mxlpy 0.16.0__py3-none-any.whl → 0.17.0__py3-none-any.whl

mxlpy/sbml/_import.py

@@ -12,7 +12,7 @@ import libsbml
 import numpy as np  # noqa: F401  # models might need it
 import sympy
 
-from mxlpy.model import Model, _sort_dependencies
+from mxlpy.model import Dependency, Model, _sort_dependencies
 from mxlpy.paths import default_tmp_dir
 from mxlpy.sbml._data import (
     AtomicUnit,
@@ -522,7 +522,10 @@ def _codgen(name: str, sbml: Parser) -> Path:
         ^ set(variables)
         ^ set(sbml.derived)
         | {"time"},
-        elements=[(k, set(v.args)) for k, v in sbml.initial_assignment.items()],
+        elements=[
+            Dependency(name=k, required=set(v.args), provided={k})
+            for k, v in sbml.initial_assignment.items()
+        ],
     )
 
     if len(initial_assignment_order) > 0:

mxlpy/surrogates/__init__.py

@@ -19,13 +19,14 @@ from __future__ import annotations
 import contextlib
 
 with contextlib.suppress(ImportError):
-    from ._torch import TorchSurrogate, train_torch_surrogate
+    from ._torch import Torch, TorchTrainer, train_torch
 
-from ._poly import PolySurrogate, train_polynomial_surrogate
+from ._poly import Polynomial, train_polynomial
 
 __all__ = [
-    "PolySurrogate",
-    "TorchSurrogate",
-    "train_polynomial_surrogate",
-    "train_torch_surrogate",
+    "Polynomial",
+    "Torch",
+    "TorchTrainer",
+    "train_polynomial",
+    "train_torch",
 ]

mxlpy/surrogates/_poly.py

@@ -9,9 +9,9 @@ from numpy import polynomial
 from mxlpy.types import AbstractSurrogate, ArrayLike
 
 __all__ = [
-    "PolySurrogate",
+    "Polynomial",
     "PolynomialExpansion",
-    "train_polynomial_surrogate",
+    "train_polynomial",
 ]
 
 # define custom type
@@ -26,23 +26,24 @@ PolynomialExpansion = (
 
 
 @dataclass(kw_only=True)
-class PolySurrogate(AbstractSurrogate):
+class Polynomial(AbstractSurrogate):
     model: PolynomialExpansion
 
     def predict_raw(self, y: np.ndarray) -> np.ndarray:
         return self.model(y)
 
 
-def train_polynomial_surrogate(
-    feature: ArrayLike,
-    target: ArrayLike,
+def train_polynomial(
+    feature: ArrayLike | pd.Series,
+    target: ArrayLike | pd.Series,
     series: Literal[
         "Power", "Chebyshev", "Legendre", "Laguerre", "Hermite", "HermiteE"
     ] = "Power",
     degrees: Iterable[int] = (1, 2, 3, 4, 5, 6, 7),
     surrogate_args: list[str] | None = None,
+    surrogate_outputs: list[str] | None = None,
     surrogate_stoichiometries: dict[str, dict[str, float]] | None = None,
-) -> tuple[PolySurrogate, pd.DataFrame]:
+) -> tuple[Polynomial, pd.DataFrame]:
     """Train a surrogate model based on function series expansion.
 
     Args:
@@ -51,7 +52,8 @@ def train_polynomial_surrogate(
         series: Base functions for the surrogate model
         degrees: Degrees of the polynomial to fit to the data.
         surrogate_args: Additional arguments for the surrogate model.
-        surrogate_stoichiometries: Stoichiometries for the surrogate model.
+        surrogate_outputs: Names of the surrogate model outputs.
+        surrogate_stoichiometries: Mapping of variables to their stoichiometries
 
