Merge pull request #770 from mlr-org/feat/inner_valid

Feat/inner valid

Author: mb706

DESCRIPTION

@@ -28,7 +28,7 @@ Authors@R:
              comment = c(ORCID = "0000-0001-9754-0393")),
       person(given = "Sebastian",
              family = "Fischer",
-             role = "ctb",
+             role = "aut",
              email = "[email protected]",
              comment = c(ORCID = "0000-0002-9609-3197")),
       person(given = "Susanne",

NAMESPACE

@@ -27,6 +27,8 @@ S3method(pos,list)
 S3method(predict,Graph)
 S3method(print,Multiplicity)
 S3method(print,Selector)
+S3method(set_validate,GraphLearner)
+S3method(set_validate,PipeOpLearner)
 S3method(unmarshal_model,Multiplicity_marshaled)
 S3method(unmarshal_model,graph_learner_model_marshaled)
 S3method(unmarshal_model,pipeop_impute_learner_state_marshaled)

NEWS.md

@@ -2,6 +2,7 @@
 
 * Compatibility with new `bbotk` release.
 * Added marshaling support to `GraphLearner`
+* Support internal tuning and validation
 
 # mlr3pipelines 0.5.2
 

R/GraphLearner.R

@@ -47,6 +47,17 @@
 #'   contain the model. Use `graph_model` to access the trained [`Graph`] after `$train()`. Read-only.
 #' * `graph_model` :: [`Learner`][mlr3::Learner]\cr
 #'   [`Graph`] that is being wrapped. This [`Graph`] contains a trained state after `$train()`. Read-only.
+#' * `internal_tuned_values` :: named `list()` or `NULL`\cr
+#'   The internal tuned parameter values collected from all `PipeOp`s.
+#'   `NULL` is returned if the learner is not trained or none of the wrapped learners supports internal tuning.
+#' * `internal_valid_scores` :: named `list()` or `NULL`\cr
+#'   The internal validation scores as retrieved from the `PipeOps`.
+#'   The names are prefixed with the respective IDs of the `PipeOp`s.
+#'   `NULL` is returned if the learner is not trained or none of the wrapped learners supports internal validation.
+#' * `validate` :: `numeric(1)`, `"predefined"`, `"test"` or `NULL`\cr
+#'   How to construct the validation data. This also has to be configured for the individual `PipeOp`s such as
+#'   `PipeOpLearner`, see [`set_validate.GraphLearner`].
+#'   For more details on the possible values, see [`mlr3::Learner`].
 #' * `marshaled` :: `logical(1)`\cr
 #'   Whether the learner is marshaled.
 #'
@@ -110,11 +121,17 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
       }
       assert_subset(task_type, mlr_reflections$task_types$type)
 
+      private$.can_validate = some(graph$pipeops, function(po) "validation" %in% po$properties)
+      private$.can_internal_tuning = some(graph$pipeops, function(po) "internal_tuning" %in% po$properties)
+
+      properties = setdiff(mlr_reflections$learner_properties[[task_type]],
+        c("validation", "internal_tuning")[!c(private$.can_validate, private$.can_internal_tuning)])
+
       super$initialize(id = id, task_type = task_type,
         feature_types = mlr_reflections$task_feature_types,
         predict_types = names(mlr_reflections$learner_predict_types[[task_type]]),
         packages = graph$packages,
-        properties = mlr_reflections$learner_properties[[task_type]],
+        properties = properties,
         man = "mlr3pipelines::GraphLearner"
       )
 
