[Fix] Refactor development reproducibility (#172)

* [Fix] pass random state to randomized algorithms

* [Fix] double instantiation of random state

* [fix] Flaky for sample configuration

* [FIX] Runtime warning

* [FIX] hardcoded budget

* [FIX] flake

* [Fix] try forked

* [Fix] try forked

* [FIX] budget

* [Fix] missing random_state in trainer

* [Fix] overwrite in random_state

* [FIX] fix seed in splits

* [Rebase]

* [FIX] Update cv score after split num change

* [FIX] CV split

Author: franchuterivera

.github/workflows/pytest.yml

@@ -29,7 +29,7 @@ jobs:
     - name: Run tests
       run: |
         if [ ${{ matrix.code-cov }} ]; then codecov='--cov=autoPyTorch --cov-report=xml'; fi
-        python -m pytest --durations=20 --timeout=600 --timeout-method=signal -v $codecov test
+        python -m pytest --forked --durations=20 --timeout=600 --timeout-method=signal -v $codecov test
     - name: Check for files left behind by test
       if: ${{ always() }}
       run: |

autoPyTorch/api/base_task.py

@@ -1235,7 +1235,8 @@ def __del__(self) -> None:
         # When a multiprocessing work is done, the
         # objects are deleted. We don't want to delete run areas
         # until the estimator is deleted
-        self._backend.context.delete_directories(force=False)
+        if hasattr(self, '_backend'):
+            self._backend.context.delete_directories(force=False)
 
     @typing.no_type_check
     def get_incumbent_results(

autoPyTorch/datasets/base_dataset.py

@@ -118,7 +118,7 @@ def __init__(
         self.train_tensors, self.val_tensors, self.test_tensors = train_tensors, val_tensors, test_tensors
         self.cross_validators: Dict[str, CrossValFunc] = {}
         self.holdout_validators: Dict[str, HoldOutFunc] = {}
-        self.rng = np.random.RandomState(seed=seed)
+        self.random_state = np.random.RandomState(seed=seed)
         self.shuffle = shuffle
         self.resampling_strategy = resampling_strategy
         self.resampling_strategy_args = resampling_strategy_args
@@ -205,7 +205,7 @@ def __len__(self) -> int:
         return self.train_tensors[0].shape[0]
 
     def _get_indices(self) -> np.ndarray:
-        return self.rng.permutation(len(self)) if self.shuffle else np.arange(len(self))
+        return self.random_state.permutation(len(self)) if self.shuffle else np.arange(len(self))
 
     def get_splits_from_resampling_strategy(self) -> List[Tuple[List[int], List[int]]]:
         """
@@ -271,7 +271,7 @@ def create_cross_val_splits(
             # we need additional information about the data for stratification
             kwargs["stratify"] = self.train_tensors[-1]
         splits = self.cross_validators[cross_val_type.name](
-            num_splits, self._get_indices(), **kwargs)
+            self.random_state, num_splits, self._get_indices(), **kwargs)
         return splits
 
     def create_holdout_val_split(
@@ -305,7 +305,8 @@ def create_holdout_val_split(
         if holdout_val_type.is_stratified():
             # we need additional information about the data for stratification
             kwargs["stratify"] = self.train_tensors[-1]
-        train, val = self.holdout_validators[holdout_val_type.name](val_share, self._get_indices(), **kwargs)
+        train, val = self.holdout_validators[holdout_val_type.name](
+            self.random_state, val_share, self._get_indices(), **kwargs)
         return train, val
 
     def get_dataset_for_training(self, split_id: int) -> Tuple[Dataset, Dataset]:

autoPyTorch/datasets/resampling_strategy.py

@@ -18,14 +18,16 @@
 # Use callback protocol as workaround, since callable with function fields count 'self' as argument
 class CrossValFunc(Protocol):
     def __call__(self,
+                 random_state: np.random.RandomState,
                  num_splits: int,
                  indices: np.ndarray,
                  stratify: Optional[Any]) -> List[Tuple[np.ndarray, np.ndarray]]:
         ...
 
 
 class HoldOutFunc(Protocol):
-    def __call__(self, val_share: float, indices: np.ndarray, stratify: Optional[Any]
+    def __call__(self, random_state: np.random.RandomState, val_share: float,
+                 indices: np.ndarray, stratify: Optional[Any]
                  ) -> Tuple[np.ndarray, np.ndarray]:
         ...
 