     Returns:
         PolySurrogate: Polynomial surrogate model.
@@ -83,9 +85,10 @@ def train_polynomial_surrogate(
     # Choose the model with the lowest AIC
     model = models[np.argmin(score)]
     return (
-        PolySurrogate(
+        Polynomial(
             model=model,
             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 {},

mxlpy/surrogates/_torch.py

@@ -1,5 +1,6 @@
 from collections.abc import Callable
 from dataclasses import dataclass
+from typing import Self
 
 import numpy as np
 import pandas as pd
@@ -12,14 +13,32 @@ from torch.optim.optimizer import ParamsT
 from mxlpy.nn._torch import MLP, DefaultDevice
 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:
@@ -48,6 +67,91 @@ class TorchSurrogate(AbstractSurrogate):
             ).numpy()
 
 
+@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:
+        if batch_size is None:
+            losses = _train_full(
+                aprox=self.approximator,
+                features=self.features,
+                targets=self.targets,
+                epochs=epochs,
+                optimizer=self.optimizer,
+                device=self.device,
+                loss_fn=self.loss_fn,
+            )
+        else:
+            losses = _train_batched(
+                aprox=self.approximator,
+                features=self.features,
+                targets=self.targets,
+                epochs=epochs,
+                optimizer=self.optimizer,
+                device=self.device,
+                batch_size=batch_size,
+                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_batched(
     aprox: nn.Module,
     features: pd.DataFrame,
@@ -56,6 +160,7 @@ def _train_batched(
     optimizer: Adam,
     device: torch.device,
     batch_size: int,
+    loss_fn: LossFn,
 ) -> pd.Series:
     """Train the neural network using mini-batch gradient descent.
 
@@ -67,6 +172,7 @@ def _train_batched(
         optimizer: Optimizer for training.
         device: torch device
         batch_size: Size of mini-batches for training.
+        loss_fn: Loss function
 
     Returns:
         pd.Series: Series containing the training loss history.
@@ -79,7 +185,7 @@ def _train_batched(
         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 = loss_fn(aprox(X), Y)
         loss.backward()
         optimizer.step()
         losses[i] = loss.detach().numpy()
@@ -93,6 +199,7 @@ def _train_full(
     epochs: int,
     optimizer: Adam,
     device: torch.device,
+    loss_fn: Callable,
 ) -> pd.Series:
     """Train the neural network using full-batch gradient descent.
 
@@ -103,6 +210,7 @@ def _train_full(
         epochs: Number of training epochs.
         optimizer: Optimizer for training.
         device: Torch device
+        loss_fn: Loss function
 
     Returns:
         pd.Series: Series containing the training loss history.
@@ -114,24 +222,26 @@ def _train_full(
     losses = {}
     for i in tqdm.trange(epochs):
         optimizer.zero_grad()
-        loss = torch.mean(torch.abs(aprox(X) - Y))
+        loss = loss_fn(aprox(X), Y)
         loss.backward()
         optimizer.step()
         losses[i] = loss.detach().numpy()
     return pd.Series(losses, dtype=float)
 
 
-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 +253,38 @@ 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",
@@ -444,7 +445,8 @@ 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 +457,7 @@ class AbstractSurrogate:
         """Predict outputs based on input data."""
         return dict(
             zip(
-                self.stoichiometries,
+                self.outputs,
                 self.predict_raw(y),
                 strict=True,
             )
@@ -475,7 +477,7 @@ 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 +493,15 @@ 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-0.17.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.16.0
+Version: 0.17.0
 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>
@@ -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'

{mxlpy-0.16.0.dist-info → mxlpy-0.17.0.dist-info}/RECORD

@@ -1,50 +1,51 @@
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 mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
 mxlpy/fit.py,sha256=LwSoLfNVrqSlTtuUApwH36LjzGU0HLs4C_2qqTTjXFE,7859
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 mxlpy/identify.py,sha256=af52SCG4nlY9sSw22goaIheuvXR09QYK4ksCT24QHWI,1946
 mxlpy/label_map.py,sha256=urv-QTb0MUEKjwWvKtJSB8H2kvhLn1EKfRIH7awQQ8Y,17769
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