docs for forecasting task (#443)

* docs for forecasting task * avoid directly import extra dependencies * Update docs/dev.rst Co-authored-by: Ravin Kohli <13005107+ravinkohli@users.noreply.github.com> * make ForecastingDependenciesNotInstalledError a str message * make ForecastingDependenciesNotInstalledError a str message * update readme and examples * add explanation for univariant models in example Co-authored-by: Ravin Kohli <13005107+ravinkohli@users.noreply.github.com>
automl · Jul 6, 2022 · dcd2bc5 · dcd2bc5
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diff --git a/README.md b/README.md
@@ -4,8 +4,9 @@ Copyright (C) 2021  [AutoML Groups Freiburg and Hannover](http://www.automl.org/
 
 While early AutoML frameworks focused on optimizing traditional ML pipelines and their hyperparameters, another trend in AutoML is to focus on neural architecture search. To bring the best of these two worlds together, we developed **Auto-PyTorch**, which jointly and robustly optimizes the network architecture and the training hyperparameters to enable fully automated deep learning (AutoDL).
 
-Auto-PyTorch is mainly developed to support tabular data (classification, regression).
+Auto-PyTorch is mainly developed to support tabular data (classification, regression) and time series data (forecasting).
 The newest features in Auto-PyTorch for tabular data are described in the paper ["Auto-PyTorch Tabular: Multi-Fidelity MetaLearning for Efficient and Robust AutoDL"](https://arxiv.org/abs/2006.13799) (see below for bibtex ref).
+Details about Auto-PyTorch for multi-horizontal time series forecasting tasks can be found in the paper ["Efficient Automated Deep Learning for Time Series Forecasting"](https://arxiv.org/abs/2205.05511) (also see below for bibtex ref).
 
 Also, find the documentation [here](https://automl.github.io/Auto-PyTorch/master).
 
@@ -27,7 +28,9 @@ In other words, we evaluate the portfolio on a provided data as initial configur
 Then API starts the following procedures:
 1. **Validate input data**: Process each data type, e.g. encoding categorical data, so that Auto-Pytorch can handled.
 2. **Create dataset**: Create a dataset that can be handled in this API with a choice of cross validation or holdout splits.
-3. **Evaluate baselines** *1: Train each algorithm in the predefined pool with a fixed hyperparameter configuration and dummy model from `sklearn.dummy` that represents the worst possible performance.
+3. **Evaluate baselines** 
+   * ***Tabular dataset*** *1: Train each algorithm in the predefined pool with a fixed hyperparameter configuration and dummy model from `sklearn.dummy` that represents the worst possible performance.
+   * ***Time Series Forecasting dataset*** : Train a dummy predictor that repeats the last observed value in each series
 4. **Search by [SMAC](https://github.com/automl/SMAC3)**:\
     a. Determine budget and cut-off rules by [Hyperband](https://jmlr.org/papers/volume18/16-558/16-558.pdf)\
     b. Sample a pipeline hyperparameter configuration *2 by SMAC\
@@ -50,6 +53,14 @@ pip install autoPyTorch
 
 ```
 
+Auto-PyTorch for Time Series Forecasting requires additional dependencies 
+
+```sh
+
+pip install autoPyTorch[forecasting]
+
+```
+
 ### Manual Installation
 
 We recommend using Anaconda for developing as follows:
@@ -70,6 +81,20 @@ python setup.py install
 
 ```
 
+Similarly, to install all the dependencies for Auto-PyTorch-TimeSeriesForecasting:
+
+
+```sh
+
+git submodule update --init --recursive
+
+conda create -n auto-pytorch python=3.8
+conda activate auto-pytorch
+conda install swig
+pip install -e[forecasting]
+
+```
+
 ## Examples
 
