mxlpy 0.17.0__py3-none-any.whl → 0.19.0__py3-none-any.whl

mxlpy/npe/__init__.py

@@ -16,23 +16,28 @@ Functions:
 
 from __future__ import annotations
 
-import contextlib
-
-with contextlib.suppress(ImportError):
-    from ._torch import (
-        TorchSteadyState,
-        TorchSteadyStateTrainer,
-        TorchTimeCourse,
-        TorchTimeCourseTrainer,
-        train_torch_steady_state,
-        train_torch_time_course,
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import contextlib
+
+    with contextlib.suppress(ImportError):
+        from . import _keras as keras
+        from . import _torch as torch
+else:
+    from lazy_import import lazy_module
+
+    keras = lazy_module(
+        "mxlpy.npe._keras",
+        error_strings={"module": "keras", "install_name": "mxlpy[tf]"},
     )
+    torch = lazy_module(
+        "mxlpy.npe._torch",
+        error_strings={"module": "torch", "install_name": "mxlpy[torch]"},
+    )
+
 
 __all__ = [
-    "TorchSteadyState",
-    "TorchSteadyStateTrainer",
-    "TorchTimeCourse",
-    "TorchTimeCourseTrainer",
-    "train_torch_steady_state",
-    "train_torch_time_course",
+    "keras",
+    "torch",
 ]

