gcdnet: Fits the regularization paths for large margin classifiers

In gcdnet: The (Adaptive) LASSO and Elastic Net Penalized Least Squares, Logistic Regression, Hybrid Huberized Support Vector Machines, Squared Hinge Loss Support Vector Machines and Expectile Regression using a Fast Generalized Coordinate Descent Algorithm

Fits the regularization paths for large margin classifiers

Description

Fits a regularization path for large margin classifiers at a sequence of regularization parameters lambda.

Usage

gcdnet(
  x,
  y,
  nlambda = 100,
  method = c("hhsvm", "logit", "sqsvm", "ls", "er"),
  lambda.factor = ifelse(nobs < nvars, 0.01, 1e-04),
  lambda = NULL,
  lambda2 = 0,
  pf = rep(1, nvars),
  pf2 = rep(1, nvars),
  exclude,
  dfmax = nvars + 1,
  pmax = min(dfmax * 1.2, nvars),
  standardize = FALSE,
  intercept = TRUE,
  eps = 1e-08,
  maxit = 1e+06,
  delta = 2,
  omega = 0.5
)

Arguments

x	matrix of predictors, of dimension N*p; each row is an observation vector.
y	response variable. This argument should be a two-level factor for classification.
nlambda	the number of lambda values - default is 100.
method	a character string specifying the loss function to use, valid options are: "hhsvm" Huberized squared hinge loss, "sqsvm" Squared hinge loss, "logit" logistic loss, "ls" least square loss. "er" expectile regression loss. Default is "hhsvm".
lambda.factor	The factor for getting the minimal lambda in lambda sequence, where min(lambda) = lambda.factor * max(lambda), where max(lambda) is the smallest value of lambda for which all coefficients are zero. The default depends on the relationship between N (the number of rows in the matrix of predictors) and p (the number of predictors). If N > p, the default is 0.0001, close to zero. If N<p, the default is 0.01. A very small value of lambda.factor will lead to a saturated fit. It takes no effect if there is user-defined lambda sequence.
lambda	a user supplied lambda sequence. Typically, by leaving this option unspecified users can have the program compute its own lambda sequence based on nlambda and lambda.factor. Supplying a value of lambda overrides this. It is better to supply a decreasing sequence of lambda values than a single (small) value, if not, the program will sort user-defined lambda sequence in decreasing order automatically.
lambda2	regularization parameter lambda2 for the quadratic penalty of the coefficients.
pf	L1 penalty factor of length p used for adaptive LASSO or adaptive elastic net. Separate L1 penalty weights can be applied to each coefficient of beta to allow differential L1 shrinkage. Can be 0 for some variables, which implies no L1 shrinkage, and results in that variable always being included in the model. Default is 1 for all variables (and implicitly infinity for variables listed in exclude).
pf2	L2 penalty factor of length p used for adaptive LASSO or adaptive elastic net. Separate L2 penalty weights can be applied to each coefficient of beta to allow differential L2 shrinkage. Can be 0 for some variables, which implies no L2 shrinkage. Default is 1 for all variables.
exclude	indices of variables to be excluded from the model. Default is none. Equivalent to an infinite penalty factor.
dfmax	limit the maximum number of variables in the model. Useful for very large p, if a partial path is desired. Default is p+1.
pmax	limit the maximum number of variables ever to be nonzero. For example once β enters the model, no matter how many times it exits or re-enters model through the path, it will be counted only once. Default is min(dfmax*1.2,p).
standardize	logical flag for variable standardization, prior to fitting the model sequence. If TRUE, x matrix is normalized such that x is centered (i.e. sum(Xj)=0), and sum squares of each column <Xj,Xj>/N=1. If x matrix is standardized, the ending coefficients will be transformed back to the original scale. Default is FALSE.
intercept	logical flag to indicate whether to include or exclude the intercept in the model.
eps	convergence threshold for coordinate majorization descent. Each inner coordinate majorization descent loop continues until the relative change in any coefficient (i.e., max(j)(beta_new[j]-beta_old[j])^2) is less than eps. For HHSVM, i.e., method="hhsvm", it is 2*max(j) (beta_new[j]-beta_old[j])^2/delta. For expectile regression, i.e., method="er", it is 2*max(1-omega,omega)*max(j) (beta_new[j]-beta_old[j])^2. Defaults value is 1e-8.
maxit	maximum number of outer-loop iterations allowed at fixed lambda value. Default is 1e6. If models do not converge, consider increasing maxit.
delta	the parameter delta in the HHSVM model. The value must be greater than 0. Default is 2.
omega	the parameter omega in the expectile regression model. The value must be in (0,1). Default is 0.5.

