Merge pull request #264 from mlr-org/add_rcll

add RCLL

Author: RaphaelS1

DESCRIPTION

@@ -94,6 +94,7 @@ Collate:
     'MeasureSurvMSE.R'
     'MeasureSurvNagelkR2.R'
     'MeasureSurvOQuigleyR2.R'
+    'MeasureSurvRCLL.R'
     'MeasureSurvRMSE.R'
     'MeasureSurvSchmid.R'
     'MeasureSurvSongAUC.R'

NAMESPACE

@@ -53,6 +53,7 @@ export(MeasureSurvMAE)
 export(MeasureSurvMSE)
 export(MeasureSurvNagelkR2)
 export(MeasureSurvOQuigleyR2)
+export(MeasureSurvRCLL)
 export(MeasureSurvRMSE)
 export(MeasureSurvSchmid)
 export(MeasureSurvSongAUC)

NEWS.md

@@ -1,5 +1,6 @@
 # mlr3proba 0.4.7
 
+* Add right-censored log loss
 * Fix bug in {rpart} where model was being discarded when set to be kept. Parameter `model` now called `keep_model`.
 
 # mlr3proba 0.4.6

R/MeasureSurvRCLL.R

@@ -0,0 +1,72 @@
+#' @template surv_measure
+#' @templateVar title Right-Censored Log loss
+#' @templateVar fullname MeasureSurvRCLL
+#'
+#' @description
+#' Calculates the right-censored logarithmic (log), loss.
+#'
+#' The RCLL, in the context of probabilistic predictions, is defined by
+#' \deqn{L(f, t, \Delta) = -log(\Delta f(t) + (1 - \Delta) S(t))}
+#' where \eqn{\Delta} is the censoring indicator.
+#'
+#' @template param_id
+#' @template param_eps
+#'
+#' @references
+#' Avati, A., Duan, T., Zhou, S., Jung, K., Shah, N. H., & Ng, A. (2018).
+#' Countdown Regression: Sharp and Calibrated Survival Predictions.
+#' http://arxiv.org/abs/1806.08324
+#'
+#' @family Probabilistic survival measures
+#' @family distr survival measures
+#' @export
+MeasureSurvRCLL = R6::R6Class("MeasureSurvRCLL",
+  inherit = MeasureSurv,
+  public = list(
+    #' @description
+    #' Creates a new instance of this [R6][R6::R6Class] class.
+    initialize = function() {
+      ps = ps(
+        eps = p_dbl(0, 1, default = 1e-15),
+        se = p_lgl(default = FALSE)
+      )
+      ps$values = list(eps = 1e-15, se = FALSE)
+
+      super$initialize(
+        id = "surv.rcll",
+        minimize = TRUE,
+        predict_type = "distr",
+        packages = "distr6",
+        label = "RCLL",
+        man = "mlr3proba::mlr_measures_surv.rcll",
+        range = c(-Inf, Inf),
+        param_set = ps
+      )
+
+      invisible(self)
+    }
+  ),
+
+  private = list(
+    .score = function(prediction, ...) {
+      out = numeric(length(prediction$row_ids))
+      truth = prediction$truth
+      event = truth[, 2] == 1
+
+      # uncensored -> pdf at outcome time (survived *this* long)
+      out[event] = diag(prediction$distr$pdf(truth[event, 1]))
+      # censored -> survival at outcome time (survived *at least* this long)
+      out[!event] = diag(prediction$distr$survival(truth[!event, 1]))
+      # prevent infinite log errors
+      out[out == 0] = self$param_set$values$eps
+
+      out = -log(out)
+
+      if (self$param_set$values$se) {
+        sd(out) / sqrt(length(out))
+      } else {
+        mean(out)
+      }
+    }
+  )
+)

R/zzz.R

@@ -109,6 +109,7 @@ register_mlr3 = function() {
   x$add("surv.brier", MeasureSurvGraf)
   x$add("surv.schmid", MeasureSurvSchmid)
   x$add("surv.logloss", MeasureSurvLogloss)
+  x$add("surv.rcll", MeasureSurvRCLL)
   x$add("surv.intlogloss", MeasureSurvIntLogloss)
 
   x$add("surv.cindex", MeasureSurvCindex)