Feature weights (#5962)

amalgamation/xgboost-all0.cc

@@ -68,6 +68,7 @@
 #include "../src/learner.cc"
 #include "../src/logging.cc"
 #include "../src/common/common.cc"
+#include "../src/common/random.cc"
 #include "../src/common/charconv.cc"
 #include "../src/common/timer.cc"
 #include "../src/common/quantile.cc"

demo/guide-python/feature_weights.py

@@ -0,0 +1,49 @@
+'''Using feature weight to change column sampling.
+
+    .. versionadded:: 1.3.0
+'''
+
+import numpy as np
+import xgboost
+from matplotlib import pyplot as plt
+import argparse
+
+
+def main(args):
+    rng = np.random.RandomState(1994)
+
+    kRows = 1000
+    kCols = 10
+
+    X = rng.randn(kRows, kCols)
+    y = rng.randn(kRows)
+    fw = np.ones(shape=(kCols,))
+    for i in range(kCols):
+        fw[i] *= float(i)
+
+    dtrain = xgboost.DMatrix(X, y)
+    dtrain.set_info(feature_weights=fw)
+
+    bst = xgboost.train({'tree_method': 'hist',
+                         'colsample_bynode': 0.5},
+                        dtrain, num_boost_round=10,
+                        evals=[(dtrain, 'd')])
+    featue_map = bst.get_fscore()
+    # feature zero has 0 weight
+    assert featue_map.get('f0', None) is None
+    assert max(featue_map.values()) == featue_map.get('f9')
+
+    if args.plot:
+        xgboost.plot_importance(bst)
+        plt.show()
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '--plot',
+        type=int,
+        default=1,
+        help='Set to 0 to disable plotting the evaluation history.')
+    args = parser.parse_args()
+    main(args)

demo/json-model/json_parser.py

@@ -94,7 +94,7 @@ class Tree:
 
 class Model:
     '''Gradient boosted tree model.'''
-    def __init__(self, m: dict):
+    def __init__(self, model: dict):
         '''Construct the Model from JSON object.
 
          parameters

doc/parameter.rst

@@ -107,6 +107,10 @@ Parameters for Tree Booster
     'colsample_bynode':0.5}`` with 64 features will leave 8 features to choose from at
     each split.
 
+    On Python interface, one can set the ``feature_weights`` for DMatrix to define the
+    probability of each feature being selected when using column sampling.  There's a
+    similar parameter for ``fit`` method in sklearn interface.
+
 * ``lambda`` [default=1, alias: ``reg_lambda``]
 
   - L2 regularization term on weights. Increasing this value will make model more conservative.
@@ -224,7 +228,7 @@ Parameters for Tree Booster
     list is a group of indices of features that are allowed to interact with each other.
     See tutorial for more information
 
-Additional parameters for ``hist`` and ```gpu_hist`` tree method
+Additional parameters for ``hist`` and ``gpu_hist`` tree method
 ================================================================
 
 * ``single_precision_histogram``, [default=``false``]

include/xgboost/c_api.h

@@ -483,6 +483,34 @@ XGB_DLL int XGDMatrixGetStrFeatureInfo(DMatrixHandle handle, const char *field,
                                        bst_ulong *size,
                                        const char ***out_features);
 
+/*!
+ * \brief Set meta info from dense matrix.  Valid field names are:
+ *
+ *  - label
+ *  - weight
+ *  - base_margin
+ *  - group
+ *  - label_lower_bound
+ *  - label_upper_bound
+ *  - feature_weights
+ *
+ * \param handle An instance of data matrix
+ * \param field  Feild name
+ * \param data   Pointer to consecutive memory storing data.
+ * \param size   Size of the data, this is relative to size of type.  (Meaning NOT number
+ *               of bytes.)
+ * \param type   Indicator of data type.  This is defined in xgboost::DataType enum class.
+ *
+ *    float    = 1
+ *    double   = 2
+ *    uint32_t = 3
+ *    uint64_t = 4
+ *
+ * \return 0 when success, -1 when failure happens
+ */
+XGB_DLL int XGDMatrixSetDenseInfo(DMatrixHandle handle, const char *field,
+                                  void *data, bst_ulong size, int type);
+
 /*!
  * \brief (deprecated) Use XGDMatrixSetUIntInfo instead. Set group of the training matrix
  * \param handle a instance of data matrix

include/xgboost/data.h

@@ -88,34 +88,17 @@ class MetaInfo {
    * \brief Type of each feature.  Automatically set when feature_type_names is specifed.
    */
   HostDeviceVector<FeatureType> feature_types;
+  /*
+   * \brief Weight of each feature, used to define the probability of each feature being
+   *        selected when using column sampling.
+   */
+  HostDeviceVector<float> feature_weigths;
 
   /*! \brief default constructor */
   MetaInfo()  = default;
   MetaInfo(MetaInfo&& that) = default;
   MetaInfo& operator=(MetaInfo&& that) = default;
-  MetaInfo& operator=(MetaInfo const& that) {
+  MetaInfo& operator=(MetaInfo const& that) = delete;
-    this->num_row_ = that.num_row_;
-    this->num_col_ = that.num_col_;
-    this->num_nonzero_ = that.num_nonzero_;
-
-    this->labels_.Resize(that.labels_.Size());
-    this->labels_.Copy(that.labels_);
-
-    this->group_ptr_ = that.group_ptr_;
-
-    this->weights_.Resize(that.weights_.Size());
-    this->weights_.Copy(that.weights_);
-
-    this->base_margin_.Resize(that.base_margin_.Size());
-    this->base_margin_.Copy(that.base_margin_);
-
-    this->labels_lower_bound_.Resize(that.labels_lower_bound_.Size());
-    this->labels_lower_bound_.Copy(that.labels_lower_bound_);
-
-    this->labels_upper_bound_.Resize(that.labels_upper_bound_.Size());
-    this->labels_upper_bound_.Copy(that.labels_upper_bound_);
-    return *this;
-  }
 