 In a nutshell:
@@ -105,6 +130,66 @@ score = api.score(y_pred, y_test)
 print("Accuracy score", score)
 ```
 
+For Time Series Forecasting Tasks
+```py
+
+from autoPyTorch.api.time_series_forecasting import TimeSeriesForecastingTask
+
+# data and metric imports
+from sktime.datasets import load_longley
+targets, features = load_longley()
+
+# define the forecasting horizon
+forecasting_horizon = 3
+
+# Dataset optimized by APT-TS can be a list of np.ndarray/ pd.DataFrame where each series represents an element in the 
+# list, or a single pd.DataFrame that records the series
+# index information: to which series the timestep belongs? This id can be stored as the DataFrame's index or a separate
+# column
+# Within each series, we take the last forecasting_horizon as test targets. The items before that as training targets
+# Normally the value to be forecasted should follow the training sets
+y_train = [targets[: -forecasting_horizon]]
+y_test = [targets[-forecasting_horizon:]]
+
+# same for features. For uni-variant models, X_train, X_test can be omitted and set as None
+X_train = [features[: -forecasting_horizon]]
+# Here x_test indicates the 'known future features': they are the features known previously, features that are unknown
+# could be replaced with NAN or zeros (which will not be used by our networks). If no feature is known beforehand,
+# we could also omit X_test
+known_future_features = list(features.columns)
+X_test = [features[-forecasting_horizon:]]
+
+start_times = [targets.index.to_timestamp()[0]]
+freq = '1Y'
+
+# initialise Auto-PyTorch api
+api = TimeSeriesForecastingTask()
+
+# Search for an ensemble of machine learning algorithms
+api.search(
+    X_train=X_train,
+    y_train=y_train,
+    X_test=X_test, 
+    optimize_metric='mean_MAPE_forecasting',
+    n_prediction_steps=forecasting_horizon,
+    memory_limit=16 * 1024,  # Currently, forecasting models use much more memories
+    freq=freq,
+    start_times=start_times,
+    func_eval_time_limit_secs=50,
+    total_walltime_limit=60,
+    min_num_test_instances=1000,  # proxy validation sets. This only works for the tasks with more than 1000 series
+    known_future_features=known_future_features,
+)
+
+# our dataset could directly generate sequences for new datasets
+test_sets = api.dataset.generate_test_seqs()
+
+# Calculate test accuracy
+y_pred = api.predict(test_sets)
+score = api.score(y_pred, y_test)
+print("Forecasting score", score)
+```
+
 For more examples including customising the search space, parellising the code, etc, checkout the `examples` folder
 