Details

Note that the objective function in gcdnet is

Loss(y, X, beta))/N + lambda1 * |beta| + 0.5 * lambda2 * |beta|^2

where the penalty is a combination of L1 and L2 term. Users can specify the loss function to use, options include Huberized squared hinge loss, Squared hinge loss, least square loss, logistic regression and expectile regression loss. Users can also tweak the penalty by choosing different lambda2 and penalty factor.

For computing speed reason, if models are not converging or running slow, consider increasing eps, decreasing nlambda, or increasing lambda.factor before increasing maxit.

FAQ:

Question: “I couldn't get an idea how to specify an option to get adaptive LASSO, how to specify an option to get elastic net and adaptive elastic net? Could you please give me a quick hint?”

Answer: lambda2 is the regularize parameter for L2 penalty part. To use LASSO, set lambda2=0. To use elastic net, set lambda2 as nonzero.

pf is the L1 penalty factor of length p (p is the number of predictors). Separate L1 penalty weights can be applied to each coefficient to allow differential L1 shrinkage. Similiarly pf2 is the L2 penalty factor of length p.

To use adaptive LASSO, you should set lambda2=0 and also specify pf and pf2. To use adaptive elastic net, you should set lambda2 as nonzero and specify pf and pf2,

For example:

    library('gcdnet')
    # Dataset N = 100, p = 10
    x_log <- matrix(rnorm(100*10),100,10)
    y_log <- sample(c(-1,1),100,replace=TRUE)

    # LASSO
    m <- gcdnet(x=x_log,y=y_log,lambda2=0,method="log")
    plot(m)

    # elastic net with lambda2 = 1
    m <- gcdnet(x=x_log,y=y_log,lambda2=1,method="log")
    plot(m)

    # adaptive lasso with penalty factor
    # pf = 0.5 0.5 0.5 0.5 0.5 1.0 1.0 1.0 1.0 1.0
    m <- gcdnet(x=x_log,y=y_log,lambda2=0,method="log",
                pf=c(rep(0.5,5),rep(1,5)))
    plot(m)

    # adaptive elastic net with lambda2 = 1 and penalty factor pf =
    # c(rep(0.5,5),rep(1,5)) pf2 = 3 3 3 3 3 1 1 1 1 1
    m <- gcdnet(x=x_log,y=y_log,lambda2=1,method="log",
                pf=c(rep(0.5,5),rep(1,5)),
                pf2 = c(rep(3,5),rep(1,5)))
    plot(m)
  

Question: “what is the meaning of the parameter pf? On the package documentation, it said pf is the penalty weight applied to each coefficient of beta?”

Answer: Yes, pf and pf2 are L1 and L2 penalty factor of length p used for adaptive LASSO or adaptive elastic net. 0 means that the feature (variable) is always excluded, 1 means that the feature (variable) is included with weight 1.

Question: “Does gcdnet deal with both continuous and categorical response variables?”

Answer: Yes, both are supported, you can use a continuous type response variable with the least squares regression loss, or a categorical type response with losses for classification problem.

Question: “Why does predict function not work? predict should return the predicted probability of the positive class. Instead I get:”

    Error in as.matrix(as.matrix(cbind2(1, newx)) %*% nbeta):
    error in evaluating the argument 'x' in selecting a method for function 'as.matrix':
    Error in t(.Call(Csparse_dense_crossprod, y, t(x))):
    error in evaluating the argument 'x' in selecting a method for function 't':
    Error: Cholmod error 'X and/or Y have wrong dimensions' at
      file ../MatrixOps/cholmod_sdmult.c, line 90?
  