@@ -85,35 +87,42 @@ def is_stratified(self) -> bool:
         'val_share': 0.33,
     },
     CrossValTypes.k_fold_cross_validation: {
-        'num_splits': 3,
+        'num_splits': 5,
     },
     CrossValTypes.stratified_k_fold_cross_validation: {
-        'num_splits': 3,
+        'num_splits': 5,
     },
     CrossValTypes.shuffle_split_cross_validation: {
-        'num_splits': 3,
+        'num_splits': 5,
     },
     CrossValTypes.time_series_cross_validation: {
-        'num_splits': 3,
+        'num_splits': 5,
     },
 }  # type: Dict[Union[HoldoutValTypes, CrossValTypes], Dict[str, Any]]
 
 
 class HoldOutFuncs():
     @staticmethod
-    def holdout_validation(val_share: float,
+    def holdout_validation(random_state: np.random.RandomState,
+                           val_share: float,
                            indices: np.ndarray,
                            **kwargs: Any
                            ) -> Tuple[np.ndarray, np.ndarray]:
-        train, val = train_test_split(indices, test_size=val_share, shuffle=False)
+        shuffle = kwargs.get('shuffle', True)
+        train, val = train_test_split(indices, test_size=val_share,
+                                      shuffle=shuffle,
+                                      random_state=random_state if shuffle else None,
+                                      )
         return train, val
 
     @staticmethod
-    def stratified_holdout_validation(val_share: float,
+    def stratified_holdout_validation(random_state: np.random.RandomState,
+                                      val_share: float,
                                       indices: np.ndarray,
                                       **kwargs: Any
                                       ) -> Tuple[np.ndarray, np.ndarray]:
-        train, val = train_test_split(indices, test_size=val_share, shuffle=True, stratify=kwargs["stratify"])
+        train, val = train_test_split(indices, test_size=val_share, shuffle=True, stratify=kwargs["stratify"],
+                                      random_state=random_state)
         return train, val
 
     @classmethod
@@ -128,34 +137,38 @@ def get_holdout_validators(cls, *holdout_val_types: HoldoutValTypes) -> Dict[str
 
 class CrossValFuncs():
     @staticmethod
-    def shuffle_split_cross_validation(num_splits: int,
+    def shuffle_split_cross_validation(random_state: np.random.RandomState,
+                                       num_splits: int,
                                        indices: np.ndarray,
                                        **kwargs: Any
                                        ) -> List[Tuple[np.ndarray, np.ndarray]]:
-        cv = ShuffleSplit(n_splits=num_splits)
+        cv = ShuffleSplit(n_splits=num_splits, random_state=random_state)
         splits = list(cv.split(indices))
         return splits
 
     @staticmethod
-    def stratified_shuffle_split_cross_validation(num_splits: int,
+    def stratified_shuffle_split_cross_validation(random_state: np.random.RandomState,
+                                                  num_splits: int,
                                                   indices: np.ndarray,
                                                   **kwargs: Any
                                                   ) -> List[Tuple[np.ndarray, np.ndarray]]:
-        cv = StratifiedShuffleSplit(n_splits=num_splits)
+        cv = StratifiedShuffleSplit(n_splits=num_splits, random_state=random_state)
         splits = list(cv.split(indices, kwargs["stratify"]))
         return splits
 
     @staticmethod
-    def stratified_k_fold_cross_validation(num_splits: int,
+    def stratified_k_fold_cross_validation(random_state: np.random.RandomState,
+                                           num_splits: int,
                                            indices: np.ndarray,
                                            **kwargs: Any
                                            ) -> List[Tuple[np.ndarray, np.ndarray]]:
-        cv = StratifiedKFold(n_splits=num_splits)
+        cv = StratifiedKFold(n_splits=num_splits, random_state=random_state)
         splits = list(cv.split(indices, kwargs["stratify"]))
         return splits
 
     @staticmethod
-    def k_fold_cross_validation(num_splits: int,
+    def k_fold_cross_validation(random_state: np.random.RandomState,
+                                num_splits: int,
                                 indices: np.ndarray,
                                 **kwargs: Any
                                 ) -> List[Tuple[np.ndarray, np.ndarray]]:
@@ -169,12 +182,14 @@ def k_fold_cross_validation(num_splits: int,
         Returns:
             splits (List[Tuple[List, List]]): list of tuples of training and validation indices
         """
-        cv = KFold(n_splits=num_splits)
+        shuffle = kwargs.get('shuffle', True)
+        cv = KFold(n_splits=num_splits, random_state=random_state if shuffle else None, shuffle=shuffle)
         splits = list(cv.split(indices))
         return splits
 
