[pyspark] Make Xgboost estimator support using sparse matrix as optimization (#8145)

Signed-off-by: Weichen Xu <weichen.xu@databricks.com>

python-package/xgboost/spark/core.py

@@ -1,7 +1,7 @@
 # type: ignore
 """Xgboost pyspark integration submodule for core code."""
 # pylint: disable=fixme, too-many-ancestors, protected-access, no-member, invalid-name
-# pylint: disable=too-few-public-methods
+# pylint: disable=too-few-public-methods, too-many-lines
 from typing import Iterator, Optional, Tuple
 
 import numpy as np
@@ -37,14 +37,24 @@ from xgboost.training import train as worker_train
 import xgboost
 from xgboost import XGBClassifier, XGBRegressor
 
-from .data import alias, create_dmatrix_from_partitions, stack_series
+from .data import (
+    _read_csr_matrix_from_unwrapped_spark_vec,
+    alias,
+    create_dmatrix_from_partitions,
+    stack_series,
+)
 from .model import (
     SparkXGBModelReader,
     SparkXGBModelWriter,
     SparkXGBReader,
     SparkXGBWriter,
 )
-from .params import HasArbitraryParamsDict, HasBaseMarginCol, HasFeaturesCols
+from .params import (
+    HasArbitraryParamsDict,
+    HasBaseMarginCol,
+    HasEnableSparseDataOptim,
+    HasFeaturesCols,
+)
 from .utils import (
     RabitContext,
     _get_args_from_message_list,
@@ -75,6 +85,7 @@ _pyspark_specific_params = [
     "use_gpu",
     "feature_names",
     "features_cols",
+    "enable_sparse_data_optim",
 ]
 
 _non_booster_params = ["missing", "n_estimators", "feature_types", "feature_weights"]
@@ -124,6 +135,7 @@ class _SparkXGBParams(
     HasArbitraryParamsDict,
     HasBaseMarginCol,
     HasFeaturesCols,
+    HasEnableSparseDataOptim,
 ):
     num_workers = Param(
         Params._dummy(),
@@ -237,6 +249,7 @@ class _SparkXGBParams(
         return predict_params
 
     def _validate_params(self):
+        # pylint: disable=too-many-branches
         init_model = self.getOrDefault(self.xgb_model)
         if init_model is not None and not isinstance(init_model, Booster):
             raise ValueError(
@@ -267,6 +280,26 @@ class _SparkXGBParams(
                 "If features_cols param set, then features_col param is ignored."
             )
 
+        if self.getOrDefault(self.enable_sparse_data_optim):
+            if self.getOrDefault(self.missing) != 0.0:
+                # If DMatrix is constructed from csr / csc matrix, then inactive elements
+                # in csr / csc matrix are regarded as missing value, but, in pyspark, we
+                # are hard to control elements to be active or inactive in sparse vector column,
+                # some spark transformers such as VectorAssembler might compress vectors
+                # to be dense or sparse format automatically, and when a spark ML vector object
+                # is compressed to sparse vector, then all zero value elements become inactive.
+                # So we force setting missing param to be 0 when enable_sparse_data_optim config
+                # is True.
+                raise ValueError(
+                    "If enable_sparse_data_optim is True, missing param != 0 is not supported."
+                )
+            if self.getOrDefault(self.features_cols):
+                raise ValueError(
+                    "If enable_sparse_data_optim is True, you cannot set multiple feature columns "
+                    "but you should set one feature column with values of "
+                    "`pyspark.ml.linalg.Vector` type."
+                )
+
         if self.getOrDefault(self.use_gpu):
             tree_method = self.getParam("tree_method")
             if (
@@ -363,6 +396,52 @@ def _validate_and_convert_feature_col_as_array_col(dataset, features_col_name):
     return features_array_col
 