“Using the Arcene dataset and executing the following code will give the above error:”

    library(gcdnet)
    arc <- read.csv("arcene.csv", header=FALSE)
    fit <- gcdnet(arc[,-10001], arc[,10001], standardize=FALSE,
                  method="logit")
    pred <- rnorm(10000)
    predict(fit, pred, type="link")
  

Answer: It is actually NOT a bug of gcdnet. When make prediction using a new matrix x, each observation of x should be arranged as a row of a matrix. In your code, because "pred" is a vector, you need to convert "pred" into a matrix, try the following code:

     pred <- rnorm(10000)
     pred <- matrix(pred,1,10000)
     predict(fit, pred, type="link")
  

Value

An object with S3 class gcdnet.

call	the call that produced this object
b0	intercept sequence of length length(lambda)
beta	a p*length(lambda) matrix of coefficients, stored as a sparse matrix (dgCMatrix class, the standard class for sparse numeric matrices in the Matrix package.). To convert it into normal type matrix use as.matrix().
lambda	the actual sequence of lambda values used
df	the number of nonzero coefficients for each value of lambda.
dim	dimension of coefficient matrix (ices)
npasses	total number of iterations (the most inner loop) summed over all lambda values
jerr	error flag, for warnings and errors, 0 if no error.

Author(s)

Yi Yang, Yuwen Gu and Hui Zou
Maintainer: Yi Yang <[e-mail]>

References

Yang, Y. and Zou, H. (2012). "An Efficient Algorithm for Computing The HHSVM and Its Generalizations." Journal of Computational and Graphical Statistics, 22, 396-415.
BugReport: https://github.com/emeryyi/gcdnet

Gu, Y., and Zou, H. (2016). "High-dimensional generalizations of asymmetric least squares regression and their applications." The Annals of Statistics, 44(6), 2661–2694.

See Also

plot.gcdnet

Examples

data(FHT)
# 1. solution paths for the LASSO penalized least squares.
# To use LASSO set lambda2 = 0.

m1 <- gcdnet(x = FHT$x, y = FHT$y_reg, lambda2 = 0, method = "ls")
plot(m1)

# 2. solution paths for the elastic net penalized HHSVM.
# lambda2 is the parameter controlling the L2 penalty.
m2 <- gcdnet(x = FHT$x, y = FHT$y, delta = 1, lambda2 = 1, method = "hhsvm")
plot(m2)

# 3. solution paths for the adaptive LASSO penalized SVM
# with the squared hinge loss. To use the adaptive LASSO,
# set lambda2 = 0 and meanwhile specify the L1 penalty weights.
p <- ncol(FHT$x)
# set the first three L1 penalty weights as 0.1 and the rest are 1
pf = c(0.1, 0.1, 0.1, rep(1, p-3))
m3 <- gcdnet(x = FHT$x, y = FHT$y, pf = pf, lambda2 = 0, method = "sqsvm")
plot(m3)

# 4. solution paths for the adaptive elastic net penalized
# logistic regression.

p <- ncol(FHT$x)
# set the first three L1 penalty weights as 10 and the rest are 1.
pf <- c(10, 10, 10, rep(1, p-3))
# set the last three L2 penalty weights as 0.1 and the rest are 1.
pf2 <- c(rep(1, p-3), 0.1, 0.1, 0.1)
# set the L2 penalty parameter lambda2=0.01.
m4 <- gcdnet(x = FHT$x, y = FHT$y, pf = pf, pf2 = pf2,
             lambda2 = 0.01, method = "logit")
plot(m4)

# 5. solution paths for the LASSO penalized expectile regression
# with the asymmetric least square parameter omega=0.9.

m5 <- gcdnet(x = FHT$x, y = FHT$y_reg, omega = 0.9,
             lambda2 = 0, method = "er")
plot(m5)

gcdnet documentation built on Aug. 14, 2022, 9:05 a.m.