   /*!
    * \brief Validate all metainfo.

python-package/xgboost/core.py

@@ -455,7 +455,8 @@ class DMatrix:                  # pylint: disable=too-many-instance-attributes
                  label_lower_bound=None,
                  label_upper_bound=None,
                  feature_names=None,
-                 feature_types=None):
+                 feature_types=None,
+                 feature_weights=None):
         '''Set meta info for DMatrix.'''
         if label is not None:
             self.set_label(label)
@@ -473,6 +474,10 @@ class DMatrix:                  # pylint: disable=too-many-instance-attributes
             self.feature_names = feature_names
         if feature_types is not None:
             self.feature_types = feature_types
+        if feature_weights is not None:
+            from .data import dispatch_meta_backend
+            dispatch_meta_backend(matrix=self, data=feature_weights,
+                                  name='feature_weights')
 
     def get_float_info(self, field):
         """Get float property from the DMatrix.

python-package/xgboost/data.py

@@ -530,22 +530,38 @@ def dispatch_data_backend(data, missing, threads,
     raise TypeError('Not supported type for data.' + str(type(data)))
 
 
+def _to_data_type(dtype: str, name: str):
+    dtype_map = {'float32': 1, 'float64': 2, 'uint32': 3, 'uint64': 4}
+    if dtype not in dtype_map.keys():
+        raise TypeError(
+            f'Expecting float32, float64, uint32, uint64, got {dtype} ' +
+            f'for {name}.')
+    return dtype_map[dtype]
+
+
+def _validate_meta_shape(data):
+    if hasattr(data, 'shape'):
+        assert len(data.shape) == 1 or (
+            len(data.shape) == 2 and
+            (data.shape[1] == 0 or data.shape[1] == 1))
+
+
 def _meta_from_numpy(data, field, dtype, handle):
     data = _maybe_np_slice(data, dtype)
-    if dtype == 'uint32':
+    interface = data.__array_interface__
-        c_data = c_array(ctypes.c_uint32, data)
+    assert interface.get('mask', None) is None, 'Masked array is not supported'
-        _check_call(_LIB.XGDMatrixSetUIntInfo(handle,
+    size = data.shape[0]
+
+    c_type = _to_data_type(str(data.dtype), field)
+    ptr = interface['data'][0]
+    ptr = ctypes.c_void_p(ptr)
+    _check_call(_LIB.XGDMatrixSetDenseInfo(
+        handle,
         c_str(field),
-                                              c_array(ctypes.c_uint, data),
+        ptr,
-                                              c_bst_ulong(len(data))))
+        c_bst_ulong(size),
-    elif dtype == 'float':
+        c_type
-        c_data = c_array(ctypes.c_float, data)
+    ))
-        _check_call(_LIB.XGDMatrixSetFloatInfo(handle,
-                                               c_str(field),
-                                               c_data,
-                                               c_bst_ulong(len(data))))
-    else:
-        raise TypeError('Unsupported type ' + str(dtype) + ' for:' + field)
 
 
 def _meta_from_list(data, field, dtype, handle):
@@ -595,6 +611,7 @@ def _meta_from_dt(data, field, dtype, handle):
 def dispatch_meta_backend(matrix: DMatrix, data, name: str, dtype: str = None):
     '''Dispatch for meta info.'''
     handle = matrix.handle
+    _validate_meta_shape(data)
     if data is None:
         return
     if _is_list(data):

python-package/xgboost/sklearn.py

@@ -441,6 +441,7 @@ class XGBModel(XGBModelBase):
     def fit(self, X, y, sample_weight=None, base_margin=None,
             eval_set=None, eval_metric=None, early_stopping_rounds=None,
             verbose=True, xgb_model=None, sample_weight_eval_set=None,
+            feature_weights=None,
             callbacks=None):
         # pylint: disable=invalid-name,attribute-defined-outside-init
         """Fit gradient boosting model
@@ -459,9 +460,6 @@ class XGBModel(XGBModelBase):
             A list of (X, y) tuple pairs to use as validation sets, for which
             metrics will be computed.
             Validation metrics will help us track the performance of the model.
-        sample_weight_eval_set : list, optional
-            A list of the form [L_1, L_2, ..., L_n], where each L_i is a list of
-            instance weights on the i-th validation set.
         eval_metric : str, list of str, or callable, optional
             If a str, should be a built-in evaluation metric to use. See
             doc/parameter.rst.
@@ -490,6 +488,13 @@ class XGBModel(XGBModelBase):
         xgb_model : str
             file name of stored XGBoost model or 'Booster' instance XGBoost model to be
             loaded before training (allows training continuation).
+        sample_weight_eval_set : list, optional
+            A list of the form [L_1, L_2, ..., L_n], where each L_i is a list of
+            instance weights on the i-th validation set.
+        feature_weights: array_like
+            Weight for each feature, defines the probability of each feature
+            being selected when colsample is being used.  All values must be
+            greater than 0, otherwise a `ValueError` is thrown.
         callbacks : list of callback functions
             List of callback functions that are applied at end of each iteration.
             It is possible to use predefined callbacks by using :ref:`callback_api`.
@@ -498,6 +503,7 @@ class XGBModel(XGBModelBase):
             .. code-block:: python
 
                 [xgb.callback.reset_learning_rate(custom_rates)]
+
         """
         self.n_features_in_ = X.shape[1]
 
