[ADD] Calculate memory of dataset after one hot encoding (pytorch emb…

…edding) (#437) * add updates for apt1.0+reg_cocktails * debug loggers for checking data and network memory usage * add support for pandas, test for data passing, remove debug loggers * remove unwanted changes * : * Adjust formula to account for embedding columns * Apply suggestions from code review Co-authored-by: nabenabe0928 <[email protected]> * remove unwanted additions * Update autoPyTorch/pipeline/components/preprocessing/tabular_preprocessing/TabularColumnTransformer.py Co-authored-by: nabenabe0928 <[email protected]>
automl · Jul 16, 2022 · 95a5969 · 95a5969
1 parent 9573358
commit 95a5969
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Showing 11 changed files with 98 additions and 41 deletions.
diff --git a/autoPyTorch/api/base_task.py b/autoPyTorch/api/base_task.py
@@ -111,23 +111,6 @@ def send_warnings_to_log(
     return prediction
 
 
-def get_search_updates(categorical_indicator: List[bool]) -> HyperparameterSearchSpaceUpdates:
-    """
-    These updates mimic the autopytorch tabular paper.
-    Returns:
-    ________
-    search_space_updates - HyperparameterSearchSpaceUpdates
-        The search space updates like setting different hps to different values or ranges.
-    """
-
-    # has_cat_features = any(categorical_indicator)
-    # has_numerical_features = not all(categorical_indicator)
-
-    search_space_updates = HyperparameterSearchSpaceUpdates()
-
-    return search_space_updates
-
-
 class BaseTask(ABC):
     """
     Base class for the tasks that serve as API to the pipelines.
@@ -200,7 +183,6 @@ def __init__(
         resampling_strategy_args: Optional[Dict[str, Any]] = None,
         search_space_updates: Optional[HyperparameterSearchSpaceUpdates] = None,
         task_type: Optional[str] = None,
-        categorical_indicator: Optional[List[bool]] = None
     ) -> None:
 
         if isinstance(resampling_strategy, NoResamplingStrategyTypes) and ensemble_size != 0:

diff --git a/autoPyTorch/api/tabular_classification.py b/autoPyTorch/api/tabular_classification.py
@@ -98,7 +98,6 @@ def __init__(
         resampling_strategy_args: Optional[Dict[str, Any]] = None,
         backend: Optional[Backend] = None,
         search_space_updates: Optional[HyperparameterSearchSpaceUpdates] = None,
-        categorical_indicator: Optional[List[bool]] = None
     ):
         super().__init__(
             seed=seed,
@@ -119,7 +118,6 @@ def __init__(
             resampling_strategy_args=resampling_strategy_args,
             search_space_updates=search_space_updates,
             task_type=TASK_TYPES_TO_STRING[TABULAR_CLASSIFICATION],
-            categorical_indicator=categorical_indicator
         )
 
     def build_pipeline(

diff --git a/autoPyTorch/constants.py b/autoPyTorch/constants.py
@@ -54,3 +54,5 @@
 
 CLASSIFICATION_OUTPUTS = [BINARY, MULTICLASS, MULTICLASSMULTIOUTPUT]
 REGRESSION_OUTPUTS = [CONTINUOUS, CONTINUOUSMULTIOUTPUT]
+
+MIN_CATEGORIES_FOR_EMBEDDING_MAX = 7
diff --git a/autoPyTorch/data/tabular_validator.py b/autoPyTorch/data/tabular_validator.py
@@ -104,6 +104,8 @@ def _compress_dataset(
                 y=y,
                 is_classification=self.is_classification,
                 random_state=self.seed,
+                categorical_columns=self.feature_validator.categorical_columns,
+                n_categories_per_cat_column=self.feature_validator.num_categories_per_col,
                 **self.dataset_compression  # type: ignore [arg-type]
             )
             self._reduced_dtype = dict(X.dtypes) if is_dataframe else X.dtype

diff --git a/autoPyTorch/data/utils.py b/autoPyTorch/data/utils.py
@@ -25,6 +25,7 @@
 from sklearn.utils import _approximate_mode, check_random_state
 from sklearn.utils.validation import _num_samples, check_array
 
+from autoPyTorch.constants import MIN_CATEGORIES_FOR_EMBEDDING_MAX
 from autoPyTorch.data.base_target_validator import SupportedTargetTypes
 from autoPyTorch.utils.common import ispandas
 
