mxlpy 0.16.0__py3-none-any.whl → 0.18.0__py3-none-any.whl

mxlpy/surrogates/_torch.py

@@ -1,25 +1,43 @@
 from collections.abc import Callable
 from dataclasses import dataclass
+from typing import Self
 
 import numpy as np
 import pandas as pd
 import torch
-import tqdm
 from torch import nn
 from torch.optim.adam import Adam
 from torch.optim.optimizer import ParamsT
 
-from mxlpy.nn._torch import MLP, DefaultDevice
+from mxlpy.nn._torch import MLP, DefaultDevice, train
 from mxlpy.types import AbstractSurrogate
 
+type LossFn = Callable[[torch.Tensor, torch.Tensor], torch.Tensor]
+
 __all__ = [
-    "TorchSurrogate",
-    "train_torch_surrogate",
+    "LossFn",
+    "Torch",
+    "TorchTrainer",
+    "train_torch",
 ]
 
 
+def _mean_abs(x: torch.Tensor, y: torch.Tensor) -> torch.Tensor:
+    """Standard loss for surrogates.
+
+    Args:
+        x: Predictions of a model.
+        y: Targets.
+
+    Returns:
+        torch.Tensor: loss.
+
+    """
+    return torch.mean(torch.abs(x - y))
+
+
 @dataclass(kw_only=True)
-class TorchSurrogate(AbstractSurrogate):
+class Torch(AbstractSurrogate):
     """Surrogate model using PyTorch.
 
     Attributes:
@@ -48,90 +66,92 @@ class TorchSurrogate(AbstractSurrogate):
             ).numpy()
 
 
-def _train_batched(
-    aprox: nn.Module,
-    features: pd.DataFrame,
-    targets: pd.DataFrame,
-    epochs: int,
-    optimizer: Adam,
-    device: torch.device,
-    batch_size: int,
-) -> pd.Series:
-    """Train the neural network using mini-batch gradient descent.
-
-    Args:
-        aprox: Neural network model to train.
-        features: Input features as a tensor.
-        targets: Target values as a tensor.
-        epochs: Number of training epochs.
-        optimizer: Optimizer for training.
-        device: torch device
-        batch_size: Size of mini-batches for training.
-
-    Returns:
-        pd.Series: Series containing the training loss history.
-
-    """
-    rng = np.random.default_rng()
-    losses = {}
-    for i in tqdm.trange(epochs):
-        idxs = rng.choice(features.index, size=batch_size)
-        X = torch.Tensor(features.iloc[idxs].to_numpy(), device=device)
-        Y = torch.Tensor(targets.iloc[idxs].to_numpy(), device=device)
-        optimizer.zero_grad()
-        loss = torch.mean(torch.abs(aprox(X) - Y))
-        loss.backward()
-        optimizer.step()
-        losses[i] = loss.detach().numpy()
-    return pd.Series(losses, dtype=float)
-
-
-def _train_full(
-    aprox: nn.Module,
-    features: pd.DataFrame,
-    targets: pd.DataFrame,
-    epochs: int,
-    optimizer: Adam,
-    device: torch.device,
-) -> pd.Series:
-    """Train the neural network using full-batch gradient descent.
-
-    Args:
-        aprox: Neural network model to train.
-        features: Input features as a tensor.
-        targets: Target values as a tensor.
-        epochs: Number of training epochs.
-        optimizer: Optimizer for training.
-        device: Torch device
-
-    Returns:
-        pd.Series: Series containing the training loss history.
-
-    """
-    X = torch.Tensor(features.to_numpy(), device=device)
-    Y = torch.Tensor(targets.to_numpy(), device=device)
-
-    losses = {}
-    for i in tqdm.trange(epochs):
-        optimizer.zero_grad()
-        loss = torch.mean(torch.abs(aprox(X) - Y))
-        loss.backward()
-        optimizer.step()
-        losses[i] = loss.detach().numpy()
-    return pd.Series(losses, dtype=float)
+@dataclass(init=False)
+class TorchTrainer:
+    features: pd.DataFrame
+    targets: pd.DataFrame
+    approximator: nn.Module
+    optimizer: Adam
+    device: torch.device
+    losses: list[pd.Series]
+    loss_fn: LossFn
+
+    def __init__(
+        self,
+        features: pd.DataFrame,
+        targets: pd.DataFrame,
+        approximator: nn.Module | None = None,
+        optimimzer_cls: Callable[[ParamsT], Adam] = Adam,
+        device: torch.device = DefaultDevice,
+        loss_fn: LossFn = _mean_abs,
+    ) -> None:
+        self.features = features
+        self.targets = targets
+
+        if approximator is None:
+            approximator = MLP(
+                n_inputs=len(features.columns),
+                neurons_per_layer=[50, 50, len(targets.columns)],
+            )
+        self.approximator = approximator.to(device)
+
+        self.optimizer = optimimzer_cls(approximator.parameters())
+        self.device = device
+        self.loss_fn = loss_fn
+        self.losses = []
+
+    def train(
+        self,
+        epochs: int,
+        batch_size: int | None = None,
+    ) -> Self:
+        losses = train(
+            aprox=self.approximator,
+            features=self.features.to_numpy(),
+            targets=self.targets.to_numpy(),
+            epochs=epochs,
+            optimizer=self.optimizer,
+            batch_size=batch_size,
+            device=self.device,
+            loss_fn=self.loss_fn,
+        )
+        if len(self.losses) > 0:
+            losses.index += self.losses[-1].index[-1]
+        self.losses.append(losses)
+        return self
+
+    def get_loss(self) -> pd.Series:
+        return pd.concat(self.losses)
+
+    def get_surrogate(
+        self,
+        surrogate_args: list[str] | None = None,
+        surrogate_outputs: list[str] | None = None,
+        surrogate_stoichiometries: dict[str, dict[str, float]] | None = None,
+    ) -> Torch:
+        return Torch(
+            model=self.approximator,
+            args=surrogate_args if surrogate_args is not None else [],
+            outputs=surrogate_outputs if surrogate_outputs is not None else [],
+            stoichiometries=surrogate_stoichiometries
+            if surrogate_stoichiometries is not None
+            else {},
+        )
 