@@ -505,6 +511,7 @@ class XGBModel(XGBModelBase):
                                 base_margin=base_margin,
                                 missing=self.missing,
                                 nthread=self.n_jobs)
+        train_dmatrix.set_info(feature_weights=feature_weights)
 
         evals_result = {}
 
@@ -759,7 +766,7 @@ class XGBClassifier(XGBModel, XGBClassifierBase):
     def fit(self, X, y, sample_weight=None, base_margin=None,
             eval_set=None, eval_metric=None,
             early_stopping_rounds=None, verbose=True, xgb_model=None,
-            sample_weight_eval_set=None, callbacks=None):
+            sample_weight_eval_set=None, feature_weights=None, callbacks=None):
         # pylint: disable = attribute-defined-outside-init,arguments-differ
 
         evals_result = {}
@@ -821,6 +828,7 @@ class XGBClassifier(XGBModel, XGBClassifierBase):
         train_dmatrix = DMatrix(X, label=training_labels, weight=sample_weight,
                                 base_margin=base_margin,
                                 missing=self.missing, nthread=self.n_jobs)
+        train_dmatrix.set_info(feature_weights=feature_weights)
 
         self._Booster = train(xgb_options, train_dmatrix,
                               self.get_num_boosting_rounds(),
@@ -1101,10 +1109,10 @@ class XGBRanker(XGBModel):
             raise ValueError("please use XGBRanker for ranking task")
 
     def fit(self, X, y, group, sample_weight=None, base_margin=None,
-            eval_set=None,
+            eval_set=None, sample_weight_eval_set=None,
-            sample_weight_eval_set=None, eval_group=None, eval_metric=None,
+            eval_group=None, eval_metric=None,
             early_stopping_rounds=None, verbose=False, xgb_model=None,
-            callbacks=None):
+            feature_weights=None, callbacks=None):
         # pylint: disable = attribute-defined-outside-init,arguments-differ
         """Fit gradient boosting ranker
 
@@ -1170,6 +1178,10 @@ class XGBRanker(XGBModel):
         xgb_model : str
             file name of stored XGBoost model or 'Booster' instance XGBoost
             model to be loaded before training (allows training continuation).
+        feature_weights: array_like
+            Weight for each feature, defines the probability of each feature
+            being selected when colsample is being used.  All values must be
+            greater than 0, otherwise a `ValueError` is thrown.
         callbacks : list of callback functions
             List of callback functions that are applied at end of each
             iteration.  It is possible to use predefined callbacks by using
@@ -1205,6 +1217,7 @@ class XGBRanker(XGBModel):
         train_dmatrix = DMatrix(data=X, label=y, weight=sample_weight,
                                 base_margin=base_margin,
                                 missing=self.missing, nthread=self.n_jobs)
+        train_dmatrix.set_info(feature_weights=feature_weights)
         train_dmatrix.set_group(group)
 
         evals_result = {}

src/c_api/c_api.cc

@@ -316,6 +316,17 @@ XGB_DLL int XGDMatrixGetStrFeatureInfo(DMatrixHandle handle, const char *field,
   API_END();
 }
 
+XGB_DLL int XGDMatrixSetDenseInfo(DMatrixHandle handle, const char *field,
+                                  void *data, xgboost::bst_ulong size,
+                                  int type) {
+  API_BEGIN();
+  CHECK_HANDLE();
+  auto &info = static_cast<std::shared_ptr<DMatrix> *>(handle)->get()->Info();
+  CHECK(type >= 1 && type <= 4);
+  info.SetInfo(field, data, static_cast<DataType>(type), size);
+  API_END();
+}
+
 XGB_DLL int XGDMatrixSetGroup(DMatrixHandle handle,
                               const unsigned* group,
                               xgboost::bst_ulong len) {

src/common/common.h

@@ -9,12 +9,15 @@
 #include <xgboost/base.h>
 #include <xgboost/logging.h>
 
+#include <algorithm>
 #include <exception>
+#include <functional>
 #include <limits>
 #include <type_traits>
 #include <vector>
 #include <string>
 #include <sstream>
+#include <numeric>
 
 #if defined(__CUDACC__)
 #include <thrust/system/cuda/error.h>
@@ -160,6 +163,15 @@ inline void AssertOneAPISupport() {
 #endif  // XGBOOST_USE_ONEAPI
 }
 
+template <typename Idx, typename V, typename Comp = std::less<V>>
+std::vector<Idx> ArgSort(std::vector<V> const &array, Comp comp = std::less<V>{}) {
+  std::vector<Idx> result(array.size());
+  std::iota(result.begin(), result.end(), 0);
+  std::stable_sort(
+      result.begin(), result.end(),
+      [&array, comp](Idx const &l, Idx const &r) { return comp(array[l], array[r]); });
+  return result;
+}
 }  // namespace common
 }  // namespace xgboost
 #endif  // XGBOOST_COMMON_COMMON_H_

src/common/random.cc

@@ -0,0 +1,38 @@
+/*!
+ * Copyright 2020 by XGBoost Contributors
+ * \file random.cc
+ */
+#include "random.h"
+
+namespace xgboost {
+namespace common {
+std::shared_ptr<HostDeviceVector<bst_feature_t>> ColumnSampler::ColSample(
+    std::shared_ptr<HostDeviceVector<bst_feature_t>> p_features,
+    float colsample) {
+  if (colsample == 1.0f) {
+    return p_features;
+  }
+  const auto &features = p_features->HostVector();
+  CHECK_GT(features.size(), 0);
+
+  int n = std::max(1, static_cast<int>(colsample * features.size()));
+  auto p_new_features = std::make_shared<HostDeviceVector<bst_feature_t>>();
+  auto &new_features = *p_new_features;
+
+  if (feature_weights_.size() != 0) {
+    new_features.HostVector() = WeightedSamplingWithoutReplacement(
+        p_features->HostVector(), feature_weights_, n);
+  } else {
+    new_features.Resize(features.size());
+    std::copy(features.begin(), features.end(),
+              new_features.HostVector().begin());
+    std::shuffle(new_features.HostVector().begin(),
+                 new_features.HostVector().end(), rng_);
+    new_features.Resize(n);
+  }
+  std::sort(new_features.HostVector().begin(), new_features.HostVector().end());
+  return p_new_features;
+}
+
+}  // namespace common
+}  // namespace xgboost

src/common/random.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2015 by Contributors
+ * Copyright 2015-2020 by Contributors
  * \file random.h
  * \brief Utility related to random.
  * \author Tianqi Chen
@@ -10,14 +10,17 @@
 #include <rabit/rabit.h>
 #include <xgboost/logging.h>
 #include <algorithm>
+#include <functional>
 #include <vector>
 #include <limits>
 #include <map>
 #include <memory>
 #include <numeric>
 #include <random>
+#include <utility>
 
