Fast big-memory workflows with bigPLScox

In bigPLScox: Partial Least Squares for Cox Models with Big Matrices

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "figures/fast-big--",
  fig.width = 7,
  fig.height = 4.5,
  dpi = 150,
  message = FALSE,
  warning = FALSE
)

LOCAL <- identical(Sys.getenv("LOCAL"), "TRUE")

Introduction

Large survival datasets often outgrow the capabilities of purely in-memory algorithms. bigPLScox therefore offers three flavours of Partial Least Squares (PLS) components for Cox models:

1. big_pls_cox() – the original R/C++ hybrid that expects dense matrices;
2. big_pls_cox_fast() – the new Armadillo backend with variance-one components and support for both dense matrices and bigmemory::big.matrix objects; and
3. big_pls_cox_gd() – a stochastic gradient descent (SGD) solver for streaming or disk-backed data. allowing datasets too large to fit in RAM.

This vignette demonstrates how to build file-backed matrices, run the fast backends, and reconcile their outputs. It complements the introductory vignette vignette("getting-started", package = "bigPLScox") and focuses on workflow patterns specific to large datasets.

Simulating a large survival dataset

We generate a synthetic dataset with correlated predictors and a known linear predictor. The same object is used to illustrate the dense and big-memory interfaces.

library(bigPLScox)
set.seed(2024)

n_obs  <- 5000
n_pred <- 100
k_true <- 3

Sigma <- diag(n_pred)
for (b in 0:2) {
  idx <- (b * 10 + 1):(b * 10 + 10)
  Sigma[idx, idx] <- 0.7
  diag(Sigma[idx, idx]) <- 1
}

L <- chol(Sigma)
Z <- matrix(rnorm(n_obs * n_pred), nrow = n_obs)
X_dense <- Z %*% L

w1 <- numeric(n_pred); w1[1:4]   <- c( 1.0,  0.8,  0.6, -0.5)
w2 <- numeric(n_pred); w2[5:8]   <- c(-0.7,  0.9, -0.4,  0.5)
w3 <- numeric(n_pred); w3[9:12]  <- c( 0.6, -0.5,  0.7,  0.8)
w1 <- w1 / sqrt(sum(w1^2))
w2 <- w2 / sqrt(sum(w2^2))
w3 <- w3 / sqrt(sum(w3^2))

t1 <- as.numeric(scale(drop(X_dense %*% w1), center = TRUE, scale = TRUE))
t2 <- as.numeric(scale(drop(X_dense %*% w2), center = TRUE, scale = TRUE))
t3 <- as.numeric(scale(drop(X_dense %*% w3), center = TRUE, scale = TRUE))

beta_true <- c(1.0, 0.6, 0.3)
eta       <- beta_true[1]*t1 + beta_true[2]*t2 + beta_true[3]*t3

lambda0 <- 0.05
u <- runif(n_obs)
time_event <- -log(u) / (lambda0 * exp(eta))

target_event <- 0.65

f <- function(lc) {
  mean(time_event <= rexp(n_obs, rate = lc)) - target_event
}
lambda_c <- uniroot(f, c(1e-4, 1), tol = 1e-4)$root
time_cens <- rexp(n_obs, rate = lambda_c)

time   <- pmin(time_event, time_cens)
status <- as.integer(time_event <= time_cens)

if (requireNamespace("bigmemory", quietly = TRUE)) {
  library(bigmemory)
  big_dir <- tempfile("bigPLScox-")
  dir.create(big_dir)
  if(file.exists(paste(big_dir,"X.bin",sep="/"))){unlink(paste(big_dir,"X.bin",sep="/"))}
  if(file.exists(paste(big_dir,"X.desc",sep="/"))){unlink(paste(big_dir,"X.desc",sep="/"))}
  X_big <- bigmemory::as.big.matrix(
    X_dense,
    backingpath = big_dir,
    backingfile = "X.bin",
    descriptorfile = "X.desc"
  )
  X_big[1:6, 1:6]
}

Dense-matrix solvers

The legacy solver big_pls_cox() performs the component extraction in R before fitting the Cox model. The new big_pls_cox_fast() backend exposes the same arguments but runs entirely in C++ for a substantial speed-up.

fit_legacy <- big_pls_cox(
  X = X_dense,
  time = time,
  status = status,
  ncomp = k_true
)
fit_fast_dense <- big_pls_cox_fast(
  X = X_dense,
  time = time,
  status = status,
  ncomp = k_true
)

list(
  legacy = head(fit_legacy$scores),
  fast = head(fit_fast_dense$scores)
)

list(
  legacy = apply(fit_legacy$scores, 2, var),
  fast = apply(fit_fast_dense$scores, 2, var)
)

The summary() method reports key diagnostics, including the final Cox coefficients and the number of predictors retained per component.

summary(fit_fast_dense)

Switching to file-backed matrices

When working with a big.matrix, the same function operates on the shared memory pointer without copying data back to R. This is ideal for datasets that do not fit entirely in RAM.

if (exists("X_big")) {
  fit_fast_big <- big_pls_cox_fast(
    X = X_big,
    time = time,
    status = status,
    ncomp = k_true
  )
  summary(fit_fast_big)
}

The resulting scores, loadings, and centring parameters mirror the dense fit, which simplifies debugging and incremental model building.

