Combine TreeModel and RegTree

src/gbm/gbtree.cc

@@ -283,7 +283,6 @@ class GBTree : public GradientBooster {
         // create new tree
         std::unique_ptr<RegTree> ptr(new RegTree());
         ptr->param.InitAllowUnknown(this->cfg_);
-        ptr->InitModel();
         new_trees.push_back(ptr.get());
         ret->push_back(std::move(ptr));
       } else if (tparam_.process_type == kUpdate) {

src/tree/tree_model.cc

@@ -169,4 +169,240 @@ std::string RegTree::DumpModel(const FeatureMap& fmap,
   }
   return fo.str();
 }
+void RegTree::FillNodeMeanValues() {
+  size_t num_nodes = this->param.num_nodes;
+  if (this->node_mean_values_.size() == num_nodes) {
+    return;
+  }
+  this->node_mean_values_.resize(num_nodes);
+  for (int root_id = 0; root_id < param.num_roots; ++root_id) {
+    this->FillNodeMeanValue(root_id);
+  }
+}
+
+bst_float RegTree::FillNodeMeanValue(int nid) {
+  bst_float result;
+  auto& node = (*this)[nid];
+  if (node.IsLeaf()) {
+    result = node.LeafValue();
+  } else {
+    result  = this->FillNodeMeanValue(node.LeftChild()) * this->Stat(node.LeftChild()).sum_hess;
+    result += this->FillNodeMeanValue(node.RightChild()) * this->Stat(node.RightChild()).sum_hess;
+    result /= this->Stat(nid).sum_hess;
+  }
+  this->node_mean_values_[nid] = result;
+  return result;
+}
+
+void RegTree::CalculateContributionsApprox(const RegTree::FVec &feat,
+                                           unsigned root_id,
+                                           bst_float *out_contribs) const {
+  CHECK_GT(this->node_mean_values_.size(), 0U);
+  // this follows the idea of http://blog.datadive.net/interpreting-random-forests/
+  unsigned split_index = 0;
+  auto pid = static_cast<int>(root_id);
+  // update bias value
+  bst_float node_value = this->node_mean_values_[pid];
+  out_contribs[feat.Size()] += node_value;
+  if ((*this)[pid].IsLeaf()) {
+    // nothing to do anymore
+    return;
+  }
+  while (!(*this)[pid].IsLeaf()) {
+    split_index = (*this)[pid].SplitIndex();
+    pid = this->GetNext(pid, feat.Fvalue(split_index), feat.IsMissing(split_index));
+    bst_float new_value = this->node_mean_values_[pid];
+    // update feature weight
+    out_contribs[split_index] += new_value - node_value;
+    node_value = new_value;
+  }
+  bst_float leaf_value = (*this)[pid].LeafValue();
+  // update leaf feature weight
+  out_contribs[split_index] += leaf_value - node_value;
+}
+
+// Used by TreeShap
+// data we keep about our decision path
+// note that pweight is included for convenience and is not tied with the other attributes
+// the pweight of the i'th path element is the permuation weight of paths with i-1 ones in them
+struct PathElement {
+  int feature_index;
+  bst_float zero_fraction;
+  bst_float one_fraction;
+  bst_float pweight;
+  PathElement() = default;
+  PathElement(int i, bst_float z, bst_float o, bst_float w) :
+    feature_index(i), zero_fraction(z), one_fraction(o), pweight(w) {}
+};
+
+// extend our decision path with a fraction of one and zero extensions
+void ExtendPath(PathElement *unique_path, unsigned unique_depth,
+                bst_float zero_fraction, bst_float one_fraction,
+                int feature_index) {
+  unique_path[unique_depth].feature_index = feature_index;
+  unique_path[unique_depth].zero_fraction = zero_fraction;
+  unique_path[unique_depth].one_fraction = one_fraction;
+  unique_path[unique_depth].pweight = (unique_depth == 0 ? 1.0f : 0.0f);
+  for (int i = unique_depth - 1; i >= 0; i--) {
+    unique_path[i+1].pweight += one_fraction * unique_path[i].pweight * (i + 1)
+                                / static_cast<bst_float>(unique_depth + 1);