mxlpy/npe/_keras.py

@@ -0,0 +1,326 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Self, cast
+
+import keras
+import numpy as np
+import pandas as pd
+
+from mxlpy.nn._keras import LSTM, MLP, train
+from mxlpy.types import AbstractEstimator
+
+__all__ = [
+    "DefaultLoss",
+    "DefaultOptimizer",
+    "LossFn",
+    "Optimizer",
+    "SteadyState",
+    "SteadyStateTrainer",
+    "TimeCourse",
+    "TimeCourseTrainer",
+    "train_steady_state",
+    "train_time_course",
+]
+
+type Optimizer = keras.optimizers.Optimizer | str
+type LossFn = keras.losses.Loss | str
+
+DefaultOptimizer = keras.optimizers.Adam()
+DefaultLoss = keras.losses.MeanAbsoluteError()
+
+
+@dataclass(kw_only=True)
+class SteadyState(AbstractEstimator):
+    """Estimator for steady state data using Keras models."""
+
+    model: keras.Model
+
+    def predict(self, features: pd.Series | pd.DataFrame) -> pd.DataFrame:
+        """Predict the target values for the given features."""
+        return pd.DataFrame(
+            self.model.predict(features),
+            columns=self.parameter_names,
+            dtype=float,
+        )
+
+
+@dataclass(kw_only=True)
+class TimeCourse(AbstractEstimator):
+    """Estimator for time course data using Keras models."""
+
+    model: keras.Model
+
+    def predict(self, features: pd.Series | pd.DataFrame) -> pd.DataFrame:
+        """Predict the target values for the given features."""
+        idx = cast(pd.MultiIndex, features.index)
+        features_ = (
+            np.swapaxes(
+                features.to_numpy().reshape(
+                    (
+                        len(idx.levels[0]),
+                        len(idx.levels[1]),
+                        len(features.columns),
+                    )
+                ),
+                axis1=0,
+                axis2=1,
+            ),
+        )
+        return pd.DataFrame(
+            self.model.predict(features_),
+            columns=self.parameter_names,
+            dtype=float,
+        )
+
+
+@dataclass
+class SteadyStateTrainer:
+    """Trainer for steady state data using Keras models."""
+
+    features: pd.DataFrame
+    targets: pd.DataFrame
+    model: keras.Model
+    optimizer: Optimizer
+    losses: list[pd.Series]
+    loss_fn: LossFn
+
+    def __init__(
+        self,
+        features: pd.DataFrame,
+        targets: pd.DataFrame,
+        model: keras.Model | None = None,
+        optimizer: Optimizer = DefaultOptimizer,
+        loss: LossFn = DefaultLoss,
+    ) -> None:
+        """Initialize the trainer with features, targets, and model.
+
+        Args:
+            features: DataFrame containing the input features for training
+            targets: DataFrame containing the target values for training
+            model: Predefined neural network model (None to use default MLP)
+            optimizer: Optimizer class to use for training (default: Adam)
+            loss: Loss function
+
+        """
+        self.features = features
+        self.targets = targets
+
+        if model is None:
+            n_hidden = max(2 * len(features.columns) * len(targets.columns), 10)
+            n_outputs = len(targets.columns)
+            model = MLP(
+                n_inputs=len(features.columns),
+                neurons_per_layer=[n_hidden, n_hidden, n_outputs],
+            )
+        self.model = model
+        model.compile(optimizer=cast(str, optimizer), loss=loss)
+
+        self.loss_fn = loss
+        self.losses = []
+
+    def train(
+        self,
+        epochs: int,
+        batch_size: int | None = None,
+    ) -> Self:
+        """Train the model using the provided features and targets.
+
+        Args:
+            epochs: Number of training epochs
+            batch_size: Size of mini-batches for training (None for full-batch)
+
+        """
+        losses = train(
+            model=self.model,
+            features=self.features,
+            targets=self.targets,
+            epochs=epochs,
+            batch_size=batch_size,
+        )
+
+        if len(self.losses) > 0:
+            losses.index += self.losses[-1].index[-1]
+        self.losses.append(losses)
+        return self
+
+    def get_loss(self) -> pd.Series:
+        """Get the loss history of the training process."""
+        return pd.concat(self.losses)
+
+    def get_estimator(self) -> SteadyState:
+        """Get the trained estimator."""
+        return SteadyState(
+            model=self.model,
+            parameter_names=list(self.targets.columns),
+        )
+
+
+@dataclass
+class TimeCourseTrainer:
+    """Trainer for time course data using Keras models."""
+
+    features: pd.DataFrame
+    targets: pd.DataFrame
+    model: keras.Model
+    optimizer: Optimizer
+
+    losses: list[pd.Series]
+    loss_fn: LossFn
+
+    def __init__(
+        self,
+        features: pd.DataFrame,
+        targets: pd.DataFrame,
+        model: keras.Model | None = None,
+        optimizer: Optimizer = DefaultOptimizer,
+        loss: LossFn = DefaultLoss,
+    ) -> None:
+        """Initialize the trainer with features, targets, and model.
+
+        Args:
+            features: DataFrame containing the input features for training
+            targets: DataFrame containing the target values for training
+            model: Predefined neural network model (None to use default LSTM)
+            optimizer: Optimizer class to use for training
+            loss: Loss function
+
+        """
+        self.features = features
+        self.targets = targets
+
+        if model is None:
+            model = LSTM(
+                n_inputs=len(features.columns),
+                n_outputs=len(targets.columns),
+                n_hidden=1,
+            )
+        self.model = model
+        model.compile(optimizer=cast(str, optimizer), loss=loss)
+        self.losses = []
+
+    def train(
+        self,
+        epochs: int,
+        batch_size: int | None = None,
+    ) -> Self:
+        """Train the model using the provided features and targets.
+
+        Args:
+            epochs: Number of training epochs
+            batch_size: Size of mini-batches for training (None for full-batch)
+
+        """
+        losses = train(
+            model=self.model,
+            features=np.swapaxes(
+                self.features.to_numpy().reshape(
+                    (len(self.targets), -1, len(self.features.columns))
+                ),
+                axis1=0,
+                axis2=1,
+            ),
+            targets=self.targets,
+            epochs=epochs,
+            batch_size=batch_size,
+        )
+
+        if len(self.losses) > 0:
+            losses.index += self.losses[-1].index[-1]
+        self.losses.append(losses)
+        return self
+
+    def get_loss(self) -> pd.Series:
+        """Get the loss history of the training process."""
+        return pd.concat(self.losses)
+
+    def get_estimator(self) -> TimeCourse:
+        """Get the trained estimator."""
+        return TimeCourse(
+            model=self.model,
+            parameter_names=list(self.targets.columns),
+        )
+
+
+def train_steady_state(
+    features: pd.DataFrame,
+    targets: pd.DataFrame,
+    epochs: int,
+    batch_size: int | None = None,
+    model: keras.Model | None = None,
+    optimizer: Optimizer = DefaultOptimizer,
+    loss: LossFn = DefaultLoss,
+) -> tuple[SteadyState, pd.Series]:
+    """Train a Keras steady state estimator.
+
+    This function trains a neural network model to estimate steady state data
+    using the provided features and targets. It supports both full-batch and
+    mini-batch training.
+
+    Examples:
+        >>> train_keras_ss_estimator(features, targets, epochs=100)
+
+    Args:
+        features: DataFrame containing the input features for training
+        targets: DataFrame containing the target values for training
+        epochs: Number of training epochs
+        batch_size: Size of mini-batches for training (None for full-batch)
+        model: Predefined neural network model (None to use default MLP)
+        optimizer: Optimizer class to use for training (default: Adam)
+        loss: Loss function for the training
+
+    Returns:
+        tuple[KerasTimeSeriesEstimator, pd.Series]: Trained estimator and loss history
+
+    """
+    trainer = SteadyStateTrainer(
+        features=features,
+        targets=targets,
+        model=model,
+        optimizer=optimizer,
+        loss=loss,
+    ).train(epochs=epochs, batch_size=batch_size)
+
+    return trainer.get_estimator(), trainer.get_loss()
+
+
+def train_time_course(
+    features: pd.DataFrame,
+    targets: pd.DataFrame,
+    epochs: int,
+    batch_size: int | None = None,
+    model: keras.Model | None = None,
+    optimizer: Optimizer = DefaultOptimizer,
+    loss: LossFn = DefaultLoss,
+) -> tuple[TimeCourse, pd.Series]:
+    """Train a Keras time course estimator.
+
+    This function trains a neural network model to estimate time course data
+    using the provided features and targets. It supports both full-batch and
+    mini-batch training.
+
+    Examples:
+        >>> train_keras_time_course_estimator(features, targets, epochs=100)
+
+    Args:
+        features: DataFrame containing the input features for training
+        targets: DataFrame containing the target values for training
+        epochs: Number of training epochs
+        batch_size: Size of mini-batches for training (None for full-batch)
+        model: Predefined neural network model (None to use default LSTM)
+        optimizer: Optimizer class to use for training (default: Adam)
+        loss: Loss function for the training
+
+    Returns:
+        tuple[KerasTimeSeriesEstimator, pd.Series]: Trained estimator and loss history
+
+    """
+    trainer = TimeCourseTrainer(
+        features=features,
+        targets=targets,
+        model=model,
+        optimizer=optimizer,
+        loss=loss,
+    ).train(epochs=epochs, batch_size=batch_size)
+
+    return trainer.get_estimator(), trainer.get_loss()