 ```sh
@@ -163,6 +248,17 @@ Please refer to the branch `TPAMI.2021.3067763` to reproduce the paper *Auto-PyT
 }
 ```
 
+```bibtex
+@article{deng-ecml22,
+  author    = {Difan Deng and Florian Karl and Frank Hutter and Bernd Bischl and Marius Lindauer},
+  title     = {Efficient Automated Deep Learning for Time Series Forecasting},
+  year      = {2022},
+  booktitle = {Machine Learning and Knowledge Discovery in Databases. Research Track
+               - European Conference, {ECML} {PKDD} 2022},
+  url       = {https://doi.org/10.48550/arXiv.2205.05511},
+}
+```
+
 ## Contact
 
 Auto-PyTorch is developed by the [AutoML Groups of the University of Freiburg and Hannover](http://www.automl.org/).
diff --git a/autoPyTorch/api/time_series_forecasting.py b/autoPyTorch/api/time_series_forecasting.py
@@ -7,8 +7,7 @@
 from autoPyTorch.api.base_task import BaseTask
 from autoPyTorch.automl_common.common.utils.backend import Backend
 from autoPyTorch.constants import MAX_WINDOW_SIZE_BASE, TASK_TYPES_TO_STRING, TIMESERIES_FORECASTING
-from autoPyTorch.data.time_series_forecasting_validator import \
-    TimeSeriesForecastingInputValidator
+from autoPyTorch.data.time_series_forecasting_validator import TimeSeriesForecastingInputValidator
 from autoPyTorch.data.utils import (
     DatasetCompressionSpec,
     get_dataset_compression_mapping

diff --git a/autoPyTorch/constants.py b/autoPyTorch/constants.py
@@ -54,7 +54,10 @@
 CLASSIFICATION_OUTPUTS = [BINARY, MULTICLASS, MULTICLASSMULTIOUTPUT]
 REGRESSION_OUTPUTS = [CONTINUOUS, CONTINUOUSMULTIOUTPUT]
 
-# Constants for Forecasting Tasks
+ForecastingDependenciesNotInstalledMSG = "Additional dependencies must be installed to work with time series " \
+                                         "forecasting tasks! Please run \n pip install autoPyTorch[forecasting] \n to "\
+                                         "install the corresponding dependencies!"
+
 
 # The constant values for time series forecasting comes from
 # https://github.com/rakshitha123/TSForecasting/blob/master/experiments/deep_learning_experiments.py

diff --git a/autoPyTorch/evaluation/abstract_evaluator.py b/autoPyTorch/evaluation/abstract_evaluator.py
@@ -19,14 +19,19 @@
 import autoPyTorch.pipeline.image_classification
 import autoPyTorch.pipeline.tabular_classification
 import autoPyTorch.pipeline.tabular_regression
-import autoPyTorch.pipeline.time_series_forecasting
+try:
+    import autoPyTorch.pipeline.time_series_forecasting
+    forecasting_dependencies_installed = True
+except ModuleNotFoundError:
+    forecasting_dependencies_installed = False
 import autoPyTorch.pipeline.traditional_tabular_classification
 import autoPyTorch.pipeline.traditional_tabular_regression
 from autoPyTorch.automl_common.common.utils.backend import Backend
 from autoPyTorch.constants import (
     CLASSIFICATION_TASKS,
     FORECASTING_BUDGET_TYPE,
     FORECASTING_TASKS,
+    ForecastingDependenciesNotInstalledMSG,
     IMAGE_TASKS,
     MULTICLASS,
     REGRESSION_TASKS,
@@ -38,12 +43,16 @@
     BaseDataset,
     BaseDatasetPropertiesType
 )
-from autoPyTorch.datasets.time_series_dataset import TimeSeriesSequence
 from autoPyTorch.evaluation.utils import (
     DisableFileOutputParameters,
     VotingRegressorWrapper,
     convert_multioutput_multiclass_to_multilabel
 )
+try:
+    from autoPyTorch.evaluation.utils_extra import DummyTimeSeriesForecastingPipeline
+    forecasting_dependencies_installed = True
+except ModuleNotFoundError:
+    forecasting_dependencies_installed = False
 from autoPyTorch.pipeline.base_pipeline import BasePipeline
 from autoPyTorch.pipeline.components.training.metrics.base import autoPyTorchMetric
 from autoPyTorch.pipeline.components.training.metrics.utils import (
@@ -314,61 +323,6 @@ def get_default_pipeline_options() -> Dict[str, Any]:
                 'runtime': 1}
 
 
-class DummyTimeSeriesForecastingPipeline(DummyClassificationPipeline):
-    """
-    A wrapper class that holds a pipeline for dummy forecasting. For each series, it simply repeats the last element
-    in the training series
-
-
-    Attributes:
-        random_state (Optional[Union[int, np.random.RandomState]]):
-            Object that contains a seed and allows for reproducible results