 #include "xgboost/host_device_vector.h"
+#include "common.h"
 
 namespace xgboost {
 namespace common {
@@ -75,6 +78,38 @@ using GlobalRandomEngine = RandomEngine;
  */
 GlobalRandomEngine& GlobalRandom(); // NOLINT(*)
 
+/*
+ * Original paper:
+ * Weighted Random Sampling (2005; Efraimidis, Spirakis)
+ *
+ * Blog:
+ * https://timvieira.github.io/blog/post/2019/09/16/algorithms-for-sampling-without-replacement/
+*/
+template <typename T>
+std::vector<T> WeightedSamplingWithoutReplacement(
+    std::vector<T> const &array, std::vector<float> const &weights, size_t n) {
+  // ES sampling.
+  CHECK_EQ(array.size(), weights.size());
+  std::vector<float> keys(weights.size());
+  std::uniform_real_distribution<float> dist;
+  auto& rng = GlobalRandom();
+  for (size_t i = 0; i < array.size(); ++i) {
+    auto w = std::max(weights.at(i), kRtEps);
+    auto u = dist(rng);
+    auto k = std::log(u) / w;
+    keys[i] = k;
+  }
+  auto ind = ArgSort<size_t>(keys, std::greater<>{});
+  ind.resize(n);
+
+  std::vector<T> results(ind.size());
+  for (size_t k = 0; k < ind.size(); ++k) {
+    auto idx = ind[k];
+    results[k] = array[idx];
+  }
+  return results;
+}
+
 /**
  * \class ColumnSampler
  *
@@ -82,36 +117,18 @@ GlobalRandomEngine& GlobalRandom(); // NOLINT(*)
  * colsample_bynode parameters. Should be initialised before tree construction and to
  * reset when tree construction is completed.
  */
-
 class ColumnSampler {
   std::shared_ptr<HostDeviceVector<bst_feature_t>> feature_set_tree_;
   std::map<int, std::shared_ptr<HostDeviceVector<bst_feature_t>>> feature_set_level_;
+  std::vector<float> feature_weights_;
   float colsample_bylevel_{1.0f};
   float colsample_bytree_{1.0f};
   float colsample_bynode_{1.0f};
   GlobalRandomEngine rng_;
 
-  std::shared_ptr<HostDeviceVector<bst_feature_t>> ColSample(
-      std::shared_ptr<HostDeviceVector<bst_feature_t>> p_features, float colsample) {
-    if (colsample == 1.0f) return p_features;
-    const auto& features = p_features->HostVector();
-    CHECK_GT(features.size(), 0);
-    int n = std::max(1, static_cast<int>(colsample * features.size()));
-    auto p_new_features = std::make_shared<HostDeviceVector<bst_feature_t>>();
-    auto& new_features = *p_new_features;
-    new_features.Resize(features.size());
-    std::copy(features.begin(), features.end(),
-              new_features.HostVector().begin());
-    std::shuffle(new_features.HostVector().begin(),
-                 new_features.HostVector().end(), rng_);
-    new_features.Resize(n);
-    std::sort(new_features.HostVector().begin(),
-              new_features.HostVector().end());
-
-    return p_new_features;
-  }
-
  public:
+  std::shared_ptr<HostDeviceVector<bst_feature_t>> ColSample(
+      std::shared_ptr<HostDeviceVector<bst_feature_t>> p_features, float colsample);
   /**
    * \brief Column sampler constructor.
    * \note This constructor manually sets the rng seed
@@ -139,8 +156,10 @@ class ColumnSampler {
    * \param colsample_bytree
    * \param skip_index_0      (Optional) True to skip index 0.
    */
-  void Init(int64_t num_col, float colsample_bynode, float colsample_bylevel,
+  void Init(int64_t num_col, std::vector<float> feature_weights,
+            float colsample_bynode, float colsample_bylevel,
             float colsample_bytree, bool skip_index_0 = false) {
+    feature_weights_ = std::move(feature_weights);
     colsample_bylevel_ = colsample_bylevel;
     colsample_bytree_ = colsample_bytree;
     colsample_bynode_ = colsample_bynode;

src/data/data.cc

@@ -293,6 +293,9 @@ MetaInfo MetaInfo::Slice(common::Span<int32_t const> ridxs) const {
   } else {
     out.base_margin_.HostVector() = Gather(this->base_margin_.HostVector(), ridxs);
   }
+
+  out.feature_weigths.Resize(this->feature_weigths.Size());
+  out.feature_weigths.Copy(this->feature_weigths);
   return out;
 }
 