 
+def _get_unwrap_udt_fn():
+    try:
+        from pyspark.sql.functions import unwrap_udt
+
+        return unwrap_udt
+    except ImportError:
+        pass
+
+    try:
+        from pyspark.databricks.sql.functions import unwrap_udt
+
+        return unwrap_udt
+    except ImportError as exc:
+        raise RuntimeError(
+            "Cannot import pyspark `unwrap_udt` function. Please install pyspark>=3.4 "
+            "or run on Databricks Runtime."
+        ) from exc
+
+
+def _get_unwrapped_vec_cols(feature_col):
+    unwrap_udt = _get_unwrap_udt_fn()
+    features_unwrapped_vec_col = unwrap_udt(feature_col)
+
+    # After a `pyspark.ml.linalg.VectorUDT` type column being unwrapped, it becomes
+    # a pyspark struct type column, the struct fields are:
+    #  - `type`: byte
+    #  - `size`: int
+    #  - `indices`: array<int>
+    #  - `values`: array<double>
+    # For sparse vector, `type` field is 0, `size` field means vector length,
+    # `indices` field is the array of active element indices, `values` field
+    # is the array of active element values.
+    # For dense vector, `type` field is 1, `size` and `indices` fields are None,
+    # `values` field is the array of the vector element values.
+    return [
+        features_unwrapped_vec_col.type.alias("featureVectorType"),
+        features_unwrapped_vec_col.size.alias("featureVectorSize"),
+        features_unwrapped_vec_col.indices.alias("featureVectorIndices"),
+        # Note: the value field is double array type, cast it to float32 array type
+        # for speedup following repartitioning.
+        features_unwrapped_vec_col.values.cast(ArrayType(FloatType())).alias(
+            "featureVectorValues"
+        ),
+    ]
+
+
 class _SparkXGBEstimator(Estimator, _SparkXGBParams, MLReadable, MLWritable):
     def __init__(self):
         super().__init__()
@@ -527,17 +606,28 @@ class _SparkXGBEstimator(Estimator, _SparkXGBParams, MLReadable, MLWritable):
 
         select_cols = [label_col]
         features_cols_names = None
-        if self.getOrDefault(self.features_cols):
-            features_cols_names = self.getOrDefault(self.features_cols)
-            features_cols = _validate_and_convert_feature_col_as_float_col_list(
-                dataset, features_cols_names
-            )
-            select_cols.extend(features_cols)
+        enable_sparse_data_optim = self.getOrDefault(self.enable_sparse_data_optim)
+        if enable_sparse_data_optim:
+            features_col_name = self.getOrDefault(self.featuresCol)
+            features_col_datatype = dataset.schema[features_col_name].dataType
+            if not isinstance(features_col_datatype, VectorUDT):
+                raise ValueError(
+                    "If enable_sparse_data_optim is True, the feature column values must be "
+                    "`pyspark.ml.linalg.Vector` type."
+                )
+            select_cols.extend(_get_unwrapped_vec_cols(col(features_col_name)))
         else:
-            features_array_col = _validate_and_convert_feature_col_as_array_col(
-                dataset, self.getOrDefault(self.featuresCol)
-            )
-            select_cols.append(features_array_col)
+            if self.getOrDefault(self.features_cols):
+                features_cols_names = self.getOrDefault(self.features_cols)
+                features_cols = _validate_and_convert_feature_col_as_float_col_list(
+                    dataset, features_cols_names
+                )
+                select_cols.extend(features_cols)
+            else:
+                features_array_col = _validate_and_convert_feature_col_as_array_col(
+                    dataset, self.getOrDefault(self.featuresCol)
+                )
+                select_cols.append(features_array_col)
 