@@ -123,8 +140,9 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
       }
       if (!is.null(predict_type)) self$predict_type = predict_type
     },
-    base_learner = function(recursive = Inf) {
+    base_learner = function(recursive = Inf, return_po = FALSE) {
       assert(check_numeric(recursive, lower = Inf), check_int(recursive))
+      assert_flag(return_po)
       if (recursive <= 0) return(self)
       gm = self$graph_model
       gm_output = gm$output
@@ -143,7 +161,11 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
         if (length(last_pipeop_id) > 1) stop("Graph has no unique PipeOp containing a Learner")
         if (length(last_pipeop_id) == 0) stop("No Learner PipeOp found.")
       }
-      learner_model$base_learner(recursive - 1)
+      if (return_po) {
+        last_pipeop
+      } else {
+        learner_model$base_learner(recursive - 1)
+      }
     },
     marshal = function(...) {
       learner_marshal(.learner = self, ...)
@@ -153,15 +175,32 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
     }
   ),
   active = list(
+    internal_valid_scores = function(rhs) {
+      assert_ro_binding(rhs)
+      self$state$internal_valid_scores
+    },
+    internal_tuned_values = function(rhs) {
+      assert_ro_binding(rhs)
+      self$state$internal_tuned_values
+    },
+    validate = function(rhs) {
+      if (!missing(rhs)) {
+        if (!private$.can_validate) {
+          stopf("None of the PipeOps in Graph '%s' supports validation.", self$id)
+        }
+        private$.validate = assert_validate(rhs)
+      }
+      private$.validate
+    },
     marshaled = function() {
       learner_marshaled(self)
     },
     hash = function() {
-      digest(list(class(self), self$id, self$graph$hash, private$.predict_type,
+      digest(list(class(self), self$id, self$graph$hash, private$.predict_type, private$.validate,
         self$fallback$hash, self$parallel_predict), algo = "xxhash64")
     },
     phash = function() {
-      digest(list(class(self), self$id, self$graph$phash, private$.predict_type,
+      digest(list(class(self), self$id, self$graph$phash, private$.predict_type, private$.validate,
         self$fallback$hash, self$parallel_predict), algo = "xxhash64")
     },
     predict_type = function(rhs) {
@@ -195,6 +234,21 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
   ),
   private = list(
     .graph = NULL,
+    .validate = NULL,
+    .can_validate = NULL,
+    .can_internal_tuning = NULL,
+    .extract_internal_tuned_values = function() {
+      if (!private$.can_validate) return(NULL)
+      itvs = unlist(map(pos_with_property(self$graph_model, "internal_tuning"), "internal_tuned_values"), recursive = FALSE)
+      if (!length(itvs)) return(named_list())
+      itvs
+    },
+    .extract_internal_valid_scores = function() {
+      if (!private$.can_internal_tuning) return(NULL)
+      ivs = unlist(map(pos_with_property(self$graph_model, "validation"), "internal_valid_scores"), recursive = FALSE)
+      if (!length(ivs)) return(named_list())
+      ivs
+    },
     deep_clone = function(name, value) {
       # FIXME this repairs the mlr3::Learner deep_clone() method which is broken.
       if (is.environment(value) && !is.null(value[[".__enclos_env__"]])) {
@@ -207,6 +261,13 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
     },
 
     .train = function(task) {
+      if (!is.null(get0("validate", self))) {
+        some_pipeops_validate = some(pos_with_property(self, "validation"), function(po) !is.null(po$validate))
+        if (!some_pipeops_validate) {
+          lg$warn("GraphLearner '%s' specifies a validation set, but none of its PipeOps use it.", self$id)
+        }
+      }
+
       on.exit({self$graph$state = NULL})
       self$graph$train(task)
       state = self$graph$state
@@ -255,6 +316,109 @@ GraphLearner = R6Class("GraphLearner", inherit = Learner,
   )
 )
 
+#' @title Configure Validation for a GraphLearner
+#'
+#' @description
+#' Configure validation for a graph learner.
+#'
+#' In a [`GraphLearner`], validation can be configured on two levels:
+#' 1. On the [`GraphLearner`] level, which specifies **how** the validation set is constructed before entering the graph.
+#' 2. On the level of the individual `PipeOp`s (such as `PipeOpLearner`), which specifies
+#'    which pipeops actually make use of the validation data (set its `$validate` field to `"predefined"`) or not (set it to `NULL`).
+#'    This can be specified via the argument `ids`.
+#'
+#' @param learner ([`GraphLearner`])\cr
+#'   The graph learner to configure.
+#' @param validate (`numeric(1)`, `"predefined"`, `"test"`, or `NULL`)\cr
+#'   How to set the `$validate` field of the learner.
+#'   If set to `NULL` all validation is disabled, both on the graph learner level, but also for all pipeops.
+#' @param ids (`NULL` or `character()`)\cr
+#'   For which pipeops to enable validation.
+#'   This parameter is ignored when `validate` is set to `NULL`.
+#'   By default, validation is enabled for the final `PipeOp` in the `Graph`.
+#' @param args_all (`list()`)\cr
+#'  Rarely needed. A named list of parameter values that are passed to all subsequet [`set_validate()`] calls on the individual
+#'  `PipeOp`s.
+#' @param args (named `list()`)\cr
+#'   Rarely needed.
+#'   A named list of lists, specifying additional argments to be passed to [`set_validate()`] when calling it on the individual
+#'   `PipeOp`s.
+#' @param ... (any)\cr
+#'   Currently unused.
+#'
+#' @export
+#' @examples
+#' library(mlr3)
+#'
+#' glrn = as_learner(po("pca") %>>% lrn("classif.debug"))
+#' set_validate(glrn, 0.3)
+#' glrn$validate
+#' glrn$graph$pipeops$classif.debug$learner$validate
+#'
+#' set_validate(glrn, NULL)
+#' glrn$validate
+#' glrn$graph$pipeops$classif.debug$learner$validate
+#'
+#' set_validate(glrn, 0.2, ids = "classif.debug")
+#' glrn$validate
+#' glrn$graph$pipeops$classif.debug$learner$validate
+set_validate.GraphLearner = function(learner, validate, ids = NULL, args_all = list(), args = list(), ...) {
+  prev_validate_pos = map(pos_with_property(learner$graph$pipeops, "validation"), "validate")
+  prev_validate = learner$validate
+  on.exit({
+    iwalk(prev_validate_pos, function(prev_val, poid) {
+      # Here we don't call into set_validate() as this also does not ensure that we are able to correctly
+      # reset the configuration to the previous state, is less transparent and might fail again
+      # The error message informs the user about this though via the calling handlers below
+      learner$graph$pipeops[[poid]]$validate = prev_val
+    })
+    learner$validate = prev_validate
+  }, add = TRUE)
+
+  if (is.null(validate)) {
+    learner$validate = NULL
+    walk(pos_with_property(learner$graph$pipeops, "validation"), function(po) {
+      invoke(set_validate, po, validate = NULL, args_all = args_all, args = args[[po$id]] %??% list())
+    })
+    on.exit()
+    return(invisible(learner))
+  }
+
+  if (is.null(ids)) {
+    ids = learner$base_learner(return_po = TRUE)$id
+  } else {
+    assert_subset(ids, ids(pos_with_property(learner$graph$pipeops, "validation")))
+  }
+
+  assert_list(args, types = "list")
+  assert_list(args_all)
+  assert_subset(names(args), ids)
+
+  learner$validate = validate
+
+  walk(ids, function(poid) {
+    # learner might be another GraphLearner / AutoTuner so we call into set_validate() again
+    withCallingHandlers({
+      args = insert_named(insert_named(list(validate = "predefined"), args_all), args[[poid]])
+      invoke(set_validate, learner$graph$pipeops[[poid]], .args = args)
+    }, error = function(e) {
+      e$message = sprintf(paste0(
+        "Failed to set validate for PipeOp '%s':\n%s\n",
+        "Trying to heuristically reset validation to its previous state, please check the results"), poid, e$message)
+      stop(e)
+    }, warning = function(w) {
+      w$message = sprintf(paste0(
+        "Failed to set validate for PipeOp '%s':\n%s\n",
+        "Trying to heuristically reset validation to its previous state, please check the results"), poid, w$message)
+      warning(w)
+      invokeRestart("muffleWarning")
+    })
+  })
+  on.exit()
+
+  invisible(learner)
+}
+
 #' @export
 marshal_model.graph_learner_model = function(model, inplace = FALSE, ...) {
   xm = map(.x = model, .f = marshal_model, inplace = inplace, ...)

