A Graph-Based Cross-Fitting Engine in R

Provides a general cross-fitting engine for semiparametric estimation (e.g., double/debiased machine learning). Supports user-defined target functionals and directed acyclic graphs of nuisance learners with per-node training fold widths, target-specific evaluation windows, and fold-allocation modes ("overlap", "disjoint", "independence"). Returns either numeric estimates (mode = "estimate") or cross-fitted prediction functions (mode = "predict"), with configurable aggregation over panels and repetitions, reuse-aware caching, and failure isolation, making it well-suited for simulation studies and large benchmarks.

crossfit: A Graph-Based Cross-Fitting Engine in R

A graph-based, estimator-agnostic cross-fitting engine for semiparametric estimation (e.g. double/debiased machine learning) and related meta-learners. crossfit makes the cross-fitting schedule explicit and auditable, supports DAGs of nuisance learners, and is well-suited for simulation studies and benchmarking grids.

The package lets you define:

• a target functional (e.g. ATE, risk, regression error),
• a graph of nuisance models (propensity scores, regressions, etc.),
• how many folds each node trains on (train_fold),
• the width, in folds, of the target’s evaluation window (eval_fold),

and then runs a cross-fitting schedule with configurable aggregation over panels and repetitions.

Installation

You can install the released version from CRAN or the development version from GitHub:

# Install the released version from CRAN
install.packages("crossfit")

# Install the development version from GitHub
install.packages("remotes")
remotes::install_github("EtiennePeyrot/crossfit-R", build_vignettes = TRUE)

Then load it as usual:

library(crossfit)

Overview

crossfit is designed for settings where:

• you care about a low-dimensional target (ATE, a coefficient, a risk, …),
• the target depends on high-dimensional nuisance functions estimated by ML.

The engine:

• enforces out-of-sample use of nuisances via K-fold cross-fitting,

• executes an explicit schedule over folds, panels and repetitions (useful for auditing and benchmarking),

• includes reuse-aware caching (avoid redundant refits) and failure isolation for large experiment grids,

• supports an arbitrary DAG of nuisances (not just one or two),

• lets each node choose its own train_fold (how many folds it trains on),

• lets the target choose its evaluation-window width (eval_fold),

• supports several fold allocation schemes: "independence", "overlap", "disjoint",

• has two modes:

  • mode = "estimate" → returns a numeric estimate of the target,
  • mode = "predict" → returns a cross-fitted prediction function.

Internally, the graph is normalized into a set of instances with structural signatures, so that identical models can share fits and be cached efficiently.

Quick example: cross-fitted MSE

Here is a minimal example on a simple regression problem. We define a nuisance $m(x) = E[Y \mid X]$ and use the cross-fitted mean squared error of this nuisance as our target.

library(crossfit)

set.seed(1)
n <- 200
x <- rnorm(n)
y <- x + rnorm(n)
data <- data.frame(x = x, y = y)

# 1) Nuisance: regression m(x) = E[Y | X]
nuis_y <- create_nuisance(
  fit = function(data, ...) lm(y ~ x, data = data),
  predict = function(model, data, ...) {
    as.numeric(predict(model, newdata = data))
  }
)

# 2) Target: cross-fitted MSE of m(x)
target_mse <- function(data, nuis_y, ...) {
  mean((data$y - nuis_y)^2)
}

# 3) Method: use 4 folds, 3 repetitions, and "independence" allocation
method <- create_method(
  target = target_mse,
  list_nuisance = list(nuis_y = nuis_y),
  folds = 4,
  repeats = 3,
  eval_fold = 1,
  mode = "estimate",
  fold_allocation = "independence",
  aggregate_panels  = mean_estimate,
  aggregate_repeats = mean_estimate
)

res <- crossfit(data, method)

str(res$estimate)
res$estimate

The crossfit() call:

• builds the nuisance / target graph,

• runs K-fold cross-fitting for repeats repetitions,

• aggregates over panels and repetitions using mean_estimate(),

• returns a list with:

  • estimate – the final estimate (or prediction function),

  • results – repetition-wise values and error traces,

  • repeats_done – number of successful repetitions,

  • K, K_required, method, plan – diagnostics and internals.

