control.minQuad: control.minQuad
In aucm: AUC Maximization

Description Usage Arguments Details Value Author(s) References See Also

View source: R/minQuad.R

Control function to minQuad

       
control.minQuad(
    maxit = 1e4, tol = 1e-04, 
    q = 0,
    ws = c("v","v2","greedy","rv2wg","rvwg","rv","rv2"),
    method = c("default","tron","loqo","exhaustive","x"),
	optim.control = list(),
    rank = 0,
	DUP = FALSE,
	NAOK = FALSE,
	verbose = FALSE, 
	ret.ws = FALSE,
	ret.data = FALSE
)

`rank`	a nonnegative integer indicating the 'rank' of the design matrix, only used by by method 'exhaustive' or 'x'. if zero it is estimated by the singular value decomposition of each 'sub-matrix' associated with the sub-optimization problem in the decomposition method.
`method`	a character string (first letter is sufficient) indicating which quadratic optmizer to use, defaults to 'default'. See details.
`optim.control`	a list of control parameters to methods 'tron' or 'loqo'; 'tron' : list(maxfev = 1000,fatol = tol,frtol = tol,cgtol=tol,gtol=tol,fmin = -.Machine$double.xmax), 'loqo' : list(bound = 10,margin=0.05,maxiter=40,sigfig = 7,inf = 1e6)
`q`	size of the working set, will be set to 2 for all methods except for method = 'tron' when it defaults to NULL. In that case workings set size is automatically chosen to be sqrt(#violators) at each iteration.
`ws`	a character string indicating the strategy of how to select the working set, defaults to "rv2wg", see details.
`maxit`	maximum number of iterations whose `typeof` returns "integer".
`tol`	tolerance for termination criterion whose `typeof` returns "double".
`DUP`	should arguments be passed by reference ? defaults to FALSE.
`NAOK`	should NA's,NaN's be allowed to be passed to C code (no checking) ? defaults to FALSE.
`verbose`	some output at each iteration, possible values are FALSE/TRUE or and integer if more details are wanted, defaults to FALSE.
`ret.ws`	defaults to FALSE, indicates whether to return the working set selected at each iteration.
`ret.data`	defaults to FALSE, indicates whether to return the data passed to minQuad.

Four quadratic optimizers are available within minQuad, "default", "tron", "loqo" and "exhaustive" (optimizer 'x' is a slightly faster implementation of the exhaustive method). For working set size q = 2, the 'default' option is a fast implementation that loosely minimizes the quadratic objective function, which is often sufficient to achieve convergence in the DCA-loop in rauc. For working set size q = 2, the 'default' option minimizes the quadratic objective function by "solving" an associated equation at each data point. The "exhaustive" method is a brute-force method that gives an exact solution to each quadratic sub-problem in minQuad and should probably not be used beyond working set size q = 8,10 on most computers. Method 'tron' is a positive semidefinite quadratic optimizer and thus well suited for low-rank problems - for this method 'q' can be larger, ~100 or perhaps even ~1000. Method 'loqo' is a positive definite quadratic optimizer that accepts 'm' constraints specified by (m x n) matrix A in the form v <= A*x <= v+r with both v and r finite. The default value of the size of the working set 'q' is 0. This means that if 'method' is 'tron' then 'q' is automatically set to the sqrt(no. of violators) at the current iteration in minQuad (rounded up). Otherwise 'q' defaults to 2 but may be set to any nonzero integer that is greater than 1. The "ws" argument sets the type of strategy to select the working set. Denote the two sets of violators as V0 = {1 if (a[p] > 0.0),(df[p] > 0.0), 0 ow.}, VC = {1 if (a[p] < C),(df[p] < 0.0), 0 ow.} where "df[a]" stands for the gradient of the objective function at 'a'. "greedy" selects the extremes pairs (max,min) from the two sets (M,m) where M = {-df[i] , a[i] < C} and m = {-df[j] | a[j] > 0}. "v" selects from violators V = V0 U VC ranked by |df|. "v2" selects separately from V0 and VC separately, ranked by |df|. "rv" selects without replacement (WOR) from all violators. "rvwg" selects WOR from all violators V with probability ~ |df[V]|. "rv2wg" selects WOR from the two sets of violators V0 and VC with probability ~ |df[V]|.

A list with the following elements:

`convergence`	0 if converged, 1 if maximum iteration is reached.
`alpha`	estimated vector of coefficients.
`value`	value of the objective function.
`iterations`	number of iterations until convergence or "maxit" reached.
`epsilon`	stopping rule value to be compared to "tol".
`n`
`nSV`	#{0 < a}, no. of support vectors.
`nBSV`	#{a==C}, no. of bounded support vectors.
`nFSV`	#{0 < alpha < C}, no. of unbounded support vectors.
`control`	the control argument.
`ws`	if requested, the working set selected at current iteration.

Krisztian Sebestyen ksebestyen@gmail.com
Youyi Fong youyifong@gmail.com
Shuxin Yin

Combining Biomarkers Nonlinearly for Classification Using the Area Under the ROC Curve Y. FONG, S. YIN, Y. HUANG Biometrika (2012), pp 1-28

Newton's method for large bound-constrained optimization problems Lin, C.J. and More, J.J. SIAM Journal on Optimization (1999), volume 9, pp 1100-1127.

kernlab - An S4 Package for Kernel Methods in R. Alexandros Karatzoglou, Alex Smola, Kurt Hornik, Achim Zeileis Journal of Statistical Software (2004) 11(9), 1-20. URL http://www.jstatsoft.org/v11/i09/

rauc, minQuad

aucm documentation built on Jan. 11, 2020, 9:43 a.m.