nmfkc.bicv: Bi-cross-validation for NMF rank selection

In nmfkc: Non-Negative Matrix Factorization with Kernel Covariates

Bi-cross-validation for NMF rank selection

Description

Owen & Perry's (2009) bi-cross-validation (BCV) for choosing the NMF rank. A lightweight CV engine in the spirit of nmfkc.ecv: it returns the held-out error per rank and nothing more (no plot, no table) – pass the result to which.min(sigma), or build your own diagnostics.

Unlike the element-wise CV of nmfkc.ecv (which holds out scattered entries and refits with weights), BCV holds out a whole row-block and column-block simultaneously: the model is fit only on the retained block D, and the held-out block A is predicted by folding the held-out rows/columns onto the fixed D-factors via non-negative regression (\hat A = L_I R_J). Because the held-out rows and columns never enter the fit, there is no information leakage. Covariates are ignored (plain NMF). The recommended setting is to leave out roughly half the rows and half the columns (nfolds = 2).

Usage

nmfkc.bicv(Y, rank = 1:3, ...)

Arguments

Y	Observation matrix (P \times N), non-negative.
rank	Integer vector of ranks to evaluate.
...	Advanced options, rarely needed (defaults in parentheses): nfolds (2), the number of row and column folds (the grid is nfolds x nfolds; 2 leaves out half the rows / columns, Owen & Perry's recommendation); seed (123, fold-assignment seed); and nnls.maxit (100, multiplicative-update iterations for the fold-in non-negative regressions). Any other arguments are passed to nmfkc for the per-block fits (e.g.\ maxit).

Details

Each fold keeps about (1 - 1/\text{nfolds}) of the rows and columns, so the retained block D must have more than rank rows and columns. The largest testable rank is therefore about (1 - 1/\text{nfolds})\min(P, N) - 1; with nfolds = 2 this is roughly \min(P, N)/2 - 1. Ranks above this return NA and trigger a warning that names the limit and the nfolds (or nmfkc.ecv) that would reach the requested ranks. Raising nfolds lifts the limit at the cost of a smaller hold-out and more compute ((\text{nfolds} - 1)^2 full fits per rank).

Value

A list (cf.\ nmfkc.ecv) with:

objfunc	Held-out mean squared error for each rank.
sigma	Its square root (RMSE) for each rank.
rank	The evaluated rank vector.
nfolds	The number of folds used.

References

A. B. Owen and P. O. Perry (2009). Bi-cross-validation of the SVD and the nonnegative matrix factorization. Ann. Appl. Stat. 3(2):564–594. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1214/08-AOAS227")}.

See Also

nmfkc.rank, nmfkc.ecv, nmfkc.consensus, nmfkc.ard

Examples

## rank-3 non-negative data; bi-CV needs enough kept rows/cols per
## fold (> rank), so use a matrix with ample dimensions.
set.seed(1)
X <- matrix(abs(rnorm(30 * 3)), 30, 3)
B <- matrix(abs(rnorm(3 * 40)), 3, 40)
bv <- nmfkc.bicv(X %*% B, rank = 1:6)   # nfolds = 2 (Owen & Perry) by default
bv$sigma                  # held-out RMSE per rank
bv$rank[which.min(bv$sigma)]

nmfkc documentation built on July 14, 2026, 1:07 a.m.