         if self.isDefined(self.weightCol) and self.getOrDefault(self.weightCol):
             select_cols.append(
@@ -589,7 +679,7 @@ class _SparkXGBEstimator(Estimator, _SparkXGBParams, MLReadable, MLWritable):
             "feature_types": self.getOrDefault(self.feature_types),
             "feature_names": self.getOrDefault(self.feature_names),
             "feature_weights": self.getOrDefault(self.feature_weights),
-            "missing": self.getOrDefault(self.missing),
+            "missing": float(self.getOrDefault(self.missing)),
         }
         booster_params["nthread"] = cpu_per_task
         use_gpu = self.getOrDefault(self.use_gpu)
@@ -627,7 +717,11 @@ class _SparkXGBEstimator(Estimator, _SparkXGBParams, MLReadable, MLWritable):
             evals_result = {}
             with RabitContext(_rabit_args, context):
                 dtrain, dvalid = create_dmatrix_from_partitions(
-                    pandas_df_iter, features_cols_names, gpu_id, dmatrix_kwargs
+                    pandas_df_iter,
+                    features_cols_names,
+                    gpu_id,
+                    dmatrix_kwargs,
+                    enable_sparse_data_optim=enable_sparse_data_optim,
                 )
                 if dvalid is not None:
                     dval = [(dtrain, "training"), (dvalid, "validation")]
@@ -732,6 +826,12 @@ class _SparkXGBModel(Model, _SparkXGBParams, MLReadable, MLWritable):
         vector or array feature type. But first we need to check features_cols
         and then featuresCol
         """
+        if self.getOrDefault(self.enable_sparse_data_optim):
+            feature_col_names = None
+            features_col = _get_unwrapped_vec_cols(
+                col(self.getOrDefault(self.featuresCol))
+            )
+            return features_col, feature_col_names
 
         feature_col_names = self.getOrDefault(self.features_cols)
         features_col = []
@@ -783,15 +883,19 @@ class SparkXGBRegressorModel(_SparkXGBModel):
             )
 
         features_col, feature_col_names = self._get_feature_col(dataset)
+        enable_sparse_data_optim = self.getOrDefault(self.enable_sparse_data_optim)
 
         @pandas_udf("double")
         def predict_udf(iterator: Iterator[pd.DataFrame]) -> Iterator[pd.Series]:
             model = xgb_sklearn_model
             for data in iterator:
-                if feature_col_names is not None:
-                    X = data[feature_col_names]
+                if enable_sparse_data_optim:
+                    X = _read_csr_matrix_from_unwrapped_spark_vec(data)
                 else:
-                    X = stack_series(data[alias.data])
+                    if feature_col_names is not None:
+                        X = data[feature_col_names]
+                    else:
+                        X = stack_series(data[alias.data])
 
                 if has_base_margin:
                     base_margin = data[alias.margin].to_numpy()
@@ -828,6 +932,7 @@ class SparkXGBClassifierModel(_SparkXGBModel, HasProbabilityCol, HasRawPredictio
         return XGBClassifier
 
     def _transform(self, dataset):
+        # pylint: disable=too-many-locals
         # Save xgb_sklearn_model and predict_params to be local variable
         # to avoid the `self` object to be pickled to remote.
         xgb_sklearn_model = self._xgb_sklearn_model
@@ -856,6 +961,7 @@ class SparkXGBClassifierModel(_SparkXGBModel, HasProbabilityCol, HasRawPredictio
             return raw_preds, class_probs
 
         features_col, feature_col_names = self._get_feature_col(dataset)
+        enable_sparse_data_optim = self.getOrDefault(self.enable_sparse_data_optim)
 
         @pandas_udf(
             "rawPrediction array<double>, prediction double, probability array<double>"
@@ -865,10 +971,13 @@ class SparkXGBClassifierModel(_SparkXGBModel, HasProbabilityCol, HasRawPredictio
         ) -> Iterator[pd.DataFrame]:
             model = xgb_sklearn_model
             for data in iterator:
-                if feature_col_names is not None:
-                    X = data[feature_col_names]
+                if enable_sparse_data_optim:
+                    X = _read_csr_matrix_from_unwrapped_spark_vec(data)
                 else:
-                    X = stack_series(data[alias.data])
+                    if feature_col_names is not None:
+                        X = data[feature_col_names]
+                    else:
+                        X = stack_series(data[alias.data])
 
                 if has_base_margin:
                     base_margin = stack_series(data[alias.margin])

python-package/xgboost/spark/data.py

@@ -4,6 +4,7 @@ from typing import Any, Callable, Dict, Iterator, List, Optional, Sequence, Tupl
 
 import numpy as np
 import pandas as pd
+from scipy.sparse import csr_matrix
 from xgboost.compat import concat
 
 from xgboost import DataIter, DeviceQuantileDMatrix, DMatrix
@@ -101,11 +102,55 @@ class PartIter(DataIter):
         self._iter = 0
 