+    unique_path[i].pweight = zero_fraction * unique_path[i].pweight * (unique_depth - i)
+                             / static_cast<bst_float>(unique_depth + 1);
+  }
+}
+
+// undo a previous extension of the decision path
+void UnwindPath(PathElement *unique_path, unsigned unique_depth,
+                unsigned path_index) {
+  const bst_float one_fraction = unique_path[path_index].one_fraction;
+  const bst_float zero_fraction = unique_path[path_index].zero_fraction;
+  bst_float next_one_portion = unique_path[unique_depth].pweight;
+
+  for (int i = unique_depth - 1; i >= 0; --i) {
+    if (one_fraction != 0) {
+      const bst_float tmp = unique_path[i].pweight;
+      unique_path[i].pweight = next_one_portion * (unique_depth + 1)
+                               / static_cast<bst_float>((i + 1) * one_fraction);
+      next_one_portion = tmp - unique_path[i].pweight * zero_fraction * (unique_depth - i)
+                               / static_cast<bst_float>(unique_depth + 1);
+    } else {
+      unique_path[i].pweight = (unique_path[i].pweight * (unique_depth + 1))
+                               / static_cast<bst_float>(zero_fraction * (unique_depth - i));
+    }
+  }
+
+  for (auto i = path_index; i < unique_depth; ++i) {
+    unique_path[i].feature_index = unique_path[i+1].feature_index;
+    unique_path[i].zero_fraction = unique_path[i+1].zero_fraction;
+    unique_path[i].one_fraction = unique_path[i+1].one_fraction;
+  }
+}
+
+// determine what the total permuation weight would be if
+// we unwound a previous extension in the decision path
+bst_float UnwoundPathSum(const PathElement *unique_path, unsigned unique_depth,
+                         unsigned path_index) {
+  const bst_float one_fraction = unique_path[path_index].one_fraction;
+  const bst_float zero_fraction = unique_path[path_index].zero_fraction;
+  bst_float next_one_portion = unique_path[unique_depth].pweight;
+  bst_float total = 0;
+  for (int i = unique_depth - 1; i >= 0; --i) {
+    if (one_fraction != 0) {
+      const bst_float tmp = next_one_portion * (unique_depth + 1)
+                            / static_cast<bst_float>((i + 1) * one_fraction);
+      total += tmp;
+      next_one_portion = unique_path[i].pweight - tmp * zero_fraction * ((unique_depth - i)
+                         / static_cast<bst_float>(unique_depth + 1));
+    } else {
+      total += (unique_path[i].pweight / zero_fraction) / ((unique_depth - i)
+               / static_cast<bst_float>(unique_depth + 1));
+    }
+  }
+  return total;
+}
+
+// recursive computation of SHAP values for a decision tree
+void RegTree::TreeShap(const RegTree::FVec &feat, bst_float *phi,
+                       unsigned node_index, unsigned unique_depth,
+                       PathElement *parent_unique_path,
+                       bst_float parent_zero_fraction,
+                       bst_float parent_one_fraction, int parent_feature_index,
+                       int condition, unsigned condition_feature,
+                       bst_float condition_fraction) const {
+  const auto node = (*this)[node_index];
+
+  // stop if we have no weight coming down to us
+  if (condition_fraction == 0) return;
+
+  // extend the unique path
+  PathElement *unique_path = parent_unique_path + unique_depth + 1;
+  std::copy(parent_unique_path, parent_unique_path + unique_depth + 1, unique_path);
+
+  if (condition == 0 || condition_feature != static_cast<unsigned>(parent_feature_index)) {
+    ExtendPath(unique_path, unique_depth, parent_zero_fraction,
+               parent_one_fraction, parent_feature_index);