 
-def train_torch_surrogate(
+def train_torch(
     features: pd.DataFrame,
     targets: pd.DataFrame,
     epochs: int,
     surrogate_args: list[str] | None = None,
+    surrogate_outputs: list[str] | None = None,
     surrogate_stoichiometries: dict[str, dict[str, float]] | None = None,
     batch_size: int | None = None,
     approximator: nn.Module | None = None,
     optimimzer_cls: Callable[[ParamsT], Adam] = Adam,
     device: torch.device = DefaultDevice,
-) -> tuple[TorchSurrogate, pd.Series]:
+    loss_fn: LossFn = _mean_abs,
+) -> tuple[Torch, pd.Series]:
     """Train a PyTorch surrogate model.
 
     Examples:
@@ -143,54 +163,38 @@ def train_torch_surrogate(
         ...     surrogate_stoichiometries={
         ...         "v1": {"x1": -1, "x2": 1, "ATP": -1},
         ...     },
-        ...)
+        ...)surrogate_stoichiometries
 
     Args:
         features: DataFrame containing the input features for training.
         targets: DataFrame containing the target values for training.
         epochs: Number of training epochs.
-        surrogate_args: List of input variable names for the surrogate model.
-        surrogate_stoichiometries: Dictionary mapping reaction names to stoichiometries.
+        surrogate_args: Names of inputs arguments for the surrogate model.
+        surrogate_outputs: Names of output arguments from the surrogate.
+        surrogate_stoichiometries: Mapping of variables to their stoichiometries
         batch_size: Size of mini-batches for training (None for full-batch).
         approximator: Predefined neural network model (None to use default MLP features-50-50-output).
         optimimzer_cls: Optimizer class to use for training (default: Adam).
         device: Device to run the training on (default: DefaultDevice).
+        loss_fn: Custom loss function or instance of torch loss object
 
     Returns:
         tuple[TorchSurrogate, pd.Series]: Trained surrogate model and loss history.
 
     """
-    if approximator is None:
-        approximator = MLP(
-            n_inputs=len(features.columns),
-            neurons_per_layer=[50, 50, len(targets.columns)],
-        ).to(device)
-
-    optimizer = optimimzer_cls(approximator.parameters())
-    if batch_size is None:
-        losses = _train_full(
-            aprox=approximator,
-            features=features,
-            targets=targets,
-            epochs=epochs,
-            optimizer=optimizer,
-            device=device,
-        )
-    else:
-        losses = _train_batched(
-            aprox=approximator,
-            features=features,
-            targets=targets,
-            epochs=epochs,
-            optimizer=optimizer,
-            device=device,
-            batch_size=batch_size,
-        )
-    surrogate = TorchSurrogate(
-        model=approximator,
-        args=surrogate_args if surrogate_args is not None else [],
-        stoichiometries=surrogate_stoichiometries
-        if surrogate_stoichiometries is not None
-        else {},
+    trainer = TorchTrainer(
+        features=features,
+        targets=targets,
+        approximator=approximator,
+        optimimzer_cls=optimimzer_cls,
+        device=device,
+        loss_fn=loss_fn,
+    ).train(
+        epochs=epochs,
+        batch_size=batch_size,
     )
-    return surrogate, losses
+    return trainer.get_surrogate(
+        surrogate_args=surrogate_args,
+        surrogate_outputs=surrogate_outputs,
+        surrogate_stoichiometries=surrogate_stoichiometries,
+    ), trainer.get_loss()

mxlpy/symbolic/strikepy.py

@@ -27,9 +27,7 @@ import tqdm
 from sympy import Matrix
 from sympy.matrices import zeros
 
-from mxlpy.model import Model
-
-from .symbolic_model import SymbolicModel, to_symbolic_model
+from .symbolic_model import SymbolicModel
 