@@ -377,6 +380,16 @@ void MetaInfo::SetInfo(const char* key, const void* dptr, DataType dtype, size_t
     labels.resize(num);
     DISPATCH_CONST_PTR(dtype, dptr, cast_dptr,
                        std::copy(cast_dptr, cast_dptr + num, labels.begin()));
+  } else if (!std::strcmp(key, "feature_weights")) {
+    auto &h_feature_weights = feature_weigths.HostVector();
+    h_feature_weights.resize(num);
+    DISPATCH_CONST_PTR(
+        dtype, dptr, cast_dptr,
+        std::copy(cast_dptr, cast_dptr + num, h_feature_weights.begin()));
+    bool valid =
+        std::all_of(h_feature_weights.cbegin(), h_feature_weights.cend(),
+                    [](float w) { return w >= 0; });
+    CHECK(valid) << "Feature weight must be greater than 0.";
   } else {
     LOG(FATAL) << "Unknown key for MetaInfo: " << key;
   }
@@ -396,6 +409,8 @@ void MetaInfo::GetInfo(char const *key, bst_ulong *out_len, DataType dtype,
       vec = &this->labels_lower_bound_.HostVector();
     } else if (!std::strcmp(key, "label_upper_bound")) {
       vec = &this->labels_upper_bound_.HostVector();
+    } else if (!std::strcmp(key, "feature_weights")) {
+      vec = &this->feature_weigths.HostVector();
     } else {
       LOG(FATAL) << "Unknown float field name: " << key;
     }
@@ -497,6 +512,11 @@ void MetaInfo::Extend(MetaInfo const& that, bool accumulate_rows) {
     auto &h_feature_types = feature_types.HostVector();
     LoadFeatureType(this->feature_type_names, &h_feature_types);
   }
+  if (!that.feature_weigths.Empty()) {
+    this->feature_weigths.Resize(that.feature_weigths.Size());
+    this->feature_weigths.SetDevice(that.feature_weigths.DeviceIdx());
+    this->feature_weigths.Copy(that.feature_weigths);
+  }
 }
 
 void MetaInfo::Validate(int32_t device) const {
@@ -538,6 +558,11 @@ void MetaInfo::Validate(int32_t device) const {
     check_device(labels_lower_bound_);
     return;
   }
+  if (feature_weigths.Size() != 0) {
+    CHECK_EQ(feature_weigths.Size(), num_col_)
+        << "Size of feature_weights must equal to number of columns.";
+    check_device(feature_weigths);
+  }
   if (labels_upper_bound_.Size() != 0) {
     CHECK_EQ(labels_upper_bound_.Size(), num_row_)
         << "Size of label_upper_bound must equal to number of rows.";

src/data/data.cu

@@ -58,6 +58,15 @@ void CopyGroupInfoImpl(ArrayInterface column, std::vector<bst_group_t>* out) {
   std::partial_sum(out->begin(), out->end(), out->begin());
 }
 
+namespace {
+// thrust::all_of tries to copy lambda function.
+struct AllOfOp {
+  __device__ bool operator()(float w) {
+    return w >= 0;
+  }
+};
+}  // anonymous namespace
+
 void MetaInfo::SetInfo(const char * c_key, std::string const& interface_str) {
   Json j_interface = Json::Load({interface_str.c_str(), interface_str.size()});
   auto const& j_arr = get<Array>(j_interface);
@@ -82,6 +91,21 @@ void MetaInfo::SetInfo(const char * c_key, std::string const& interface_str) {
   } else if (key == "group") {
     CopyGroupInfoImpl(array_interface, &group_ptr_);
     return;
+  } else if (key == "label_lower_bound") {
+    CopyInfoImpl(array_interface, &labels_lower_bound_);
+    return;
+  } else if (key == "label_upper_bound") {
+    CopyInfoImpl(array_interface, &labels_upper_bound_);
+    return;
+  } else if (key == "feature_weights") {
+    CopyInfoImpl(array_interface, &feature_weigths);
+    auto d_feature_weights = feature_weigths.ConstDeviceSpan();
+    auto valid =
+        thrust::all_of(thrust::device, d_feature_weights.data(),
+                       d_feature_weights.data() + d_feature_weights.size(),
+                       AllOfOp{});
+    CHECK(valid) << "Feature weight must be greater than 0.";
+    return;
   } else {
     LOG(FATAL) << "Unknown metainfo: " << key;
   }

src/tree/updater_colmaker.cc

@@ -235,8 +235,10 @@ class ColMaker: public TreeUpdater {
         }
       }
       {
-        column_sampler_.Init(fmat.Info().num_col_, param_.colsample_bynode,
+        column_sampler_.Init(fmat.Info().num_col_,
-                             param_.colsample_bylevel, param_.colsample_bytree);
+                             fmat.Info().feature_weigths.ConstHostVector(),
+                             param_.colsample_bynode, param_.colsample_bylevel,
+                             param_.colsample_bytree);
       }
       {
         // setup temp space for each thread

src/tree/updater_gpu_hist.cu

@@ -266,8 +266,10 @@ struct GPUHistMakerDevice {
   // Note that the column sampler must be passed by value because it is not
   // thread safe
   void Reset(HostDeviceVector<GradientPair>* dh_gpair, DMatrix* dmat, int64_t num_columns) {
-    this->column_sampler.Init(num_columns, param.colsample_bynode,
+    auto const& info = dmat->Info();
-      param.colsample_bylevel, param.colsample_bytree);
+    this->column_sampler.Init(num_columns, info.feature_weigths.HostVector(),
+                              param.colsample_bynode, param.colsample_bylevel,
+                              param.colsample_bytree);
     dh::safe_cuda(cudaSetDevice(device_id));
     this->interaction_constraints.Reset();
     std::fill(node_sum_gradients.begin(), node_sum_gradients.end(),