     @staticmethod
-    def time_series_cross_validation(num_splits: int,
+    def time_series_cross_validation(random_state: np.random.RandomState,
+                                     num_splits: int,
                                      indices: np.ndarray,
                                      **kwargs: Any
                                      ) -> List[Tuple[np.ndarray, np.ndarray]]:
@@ -196,7 +211,7 @@ def time_series_cross_validation(num_splits: int,
                  ([0, 1, 2], [3])]
 
         """
-        cv = TimeSeriesSplit(n_splits=num_splits)
+        cv = TimeSeriesSplit(n_splits=num_splits, random_state=random_state)
         splits = list(cv.split(indices))
         return splits
 

autoPyTorch/evaluation/abstract_evaluator.py

@@ -80,7 +80,8 @@ def __init__(self, config: str,
         self.random_state = random_state
         self.init_params = init_params
         self.pipeline = autoPyTorch.pipeline.traditional_tabular_classification.\
-            TraditionalTabularClassificationPipeline(dataset_properties=dataset_properties)
+            TraditionalTabularClassificationPipeline(dataset_properties=dataset_properties,
+                                                     random_state=self.random_state)
         configuration_space = self.pipeline.get_hyperparameter_search_space()
         default_configuration = configuration_space.get_default_configuration().get_dictionary()
         default_configuration['model_trainer:tabular_classifier:classifier'] = config

autoPyTorch/evaluation/tae.py

@@ -4,6 +4,7 @@
 import logging
 import math
 import multiprocessing
+import os
 import time
 import traceback
 import typing
@@ -25,6 +26,7 @@
 from autoPyTorch.evaluation.utils import empty_queue, extract_learning_curve, read_queue
 from autoPyTorch.pipeline.components.training.metrics.base import autoPyTorchMetric
 from autoPyTorch.utils.backend import Backend
+from autoPyTorch.utils.common import replace_string_bool_to_bool
 from autoPyTorch.utils.hyperparameter_search_space_update import HyperparameterSearchSpaceUpdates
 from autoPyTorch.utils.logging_ import PicklableClientLogger, get_named_client_logger
 
@@ -144,7 +146,12 @@ def __init__(
         self.exclude = exclude
         self.disable_file_output = disable_file_output
         self.init_params = init_params
-        self.pipeline_config = pipeline_config
+        self.pipeline_config: typing.Dict[str, typing.Union[int, str, float]] = dict()
+        if pipeline_config is None:
+            pipeline_config = replace_string_bool_to_bool(json.load(open(
+                os.path.join(os.path.dirname(__file__), '../configs/default_pipeline_options.json'))))
+        self.pipeline_config.update(pipeline_config)
+
         self.budget_type = pipeline_config['budget_type'] if pipeline_config is not None else budget_type
         self.logger_port = logger_port
         if self.logger_port is None:
@@ -199,7 +206,7 @@ def run_wrapper(
                 )
         else:
             if run_info.budget == 0:
-                run_info = run_info._replace(budget=100.0)
+                run_info = run_info._replace(budget=self.pipeline_config[self.budget_type])
             elif run_info.budget <= 0 or run_info.budget > 100:
                 raise ValueError('Illegal value for budget, must be >0 and <=100, but is %f' %
                                  run_info.budget)

autoPyTorch/pipeline/base_pipeline.py

@@ -70,6 +70,10 @@ def __init__(
         self.include = include if include is not None else {}
         self.exclude = exclude if exclude is not None else {}
         self.search_space_updates = search_space_updates
+        if random_state is None:
+            self.random_state = check_random_state(1)
+        else:
+            self.random_state = check_random_state(random_state)
 
         if steps is None:
             self.steps = self._get_pipeline_steps(dataset_properties)
@@ -98,10 +102,6 @@ def __init__(
 
         self.set_hyperparameters(self.config, init_params=init_params)
 
-        if random_state is None:
-            self.random_state = check_random_state(1)
-        else:
-            self.random_state = check_random_state(random_state)
         super().__init__(steps=self.steps)
 
         self._additional_run_info = {}  # type: Dict[str, str]

autoPyTorch/pipeline/components/base_component.py

@@ -8,7 +8,10 @@
 
 from ConfigSpace.configuration_space import Configuration, ConfigurationSpace
 
+import numpy as np
+
 from sklearn.base import BaseEstimator
+from sklearn.utils import check_random_state
 
 from autoPyTorch.utils.common import FitRequirement, HyperparameterSearchSpace
 from autoPyTorch.utils.hyperparameter_search_space_update import HyperparameterSearchSpaceUpdate
@@ -93,8 +96,12 @@ def add_component(self, obj: BaseEstimator) -> None:
 class autoPyTorchComponent(BaseEstimator):
     _required_properties: Optional[List[str]] = None
 