@@ -459,8 +460,8 @@ def _subsample_by_indices(
     return X, y
 
 
-def megabytes(arr: DatasetCompressionInputType) -> float:
-
+def get_raw_memory_usage(arr: DatasetCompressionInputType) -> float:
+    memory_in_bytes: float
     if isinstance(arr, np.ndarray):
         memory_in_bytes = arr.nbytes
     elif issparse(arr):
@@ -470,19 +471,57 @@ def megabytes(arr: DatasetCompressionInputType) -> float:
     else:
         raise ValueError(f"Unrecognised data type of X, expected data type to "
                          f"be in (np.ndarray, spmatrix, pd.DataFrame) but got :{type(arr)}")
+    return memory_in_bytes
+
+
+def get_approximate_mem_usage_in_mb(
+    arr: DatasetCompressionInputType,
+    categorical_columns: List,
+    n_categories_per_cat_column: Optional[List[int]] = None
+) -> float:
+
+    err_msg = "Value number of categories per categorical is required when the data has categorical columns"
+    if ispandas(arr):
+        arr_dtypes = arr.dtypes.to_dict()
+        multipliers = [dtype.itemsize for col, dtype in arr_dtypes.items() if col not in categorical_columns]
+        if len(categorical_columns) > 0:
+            if n_categories_per_cat_column is None:
+                raise ValueError(err_msg)
+            for col, num_cat in zip(categorical_columns, n_categories_per_cat_column):
+                if num_cat < MIN_CATEGORIES_FOR_EMBEDDING_MAX:
+                    multipliers.append(num_cat * arr_dtypes[col].itemsize)
+                else:
+                    multipliers.append(arr_dtypes[col].itemsize)
+        size_one_row = sum(multipliers)
+
+    elif isinstance(arr, (np.ndarray, spmatrix)):
+        n_cols = arr.shape[-1] - len(categorical_columns)
+        multiplier = arr.dtype.itemsize
+        if len(categorical_columns) > 0:
+            if n_categories_per_cat_column is None:
+                raise ValueError(err_msg)
+            # multiply num categories with the size of the column to capture memory after one hot encoding
+            n_cols += sum(num_cat if num_cat < MIN_CATEGORIES_FOR_EMBEDDING_MAX else 1 for num_cat in n_categories_per_cat_column)
+        size_one_row = n_cols * multiplier
+    else:
+        raise ValueError(f"Unrecognised data type of X, expected data type to "
+                         f"be in (np.ndarray, spmatrix, pd.DataFrame), but got :{type(arr)}")
 
-    return float(memory_in_bytes / (2**20))
+    return float(arr.shape[0] * size_one_row / (2**20))
 
 
 def reduce_dataset_size_if_too_large(
     X: DatasetCompressionInputType,
     memory_allocation: Union[int, float],
     is_classification: bool,
     random_state: Union[int, np.random.RandomState],
+    categorical_columns: List,
+    n_categories_per_cat_column: Optional[List[int]] = None,
     y: Optional[SupportedTargetTypes] = None,
     methods: List[str] = ['precision', 'subsample'],
 ) -> DatasetCompressionInputType:
-    f""" Reduces the size of the dataset if it's too close to the memory limit.
+    f"""
+    Reduces the size of the dataset if it's too close to the memory limit.
 
     Follows the order of the operations passed in and retains the type of its
     input.
@@ -513,7 +552,6 @@ def reduce_dataset_size_if_too_large(
                 Reduce the amount of samples of the dataset such that it fits into the allocated
                 memory. Ensures stratification and that unique labels are present
 
-
         memory_allocation (Union[int, float]):
             The amount of memory to allocate to the dataset. It should specify an
             absolute amount.
@@ -524,7 +562,7 @@ def reduce_dataset_size_if_too_large(
     """
 
     for method in methods:
-        if megabytes(X) <= memory_allocation:
+        if get_approximate_mem_usage_in_mb(X, categorical_columns, n_categories_per_cat_column) <= memory_allocation:
             break
 
         if method == 'precision':
@@ -540,7 +578,8 @@ def reduce_dataset_size_if_too_large(
             # into the allocated memory, we subsample it so that it does
 
             n_samples_before = X.shape[0]
-            sample_percentage = memory_allocation / megabytes(X)
+            sample_percentage = memory_allocation / get_approximate_mem_usage_in_mb(
+                X, categorical_columns, n_categories_per_cat_column)
 