 __all__ = [
     "Options",

mxlpy/types.py

@@ -22,6 +22,7 @@ from dataclasses import dataclass, field
 import pandas as pd
 
 __all__ = [
+    "AbstractEstimator",
     "AbstractSurrogate",
     "Array",
     "ArrayLike",
@@ -45,9 +46,6 @@ __all__ = [
     "unwrap2",
 ]
 
-# Re-exporting some types here, because their imports have
-# changed between Python versions and I have no interest in
-# fixing it in every file
 from collections.abc import Callable, Iterator, Mapping
 from typing import TYPE_CHECKING, Any, ParamSpec, Protocol, TypeVar, cast
 
@@ -444,7 +442,8 @@ class AbstractSurrogate:
 
     """
 
-    args: list[str] = field(default_factory=list)
+    args: list[str]
+    outputs: list[str]
     stoichiometries: dict[str, dict[str, float]] = field(default_factory=dict)
 
     @abstractmethod
@@ -455,7 +454,7 @@ class AbstractSurrogate:
         """Predict outputs based on input data."""
         return dict(
             zip(
-                self.stoichiometries,
+                self.outputs,
                 self.predict_raw(y),
                 strict=True,
             )
@@ -475,7 +474,7 @@ class AbstractSurrogate:
         args: pd.DataFrame,
     ) -> None:
         """Predict outputs based on input data."""
-        args[list(self.stoichiometries)] = pd.DataFrame(
+        args[self.outputs] = pd.DataFrame(
             [self.predict(y) for y in args.loc[:, self.args].to_numpy()],
             index=args.index,
             dtype=float,
@@ -491,4 +490,15 @@ class MockSurrogate(AbstractSurrogate):
         y: np.ndarray,
     ) -> dict[str, float]:
         """Predict outputs based on input data."""
-        return dict(zip(self.stoichiometries, y, strict=True))
+        return dict(zip(self.outputs, y, strict=True))
+
+
+@dataclass(kw_only=True)
+class AbstractEstimator:
+    """Abstract class for parameter estimation using neural networks."""
+
+    parameter_names: list[str]
+
+    @abstractmethod
+    def predict(self, features: pd.Series | pd.DataFrame) -> pd.DataFrame:
+        """Predict the target values for the given features."""

{mxlpy-0.16.0.dist-info → mxlpy-0.18.0.dist-info}/METADATA

@@ -1,17 +1,17 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.16.0
+Version: 0.18.0
 Summary: A package to build metabolic models
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
-License-Expression: GPL-3.0-or-later
+License-Expression: MIT
 License-File: LICENSE
 Keywords: metabolic,modelling,ode
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: OS Independent
@@ -47,7 +47,6 @@ Requires-Dist: jupyter>=1.1.1; extra == 'dev'
 Requires-Dist: mkdocs-jupyter>=0.25.1; extra == 'dev'
 Requires-Dist: mkdocs-material>=9.5.42; extra == 'dev'
 Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
-Requires-Dist: mypy>=1.13.0; extra == 'dev'
 Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
 Requires-Dist: pyright>=1.1.387; extra == 'dev'
 Requires-Dist: pytest-cov>=5.0.0; extra == 'dev'
@@ -68,7 +67,7 @@ Description-Content-Type: text/markdown
 
 [![pypi](https://img.shields.io/pypi/v/mxlpy.svg)](https://pypi.python.org/pypi/mxlpy)
 [![docs][docs-badge]][docs]
-![License](https://img.shields.io/badge/license-GPL--3.0-blue?style=flat-square)
+![License](https://img.shields.io/badge/license-MIT-blue?style=flat-square)
 ![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fgist.github.com%2Fmarvinvanaalst%2F98ab3ce1db511de42f9871e91d85e4cd%2Fraw%2Fcoverage.json&query=%24.message&label=Coverage&color=%24.color&suffix=%20%25)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
@@ -91,10 +90,10 @@ pixi add --pypi mxlpy[torch]
 
 ## How to cite
 
-If you use this software in your scientific work, please cite [this article](...):
+If you use this software in your scientific work, please cite [this article](https://doi.org/10.1101/2025.05.06.652335):
 
-- [doi](https://doi.org/)
-- [bibtex file](https://fillme.out)
+- [doi](https://doi.org/10.1101/2025.05.06.652335)
+- [bibtex file](https://github.com/Computational-Biology-Aachen/MxlPy/citation.bibtex)
 
 
 ## Development setup

{mxlpy-0.16.0.dist-info → mxlpy-0.18.0.dist-info}/RECORD

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 mxlpy/label_map.py,sha256=urv-QTb0MUEKjwWvKtJSB8H2kvhLn1EKfRIH7awQQ8Y,17769
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 mxlpy/sbml/_mathml.py,sha256=bNk9RQ_NQFDhY1R354p-gwqqHaIiyAwZ1xLPHHhiguQ,24436
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 mxlpy/sbml/_unit_conversion.py,sha256=dW_I6_Ou09ccwnp6LIdrPriIQnQUK5lJcjzM2Fawm6U,1927
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mxlpy-0.18.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2025] [Marvin van Aalst, Anna Matuszyńska]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.