src/tree/updater_quantile_hist.cc

@@ -841,10 +841,12 @@ void QuantileHistMaker::Builder<GradientSumT>::InitData(const GHistIndexMatrix&
   // store a pointer to the tree
   p_last_tree_ = &tree;
   if (data_layout_ == kDenseDataOneBased) {
-    column_sampler_.Init(info.num_col_, param_.colsample_bynode, param_.colsample_bylevel,
+    column_sampler_.Init(info.num_col_, info.feature_weigths.ConstHostVector(),
+                         param_.colsample_bynode, param_.colsample_bylevel,
                          param_.colsample_bytree, true);
   } else {
-    column_sampler_.Init(info.num_col_, param_.colsample_bynode, param_.colsample_bylevel,
+    column_sampler_.Init(info.num_col_, info.feature_weigths.ConstHostVector(),
+                         param_.colsample_bynode, param_.colsample_bylevel,
                          param_.colsample_bytree, false);
   }
   if (data_layout_ == kDenseDataZeroBased || data_layout_ == kDenseDataOneBased) {

tests/cpp/common/test_common.cc

@@ -0,0 +1,13 @@
+#include <gtest/gtest.h>
+#include "../../../src/common/common.h"
+
+namespace xgboost {
+namespace common {
+TEST(ArgSort, Basic) {
+  std::vector<float> inputs {3.0, 2.0, 1.0};
+  auto ret = ArgSort<bst_feature_t>(inputs);
+  std::vector<bst_feature_t> sol{2, 1, 0};
+  ASSERT_EQ(ret, sol);
+}
+}  // namespace common
+}  // namespace xgboost

tests/cpp/common/test_random.cc

@@ -8,9 +8,10 @@ namespace common {
 TEST(ColumnSampler, Test) {
   int n = 128;
   ColumnSampler cs;
+  std::vector<float> feature_weights;
 
   // No node sampling
-  cs.Init(n, 1.0f, 0.5f, 0.5f);
+  cs.Init(n, feature_weights, 1.0f, 0.5f, 0.5f);
   auto set0 = cs.GetFeatureSet(0);
   ASSERT_EQ(set0->Size(), 32);
 
@@ -23,7 +24,7 @@ TEST(ColumnSampler, Test) {
   ASSERT_EQ(set2->Size(), 32);
 
   // Node sampling
-  cs.Init(n, 0.5f, 1.0f, 0.5f);
+  cs.Init(n, feature_weights, 0.5f, 1.0f, 0.5f);
   auto set3 = cs.GetFeatureSet(0);
   ASSERT_EQ(set3->Size(), 32);
 
@@ -33,19 +34,19 @@ TEST(ColumnSampler, Test) {
   ASSERT_EQ(set4->Size(), 32);
 
   // No level or node sampling, should be the same at different depth
-  cs.Init(n, 1.0f, 1.0f, 0.5f);
+  cs.Init(n, feature_weights, 1.0f, 1.0f, 0.5f);
   ASSERT_EQ(cs.GetFeatureSet(0)->HostVector(),
             cs.GetFeatureSet(1)->HostVector());
 
-  cs.Init(n, 1.0f, 1.0f, 1.0f);
+  cs.Init(n, feature_weights, 1.0f, 1.0f, 1.0f);
   auto set5 = cs.GetFeatureSet(0);
   ASSERT_EQ(set5->Size(), n);
-  cs.Init(n, 1.0f, 1.0f, 1.0f);
+  cs.Init(n, feature_weights, 1.0f, 1.0f, 1.0f);
   auto set6 = cs.GetFeatureSet(0);
   ASSERT_EQ(set5->HostVector(), set6->HostVector());
 
   // Should always be a minimum of one feature
-  cs.Init(n, 1e-16f, 1e-16f, 1e-16f);
+  cs.Init(n, feature_weights, 1e-16f, 1e-16f, 1e-16f);
   ASSERT_EQ(cs.GetFeatureSet(0)->Size(), 1);
 }
 
@@ -56,13 +57,13 @@ TEST(ColumnSampler, ThreadSynchronisation) {
   size_t iterations = 10;
   size_t levels = 5;
   std::vector<bst_feature_t> reference_result;
-  bool success =
+  std::vector<float> feature_weights;
-      true;  // Cannot use google test asserts in multithreaded region
+  bool success = true; // Cannot use google test asserts in multithreaded region
 #pragma omp parallel num_threads(num_threads)
   {
     for (auto j = 0ull; j < iterations; j++) {
       ColumnSampler cs(j);
-      cs.Init(n, 0.5f, 0.5f, 0.5f);
+      cs.Init(n, feature_weights, 0.5f, 0.5f, 0.5f);
       for (auto level = 0ull; level < levels; level++) {
         auto result = cs.GetFeatureSet(level)->ConstHostVector();
 #pragma omp single
@@ -76,5 +77,54 @@ TEST(ColumnSampler, ThreadSynchronisation) {
   }
   ASSERT_TRUE(success);
 }
+
+TEST(ColumnSampler, WeightedSampling) {
+  auto test_basic = [](int first) {
+    std::vector<float> feature_weights(2);
+    feature_weights[0] = std::abs(first - 1.0f);
+    feature_weights[1] = first - 0.0f;
+    ColumnSampler cs{0};
+    cs.Init(2, feature_weights, 1.0, 1.0, 0.5);
+    auto feature_sets = cs.GetFeatureSet(0);
+    auto const &h_feat_set = feature_sets->HostVector();
+    ASSERT_EQ(h_feat_set.size(), 1);
+    ASSERT_EQ(h_feat_set[0], first - 0);
+  };
+
+  test_basic(0);
+  test_basic(1);
+
+  size_t constexpr kCols = 64;
+  std::vector<float> feature_weights(kCols);
+  SimpleLCG rng;
+  SimpleRealUniformDistribution<float> dist(.0f, 12.0f);
+  std::generate(feature_weights.begin(), feature_weights.end(), [&]() { return dist(&rng); });
+  ColumnSampler cs{0};
+  cs.Init(kCols, feature_weights, 0.5f, 1.0f, 1.0f);
+  std::vector<bst_feature_t> features(kCols);
+  std::iota(features.begin(), features.end(), 0);
+  std::vector<float> freq(kCols, 0);
+  for (size_t i = 0; i < 1024; ++i) {
+    auto fset = cs.GetFeatureSet(0);
+    ASSERT_EQ(kCols * 0.5, fset->Size());
+    auto const& h_fset = fset->HostVector();
+    for (auto f : h_fset) {
+      freq[f] += 1.0f;
+    }
+  }
+
+  auto norm = std::accumulate(freq.cbegin(), freq.cend(), .0f);
+  for (auto& f : freq) {
+    f /= norm;
+  }
+  norm = std::accumulate(feature_weights.cbegin(), feature_weights.cend(), .0f);
+  for (auto& f : feature_weights) {
+    f /= norm;
+  }
+
+  for (size_t i = 0; i < feature_weights.size(); ++i) {
+    EXPECT_NEAR(freq[i], feature_weights[i], 1e-2);
+  }
+}
 }  // namespace common
 }  // namespace xgboost

