flash_set_verbose: Set verbose output

In willwerscheid/flashier: Empirical Bayes Matrix Factorization

Set verbose output

Description

Used in a flash pipeline to set the output that will be printed after each greedy or backfitting iteration.

Usage

flash_set_verbose(
  flash,
  verbose = 1L,
  fns = NULL,
  colnames = NULL,
  colwidths = NULL
)

Arguments

flash	A flash or flash_fit object.
verbose	When and how to display progress updates. Set to 0 for no updates; 1 for updates after a "greedy" factor is added or a backfit is completed; 2 for additional notifications about the variational lower bound (ELBO); and 3 for updates after every iteration. By default, per-iteration update information includes the change in ELBO and the maximum (absolute) change over all L2-normalized loadings \ell_1, \ldots, \ell_K and factors f_1, \ldots, f_K. Update information is customizable via parameters fns, colnames, and colwidths. A single tab-delimited table of values may also be output using option verbose = -1. This format is especially convenient for downstream analysis of the fitting history. For example, it may be used to plot the value of the ELBO after each iteration (see the "Advanced Flashier" vignette for an illustration).
fns	A vector of functions. Used to calculate values to display after each greedy/backfit iteration when verbose is either -1 or 3 (see Details below). Ignored for other values of verbose (0, 1, or 2).
colnames	A vector of column names, one for each function in fns.
colwidths	A vector of column widths, one for each function in fns.

Details

Function flash_set_verbose can be used to customize the output that is printed to console while fitting a flash object. After each greedy or backfitting iteration (see, respectively, flash_greedy and flash_backfit), each function in argument fns is successively evaluated and the result is printed to console in a table with column names defined by argument colnames and column widths defined by argument colwidths.

Each function in fns must accept exactly three parameters, curr, prev, and k: curr refers to the flash_fit object from the current iteration; prev, to the flash_fit object from the previous iteration; and, if the iteration is a sequential backfitting iteration (that is, a flash_backfit iteration with argument extrapolate = FALSE), k identifies the factor/loadings pair that is currently being updated (in all other cases, k is NULL). Package flashier provides a number of functions that may be used to customize output: see flash_verbose_elbo, flash_verbose_elbo_diff, flash_verbose_max_chg, flash_verbose_max_chg_L, and flash_verbose_max_chg_F. Custom functions may also be defined. They might inspect the current flash_fit object via argument curr; compare the fit in curr to the fit from the previous iteration (provided by argument prev); or ignore both flash_fit objects entirely (for example, to track progress over time, one might simply call Sys.time). To facilitate working with flash_fit objects, package flashier provides a number of accessors, which are enumerated in the documentation for object flash_fit. Custom functions should return a character string that contains the output exactly as it is to displayed; see Examples below.

Value

The flash object from argument flash, with the new verbose settings reflected in updates to the "internal" flash_fit object. These settings will persist across all subsequent calls to flash_xxx functions until they are modified by another call to flash_set_verbose.

Examples

# Suppress all verbose output.
fl <- flash_init(gtex) |>
  flash_set_verbose(0) |>
  flash_greedy(Kmax = 5)

# Set custom verbose output.
sparsity_F <- function(curr, prev, k) {
  g_F <- flash_fit_get_g(curr, n = 2)
  g_F_pi0 <- g_F$pi[1] # Mixture weight of the "null" component.
  return(g_F_pi0)
}
verbose_fns <- c(flash_verbose_elbo, flash_verbose_max_chg_F, sparsity_F)
colnames <- c("ELBO", "Max Chg (Tiss)", "Sparsity (Tiss)")
colwidths <- c(12, 18, 18)
fl <- flash_init(gtex) |>
  flash_set_verbose(
    verbose = 3,
    fns = verbose_fns,
    colnames = colnames,
    colwidths = colwidths
  ) |>
  flash_greedy(Kmax = 3)

# Output can be changed as needed.
fl <- flash_init(gtex) |>
  flash_set_verbose(verbose = 1) |>
  flash_greedy(Kmax = 5L) |>
  flash_backfit(verbose = 3) |>
  flash_greedy(Kmax = 1L)

willwerscheid/flashier documentation built on Jan. 30, 2025, 11:27 p.m.