-        init_params  (Optional[Dict]):
-            An optional dictionary that is passed to the pipeline's steps. It complies
-            a similar function as the kwargs
-        n_prediction_steps (int):
-            forecasting horizon
-    """
-    def __init__(self, config: Configuration,
-                 random_state: Optional[Union[int, np.random.RandomState]] = None,
-                 init_params: Optional[Dict] = None,
-                 n_prediction_steps: int = 1,
-                 ) -> None:
-        super(DummyTimeSeriesForecastingPipeline, self).__init__(config, random_state, init_params)
-        self.n_prediction_steps = n_prediction_steps
-
-    def fit(self, X: Dict[str, Any], y: Any,
-            sample_weight: Optional[np.ndarray] = None) -> object:
-        self.n_prediction_steps = X['dataset_properties']['n_prediction_steps']
-        y_train = subsampler(X['y_train'], X['train_indices'])
-        return DummyClassifier.fit(self, np.ones((y_train.shape[0], 1)), y_train, sample_weight)
-
-    def _generate_dummy_forecasting(self, X: List[Union[TimeSeriesSequence, np.ndarray]]) -> List:
-        if isinstance(X[0], TimeSeriesSequence):
-            X_tail = [x.get_target_values(-1) for x in X]
-        else:
-            X_tail = [x[-1] for x in X]
-        return X_tail
-
-    def predict_proba(self, X: Union[np.ndarray, pd.DataFrame],
-                      batch_size: int = 1000) -> np.ndarray:
-        X_tail = self._generate_dummy_forecasting(X)
-        return np.tile(X_tail, (1, self.n_prediction_steps)).astype(np.float32).flatten()
-
-    def predict(self, X: Union[np.ndarray, pd.DataFrame],
-                batch_size: int = 1000) -> np.ndarray:
-        X_tail = np.asarray(self._generate_dummy_forecasting(X))
-        if X_tail.ndim == 1:
-            X_tail = np.expand_dims(X_tail, -1)
-        return np.tile(X_tail, (1, self.n_prediction_steps)).astype(np.float32).flatten()
-
-    @staticmethod
-    def get_default_pipeline_options() -> Dict[str, Any]:
-        return {'budget_type': 'epochs',
-                'epochs': 1,
-                'runtime': 1}
-
-
 def fit_and_suppress_warnings(logger: PicklableClientLogger, pipeline: BaseEstimator,
                               X: Dict[str, Any], y: Any
                               ) -> BaseEstimator:
@@ -543,6 +497,8 @@ def __init__(self, backend: Backend,
             self.predict_function = self._predict_proba
         elif self.task_type in FORECASTING_TASKS:
             if isinstance(self.configuration, int):
+                if not forecasting_dependencies_installed:
+                    raise ModuleNotFoundError(ForecastingDependenciesNotInstalledMSG)
                 self.pipeline_class = DummyTimeSeriesForecastingPipeline
             elif isinstance(self.configuration, str):
                 raise ValueError("Only tabular classifications tasks "

diff --git a/autoPyTorch/evaluation/tae.py b/autoPyTorch/evaluation/tae.py
@@ -25,6 +25,7 @@
 from autoPyTorch.automl_common.common.utils.backend import Backend
 from autoPyTorch.constants import (
     FORECASTING_BUDGET_TYPE,
+    ForecastingDependenciesNotInstalledMSG,
     STRING_TO_TASK_TYPES,
     TIMESERIES_FORECASTING,
 )
@@ -34,7 +35,11 @@
     NoResamplingStrategyTypes
 )
 from autoPyTorch.evaluation.test_evaluator import eval_test_function
-from autoPyTorch.evaluation.time_series_forecasting_train_evaluator import forecasting_eval_train_function
+try:
+    from autoPyTorch.evaluation.time_series_forecasting_train_evaluator import forecasting_eval_train_function
+    forecasting_dependencies_installed = True
+except ModuleNotFoundError:
+    forecasting_dependencies_installed = False
 from autoPyTorch.evaluation.train_evaluator import eval_train_function
 from autoPyTorch.evaluation.utils import (
     DisableFileOutputParameters,
@@ -152,6 +157,8 @@ def __init__(
         self.resampling_strategy_args = dm.resampling_strategy_args
 
         if STRING_TO_TASK_TYPES.get(dm.task_type, -1) == TIMESERIES_FORECASTING:
+            if not forecasting_dependencies_installed:
+                raise ModuleNotFoundError(ForecastingDependenciesNotInstalledMSG)
             eval_function: Callable = forecasting_eval_train_function