 
+def _read_csr_matrix_from_unwrapped_spark_vec(part: pd.DataFrame) -> csr_matrix:
+    # variables for constructing csr_matrix
+    csr_indices_list, csr_indptr_list, csr_values_list = [], [0], []
+
+    n_features = 0
+
+    for vec_type, vec_size_, vec_indices, vec_values in zip(
+        part.featureVectorType,
+        part.featureVectorSize,
+        part.featureVectorIndices,
+        part.featureVectorValues,
+    ):
+        if vec_type == 0:
+            # sparse vector
+            vec_size = int(vec_size_)
+            csr_indices = vec_indices
+            csr_values = vec_values
+        else:
+            # dense vector
+            # Note: According to spark ML VectorUDT format,
+            # when type field is 1, the size field is also empty.
+            # we need to check the values field to get vector length.
+            vec_size = len(vec_values)
+            csr_indices = np.arange(vec_size, dtype=np.int32)
+            csr_values = vec_values
+
+        if n_features == 0:
+            n_features = vec_size
+        assert n_features == vec_size
+
+        csr_indices_list.append(csr_indices)
+        csr_indptr_list.append(csr_indptr_list[-1] + len(csr_indices))
+        csr_values_list.append(csr_values)
+
+    csr_indptr_arr = np.array(csr_indptr_list)
+    csr_indices_arr = np.concatenate(csr_indices_list)
+    csr_values_arr = np.concatenate(csr_values_list)
+
+    return csr_matrix(
+        (csr_values_arr, csr_indices_arr, csr_indptr_arr), shape=(len(part), n_features)
+    )
+
+
 def create_dmatrix_from_partitions(
     iterator: Iterator[pd.DataFrame],
     feature_cols: Optional[Sequence[str]],
     gpu_id: Optional[int],
     kwargs: Dict[str, Any],  # use dict to make sure this parameter is passed.
+    enable_sparse_data_optim: bool,
 ) -> Tuple[DMatrix, Optional[DMatrix]]:
     """Create DMatrix from spark data partitions. This is not particularly efficient as
     we need to convert the pandas series format to numpy then concatenate all the data.
@@ -118,7 +163,7 @@ def create_dmatrix_from_partitions(
         Metainfo for DMatrix.
 
     """
-
+    # pylint: disable=too-many-locals, too-many-statements
     train_data: Dict[str, List[np.ndarray]] = defaultdict(list)
     valid_data: Dict[str, List[np.ndarray]] = defaultdict(list)
 
@@ -139,6 +184,23 @@ def create_dmatrix_from_partitions(
             else:
                 train_data[name].append(array)
 
+    def append_m_sparse(part: pd.DataFrame, name: str, is_valid: bool) -> None:
+        nonlocal n_features
+
+        if name == alias.data or name in part.columns:
+            if name == alias.data:
+                array = _read_csr_matrix_from_unwrapped_spark_vec(part)
+                if n_features == 0:
+                    n_features = array.shape[1]
+                assert n_features == array.shape[1]
+            else:
+                array = part[name]
+
+            if is_valid:
+                valid_data[name].append(array)
+            else:
+                train_data[name].append(array)
+
     def append_dqm(part: pd.DataFrame, name: str, is_valid: bool) -> None:
         """Preprocessing for DeviceQuantileDMatrix"""
         nonlocal n_features
@@ -164,13 +226,19 @@ def create_dmatrix_from_partitions(
         label = concat_or_none(values.get(alias.label, None))
         weight = concat_or_none(values.get(alias.weight, None))
         margin = concat_or_none(values.get(alias.margin, None))
+
         return DMatrix(
             data=data, label=label, weight=weight, base_margin=margin, **kwargs
         )
 