+  }
+  const unsigned split_index = node.SplitIndex();
+
+  // leaf node
+  if (node.IsLeaf()) {
+    for (unsigned i = 1; i <= unique_depth; ++i) {
+      const bst_float w = UnwoundPathSum(unique_path, unique_depth, i);
+      const PathElement &el = unique_path[i];
+      phi[el.feature_index] += w * (el.one_fraction - el.zero_fraction)
+                                 * node.LeafValue() * condition_fraction;
+    }
+
+  // internal node
+  } else {
+    // find which branch is "hot" (meaning x would follow it)
+    unsigned hot_index = 0;
+    if (feat.IsMissing(split_index)) {
+      hot_index = node.DefaultChild();
+    } else if (feat.Fvalue(split_index) < node.SplitCond()) {
+      hot_index = node.LeftChild();
+    } else {
+      hot_index = node.RightChild();
+    }
+    const unsigned cold_index = (static_cast<int>(hot_index) == node.LeftChild() ?
+                                 node.RightChild() : node.LeftChild());
+    const bst_float w = this->Stat(node_index).sum_hess;
+    const bst_float hot_zero_fraction = this->Stat(hot_index).sum_hess / w;
+    const bst_float cold_zero_fraction = this->Stat(cold_index).sum_hess / w;
+    bst_float incoming_zero_fraction = 1;
+    bst_float incoming_one_fraction = 1;
+
+    // see if we have already split on this feature,
+    // if so we undo that split so we can redo it for this node
+    unsigned path_index = 0;
+    for (; path_index <= unique_depth; ++path_index) {
+      if (static_cast<unsigned>(unique_path[path_index].feature_index) == split_index) break;
+    }
+    if (path_index != unique_depth + 1) {
+      incoming_zero_fraction = unique_path[path_index].zero_fraction;
+      incoming_one_fraction = unique_path[path_index].one_fraction;
+      UnwindPath(unique_path, unique_depth, path_index);
+      unique_depth -= 1;
+    }
+
+    // divide up the condition_fraction among the recursive calls
+    bst_float hot_condition_fraction = condition_fraction;
+    bst_float cold_condition_fraction = condition_fraction;
+    if (condition > 0 && split_index == condition_feature) {
+      cold_condition_fraction = 0;
+      unique_depth -= 1;
+    } else if (condition < 0 && split_index == condition_feature) {
+      hot_condition_fraction *= hot_zero_fraction;
+      cold_condition_fraction *= cold_zero_fraction;
+      unique_depth -= 1;
+    }
+
+    TreeShap(feat, phi, hot_index, unique_depth + 1, unique_path,
+             hot_zero_fraction * incoming_zero_fraction, incoming_one_fraction,
+             split_index, condition, condition_feature, hot_condition_fraction);
+
+    TreeShap(feat, phi, cold_index, unique_depth + 1, unique_path,
+             cold_zero_fraction * incoming_zero_fraction, 0,
+             split_index, condition, condition_feature, cold_condition_fraction);
+  }
+}
+
+void RegTree::CalculateContributions(const RegTree::FVec &feat,
+                                     unsigned root_id, bst_float *out_contribs,
+                                     int condition,
+                                     unsigned condition_feature) const {
+  // find the expected value of the tree's predictions
+  if (condition == 0) {
+    bst_float node_value = this->node_mean_values_[static_cast<int>(root_id)];
+    out_contribs[feat.Size()] += node_value;
+  }
+
+  // Preallocate space for the unique path data
+  const int maxd = this->MaxDepth(root_id) + 2;
+  auto *unique_path_data = new PathElement[(maxd * (maxd + 1)) / 2];
+
+  TreeShap(feat, out_contribs, root_id, 0, unique_path_data,
+           1, 1, -1, condition, condition_feature, 1);
+  delete[] unique_path_data;
+}
 }  // namespace xgboost