tests/cpp/tree/test_gpu_hist.cu

@@ -204,11 +204,10 @@ TEST(GpuHist, EvaluateRootSplit) {
   ASSERT_EQ(maker.hist.Data().size(), hist.size());
   thrust::copy(hist.begin(), hist.end(),
     maker.hist.Data().begin());
+  std::vector<float> feature_weights;
 
-  maker.column_sampler.Init(kNCols,
+  maker.column_sampler.Init(kNCols, feature_weights, param.colsample_bynode,
-    param.colsample_bynode,
+                            param.colsample_bylevel, param.colsample_bytree,
-    param.colsample_bylevel,
-    param.colsample_bytree,
                             false);
 
   RegTree tree;

tests/python-gpu/test_device_quantile_dmatrix.py

@@ -16,6 +16,20 @@ class TestDeviceQuantileDMatrix(unittest.TestCase):
                            match='is not supported for DeviceQuantileDMatrix'):
             xgb.DeviceQuantileDMatrix(data, np.ones(5, dtype=np.float64))
 
+    @pytest.mark.skipif(**tm.no_cupy())
+    def test_dmatrix_feature_weights(self):
+        import cupy as cp
+        rng = cp.random.RandomState(1994)
+        data = rng.randn(5, 5)
+        m = xgb.DMatrix(data)
+
+        feature_weights = rng.uniform(size=5)
+        m.set_info(feature_weights=feature_weights)
+
+        cp.testing.assert_array_equal(
+            cp.array(m.get_float_info('feature_weights')),
+            feature_weights.astype(np.float32))
+
     @pytest.mark.skipif(**tm.no_cupy())
     def test_dmatrix_cupy_init(self):
         import cupy as cp

tests/python/test_demos.py

@@ -1,12 +1,10 @@
 import os
 import subprocess
-import sys
 import pytest
 import testing as tm
 
 
-CURRENT_DIR = os.path.dirname(__file__)
+ROOT_DIR = tm.PROJECT_ROOT
-ROOT_DIR = os.path.dirname(os.path.dirname(CURRENT_DIR))
 DEMO_DIR = os.path.join(ROOT_DIR, 'demo')
 PYTHON_DEMO_DIR = os.path.join(DEMO_DIR, 'guide-python')
 
@@ -19,21 +17,27 @@ def test_basic_walkthrough():
     os.remove('dump.raw.txt')
 
 
+@pytest.mark.skipif(**tm.no_matplotlib())
 def test_custom_multiclass_objective():
     script = os.path.join(PYTHON_DEMO_DIR, 'custom_softmax.py')
     cmd = ['python', script, '--plot=0']
     subprocess.check_call(cmd)
 
 
+@pytest.mark.skipif(**tm.no_matplotlib())
 def test_custom_rmsle_objective():
-    major, minor = sys.version_info[:2]
-    if minor < 6:
-        pytest.skip('Skipping RMLSE test due to Python version being too low.')
     script = os.path.join(PYTHON_DEMO_DIR, 'custom_rmsle.py')
     cmd = ['python', script, '--plot=0']
     subprocess.check_call(cmd)
 
 
+@pytest.mark.skipif(**tm.no_matplotlib())
+def test_feature_weights_demo():
+    script = os.path.join(PYTHON_DEMO_DIR, 'feature_weights.py')
+    cmd = ['python', script, '--plot=0']
+    subprocess.check_call(cmd)
+
+
 @pytest.mark.skipif(**tm.no_sklearn())
 def test_sklearn_demo():
     script = os.path.join(PYTHON_DEMO_DIR, 'sklearn_examples.py')

tests/python/test_dmatrix.py

@@ -99,6 +99,11 @@ class TestDMatrix(unittest.TestCase):
         X = rng.randn(100, 100)
         y = rng.randint(low=0, high=3, size=100)
         d = xgb.DMatrix(X, y)
+        np.testing.assert_equal(d.get_label(), y.astype(np.float32))
+
+        fw = rng.uniform(size=100).astype(np.float32)
+        d.set_info(feature_weights=fw)
+
         eval_res_0 = {}
         booster = xgb.train(
             {'num_class': 3, 'objective': 'multi:softprob'}, d,
@@ -106,19 +111,23 @@ class TestDMatrix(unittest.TestCase):
 
         predt = booster.predict(d)
         predt = predt.reshape(100 * 3, 1)
+
         d.set_base_margin(predt)
 
         ridxs = [1, 2, 3, 4, 5, 6]
-        d = d.slice(ridxs)
+        sliced = d.slice(ridxs)
-        sliced_margin = d.get_float_info('base_margin')
+
+        sliced_margin = sliced.get_float_info('base_margin')
         assert sliced_margin.shape[0] == len(ridxs) * 3
 
         eval_res_1 = {}
-        xgb.train({'num_class': 3, 'objective': 'multi:softprob'}, d,
+        xgb.train({'num_class': 3, 'objective': 'multi:softprob'}, sliced,
-                  num_boost_round=2, evals=[(d, 'd')], evals_result=eval_res_1)
+                  num_boost_round=2, evals=[(sliced, 'd')],
+                  evals_result=eval_res_1)
 
         eval_res_0 = eval_res_0['d']['merror']
         eval_res_1 = eval_res_1['d']['merror']
+
         for i in range(len(eval_res_0)):
             assert abs(eval_res_0[i] - eval_res_1[i]) < 0.02
 