     is_dmatrix = feature_cols is None
     if is_dmatrix:
-        cache_partitions(iterator, append_m)
+        if enable_sparse_data_optim:
+            append_fn = append_m_sparse
+            assert "missing" in kwargs and kwargs["missing"] == 0.0
+        else:
+            append_fn = append_m
+        cache_partitions(iterator, append_fn)
         dtrain = make(train_data, kwargs)
     else:
         cache_partitions(iterator, append_dqm)

python-package/xgboost/spark/params.py

@@ -50,3 +50,25 @@ class HasFeaturesCols(Params):
     def __init__(self):
         super().__init__()
         self._setDefault(features_cols=[])
+
+
+class HasEnableSparseDataOptim(Params):
+
+    """
+    This is a Params based class that is extended by _SparkXGBParams
+    and holds the variable to store the boolean config of enabling sparse data optimization.
+    """
+
+    enable_sparse_data_optim = Param(
+        Params._dummy(),
+        "enable_sparse_data_optim",
+        "This stores the boolean config of enabling sparse data optimization, if enabled, "
+        "Xgboost DMatrix object will be constructed from sparse matrix instead of "
+        "dense matrix. This config is disabled by default. If most of examples in your "
+        "training dataset contains sparse features, we suggest to enable this config.",
+        typeConverter=TypeConverters.toBoolean,
+    )
+
+    def __init__(self):
+        super().__init__()
+        self._setDefault(enable_sparse_data_optim=False)

tests/ci_build/conda_env/cpu_test.yml

@@ -32,9 +32,10 @@ dependencies:
 - cffi
 - pyarrow
 - protobuf
-- pyspark>=3.3.0
 - cloudpickle
 - shap
 - modin
 - pip:
   - datatable
+  # TODO: Replace it with pyspark>=3.4 once 3.4 released.
+  - https://ml-team-public-read.s3.us-west-2.amazonaws.com/pyspark-3.4.0.dev0.tar.gz

tests/python/test_spark/test_data.py

@@ -11,7 +11,12 @@ if tm.no_spark()["condition"]:
 if sys.platform.startswith("win") or sys.platform.startswith("darwin"):
     pytest.skip("Skipping PySpark tests on Windows", allow_module_level=True)
 
-from xgboost.spark.data import alias, create_dmatrix_from_partitions, stack_series
+from xgboost.spark.data import (
+    _read_csr_matrix_from_unwrapped_spark_vec,
+    alias,
+    create_dmatrix_from_partitions,
+    stack_series,
+)
 
 
 def test_stack() -> None:
@@ -62,10 +67,12 @@ def run_dmatrix_ctor(is_dqm: bool) -> None:
     kwargs = {"feature_types": feature_types}
     if is_dqm:
         cols = [f"feat-{i}" for i in range(n_features)]
-        train_Xy, valid_Xy = create_dmatrix_from_partitions(iter(dfs), cols, 0, kwargs)
+        train_Xy, valid_Xy = create_dmatrix_from_partitions(
+            iter(dfs), cols, 0, kwargs, False
+        )
     else:
         train_Xy, valid_Xy = create_dmatrix_from_partitions(
-            iter(dfs), None, None, kwargs
+            iter(dfs), None, None, kwargs, False
         )
 
     assert valid_Xy is not None
@@ -100,3 +107,35 @@ def run_dmatrix_ctor(is_dqm: bool) -> None:
 