R/PipeOp.R

@@ -135,6 +135,20 @@
 #'   and done, if requested, by the [`Graph`] backend itself; it should *not* be done explicitly by `private$.train()` or `private$.predict()`.
 #' * `man` :: `character(1)`\cr
 #'   Identifying string of the help page that shows with `help()`.
+#' * `properties` :: `character()`\cr
+#'   The properties of the pipeop.
+#'   Currently supported values are:
+#'     * `"validation"`: the `PipeOp` can make use of the `$internal_valid_task` of an [`mlr3::Task`].
+#'        This is for example used for `PipeOpLearner`s that wrap a `Learner` with this property, see [`mlr3::Learner`].
+#'       `PipeOp`s that have this property, also have a `$validate` field, which controls whether to use the validation task,
+#'        as well as a `$internal_valid_scores` field, which allows to access the internal validation scores after training.
+#'     * `"internal_tuning"`: the `PipeOp` is able to internally optimize hyperparameters.
+#'        This works analogously to the internal tuning implementation for [`mlr3::Learner`].
+#'       `PipeOp`s with that property also implement the standardized accessor `$internal_tuned_values` and have at least one 
+#'        parameter tagged with `"internal_tuning"`.
+#'        An example for such a `PipeOp` is a `PipeOpLearner` that wraps a `Learner` with the `"internal_tuning"` property.
+#'
+#'   Programatic access to all available properties is possible via `mlr_reflections$pipeops$properties`.
 #'
 #' @section Methods:
 #' * `train(input)`\cr
@@ -235,8 +249,9 @@ PipeOp = R6Class("PipeOp",
     output = NULL,
     .result = NULL,
     tags = NULL,
+    properties = NULL,
 
-    initialize = function(id, param_set = ps(), param_vals = list(), input, output, packages = character(0), tags = "abstract") {
+    initialize = function(id, param_set = ps(), param_vals = list(), input, output, packages = character(0), tags = "abstract", properties = character(0)) {
       if (inherits(param_set, "ParamSet")) {
         private$.param_set = assert_param_set(param_set)
         private$.param_set_source = NULL
@@ -246,6 +261,7 @@ PipeOp = R6Class("PipeOp",
       }
       self$id = assert_string(id)
 
+      self$properties = assert_subset(properties, mlr_reflections$pipeops$properties)
       self$param_set$values = insert_named(self$param_set$values, param_vals)
       self$input = assert_connection_table(input)
       self$output = assert_connection_table(output)
@@ -601,4 +617,3 @@ evaluate_multiplicities = function(self, unpacked, evalcall, instate) {
     map(transpose_list(map(result, "output")), as.Multiplicity)
   }
 }
-

R/PipeOpImpute.R

@@ -195,6 +195,10 @@ PipeOpImpute = R6Class("PipeOpImpute",
 
       self$state$outtasklayout = copy(intask$feature_types)
 
+      if (!is.null(intask$internal_valid_task)) {
+        intask$internal_valid_task = private$.predict(list(intask$internal_valid_task))[[1L]]
+      }
+
       list(intask)
     },