             # NOTE: type ignore
             #

diff --git a/...Torch/pipeline/components/preprocessing/tabular_preprocessing/TabularColumnTransformer.py b/...Torch/pipeline/components/preprocessing/tabular_preprocessing/TabularColumnTransformer.py
@@ -24,6 +24,7 @@ def __init__(self, random_state: Optional[Union[np.random.RandomState, int]] = N
         self.add_fit_requirements([
             FitRequirement('numerical_columns', (List,), user_defined=True, dataset_property=True),
             FitRequirement('categorical_columns', (List,), user_defined=True, dataset_property=True)])
+
 
     def get_column_transformer(self) -> ColumnTransformer:
         """

diff --git a/...ipeline/components/preprocessing/tabular_preprocessing/column_splitting/ColumnSplitter.py b/...ipeline/components/preprocessing/tabular_preprocessing/column_splitting/ColumnSplitter.py
@@ -7,7 +7,7 @@
 
 import numpy as np
 
-
+from autoPyTorch.constants import MIN_CATEGORIES_FOR_EMBEDDING_MAX
 from autoPyTorch.datasets.base_dataset import BaseDatasetPropertiesType
 from autoPyTorch.pipeline.components.preprocessing.tabular_preprocessing.base_tabular_preprocessing import \
     autoPyTorchTabularPreprocessingComponent
@@ -72,7 +72,7 @@ def get_hyperparameter_search_space(
         dataset_properties: Optional[Dict[str, BaseDatasetPropertiesType]] = None,
         min_categories_for_embedding: HyperparameterSearchSpace = HyperparameterSearchSpace(
             hyperparameter="min_categories_for_embedding",
-            value_range=(3, 7),
+            value_range=(3, MIN_CATEGORIES_FOR_EMBEDDING_MAX),
             default_value=3,
             log=True),
     ) -> ConfigurationSpace:

diff --git a/...PyTorch/pipeline/components/preprocessing/tabular_preprocessing/encoding/OneHotEncoder.py b/...PyTorch/pipeline/components/preprocessing/tabular_preprocessing/encoding/OneHotEncoder.py
@@ -24,7 +24,8 @@ def fit(self, X: Dict[str, Any], y: Any = None) -> BaseEncoder:
             # It is safer to have the OHE produce a 0 array than to crash a good configuration
             categories='auto',
             sparse=False,
-            handle_unknown='ignore')
+            handle_unknown='ignore',
+            dtype=np.float32)
         return self
 
     @staticmethod

diff --git a/test/test_api/test_api.py b/test/test_api/test_api.py
@@ -500,10 +500,10 @@ def test_do_dummy_prediction(dask_client, fit_dictionary_tabular):
     del estimator
 
 
-@pytest.skip("Fix with new portfolio PR")
 @unittest.mock.patch('autoPyTorch.evaluation.tae.eval_train_function',
                      new=dummy_eval_train_function)
 @pytest.mark.parametrize('openml_id', (40981, ))
+@pytest.mark.skip(reason="Fix with new portfolio PR")
 def test_portfolio_selection(openml_id, backend, n_samples):
 
     # Get the data and check that contents of data-manager make sense
@@ -543,7 +543,7 @@ def test_portfolio_selection(openml_id, backend, n_samples):
     assert any(successful_config in portfolio_configs for successful_config in successful_configs)
 
 
-@pytest.skip("Fix with new portfolio PR")
+@pytest.mark.skip(reason="Fix with new portfolio PR")
 @unittest.mock.patch('autoPyTorch.evaluation.tae.eval_train_function',
                      new=dummy_eval_train_function)
 @pytest.mark.parametrize('openml_id', (40981, ))

diff --git a/test/test_data/test_utils.py b/test/test_data/test_utils.py
@@ -25,7 +25,7 @@
 from autoPyTorch.data.utils import (
     default_dataset_compression_arg,
     get_dataset_compression_mapping,
-    megabytes,
+    get_raw_memory_usage,
     reduce_dataset_size_if_too_large,
     reduce_precision,
     subsample,
@@ -45,13 +45,14 @@ def test_reduce_dataset_if_too_large(openmlid, as_frame, n_samples):
         X.copy(),
         y=y.copy(),
         is_classification=True,
+        categorical_columns=[],
         random_state=1,
-        memory_allocation=0.001)
+        memory_allocation=0.01)
 
     assert X_converted.shape[0] < X.shape[0]
     assert y_converted.shape[0] < y.shape[0]
 