@@ -196,13 +205,33 @@ class TestDMatrix(unittest.TestCase):
         dtrain.get_float_info('base_margin')
         dtrain.get_uint_info('group_ptr')
 
+    def test_feature_weights(self):
+        kRows = 10
+        kCols = 50
+        rng = np.random.RandomState(1994)
+        fw = rng.uniform(size=kCols)
+        X = rng.randn(kRows, kCols)
+        m = xgb.DMatrix(X)
+        m.set_info(feature_weights=fw)
+        np.testing.assert_allclose(fw, m.get_float_info('feature_weights'))
+        # Handle empty
+        m.set_info(feature_weights=np.empty((0, 0)))
+
+        assert m.get_float_info('feature_weights').shape[0] == 0
+
+        fw -= 1
+
+        def assign_weight():
+            m.set_info(feature_weights=fw)
+        self.assertRaises(ValueError, assign_weight)
+
     def test_sparse_dmatrix_csr(self):
         nrow = 100
         ncol = 1000
         x = rand(nrow, ncol, density=0.0005, format='csr', random_state=rng)
         assert x.indices.max() < ncol - 1
         x.data[:] = 1
-        dtrain = xgb.DMatrix(x, label=np.random.binomial(1, 0.3, nrow))
+        dtrain = xgb.DMatrix(x, label=rng.binomial(1, 0.3, nrow))
         assert (dtrain.num_row(), dtrain.num_col()) == (nrow, ncol)
         watchlist = [(dtrain, 'train')]
         param = {'max_depth': 3, 'objective': 'binary:logistic', 'verbosity': 0}
@@ -215,7 +244,7 @@ class TestDMatrix(unittest.TestCase):
         x = rand(nrow, ncol, density=0.0005, format='csc', random_state=rng)
         assert x.indices.max() < nrow - 1
         x.data[:] = 1
-        dtrain = xgb.DMatrix(x, label=np.random.binomial(1, 0.3, nrow))
+        dtrain = xgb.DMatrix(x, label=rng.binomial(1, 0.3, nrow))
         assert (dtrain.num_row(), dtrain.num_col()) == (nrow, ncol)
         watchlist = [(dtrain, 'train')]
         param = {'max_depth': 3, 'objective': 'binary:logistic', 'verbosity': 0}

tests/python/test_with_sklearn.py

@@ -1,3 +1,5 @@
+import collections
+import importlib.util
 import numpy as np
 import xgboost as xgb
 from xgboost.sklearn import XGBoostLabelEncoder
@@ -654,6 +656,7 @@ def test_validation_weights_xgbmodel():
                 eval_set=[(X_train, y_train), (X_test, y_test)],
                 sample_weight_eval_set=[weights_train])
 
+
 def test_validation_weights_xgbclassifier():
     from sklearn.datasets import make_hastie_10_2
 
@@ -920,6 +923,64 @@ def test_pandas_input():
                                np.array([0, 1]))
 
 
+def run_feature_weights(increasing):
+    with TemporaryDirectory() as tmpdir:
+        kRows = 512
+        kCols = 64
+        colsample_bynode = 0.5
+        reg = xgb.XGBRegressor(tree_method='hist',
+                               colsample_bynode=colsample_bynode)
+        X = rng.randn(kRows, kCols)
+        y = rng.randn(kRows)
+        fw = np.ones(shape=(kCols,))
+        for i in range(kCols):
+            if increasing:
+                fw[i] *= float(i)
+            else:
+                fw[i] *= float(kCols - i)
+
+        reg.fit(X, y, feature_weights=fw)
+        model_path = os.path.join(tmpdir, 'model.json')
+        reg.save_model(model_path)
+        with open(model_path) as fd:
+            model = json.load(fd)
+
+        parser_path = os.path.join(tm.PROJECT_ROOT, 'demo', 'json-model',
+                                   'json_parser.py')
+        spec = importlib.util.spec_from_file_location("JsonParser",
+                                                      parser_path)
+        foo = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(foo)
+        model = foo.Model(model)
+        splits = {}
+        total_nodes = 0
+        for tree in model.trees:
+            n_nodes = len(tree.nodes)
+            total_nodes += n_nodes
+            for n in range(n_nodes):
+                if tree.is_leaf(n):
+                    continue
+                if splits.get(tree.split_index(n), None) is None:
+                    splits[tree.split_index(n)] = 1
+                else:
+                    splits[tree.split_index(n)] += 1
+
+        od = collections.OrderedDict(sorted(splits.items()))
+        tuples = [(k, v) for k, v in od.items()]
+        k, v = list(zip(*tuples))
+        w = np.polyfit(k, v, deg=1)
+        return w
+
+
+def test_feature_weights():
+    poly_increasing = run_feature_weights(True)
+    poly_decreasing = run_feature_weights(False)
+    # Approxmated test, this is dependent on the implementation of random
+    # number generator in std library.
+    assert poly_increasing[0] > 0.08
+    assert poly_decreasing[0] < -0.08
+
+
 class TestBoostFromPrediction(unittest.TestCase):
     def run_boost_from_prediction(self, tree_method):
         from sklearn.datasets import load_breast_cancer