src/tree/updater_prune.cc

@@ -48,7 +48,7 @@ class TreePruner: public TreeUpdater {
   inline int TryPruneLeaf(RegTree &tree, int nid, int depth, int npruned) { // NOLINT(*)
     if (tree[nid].IsRoot()) return npruned;
     int pid = tree[nid].Parent();
-    RegTree::NodeStat &s = tree.Stat(pid);
+    RTreeNodeStat &s = tree.Stat(pid);
     ++s.leaf_child_cnt;
     if (s.leaf_child_cnt >= 2 && param_.NeedPrune(s.loss_chg, depth - 1)) {
       // need to be pruned

tests/cpp/predictor/test_cpu_predictor.cc

@@ -10,7 +10,6 @@ TEST(cpu_predictor, Test) {
 
   std::vector<std::unique_ptr<RegTree>> trees;
   trees.push_back(std::unique_ptr<RegTree>(new RegTree));
-  trees.back()->InitModel();
   (*trees.back())[0].SetLeaf(1.5f);
   (*trees.back()).Stat(0).sum_hess = 1.0f;
   gbm::GBTreeModel model(0.5);

tests/cpp/predictor/test_gpu_predictor.cu

@@ -35,7 +35,6 @@ TEST(gpu_predictor, Test) {
 
   std::vector<std::unique_ptr<RegTree>> trees;
   trees.push_back(std::unique_ptr<RegTree>(new RegTree()));
-  trees.back()->InitModel();
   (*trees.back())[0].SetLeaf(1.5f);
   (*trees.back()).Stat(0).sum_hess = 1.0f;
   gbm::GBTreeModel model(0.5);
@@ -181,7 +180,6 @@ TEST(gpu_predictor, MGPU_Test) {
 
     std::vector<std::unique_ptr<RegTree>> trees;
     trees.push_back(std::unique_ptr<RegTree>(new RegTree()));
-    trees.back()->InitModel();
     (*trees.back())[0].SetLeaf(1.5f);
     (*trees.back()).Stat(0).sum_hess = 1.0f;
     gbm::GBTreeModel model(0.5);

tests/cpp/tree/test_gpu_hist.cu

@@ -289,8 +289,6 @@ TEST(GpuHist, EvaluateSplits) {
                                   false);
 
   RegTree tree;
-  tree.InitModel();
-
   MetaInfo info;
   info.num_row_ = n_rows;
   info.num_col_ = n_cols;
@@ -338,7 +336,6 @@ TEST(GpuHist, ApplySplit) {
   // Initialize GPUHistMaker
   hist_maker.param_ = param;
   RegTree tree;
-  tree.InitModel();
 
   DeviceSplitCandidate candidate;
   candidate.Update(2, kLeftDir,

tests/cpp/tree/test_prune.cc

@@ -31,7 +31,6 @@ TEST(Updater, Prune) {
 
   // prepare tree
   RegTree tree = RegTree();
-  tree.InitModel();
   tree.param.InitAllowUnknown(cfg);
   std::vector<RegTree*> trees {&tree};
   // prepare pruner

tests/cpp/tree/test_quantile_hist.cc

@@ -122,7 +122,6 @@ class QuantileHistMock : public QuantileHistMaker {
     gmat.Init((*dmat).get(), max_bins);
 
     RegTree tree = RegTree();
-    tree.InitModel();
     tree.param.InitAllowUnknown(cfg);
 
     std::vector<GradientPair> gpair =
@@ -134,7 +133,6 @@ class QuantileHistMock : public QuantileHistMaker {
 
   void TestBuildHist() {
     RegTree tree = RegTree();
-    tree.InitModel();
     tree.param.InitAllowUnknown(cfg);
 
     size_t constexpr max_bins = 4;
@@ -146,7 +144,6 @@ class QuantileHistMock : public QuantileHistMaker {
 
   void TestEvaluateSplit() {
     RegTree tree = RegTree();
-    tree.InitModel();
     tree.param.InitAllowUnknown(cfg);
 
     builder_->TestEvaluateSplit(gmatb_, tree);

tests/cpp/tree/test_refresh.cc

@@ -25,7 +25,6 @@ TEST(Updater, Refresh) {
     {"reg_lambda", "1"}};
 
   RegTree tree = RegTree();
-  tree.InitModel();
   tree.param.InitAllowUnknown(cfg);
   std::vector<RegTree*> trees {&tree};
   std::unique_ptr<TreeUpdater> refresher(TreeUpdater::Create("refresh"));