-    assert megabytes(X_converted) < megabytes(X)
+    assert get_raw_memory_usage(X_converted) < get_raw_memory_usage(X)
 
 
 @pytest.mark.parametrize("X", [np.asarray([[1, 1, 1]] * 30)])
@@ -211,8 +212,18 @@ def test_unsupported_errors():
         ['a', 'b', 'c', 'a', 'b', 'c'],
         ['a', 'b', 'd', 'r', 'b', 'c']])
     with pytest.raises(ValueError, match=r'X.dtype = .*'):
-        reduce_dataset_size_if_too_large(X, is_classification=True, random_state=1, memory_allocation=0)
+        reduce_dataset_size_if_too_large(
+            X,
+            is_classification=True,
+            categorical_columns=[],
+            random_state=1,
+            memory_allocation=0)
 
     X = [[1, 2], [2, 3]]
     with pytest.raises(ValueError, match=r'Unrecognised data type of X, expected data type to be in .*'):
-        reduce_dataset_size_if_too_large(X, is_classification=True, random_state=1, memory_allocation=0)
+        reduce_dataset_size_if_too_large(
+            X,
+            is_classification=True,
+            categorical_columns=[],
+            random_state=1,
+            memory_allocation=0)
diff --git a/test/test_data/test_validation.py b/test/test_data/test_validation.py
@@ -8,7 +8,8 @@
 import sklearn.model_selection
 
 from autoPyTorch.data.tabular_validator import TabularInputValidator
-from autoPyTorch.data.utils import megabytes
+from autoPyTorch.data.utils import get_approximate_mem_usage_in_mb
+from autoPyTorch.utils.common import ispandas
 
 
 @pytest.mark.parametrize('openmlid', [2, 40975, 40984])
@@ -148,16 +149,36 @@ def test_featurevalidator_dataset_compression(input_data_featuretest):
     X_train, X_test, y_train, y_test = sklearn.model_selection.train_test_split(
         input_data_featuretest, input_data_targets, test_size=0.1, random_state=1)
     validator = TabularInputValidator(
-        dataset_compression={'memory_allocation': 0.8 * megabytes(X_train), 'methods': ['precision', 'subsample']}
+        dataset_compression={
+            'memory_allocation': 0.8 * get_approximate_mem_usage_in_mb(X_train, [], None),
+            'methods': ['precision', 'subsample']}
     )
     validator.fit(X_train=X_train, y_train=y_train)
     transformed_X_train, _ = validator.transform(X_train.copy(), y_train.copy())
 
+    if ispandas(X_train):
+        # input validator converts transformed_X_train to numpy and the cat columns are chosen as column indices
+        columns = X_train.columns
+        categorical_columns = [columns[col] for col in validator.feature_validator.categorical_columns]
+    else:
+        categorical_columns = validator.feature_validator.categorical_columns
+
     assert validator._reduced_dtype is not None
-    assert megabytes(transformed_X_train) < megabytes(X_train)
+    assert get_approximate_mem_usage_in_mb(
+        transformed_X_train,
+        validator.feature_validator.categorical_columns,
+        validator.feature_validator.num_categories_per_col
+    ) < get_approximate_mem_usage_in_mb(
+        X_train, categorical_columns, validator.feature_validator.num_categories_per_col)
 
     transformed_X_test, _ = validator.transform(X_test.copy(), y_test.copy())
-    assert megabytes(transformed_X_test) < megabytes(X_test)
+    assert get_approximate_mem_usage_in_mb(
+        transformed_X_test,
+        validator.feature_validator.categorical_columns,
+        validator.feature_validator.num_categories_per_col
+    ) < get_approximate_mem_usage_in_mb(
+        X_test, categorical_columns, validator.feature_validator.num_categories_per_col)
+
     if hasattr(transformed_X_train, 'iloc'):
         assert all(transformed_X_train.dtypes == transformed_X_test.dtypes)
         assert all(transformed_X_train.dtypes == validator._precision)