-    def __init__(self) -> None:
+    def __init__(self, random_state: Optional[np.random.RandomState] = None) -> None:
         super().__init__()
+        if random_state is None:
+            self.random_state = check_random_state(1)
+        else:
+            self.random_state = check_random_state(random_state)
         self._fit_requirements: List[FitRequirement] = list()
         self._cs_updates: Dict[str, HyperparameterSearchSpaceUpdate] = dict()
 

autoPyTorch/pipeline/components/preprocessing/tabular_preprocessing/feature_preprocessing/TruncatedSVD.py

@@ -26,7 +26,8 @@ def __init__(self, target_dim: int = 128,
 
     def fit(self, X: Dict[str, Any], y: Any = None) -> BaseEstimator:
 
-        self.preprocessor['numerical'] = sklearn.decomposition.TruncatedSVD(self.target_dim, algorithm="randomized")
+        self.preprocessor['numerical'] = sklearn.decomposition.TruncatedSVD(self.target_dim, algorithm="randomized",
+                                                                            random_state=self.random_state)
 
         return self
 

autoPyTorch/pipeline/components/setup/network_backbone/utils.py

@@ -1,4 +1,3 @@
-import random
 import typing
 import warnings
 
@@ -120,7 +119,8 @@ def shake_drop_get_bl(
     pl = 1 - ((block_index + 1) / num_blocks) * (1 - min_prob_no_shake)
 
     if not is_training:
-        bl = torch.tensor(1.0) if random.random() <= pl else torch.tensor(0.0)
+        # Move to torch.randn(1) for reproducibility
+        bl = torch.tensor(1.0) if torch.randn(1) <= pl else torch.tensor(0.0)
     if is_training:
         bl = torch.tensor(pl)
 

autoPyTorch/pipeline/components/setup/traditional_ml/base_model.py

@@ -74,6 +74,7 @@ def fit(self, X: Dict[str, Any], y: Any = None) -> autoPyTorchSetupComponent:
 
         # instantiate model
         self.model = self.build_model(input_shape=input_shape,
+                                      logger_port=X['logger_port'],
                                       output_shape=output_shape)
 
         # train model
@@ -91,7 +92,8 @@ def fit(self, X: Dict[str, Any], y: Any = None) -> autoPyTorchSetupComponent:
         return self
 
     @abstractmethod
-    def build_model(self, input_shape: Tuple[int, ...], output_shape: Tuple[int, ...]) -> BaseClassifier:
+    def build_model(self, input_shape: Tuple[int, ...], output_shape: Tuple[int, ...],
+                    logger_port: int) -> BaseClassifier:
         """
         This method returns a pytorch model, that is dynamically built using
         a self.config that is model specific, and contains the additional

autoPyTorch/pipeline/components/setup/traditional_ml/classifier_models/base_classifier.py

@@ -1,24 +1,37 @@
 import json
-import logging
+import logging.handlers
 import os as os
 from abc import abstractmethod
 from typing import Any, Dict, List, Optional
 
 import numpy as np
 
+from sklearn.utils import check_random_state
+
 from autoPyTorch.metrics import accuracy
+from autoPyTorch.utils.logging_ import get_named_client_logger
 
 
-class BaseClassifier():
+class BaseClassifier:
     """
     Base class for classifiers.
     """
 
-    def __init__(self, name: str = ''):
-
-        self.configure_logging()
+    def __init__(self, logger_port: int = logging.handlers.DEFAULT_TCP_LOGGING_PORT,
+                 random_state: Optional[np.random.RandomState] = None, name: str = ''):
 
         self.name = name
+        self.logger_port = logger_port
+        self.logger = get_named_client_logger(
+            name=name,
+            host='localhost',
+            port=logger_port,
+        )
+
+        if random_state is None:
+            self.random_state = check_random_state(1)
+        else:
+            self.random_state = check_random_state(random_state)
         self.config = self.get_config()
 
         self.categoricals: np.ndarray = np.array(())
@@ -28,17 +41,6 @@ def __init__(self, name: str = ''):
 
         self.metric = accuracy
 
-    def configure_logging(self) -> None:
-        """
-        Setup self.logger
-        """
-        self.logger = logging.getLogger(__name__)
-        self.logger.setLevel(logging.INFO)
-
-        ch = logging.StreamHandler()
-        ch.setLevel(logging.INFO)
-        self.logger.addHandler(ch)
-
     def get_config(self) -> Dict[str, Any]:
         """
         Load the parameters for the classifier model from ../classifier_configs/modelname.json.