Merge remote-tracking branch 'origin/xgboost_to_rpf' into interpolation-fix

Author: jyliuu

DESCRIPTION

@@ -22,7 +22,8 @@ Imports:
     hardhat,
     methods,
     Rcpp,
-    utils
+    utils,
+    xgboost
 Suggests:
     knitr,
     mvtnorm,
@@ -38,4 +39,4 @@ Config/Needs/website: patchwork, ggplot2
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0

NAMESPACE

@@ -11,6 +11,7 @@ S3method(rpf,formula)
 S3method(rpf,matrix)
 S3method(rpf,recipe)
 S3method(str,rpf_forest)
+export(convert_xgboost_rpf)
 export(is_purified)
 export(predict_components)
 export(purify)
@@ -19,7 +20,6 @@ import(checkmate)
 importFrom(Rcpp,loadModule)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,":=")
-importFrom(data.table,':=')
 importFrom(data.table,.BY)
 importFrom(data.table,.EACHI)
 importFrom(data.table,.GRP)
@@ -40,4 +40,5 @@ importFrom(methods,new)
 importFrom(stats,model.matrix)
 importFrom(utils,capture.output)
 importFrom(utils,combn)
+importFrom(xgboost,xgb.model.dt.tree)
 useDynLib(randomPlantedForest, .registration = TRUE)

R/convert_xgboost.R

@@ -0,0 +1,76 @@
+
+# Function to get leaf bounds from xgboost
+#FIXME: This seems to be the bottleneck, could do it in C++
+get_leaf_bounds <- function(trees, tree,x) {
+  max_node <- trees[Tree == tree, max(Node)]
+  num_nodes <- max_node + 1
+  lb <- matrix(-Inf, nrow = num_nodes, ncol = ncol(x))
+  ub <- matrix(Inf, nrow = num_nodes, ncol = ncol(x))
+  for (nn in 0:max_node) {
+    if (trees[Tree == tree & Node == nn, !is.na(Yes)]) {
+      left_child <- trees[Tree == tree & Node == nn, Yes]
+      right_child <- trees[Tree == tree & Node == nn, No]
+      splitvar <- trees[Tree == tree & Node == nn, Feature_num]
+
+      # Children inherit bounds
+      ub[left_child + 1, ] <- ub[nn + 1, ]
+      ub[right_child + 1, ] <- ub[nn + 1, ]
+      lb[left_child + 1, ] <- lb[nn + 1, ]
+      lb[right_child + 1, ] <- lb[nn + 1, ]
+
+      # Restrict by new split
+      ub[left_child + 1, splitvar] <- trees[Tree == tree & Node == nn, Split]
+      lb[right_child + 1, splitvar] <- trees[Tree == tree & Node == nn, Split]
+    }
+  }
+
+  # Return bounds of leaves only
+  leaves <- trees[Tree == tree & Feature == "Leaf", Node+1]
+  list(lower = lb[leaves, ],
+       upper = ub[leaves, ])
+}
+
+#' Convert xgboost to rpf object
+#'
+#' @param xg xgboost object
+#' @param x data used to train the xgboost model
+#' @param y target used to train the xgboost model
+#'
+#' @return rpf object
+#' @importFrom xgboost xgb.model.dt.tree
+#' @export
+convert_xgboost_rpf <- function(xg, x, y) {
+  trees <- xgboost::xgb.model.dt.tree(model = xg, use_int_id = TRUE)
+  trees[, Feature_num := as.integer(factor(Feature, levels = c("Leaf", colnames(x)))) - 1L]
+  num_trees <- trees[, max(Tree)+1]
+
+  # create a dummy rpf
+  rpfit <- rpf(x = x, y = y, max_interaction = 0, ntrees = num_trees, splits = 1,
+               purify = FALSE)
+
+  # Overwrite rpf trees
+  for (t in seq_len(num_trees)) {
+    # xgboost adds 0.5 to prediction
+    rpfit$forest[[t]]$values[[1]][[1]] <- 0.5
+    rpfit$forest[[t]]$variables[[2]] <- trees[Tree == t-1 & Feature_num > 0, sort(unique(Feature_num))]
+    rpfit$forest[[t]]$values[[2]] <- as.list(as.numeric(num_trees)*trees[Tree == t-1 & Feature == "Leaf", Quality])
+
+    rpfit$forest[[t]]$intervals[[2]] <- rep(rpfit$forest[[t]]$intervals[[1]], length(rpfit$forest[[t]]$values[[2]]))
+
+    # Get leaf bounds
+    leaf_bounds <- get_leaf_bounds(trees, t-1,x)
+    leaves <- trees[Tree == t-1 & Feature == "Leaf", Node+1]
+    for (i in seq_along(leaves)) {
+      rpfit$forest[[t]]$intervals[[2]][[i]][1, ] <- pmax(rpfit$forest[[t]]$intervals[[2]][[i]][1, ],
+                                                         leaf_bounds$lower[i, ])
+      rpfit$forest[[t]]$intervals[[2]][[i]][2, ] <- pmin(rpfit$forest[[t]]$intervals[[2]][[i]][2, ],
+                                                         leaf_bounds$upper[i, ])
+    }
+  }
+
+  # Also overwrite C++ forest
+  rpfit$fit$set_model(rpfit$forest)
+
+  # Return manipulated rpf object
+  rpfit
+}