Multiple methods and shared nuisances

You can run several methods in the same call, sharing some or all nuisances. For example, we can estimate both:

• the cross-fitted MSE of $m(x)$,
• the cross-fitted mean of $m(x)$,

in a single call:

target_mean <- function(data, nuis_y) {
  mean(nuis_y)
}

m_mse <- create_method(
  target = target_mse,
  list_nuisance = list(nuis_y = nuis_y),
  folds = 4,
  repeats = 3,
  eval_fold = 1,
  mode = "estimate",
  fold_allocation = "independence",
  aggregate_panels  = mean_estimate,
  aggregate_repeats = mean_estimate
)

m_mean <- create_method(
  target = target_mean,
  list_nuisance = list(nuis_y = nuis_y),
  folds = 4,
  repeats = 3,
  eval_fold = 1,
  mode = "estimate",
  fold_allocation = "overlap",
  aggregate_panels  = mean_estimate,
  aggregate_repeats = mean_estimate
)

cf_multi <- crossfit_multi(
  data    = data,
  methods = list(mse = m_mse, mean = m_mean),
  aggregate_panels  = mean_estimate,
  aggregate_repeats = mean_estimate
)

cf_multi$estimates

The two methods share the fitted nuisance models whenever their structure and training folds coincide, which can save a lot of computation when you compare multiple learners or targets.

Predict mode: cross-fitted predictor

In "predict" mode, the engine returns a prediction function instead of a numeric estimate. This is useful if you want a cross-fitted predictor you can re-use on new data.

Here we build a cross-fitted regression function:

library(crossfit)

set.seed(1)

# Toy nonlinear regression problem
n  <- 200
x  <- runif(n, -2, 2)
y  <- sin(x) + rnorm(n, sd = 0.3)
data <- data.frame(x = x, y = y)

# Two simple nuisances: linear and quadratic regressions
nuis_lin <- create_nuisance(
  fit = function(data, ...) lm(y ~ x, data = data),
  predict = function(model, data, ...) {
    as.numeric(predict(model, newdata = data))
  },
  train_fold = 2
)

nuis_quad <- create_nuisance(
  fit = function(data, ...) lm(y ~ poly(x, 2), data = data),
  predict = function(model, data, ...) {
    as.numeric(predict(model, newdata = data))
  },
  train_fold = 2
)

# Target in "predict" mode: ensemble of the two nuisances
target_ensemble <- function(data, m_lin, m_quad, ...) {
  0.5 * m_lin + 0.5 * m_quad
}

method_ens <- create_method(
  target        = target_ensemble,
  list_nuisance = list(m_lin  = nuis_lin,
                       m_quad = nuis_quad),
  folds         = 4,
  repeats       = 3,
  eval_fold     = 0, # no eval window in predict mode
  mode          = "predict",
  fold_allocation = "independence",
  aggregate_panels  = mean_predictor,
  aggregate_repeats = mean_predictor
)

res <- crossfit(data, method_ens)

# Cross-fitted ensemble predictor on new data
f_hat <- res$estimate
newdata <- data.frame(x = seq(-2, 2, length.out = 5))
cbind(x = newdata$x, y_hat = f_hat(newdata))

Here:

• Each repetition builds cross-fitted predictors,
• mean_predictor() aggregates the list of predictors into a single ensemble,
• f_hat(newdata) gives cross-fitted predictions on future data.

Key functions

• create_nuisance()
  Define a nuisance node via fit / predict, train_fold, and optional dependency mappings (fit_deps, pred_deps).

• create_method()
  Define a method:

  • target function,
  • nuisance list,
  • folds, repeats,
  • mode ("estimate" or "predict"),
  • eval_fold,
  • fold_allocation,
  • optional aggregate_panels, aggregate_repeats, and failure_control.

• crossfit_failure_control()
  Configure whether panel errors fail a repetition, whether failed shared fits may prune later methods, and how many failed repetitions are allowed.

• crossfit()
  Run cross-fitting for a single method.

• crossfit_multi()
  Run cross-fitting for several methods in the same call, with shared nuisances and shared K-fold splits.

• Aggregators:

  • mean_estimate(), median_estimate() – combine numeric panel / repetition results.
  • mean_predictor(), median_predictor() – combine lists of prediction functions when mode = "predict".

Further documentation

See:

?crossfit
?crossfit_multi
?create_method
?create_nuisance
?crossfit_failure_control

You can find a more detailed introduction in the package vignette:

browseVignettes("crossfit")
# or directly:
vignette("crossfit-intro", package = "crossfit")

If you encounter a bug or have a feature request, please open an issue at: https://github.com/EtiennePeyrot/crossfit-R/issues.

License

crossfit is free software released under the GPL-3 license.