Categorical data support in CPU sketching. (#7221)

src/common/hist_util.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2017-2020 by Contributors
+ * Copyright 2017-2021 by Contributors
  * \file hist_util.h
  * \brief Utility for fast histogram aggregation
  * \author Philip Cho, Tianqi Chen
@@ -128,6 +128,7 @@ inline HistogramCuts SketchOnDMatrix(DMatrix *m, int32_t max_bins,
     }
   }
   HostSketchContainer container(reduced, max_bins,
+                                m->Info().feature_types.ConstHostSpan(),
                                 HostSketchContainer::UseGroup(info), threads);
   for (auto const &page : m->GetBatches<SparsePage>()) {
     container.PushRowPage(page, info, hessian);

src/common/quantile.cc

@@ -1,29 +1,35 @@
 /*!
- * Copyright 2020 by XGBoost Contributors
+ * Copyright 2020-2021 by XGBoost Contributors
  */
 #include <limits>
 #include <utility>
 #include "quantile.h"
 #include "hist_util.h"
+#include "categorical.h"
 
 namespace xgboost {
 namespace common {
 
-HostSketchContainer::HostSketchContainer(std::vector<bst_row_t> columns_size,
-                                         int32_t max_bins, bool use_group,
-                                         int32_t n_threads)
-    : columns_size_{std::move(columns_size)}, max_bins_{max_bins},
+HostSketchContainer::HostSketchContainer(
+    std::vector<bst_row_t> columns_size, int32_t max_bins,
+    common::Span<FeatureType const> feature_types, bool use_group,
+    int32_t n_threads)
+    : feature_types_(feature_types.cbegin(), feature_types.cend()),
+      columns_size_{std::move(columns_size)}, max_bins_{max_bins},
       use_group_ind_{use_group}, n_threads_{n_threads} {
   monitor_.Init(__func__);
   CHECK_NE(columns_size_.size(), 0);
   sketches_.resize(columns_size_.size());
   CHECK_GE(n_threads_, 1);
+  categories_.resize(columns_size_.size());
   ParallelFor(sketches_.size(), n_threads_, Sched::Auto(), [&](auto i) {
     auto n_bins = std::min(static_cast<size_t>(max_bins_), columns_size_[i]);
     n_bins = std::max(n_bins, static_cast<decltype(n_bins)>(1));
     auto eps = 1.0 / (static_cast<float>(n_bins) * WQSketch::kFactor);
-    sketches_[i].Init(columns_size_[i], eps);
-    sketches_[i].inqueue.queue.resize(sketches_[i].limit_size * 2);
+    if (!IsCat(this->feature_types_, i)) {
+      sketches_[i].Init(columns_size_[i], eps);
+      sketches_[i].inqueue.queue.resize(sketches_[i].limit_size * 2);
+    }
   });
 }
 
@@ -182,13 +188,21 @@ void HostSketchContainer::PushRowPage(
           auto p_inst = inst.data();
           if (is_dense) {
             for (size_t ii = begin; ii < end; ii++) {
-              sketches_[ii].Push(p_inst[ii].fvalue, w);
+              if (IsCat(feature_types_, ii)) {
+                categories_[ii].emplace(p_inst[ii].fvalue);
+              } else {
+                sketches_[ii].Push(p_inst[ii].fvalue, w);
+              }
             }
           } else {
             for (size_t i = 0; i < inst.size(); ++i) {
               auto const& entry = p_inst[i];
               if (entry.index >= begin && entry.index < end) {
-                sketches_[entry.index].Push(entry.fvalue, w);
+                if (IsCat(feature_types_, entry.index)) {
+                  categories_[entry.index].emplace(entry.fvalue);
+                } else {
+                  sketches_[entry.index].Push(entry.fvalue, w);
+                }
               }
             }
           }
@@ -338,6 +352,13 @@ void AddCutPoint(WQuantileSketch<float, float>::SummaryContainer const &summary,
   }
 }
 
