Add SINDy model (#660)

docs/source/_rst/_code.rst

@@ -106,6 +106,7 @@ Models
     GraphNeuralKernel <model/graph_neural_operator_integral_kernel.rst>
     PirateNet <model/pirate_network.rst>
     EquivariantGraphNeuralOperator <model/equivariant_graph_neural_operator.rst>
+    SINDy <model/sindy.rst>
 
 Blocks
 -------------

docs/source/_rst/model/sindy.rst

@@ -0,0 +1,7 @@
+SINDy
+=======================
+.. currentmodule:: pina.model.sindy
+
+.. autoclass:: SINDy
+   :members:
+   :show-inheritance:

pina/model/__init__.py

@@ -15,6 +15,7 @@ __all__ = [
     "GraphNeuralOperator",
     "PirateNet",
     "EquivariantGraphNeuralOperator",
+    "SINDy",
 ]
 
 from .feed_forward import FeedForward, ResidualFeedForward
@@ -28,3 +29,4 @@ from .spline import Spline
 from .graph_neural_operator import GraphNeuralOperator
 from .pirate_network import PirateNet
 from .equivariant_graph_neural_operator import EquivariantGraphNeuralOperator
+from .sindy import SINDy

pina/model/sindy.py

@@ -0,0 +1,102 @@
+"""Module for the SINDy model class."""
+
+from typing import Callable
+import torch
+from ..utils import check_consistency, check_positive_integer
+
+
+class SINDy(torch.nn.Module):
+    r"""
+    SINDy model class.
+
+    The Sparse Identification of Nonlinear Dynamics (SINDy) model identifies the
+    governing equations of a dynamical system from data by learning a sparse
+    linear combination of non-linear candidate functions.
+
+    The output of the model is expressed as product of a library matrix and a
+    coefficient matrix:
+
+    .. math::
+
+        \dot{X} = \Theta(X) \Xi
+
+    where:
+      - :math:`X \in \mathbb{R}^{B \times D}` is the input snapshots of the
+        system state. Here, :math:`B` is the batch size and :math:`D` is the
+        number of state variables.
+      - :math:`\Theta(X) \in \mathbb{R}^{B \times L}` is the library matrix
+        obtained by evaluating a set of candidate functions on the input data.
+        Here, :math:`L` is the number of candidate functions in the library.
+      - :math:`\Xi \in \mathbb{R}^{L \times D}` is the learned coefficient
+        matrix that defines the sparse model.
+
+    .. seealso::
+
+        **Original reference**:
+        Brunton, S.L., Proctor, J.L., and Kutz, J.N. (2016).
+        *Discovering governing equations from data: Sparse identification of
+        non-linear dynamical systems.*
+        Proceedings of the National Academy of Sciences, 113(15), 3932-3937.
+        DOI: `10.1073/pnas.1517384113
+        <https://doi.org/10.1073/pnas.1517384113>`_
+    """
+
+    def __init__(self, library, output_dimension):
+        """
+        Initialization of the :class:`SINDy` class.
+
+        :param list[Callable] library: The collection of candidate functions
+            used to construct the library matrix. Each function must accept an
+            input tensor of shape ``[..., D]`` and return a tensor of shape
+            ``[..., 1]``.
+        :param int output_dimension: The number of output variables, typically
+            the number of state derivatives. It determines the number of columns
+            in the coefficient matrix.
+        :raises ValueError: If ``library`` is not a list of callables.
+        :raises AssertionError: If ``output_dimension`` is not a positive
+            integer.
+        """
+        super().__init__()
+
+        # Check consistency
+        check_positive_integer(output_dimension, strict=True)
+        check_consistency(library, Callable)
+        if not isinstance(library, list):
+            raise ValueError("`library` must be a list of callables.")
+
+        # Initialization
+        self._library = library
+        self._coefficients = torch.nn.Parameter(
+            torch.zeros(len(library), output_dimension)
+        )
+
+    def forward(self, x):
+        """
+        Forward pass of the :class:`SINDy` model.
+
+        :param torch.Tensor x: The input batch of state variables.
+        :return: The predicted time derivatives of the state variables.
+        :rtype: torch.Tensor
+        """
+        theta = torch.stack([f(x) for f in self.library], dim=-2)
+        return torch.einsum("...li , lo -> ...o", theta, self.coefficients)
+
+    @property
+    def library(self):
+        """
+        The library of candidate functions.
+
+        :return: The library.
+        :rtype: list[Callable]
+        """
+        return self._library
+
+    @property
+    def coefficients(self):
+        """
+        The coefficients of the model.
+
+        :return: The coefficients.
+        :rtype: torch.Tensor
+        """
+        return self._coefficients

tests/test_model/test_sindy.py

@@ -0,0 +1,55 @@
+import torch
+import pytest
+from pina.model import SINDy
+
+# Define a simple library of candidate functions and some test data
+library = [lambda x: torch.pow(x, 2), lambda x: torch.sin(x)]
+
+
+@pytest.mark.parametrize("data", [torch.rand((20, 1)), torch.rand((5, 20, 1))])
+def test_constructor(data):
+    SINDy(library, data.shape[-1])
+
+    # Should fail if output_dimension is not a positive integer
+    with pytest.raises(AssertionError):
+        SINDy(library, "not_int")
+    with pytest.raises(AssertionError):
+        SINDy(library, -1)
+
+    # Should fail if library is not a list
+    with pytest.raises(ValueError):
+        SINDy(lambda x: torch.pow(x, 2), 3)
+
+    # Should fail if library is not a list of callables
+    with pytest.raises(ValueError):
+        SINDy([1, 2, 3], 3)
+
+
+@pytest.mark.parametrize("data", [torch.rand((20, 1)), torch.rand((5, 20, 1))])
+def test_forward(data):
+
+    # Define model
+    model = SINDy(library, data.shape[-1])
+    with torch.no_grad():
+        model.coefficients.data.fill_(1.0)
+
+    # Evaluate model
+    output_ = model(data)
+    vals = data.pow(2) + torch.sin(data)
+
+    print(data.shape, output_.shape, vals.shape)
+
+    assert output_.shape == data.shape
+    assert torch.allclose(output_, vals, atol=1e-6, rtol=1e-6)
+
+
+@pytest.mark.parametrize("data", [torch.rand((20, 1)), torch.rand((5, 20, 1))])
+def test_backward(data):
+
+    # Define and evaluate model
+    model = SINDy(library, data.shape[-1])
+    output_ = model(data.requires_grad_())
+
+    loss = output_.mean()
+    loss.backward()
+    assert data.grad.shape == data.shape