R/learner_dbarts_classif_bart.R

In mlr-org/mlr3extralearners: Extra Learners For mlr3

#' @title Classification BART (Bayesian Additive Regression Trees) Learner
#' @author ck37
#' @name mlr_learners_classif.bart
#'
#' @description
#' Bayesian Additive Regression Trees are similar to gradient boosting algorithms.
#' The classification problem is solved by 0-1 encoding of the two-class targets and setting the
#' decision threshold to p = 0.5 during the prediction phase.
#' Calls [dbarts::bart()] from \CRANpkg{dbarts}.
#'
#' @template learner
#' @templateVar id classif.bart
#'
#' @section Parameter Changes:
#' * Parameter: keeptrees
#'
#'  * Original: FALSE
#'  * New: TRUE
#'  * Reason: Required for prediction
#'
#' * Parameter: offset
#'  * The parameter is removed, because only `dbarts::bart2` allows an offset during training,
#'    and therefore the offset parameter in `dbarts:::predict.bart` is irrelevant for
#'    `dbarts::dbart`.
#'
#' * Parameter: nchain, combineChains, combinechains
#'  * The parameters are removed as parallelization of multiple models is handled by future.
#'
#' * Parameter: sigest, sigdf, sigquant, keeptres
#'  * Regression only.
#'
#' @references
#' `r format_bib("sparapani2021nonparametric", "chipman2010bart")`
#'
#' @template seealso_learner
#' @template example
#' @export
LearnerClassifBart = R6Class("LearnerClassifBart",
  inherit = LearnerClassif,
  public = list(

    #' @description
    #' Creates a new instance of this [R6][R6::R6Class] class.
    initialize = function() {

      ps = ps(
        ntree = p_int(default = 200L, lower = 1L, tags = "train"),
        k = p_dbl(default = 2.0, lower = 0, tags = "train"),
        power = p_dbl(default = 2.0, lower = 0, tags = "train"),
        base = p_dbl(default = 0.95, lower = 0, upper = 1, tags = "train"),
        binaryOffset = p_dbl(default = 0.0, tags = "train"),
        ndpost = p_int(default = 1000L, lower = 1L, tags = "train"),
        nskip = p_int(default = 100L, lower = 0L, tags = "train"),
        printevery = p_int(default = 100L, lower = 0L, tags = "train"),
        keepevery = p_int(default = 1L, lower = 1L, tags = "train"),
        keeptrainfits = p_lgl(default = TRUE, tags = "train"),
        usequants = p_lgl(default = FALSE, tags = "train"),
        numcut = p_int(default = 100L, lower = 1L, tags = "train"),
        printcutoffs = p_int(default = 0, tags = "train"),
        verbose = p_lgl(default = FALSE, tags = "train"),
        nthread = p_int(default = 1L, tags = c("train", "threads")),
        keepcall = p_lgl(default = TRUE, tags = "train"),
        sampleronly = p_lgl(default = FALSE, tags = "train"),
        seed = p_int(default = NA_integer_, tags = "train", special_vals = list(NA_integer_)),
        proposalprobs = p_uty(default = NULL, tags = "train"),
        splitprobs = p_uty(default = NULL, tags = "train"),
        keepsampler = p_lgl(default = NO_DEF, tags = "train")
      )

      super$initialize(
        id = "classif.bart",
        packages = c("mlr3extralearners", "dbarts"),
        feature_types = c("integer", "numeric", "factor", "ordered"),
        predict_types = c("response", "prob"),
        param_set = ps,
        properties = c("weights", "twoclass"),
        man = "mlr3extralearners::mlr_learners_classif.bart",
        label = "Bayesian Additive Regression Trees"
      )
    }
  ),

  private = list(

    .train = function(task) {

      pars = self$param_set$get_values(tags = "train")

      # Extact just the features from the task data.
      x_train = task$data(cols = task$feature_names)
      y_train = task$data(cols = task$target_names)
      y_train = as.integer(y_train == task$positive)

      if ("weights" %in% task$properties) {
        pars$weights = task$weights$weight
      }

      invoke(
        dbarts::bart,
        x.train = x_train,
        y.train = y_train,
        keeptrees = TRUE,
        .args = pars
      )
    },

    .predict = function(task) {

      pars = self$param_set$get_values(tags = "predict") # get parameters with tag "predict"

      newdata = ordered_features(task, self)

      # This will return a matrix of predictions, where each column is an observation
      # and each row is a sample from the posterior.
      p = colMeans(invoke(
        predict,
        self$model,
        newdata = newdata,
        .args = pars
      ))

      if (self$predict_type == "response") {
        list(response = ifelse(p >= 0.5, task$positive, task$negative))
      } else {
        list(prob = pprob_to_matrix(p, task))
      }
    }
  )
)

.extralrns_dict$add("classif.bart", LearnerClassifBart)