R/utils.R

@@ -76,7 +76,7 @@ pca_order <- function(x, y) {
 # Sort factor predictors by outcome and re-encode as integer
 # save original factor levels for prediction step
 # Used in rpf_bridge()
-#' @importFrom data.table .SD ':=' as.data.table
+#' @importFrom data.table .SD as.data.table
 preprocess_predictors_fit <- function(processed) {
   predictors <- as.data.table(processed$predictors)
 

man/convert_xgboost_rpf.Rd

@@ -18,5 +18,6 @@ LineEndingConversion: Posix
 
 BuildType: Package
 PackageUseDevtools: Yes
+PackageCleanBeforeInstall: No
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace

randomPlantedForest.Rproj

@@ -25,6 +25,7 @@ class RandomPlantedForest
   void get_parameters();
   void set_parameters(StringVector keys, NumericVector values);
   List get_model();
+  void set_model(List& model);
   virtual ~RandomPlantedForest(){};
   bool is_purified();
 
@@ -60,4 +61,4 @@ class RandomPlantedForest
   std::vector<std::vector<double>> get_lim_list(const TreeFamily &curr_family);
 };
 
-#endif // RPF_HPP
+#endif // RPF_HPP

src/include/rpf.hpp

@@ -1036,3 +1036,54 @@ List RandomPlantedForest::get_model()
   }
   return (model);
 }
+
+// FIXME: Add checks for format of model argument
+void RandomPlantedForest::set_model(List& model) {
+
+  unsigned int n_families = model.size();
+
+  for (unsigned int i = 0; i < n_families; ++i) {
+    List family = model[i];
+    List variables = family["variables"];
+    List values = family["values"];
+    List intervals = family["intervals"];
+    unsigned int n_trees = variables.size();
+
+    TreeFamily& old_family = tree_families[i];
+
+    old_family.clear();
+
+    for (unsigned int j = 0; j < n_trees; ++j) {
+
+      // Variables
+      IntegerVector tree_variables = variables[j];
+      std::set<int> tree_variables_set(tree_variables.begin(), tree_variables.end());
+
+      // Values
+      std::vector<std::vector<double>> tree_values = values[j];
+      unsigned int n_leaves = tree_values.size();
+
+      // Intervals
+      std::vector<NumericMatrix> tree_intervals = intervals[j];
+
+      std::vector<Leaf> leaves;
+      for (unsigned int k = 0; k < n_leaves; ++k) {
+
+        Leaf temp;
+        temp.value = tree_values[k];
+
+        NumericMatrix leaf_intervals = tree_intervals[k];
+        std::vector<Interval> intervals(leaf_intervals.ncol());
+        for (int l = 0; l < feature_size; ++l) {
+          intervals[l] = Interval{leaf_intervals(0, l), leaf_intervals(1, l)};
+        }
+
+        temp.intervals = intervals;
+        leaves.push_back(temp);
+      }
+
+      old_family.insert(std::make_pair(tree_variables_set, std::make_shared<DecisionTree>(DecisionTree(tree_variables_set, leaves))));
+
+    }
+  }
+}

src/lib/rpf.cpp

@@ -20,6 +20,7 @@ RCPP_MODULE(mod_rpf)
       .method("get_parameters", &RandomPlantedForest::get_parameters)
       .method("set_parameters", &RandomPlantedForest::set_parameters)
       .method("get_model", &RandomPlantedForest::get_model)
+      .method("set_model", &RandomPlantedForest::set_model)
       .method("is_purified", &RandomPlantedForest::is_purified);
 
   class_<ClassificationRPF>("ClassificationRPF")