 def test_dmatrix_ctor() -> None:
     run_dmatrix_ctor(False)
+
+
+def test_read_csr_matrix_from_unwrapped_spark_vec() -> None:
+    from scipy.sparse import csr_matrix
+
+    pd1 = pd.DataFrame(
+        {
+            "featureVectorType": [0, 1, 1, 0],
+            "featureVectorSize": [3, None, None, 3],
+            "featureVectorIndices": [
+                np.array([0, 2], dtype=np.int32),
+                None,
+                None,
+                np.array([1, 2], dtype=np.int32),
+            ],
+            "featureVectorValues": [
+                np.array([3.0, 0.0], dtype=np.float64),
+                np.array([13.0, 14.0, 0.0], dtype=np.float64),
+                np.array([0.0, 24.0, 25.0], dtype=np.float64),
+                np.array([0.0, 35.0], dtype=np.float64),
+            ],
+        }
+    )
+    sm = _read_csr_matrix_from_unwrapped_spark_vec(pd1)
+    assert isinstance(sm, csr_matrix)
+
+    np.testing.assert_array_equal(
+        sm.data, [3.0, 0.0, 13.0, 14.0, 0.0, 0.0, 24.0, 25.0, 0.0, 35.0]
+    )
+    np.testing.assert_array_equal(sm.indptr, [0, 2, 5, 8, 10])
+    np.testing.assert_array_equal(sm.indices, [0, 2, 0, 1, 2, 0, 1, 2, 1, 2])
+    assert sm.shape == (4, 3)

tests/python/test_spark/test_spark_local.py

@@ -381,6 +381,26 @@ class XgboostLocalTest(SparkTestCase):
             ],
         )
 
+        self.reg_df_sparse_train = self.session.createDataFrame(
+            [
+                (Vectors.dense(1.0, 0.0, 3.0, 0.0, 0.0), 0),
+                (Vectors.sparse(5, {1: 1.0, 3: 5.5}), 1),
+                (Vectors.sparse(5, {4: -3.0}), 2),
+            ]
+            * 10,
+            ["features", "label"],
+        )
+
+        self.cls_df_sparse_train = self.session.createDataFrame(
+            [
+                (Vectors.dense(1.0, 0.0, 3.0, 0.0, 0.0), 0),
+                (Vectors.sparse(5, {1: 1.0, 3: 5.5}), 1),
+                (Vectors.sparse(5, {4: -3.0}), 0),
+            ]
+            * 10,
+            ["features", "label"],
+        )
+
     def get_local_tmp_dir(self):
         return self.tempdir + str(uuid.uuid4())
 
@@ -972,3 +992,35 @@ class XgboostLocalTest(SparkTestCase):
         )
         model = classifier.fit(self.cls_df_train)
         model.transform(self.cls_df_test).collect()
+
+    def test_regressor_with_sparse_optim(self):
+        regressor = SparkXGBRegressor(missing=0.0)
+        model = regressor.fit(self.reg_df_sparse_train)
+        assert model._xgb_sklearn_model.missing == 0.0
+        pred_result = model.transform(self.reg_df_sparse_train).collect()
+
+        # enable sparse optimiaztion
+        regressor2 = SparkXGBRegressor(missing=0.0, enable_sparse_data_optim=True)
+        model2 = regressor2.fit(self.reg_df_sparse_train)
+        assert model2.getOrDefault(model2.enable_sparse_data_optim)
+        assert model2._xgb_sklearn_model.missing == 0.0
+        pred_result2 = model2.transform(self.reg_df_sparse_train).collect()
+
+        for row1, row2 in zip(pred_result, pred_result2):
+            self.assertTrue(np.isclose(row1.prediction, row2.prediction, atol=1e-3))
+
+    def test_classifier_with_sparse_optim(self):
+        cls = SparkXGBClassifier(missing=0.0)
+        model = cls.fit(self.cls_df_sparse_train)
+        assert model._xgb_sklearn_model.missing == 0.0
+        pred_result = model.transform(self.cls_df_sparse_train).collect()
+
+        # enable sparse optimiaztion
+        cls2 = SparkXGBClassifier(missing=0.0, enable_sparse_data_optim=True)
+        model2 = cls2.fit(self.cls_df_sparse_train)
+        assert model2.getOrDefault(model2.enable_sparse_data_optim)
+        assert model2._xgb_sklearn_model.missing == 0.0
+        pred_result2 = model2.transform(self.cls_df_sparse_train).collect()
+
+        for row1, row2 in zip(pred_result, pred_result2):
+            self.assertTrue(np.allclose(row1.probability, row2.probability, rtol=1e-3))