+void AddCategories(std::set<bst_cat_t> const &categories, HistogramCuts *cuts) {
+  auto &cut_values = cuts->cut_values_.HostVector();
+  for (auto const &v : categories) {
+    cut_values.push_back(v);
+  }
+}
+
 void HostSketchContainer::MakeCuts(HistogramCuts* cuts) {
   monitor_.Start(__func__);
   std::vector<WQSketch::SummaryContainer> reduced;
@@ -348,6 +369,9 @@ void HostSketchContainer::MakeCuts(HistogramCuts* cuts) {
   std::vector<WQSketch::SummaryContainer> final_summaries(reduced.size());
 
   ParallelFor(reduced.size(), n_threads_, Sched::Guided(), [&](size_t fidx) {
+    if (IsCat(feature_types_, fidx)) {
+      return;
+    }
     WQSketch::SummaryContainer &a = final_summaries[fidx];
     size_t max_num_bins = std::min(num_cuts[fidx], max_bins_);
     a.Reserve(max_num_bins + 1);
@@ -367,13 +391,17 @@ void HostSketchContainer::MakeCuts(HistogramCuts* cuts) {
   for (size_t fid = 0; fid < reduced.size(); ++fid) {
     size_t max_num_bins = std::min(num_cuts[fid], max_bins_);
     WQSketch::SummaryContainer const& a = final_summaries[fid];
-    AddCutPoint(a, max_num_bins, cuts);
-    // push a value that is greater than anything
-    const bst_float cpt
-      = (a.size > 0) ? a.data[a.size - 1].value : cuts->min_vals_.HostVector()[fid];
-    // this must be bigger than last value in a scale
-    const bst_float last = cpt + (fabs(cpt) + 1e-5f);
-    cuts->cut_values_.HostVector().push_back(last);
+    if (IsCat(feature_types_, fid)) {
+      AddCategories(categories_.at(fid), cuts);
+    } else {
+      AddCutPoint(a, max_num_bins, cuts);
+      // push a value that is greater than anything
+      const bst_float cpt = (a.size > 0) ? a.data[a.size - 1].value
+                                         : cuts->min_vals_.HostVector()[fid];
+      // this must be bigger than last value in a scale
+      const bst_float last = cpt + (fabs(cpt) + 1e-5f);
+      cuts->cut_values_.HostVector().push_back(last);
+    }
 
     // Ensure that every feature gets at least one quantile point
     CHECK_LE(cuts->cut_values_.HostVector().size(), std::numeric_limits<uint32_t>::max());

src/common/quantile.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2014 by Contributors
+ * Copyright 2014-2021 by Contributors
  * \file quantile.h
  * \brief util to compute quantiles
  * \author Tianqi Chen
@@ -15,6 +15,7 @@
 #include <cstring>
 #include <algorithm>
 #include <iostream>
+#include <set>
 
 #include "timer.h"
 
@@ -707,6 +708,9 @@ class HostSketchContainer {
 
  private:
   std::vector<WQSketch> sketches_;
+  std::vector<std::set<bst_cat_t>> categories_;
+  std::vector<FeatureType> const feature_types_;
+
   std::vector<bst_row_t> columns_size_;
   int32_t max_bins_;
   bool use_group_ind_{false};
@@ -721,7 +725,8 @@ class HostSketchContainer {
    * \param use_group whether is assigned to group to data instance.
    */
   HostSketchContainer(std::vector<bst_row_t> columns_size, int32_t max_bins,
-                      bool use_group, int32_t n_threads);
+                      common::Span<FeatureType const> feature_types, bool use_group,
+                      int32_t n_threads);
 
