Tang (2013) for each regularization parameter in lambda, and the GIC can also be used for model selection instead of cross-validation.

Usage

cv_nb_grpreg(Y, X, groups, nb_size=1, penalty=c("gLASSO","gSCAD","gMCP"),
            n_folds=10, group_weights, taper, n_lambda=100, lambda, 
            max_iter=10000, tol=1e-4) 

Arguments

Y

n \times 1 vector of strictly nonnegative integer responses for training data.

X

n \times p design matrix for training data, where the jth column corresponds to the jth overall feature.

groups

p-dimensional vector of group labels. The jth entry in groups should contain either the group number or the factor level name that the feature in the jth column of X belongs to. groups must be either a vector of integers or factors.

nb_size

known size parameter \alpha in NB(\alpha,\mu_i) distribution for the responses. Default is nb_size=1.

penalty

group regularization method to use on the groups of regression coefficients. The options are "gLASSO", "gSCAD", "gMCP". To implement cross-validation for gamma regression with the SSGL penalty, use the cv_SSGL function.

n_folds

number of folds K to use in K-fold cross-validation. Default is n_folds=10.

group_weights

group-specific, nonnegative weights for the penalty. Default is to use the square roots of the group sizes.

taper

tapering term \gamma in group SCAD and group MCP controlling how rapidly the penalty tapers off. Default is taper=4 for group SCAD and taper=3 for group MCP. Ignored if "gLASSO" is specified as the penalty.

n_lambda

number of regularization parameters L. Default is n_lambda=100.

lambda

grid of L regularization parameters. The user may specify either a scalar or a vector. If the user does not provide this, the program chooses the grid automatically.

max_iter

maximum number of iterations in the algorithm. Default is max_iter=10000.

tol

convergence threshold for algorithm. Default is tol=1e-4.

Value

The function returns a list containing the following components:

lambda

L \times 1 vector of regularization parameters lambda used to fit the model. lambda is displayed in descending order.

cve

L \times 1 vector of mean cross-validation error across all K folds. The kth entry in cve corresponds to the kth regularization parameter in lambda.

cvse

L \times 1 vector of standard errors for cross-validation error across all K folds. The kth entry in cvse corresponds to the kth regularization parameter in lambda.

lambda_min

The value in lambda that minimizes mean cross-validation error cve.

min_index

The index of lambda_min in lambda.

References

Breheny, P. and Huang, J. (2015). "Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors." Statistics and Computing, 25:173-187.

Fan, Y. and Tang, C. Y. (2013). "Tuning parameter selection in high dimensional penalized likelihood." Journal of the Royal Statistical Society: Series B (Statistical Methodology), 75:531-552.

Wang, H. and Leng, C. (2007). "Unified LASSO estimation by least squares approximation." Journal of the American Statistical Association, 102:1039-1048.

Yuan, M. and Lin, Y. (2006). "Model selection and estimation in regression with grouped variables." Journal of the Royal Statistical Society: Series B (Statistical Methodology), 68:49-67.

Examples

## Generate data
set.seed(1234)
X = matrix(runif(100*14), nrow=100)
n = dim(X)[1]
groups = c(1,1,1,2,2,2,2,3,3,4,5,5,6,6)
beta_true = c(-1,1,1,0,0,0,0,-1,1,0,0,0,-1.5,1.5)

## Generate count responses from negative binomial regression
eta = crossprod(t(X), beta_true)
Y = rnbinom(n, size=1, mu=exp(eta))

## 10-fold cross-validation for group-regularized negative binomial
## regression with the group MCP penalty
nb_cv = cv_nb_grpreg(Y, X, groups, penalty="gMCP")

## Plot cross-validation curve
plot(nb_cv$lambda, nb_cv$cve, type="l", xlab="lambda", ylab="CVE")
## lambda which minimizes mean CVE
nb_cv$lambda_min 
## index of lambda_min in lambda
nb_cv$min_index