             if isinstance(self.resampling_strategy, (HoldoutValTypes, CrossValTypes)):
                 self.output_y_hat_optimization = output_y_hat_optimization

diff --git a/autoPyTorch/evaluation/time_series_forecasting_train_evaluator.py b/autoPyTorch/evaluation/time_series_forecasting_train_evaluator.py
@@ -13,9 +13,9 @@
 
 from autoPyTorch.automl_common.common.utils.backend import Backend
 from autoPyTorch.constants import SEASONALITY_MAP
-from autoPyTorch.evaluation.abstract_evaluator import DummyTimeSeriesForecastingPipeline
 from autoPyTorch.evaluation.train_evaluator import TrainEvaluator
 from autoPyTorch.evaluation.utils import DisableFileOutputParameters
+from autoPyTorch.evaluation.utils_extra import DummyTimeSeriesForecastingPipeline
 from autoPyTorch.pipeline.components.training.metrics.base import autoPyTorchMetric
 from autoPyTorch.pipeline.components.training.metrics.metrics import MASE_LOSSES
 from autoPyTorch.utils.hyperparameter_search_space_update import HyperparameterSearchSpaceUpdates

diff --git a/autoPyTorch/evaluation/utils_extra.py b/autoPyTorch/evaluation/utils_extra.py
@@ -0,0 +1,72 @@
+# The functions and classes implemented in this module all require extra requirements.
+# We put them here to make it easier to be wrapped by try-except process
+from typing import Any, Dict, List, Optional, Union
+
+from ConfigSpace import Configuration
+
+import numpy as np
+
+import pandas as pd
+
+from sklearn.dummy import DummyClassifier
+
+from autoPyTorch.datasets.time_series_dataset import TimeSeriesSequence
+from autoPyTorch.utils.common import subsampler
+
+
+class DummyTimeSeriesForecastingPipeline(DummyClassifier):
+    """
+    A wrapper class that holds a pipeline for dummy forecasting. For each series, it simply repeats the last element
+    in the training series
+
+
+    Attributes:
+        random_state (Optional[Union[int, np.random.RandomState]]):
+            Object that contains a seed and allows for reproducible results
+        init_params  (Optional[Dict]):
+            An optional dictionary that is passed to the pipeline's steps. It complies
+            a similar function as the kwargs
+        n_prediction_steps (int):
+            forecasting horizon
+    """
+    def __init__(self, config: Configuration,
+                 random_state: Optional[Union[int, np.random.RandomState]] = None,
+                 init_params: Optional[Dict] = None,
+                 n_prediction_steps: int = 1,
+                 ) -> None:
+        self.config = config
+        self.init_params = init_params
+        self.random_state = random_state
+        super(DummyTimeSeriesForecastingPipeline, self).__init__(strategy="uniform")
+        self.n_prediction_steps = n_prediction_steps
+
+    def fit(self, X: Dict[str, Any], y: Any,
+            sample_weight: Optional[np.ndarray] = None) -> object:
+        self.n_prediction_steps = X['dataset_properties']['n_prediction_steps']
+        y_train = subsampler(X['y_train'], X['train_indices'])
+        return DummyClassifier.fit(self, np.ones((y_train.shape[0], 1)), y_train, sample_weight)
+
+    def _generate_dummy_forecasting(self, X: List[Union[TimeSeriesSequence, np.ndarray]]) -> List:
+        if isinstance(X[0], TimeSeriesSequence):
+            X_tail = [x.get_target_values(-1) for x in X]
+        else:
+            X_tail = [x[-1] for x in X]
+        return X_tail
+
+    def predict_proba(self, X: Union[np.ndarray, pd.DataFrame],
+                      batch_size: int = 1000) -> np.ndarray:
+        X_tail = self._generate_dummy_forecasting(X)
+        return np.tile(X_tail, (1, self.n_prediction_steps)).astype(np.float32).flatten()
+
+    def predict(self, X: Union[np.ndarray, pd.DataFrame],
+                batch_size: int = 1000) -> np.ndarray:
+        X_tail = np.asarray(self._generate_dummy_forecasting(X))
+        if X_tail.ndim == 1:
+            X_tail = np.expand_dims(X_tail, -1)
+        return np.tile(X_tail, (1, self.n_prediction_steps)).astype(np.float32).flatten()
+
+    @staticmethod
+    def get_default_pipeline_options() -> Dict[str, Any]:
+        return {'budget_type': 'epochs',
+                'epochs': 1,
+                'runtime': 1}