EPSGO: Efficient Parameter Selection via Global Optimization

In mwsill/c060: Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models

Description

Finds an optimal solution for the Q.func function.

Usage

epsgo(Q.func, bounds,  round.n=5, parms.coding="none",
  fminlower=0, flag.find.one.min =FALSE,
  show=c("none", "final", "all"), N= NULL, maxevals = 500,
  pdf.name=NULL,  pdf.width=12,  pdf.height=12, my.mfrow=c(1,1),
  verbose=TRUE, seed=123,  ...  )

Arguments

Q.func	name of the function to be minimized.
bounds	bounds for parameters
round.n	number of digits after comma, default: 5
parms.coding	parmeters coding: none or log2, default: none.
fminlower	minimal value for the function Q.func, default is 0.
flag.find.one.min	do you want to find one min value and stop? Default: FALSE
show	show plots of DIRECT algorithm: none, final iteration, all iterations. Default: none
N	define the number of start points, see details.
maxevals	the maximum number of DIRECT function evaluations, default: 500.
pdf.name	pdf name
pdf.width	default: 12
pdf.height	default: 12
my.mfrow	default: c(1,1)
verbose	verbose? default: TRUE.
seed	seed
...	additional argument(s)

Details

if the number of start points (N) is not defined by the user, it will be defined dependent on the dimensionality of the parameter space. N=10D+1, where D is the number of parameters, but for high dimensional parameter space with more than 6 dimensions, the initial set is restricted to 65. However for one-dimensional parameter space the N is set to 21 due to stability reasons.

The idea of EPSGO (Efficient Parameter Selection via Global Optimization): Beginning from an intial Latin hypercube sampling containing N starting points we train an Online GP, look for the point with the maximal expected improvement, sample there and update the Gaussian Process(GP). Thereby it is not so important that GP really correctly models the error surface of the SVM in parameter space, but that it can give a us information about potentially interesting points in parameter space where we should sample next. We continue with sampling points until some convergence criterion is met.

DIRECT is a sampling algorithm which requires no knowledge of the objective function gradient. Instead, the algorithm samples points in the domain, and uses the information it has obtained to decide where to search next. The DIRECT algorithm will globally converge to the maximal value of the objective function. The name DIRECT comes from the shortening of the phrase 'DIviding RECTangles', which describes the way the algorithm moves towards the optimum.

The code source was adopted from MATLAB originals, special thanks to Holger Froehlich.

Value

fmin	minimal value of Q.func on the interval defined by bounds.
xmin	corresponding parameters for the minimum
iter	number of iterations
neval	number of visited points
maxevals	the maximum number of DIRECT function evaluations
seed	seed
bounds	bounds for parameters
Q.func	name of the function to be minimized.
points.fmin	the set of points with the same fmin
Xtrain	visited points
Ytrain	the output of Q.func at visited points Xtrain
gp.seed	seed for Gaussian Process
model.list	detailed information of the search process

Author(s)

Natalia Becker natalia.becker at dkfz.de

References

Froehlich, H. and Zell, A. (2005) "Effcient parameter selection for support vector machines in classification and regression via model-based global optimization" In Proc. Int. Joint Conf. Neural Networks, 1431-1438 .

Sill M., Hielscher T., Becker N. and Zucknick M. (2014), c060: Extended Inference with Lasso and Elastic-Net Regularized Cox and Generalized Linear Models, Journal of Statistical Software, Volume 62(5), pages 1–22. http://www.jstatsoft.org/v62/i05/

Examples

## Not run: 
set.seed(1010)
n=1000;p=100
nzc=trunc(p/10)
x=matrix(rnorm(n*p),n,p)
beta=rnorm(nzc)
fx= x[,seq(nzc)] %*% beta
eps=rnorm(n)*5
y=drop(fx+eps)
px=exp(fx)
px=px/(1+px)
ly=rbinom(n=length(px),prob=px,size=1)
set.seed(1011)

 
nfolds = 10
set.seed(1234)
foldid <- balancedFolds(class.column.factor=y.classes, cross.outer=nfolds)

# y - binomial
y.classes<-ifelse(y>= median(y),1, 0)
bounds <- t(data.frame(alpha=c(0, 1)))
colnames(bounds)<-c("lower","upper")
 
fit <- epsgo(Q.func="tune.glmnet.interval", 
             bounds=bounds, 
             parms.coding="none", 
             seed = 1234, 
             show="none",
             fminlower = -100,
             x = x, y = y.classes, family = "binomial", 
             foldid = foldid,
             type.min = "lambda.1se",
             type.measure = "mse")
summary(fit)

# y - multinomial: low - low 25%, middle - (25,75)-quantiles, high - larger 75%.
y.classes<-ifelse(y <= quantile(y,0.25),1, ifelse(y >= quantile(y,0.75),3, 2))
bounds <- t(data.frame(alpha=c(0, 1)))
colnames(bounds)<-c("lower","upper")
 
fit <- epsgo(Q.func="tune.glmnet.interval", 
             bounds=bounds, 
             parms.coding="none", 
             seed = 1234, 
             show="none",
             fminlower = -100,
             x = x, y = y.classes, family = "multinomial", 
             foldid = foldid,
             type.min = "lambda.1se",
             type.measure = "mse")
summary(fit)

##poisson
N=500; p=20
nzc=5
x=matrix(rnorm(N*p),N,p)
beta=rnorm(nzc)
f = x[,seq(nzc)]
mu=exp(f)
y.classes=rpois(N,mu)

nfolds = 10
set.seed(1234)
foldid <- balancedFolds(class.column.factor=y.classes, cross.outer=nfolds)


fit <- epsgo(Q.func="tune.glmnet.interval", 
             bounds=bounds, 
             parms.coding="none", 
             seed = 1234, 
             show="none",
             fminlower = -100,
             x = x, y = y.classes, family = "poisson", 
             foldid = foldid,
             type.min = "lambda.1se",
             type.measure = "mse")
summary(fit)

#gaussian
set.seed(1234)
x=matrix(rnorm(100*1000,0,1),100,1000)
y <- x[1:100,1:1000]%*%c(rep(2,5),rep(-2,5),rep(.1,990))

foldid <- rep(1:10,each=10)

fit <- epsgo(Q.func="tune.glmnet.interval", 
             bounds=bounds, 
             parms.coding="none", 
             seed = 1234, 
             show="none",
             fminlower = -100,
             x = x, y = y, family = "gaussian", 
             foldid = foldid,
             type.min = "lambda.1se",
             type.measure = "mse")
summary(fit)  

# y - cox in vingette

## End(Not run)

mwsill/c060 documentation built on Nov. 26, 2019, 12:14 a.m.