   static bool UseGroup(MetaInfo const &info) {
     size_t const num_groups =

tests/cpp/common/test_hist_util.cc

@@ -1,3 +1,6 @@
+/*!
+ * Copyright 2019-2021 by XGBoost Contributors
+ */
 #include <gtest/gtest.h>
 #include <vector>
 #include <string>
@@ -388,5 +391,16 @@ TEST(HistUtil, SketchFromWeights) {
   TestSketchFromWeights(true);
   TestSketchFromWeights(false);
 }
+
+TEST(HistUtil, SketchCategoricalFeatures) {
+  TestCategoricalSketch(1000, 256, 32, false,
+                        [](DMatrix *p_fmat, int32_t num_bins) {
+                          return SketchOnDMatrix(p_fmat, num_bins);
+                        });
+  TestCategoricalSketch(1000, 256, 32, true,
+                        [](DMatrix *p_fmat, int32_t num_bins) {
+                          return SketchOnDMatrix(p_fmat, num_bins);
+                        });
+}
 }  // namespace common
 }  // namespace xgboost

tests/cpp/common/test_hist_util.cu

@@ -1,3 +1,6 @@
+/*!
+ * Copyright 2019-2021 by XGBoost Contributors
+ */
 #include <dmlc/filesystem.h>
 #include <gtest/gtest.h>
 
@@ -126,43 +129,15 @@ TEST(HistUtil, DeviceSketchCategoricalAsNumeric) {
   }
 }
 
-void TestCategoricalSketch(size_t n, size_t num_categories, int32_t num_bins, bool weighted) {
-  auto x = GenerateRandomCategoricalSingleColumn(n, num_categories);
-  auto dmat = GetDMatrixFromData(x, n, 1);
-  dmat->Info().feature_types.HostVector().push_back(FeatureType::kCategorical);
-
-  if (weighted) {
-    std::vector<float> weights(n, 0);
-    SimpleLCG lcg;
-    SimpleRealUniformDistribution<float> dist(0, 1);
-    for (auto& v : weights) {
-      v = dist(&lcg);
-    }
-    dmat->Info().weights_.HostVector() = weights;
-  }
-
-  ASSERT_EQ(dmat->Info().feature_types.Size(), 1);
-  auto cuts = DeviceSketch(0, dmat.get(), num_bins);
-  std::sort(x.begin(), x.end());
-  auto n_uniques = std::unique(x.begin(), x.end()) - x.begin();
-  ASSERT_NE(n_uniques, x.size());
-  ASSERT_EQ(cuts.TotalBins(), n_uniques);
-  ASSERT_EQ(n_uniques, num_categories);
-
-  auto& values = cuts.cut_values_.HostVector();
-  ASSERT_TRUE(std::is_sorted(values.cbegin(), values.cend()));
-  auto is_unique = (std::unique(values.begin(), values.end()) - values.begin()) == n_uniques;
-  ASSERT_TRUE(is_unique);
-
-  x.resize(n_uniques);
-  for (size_t i = 0; i < n_uniques; ++i) {
-    ASSERT_EQ(x[i], values[i]);
-  }
-}
-
 TEST(HistUtil, DeviceSketchCategoricalFeatures) {
-  TestCategoricalSketch(1000, 256, 32, false);
-  TestCategoricalSketch(1000, 256, 32, true);
+  TestCategoricalSketch(1000, 256, 32, false,
+                        [](DMatrix *p_fmat, int32_t num_bins) {
+                          return DeviceSketch(0, p_fmat, num_bins);
+                        });
+  TestCategoricalSketch(1000, 256, 32, true,
+                        [](DMatrix *p_fmat, int32_t num_bins) {
+                          return DeviceSketch(0, p_fmat, num_bins);
+                        });
 }
 
 void TestMixedSketch() {

tests/cpp/common/test_hist_util.h

@@ -1,10 +1,15 @@
+/*!
+ * Copyright 2019-2021 by XGBoost Contributors
+ */
 #pragma once
 #include <gtest/gtest.h>
 #include <dmlc/filesystem.h>
 #include <random>
 #include <vector>
 #include <string>
 #include <fstream>
+
+#include "../helpers.h"
 #include "../../../src/common/hist_util.h"
 #include "../../../src/data/simple_dmatrix.h"
 #include "../../../src/data/adapter.h"
@@ -206,5 +211,45 @@ inline void ValidateCuts(const HistogramCuts& cuts, DMatrix* dmat,
   }
 }
 