Gradient descent for streaming data

The SGD solver trades a small amount of accuracy for drastically reduced memory usage. Provide the same big.matrix object along with the desired number of components.

if (exists("X_big")) {
  fit_gd <- big_pls_cox_gd(
    X = X_big,
    time = time,
    status = status,
    ncomp = k_true,
    max_iter = 2000,
    learning_rate = 0.05,
    tol = 1e-8
  )
  str(fit_gd)
}

Comparing the latent subspaces

Component bases are unique only up to orthogonal rotations. Comparing the linear predictors generated by each solver verifies that they span the same subspace.

if (exists("fit_fast_dense") && exists("fit_gd")) {
  eta_fast_dense <- drop(fit_fast_dense$scores %*% fit_fast_dense$cox_fit$coefficients)
  eta_fast_big <- drop(fit_fast_big$scores %*% fit_fast_big$cox_fit$coefficients)
  eta_gd <- drop(fit_gd$scores %*% fit_gd$cox_fit$coefficients)

  list(
    correlation_fast_dense_big = cor(eta_fast_dense, eta_fast_big),
    correlation_fast_dense_gd = cor(eta_fast_dense, eta_gd),
    concordance = c(
      fast_dense = survival::concordance(survival::Surv(time, status) ~ eta_fast_dense)$concordance,
      fast_big = survival::concordance(survival::Surv(time, status) ~ eta_fast_big)$concordance,
      gd = survival::concordance(survival::Surv(time, status) ~ eta_gd)$concordance
    )
  )
}

Predictions on new data

Use predict() with type = "components" to obtain latent scores for new observations. Supplying explicit centring and scaling parameters ensures consistent projections across solvers.

X_new <- matrix(rnorm(10 * n_pred), nrow = 10)

scores_new <- predict(
  fit_fast_dense,
  newdata = X_new,
  type = "components"
)

risk_new <- predict(
  fit_fast_dense,
  newdata = X_new,
  type = "risk"
)

list(scores = scores_new, risk = risk_new)

Timing snapshot

The bench package provides lightweight instrumentation for comparing solvers. The chunk below contrasts the classical implementation, the fast backend, and the SGD routine on the simulated dataset.

if (requireNamespace("bench", quietly = TRUE) && exists("X_big")) {
  bench_res <- bench::mark(
    big_pls = big_pls_cox(X_dense, time, status, ncomp = k_true),
    fast_dense = big_pls_cox_fast(X_dense, time, status, ncomp = k_true),
    fast_big = big_pls_cox_fast(X_big, time, status, ncomp = k_true),
    gd = big_pls_cox_gd(X_big, time, status, ncomp = k_true, max_iter = 1500),
    iterations = 30,
    check = FALSE
  )
  bench_res$expression <- names(bench_res$expression)
  bench_res[, c("expression", "median", "itr/sec", "mem_alloc")]
}

if (exists("bench_res")) {
  plot(bench_res, type = "jitter")
}

Cleaning up backing files

File-backed matrices can be deleted once the analysis is complete. In production workflows you typically keep the descriptor (.desc) file alongside the binary matrix for later reuse.

Cleaning up

Temporary backing files can be removed after the analysis. In production pipelines you will typically keep the descriptor file alongside the binary data.

if (exists("X_big")) {
  rm(X_big)
  file.remove(file.path(big_dir, "X.bin"))
  file.remove(file.path(big_dir, "X.desc"))
  unlink(big_dir, recursive = TRUE)
}

Further resources

• The introductory vignette demonstrates how to combine the fast backend with the matrix-based modelling functions and deviance residual utilities.
• vignette("bigPLScox-benchmarking", package = "bigPLScox") provides a reproducible benchmark that includes survival::coxph() and coxgpls().
• The help pages (?big_pls_cox_fast, ?big_pls_cox_gd) describe all tuning parameters in detail, including keepX for component-wise sparsity.

bigPLScox documentation built on Nov. 18, 2025, 5:06 p.m.