+/**
+ * \brief Test for sketching on categorical data.
+ *
+ * \param sketch Sketch function, can be on device or on host.
+ */
+template <typename Fn>
+void TestCategoricalSketch(size_t n, size_t num_categories, int32_t num_bins,
+                           bool weighted, Fn sketch) {
+  auto x = GenerateRandomCategoricalSingleColumn(n, num_categories);
+  auto dmat = GetDMatrixFromData(x, n, 1);
+  dmat->Info().feature_types.HostVector().push_back(FeatureType::kCategorical);
+
+  if (weighted) {
+    std::vector<float> weights(n, 0);
+    SimpleLCG lcg;
+    SimpleRealUniformDistribution<float> dist(0, 1);
+    for (auto& v : weights) {
+      v = dist(&lcg);
+    }
+    dmat->Info().weights_.HostVector() = weights;
+  }
+
+  ASSERT_EQ(dmat->Info().feature_types.Size(), 1);
+  auto cuts = sketch(dmat.get(), num_bins);
+  std::sort(x.begin(), x.end());
+  auto n_uniques = std::unique(x.begin(), x.end()) - x.begin();
+  ASSERT_NE(n_uniques, x.size());
+  ASSERT_EQ(cuts.TotalBins(), n_uniques);
+  ASSERT_EQ(n_uniques, num_categories);
+
+  auto& values = cuts.cut_values_.HostVector();
+  ASSERT_TRUE(std::is_sorted(values.cbegin(), values.cend()));
+  auto is_unique = (std::unique(values.begin(), values.end()) - values.begin()) == n_uniques;
+  ASSERT_TRUE(is_unique);
+
+  x.resize(n_uniques);
+  for (size_t i = 0; i < n_uniques; ++i) {
+    ASSERT_EQ(x[i], values[i]);
+  }
+}
 }  // namespace common
 }  // namespace xgboost

tests/cpp/common/test_quantile.cc

@@ -43,12 +43,14 @@ void TestDistributedQuantile(size_t rows, size_t cols) {
   // Generate cuts for distributed environment.
   auto sparsity = 0.5f;
   auto rank = rabit::GetRank();
-  HostSketchContainer sketch_distributed(column_size, n_bins, false, OmpGetNumThreads(0));
   auto m = RandomDataGenerator{rows, cols, sparsity}
                .Seed(rank)
                .Lower(.0f)
                .Upper(1.0f)
                .GenerateDMatrix();
+  HostSketchContainer sketch_distributed(
+      column_size, n_bins, m->Info().feature_types.ConstHostSpan(), false,
+      OmpGetNumThreads(0));
   for (auto const &page : m->GetBatches<SparsePage>()) {
     sketch_distributed.PushRowPage(page, m->Info());
   }
@@ -59,7 +61,9 @@ void TestDistributedQuantile(size_t rows, size_t cols) {
   rabit::Finalize();
   CHECK_EQ(rabit::GetWorldSize(), 1);
   std::for_each(column_size.begin(), column_size.end(), [=](auto& size) { size *= world; });
-  HostSketchContainer sketch_on_single_node(column_size, n_bins, false, OmpGetNumThreads(0));
+  HostSketchContainer sketch_on_single_node(
+      column_size, n_bins, m->Info().feature_types.ConstHostSpan(), false,
+      OmpGetNumThreads(0));
   for (auto rank = 0; rank < world; ++rank) {
     auto m = RandomDataGenerator{rows, cols, sparsity}
                  .Seed(rank)