Implement batched convolve1d (#1318)

Co-authored-by: Jesse Grabowski <jessegrabowski@gmail.com>
Co-authored-by: Rob Zinkov <zaxtax@users.noreply.github.com>

Author: 3 people

pytensor/link/jax/dispatch/__init__.py

@@ -14,6 +14,7 @@
 import pytensor.link.jax.dispatch.scalar
 import pytensor.link.jax.dispatch.scan
 import pytensor.link.jax.dispatch.shape
+import pytensor.link.jax.dispatch.signal
 import pytensor.link.jax.dispatch.slinalg
 import pytensor.link.jax.dispatch.sort
 import pytensor.link.jax.dispatch.sparse

pytensor/link/jax/dispatch/signal/__init__.py

@@ -0,0 +1 @@
+import pytensor.link.jax.dispatch.signal.conv

pytensor/link/jax/dispatch/signal/conv.py

@@ -0,0 +1,14 @@
+import jax
+
+from pytensor.link.jax.dispatch import jax_funcify
+from pytensor.tensor.signal.conv import Conv1d
+
+
+@jax_funcify.register(Conv1d)
+def jax_funcify_Conv1d(op, node, **kwargs):
+    mode = op.mode
+
+    def conv1d(data, kernel):
+        return jax.numpy.convolve(data, kernel, mode=mode)
+
+    return conv1d

pytensor/link/numba/dispatch/__init__.py

@@ -9,9 +9,11 @@
 import pytensor.link.numba.dispatch.random
 import pytensor.link.numba.dispatch.scan
 import pytensor.link.numba.dispatch.scalar
+import pytensor.link.numba.dispatch.signal
 import pytensor.link.numba.dispatch.slinalg
 import pytensor.link.numba.dispatch.sparse
 import pytensor.link.numba.dispatch.subtensor
 import pytensor.link.numba.dispatch.tensor_basic
 
+
 # isort: on

pytensor/link/numba/dispatch/signal/__init__.py

@@ -0,0 +1 @@
+import pytensor.link.numba.dispatch.signal.conv

pytensor/link/numba/dispatch/signal/conv.py

@@ -0,0 +1,16 @@
+import numpy as np
+
+from pytensor.link.numba.dispatch import numba_funcify
+from pytensor.link.numba.dispatch.basic import numba_njit
+from pytensor.tensor.signal.conv import Conv1d
+
+
+@numba_funcify.register(Conv1d)
+def numba_funcify_Conv1d(op, node, **kwargs):
+    mode = op.mode
+
+    @numba_njit
+    def conv1d(data, kernel):
+        return np.convolve(data, kernel, mode=mode)
+
+    return conv1d

pytensor/tensor/__init__.py

@@ -116,6 +116,7 @@ def _get_vector_length_Constant(op: Op | Variable, var: Constant) -> int:
 # isort: off
 from pytensor.tensor import linalg
 from pytensor.tensor import special
+from pytensor.tensor import signal
 
 # For backward compatibility
 from pytensor.tensor import nlinalg

pytensor/tensor/signal/__init__.py

@@ -0,0 +1,4 @@
+from pytensor.tensor.signal.conv import convolve1d
+
+
+__all__ = ("convolve1d",)

pytensor/tensor/signal/conv.py

@@ -0,0 +1,132 @@
+from typing import TYPE_CHECKING, Literal, cast
+
+from numpy import convolve as numpy_convolve
+
+from pytensor.graph import Apply, Op
+from pytensor.scalar.basic import upcast
+from pytensor.tensor.basic import as_tensor_variable, join, zeros
+from pytensor.tensor.blockwise import Blockwise
+from pytensor.tensor.math import maximum, minimum
+from pytensor.tensor.type import vector
+from pytensor.tensor.variable import TensorVariable
+
+
+if TYPE_CHECKING:
+    from pytensor.tensor import TensorLike
+
+
+class Conv1d(Op):
+    __props__ = ("mode",)
+    gufunc_signature = "(n),(k)->(o)"
+
+    def __init__(self, mode: Literal["full", "valid"] = "full"):
+        if mode not in ("full", "valid"):
+            raise ValueError(f"Invalid mode: {mode}")
+        self.mode = mode
+
+    def make_node(self, in1, in2):
+        in1 = as_tensor_variable(in1)
+        in2 = as_tensor_variable(in2)
+
+        assert in1.ndim == 1
+        assert in2.ndim == 1
+
+        dtype = upcast(in1.dtype, in2.dtype)
+
+        n = in1.type.shape[0]
+        k = in2.type.shape[0]
+
+        if n is None or k is None:
+            out_shape = (None,)
+        elif self.mode == "full":
+            out_shape = (n + k - 1,)
+        else:  # mode == "valid":
+            out_shape = (max(n, k) - min(n, k) + 1,)
+
+        out = vector(dtype=dtype, shape=out_shape)
+        return Apply(self, [in1, in2], [out])
+
+    def perform(self, node, inputs, outputs):
+        # We use numpy_convolve as that's what scipy would use if method="direct" was passed.
+        # And mode != "same", which this Op doesn't cover anyway.
+        outputs[0][0] = numpy_convolve(*inputs, mode=self.mode)
+
+    def infer_shape(self, fgraph, node, shapes):
+        in1_shape, in2_shape = shapes
+        n = in1_shape[0]
+        k = in2_shape[0]
+        if self.mode == "full":
+            shape = n + k - 1
+        else:  # mode == "valid":
+            shape = maximum(n, k) - minimum(n, k) + 1
+        return [[shape]]
+
+    def L_op(self, inputs, outputs, output_grads):
+        in1, in2 = inputs
+        [grad] = output_grads
+
+        if self.mode == "full":
+            valid_conv = type(self)(mode="valid")
+            in1_bar = valid_conv(grad, in2[::-1])
+            in2_bar = valid_conv(grad, in1[::-1])
+
+        else:  # mode == "valid":
+            full_conv = type(self)(mode="full")
+            n = in1.shape[0]
+            k = in2.shape[0]
+            kmn = maximum(0, k - n)
+            nkm = maximum(0, n - k)
+            # We need mode="full" if k >= n else "valid" for `in1_bar` (opposite for `in2_bar`), but mode is not symbolic.
+            # Instead, we always use mode="full" and slice the result so it behaves like "valid" for the input that's shorter.
+            in1_bar = full_conv(grad, in2[::-1])
+            in1_bar = in1_bar[kmn : in1_bar.shape[0] - kmn]
+            in2_bar = full_conv(grad, in1[::-1])
+            in2_bar = in2_bar[nkm : in2_bar.shape[0] - nkm]
+
+        return [in1_bar, in2_bar]
+
+
+def convolve1d(
+    in1: "TensorLike",
+    in2: "TensorLike",
+    mode: Literal["full", "valid", "same"] = "full",
+) -> TensorVariable:
+    """Convolve two one-dimensional arrays.
+
+    Convolve in1 and in2, with the output size determined by the mode argument.
+
+    Parameters
+    ----------
+    in1 : (..., N,) tensor_like
+        First input.
+    in2 : (..., M,) tensor_like
+        Second input.
+    mode : {'full', 'valid', 'same'}, optional
+        A string indicating the size of the output:
+        - 'full': The output is the full discrete linear convolution of the inputs, with shape (..., N+M-1,).
+        - 'valid': The output consists only of elements that do not rely on zero-padding, with shape (..., max(N, M) - min(N, M) + 1,).
+        - 'same': The output is the same size as in1, centered with respect to the 'full' output.
+
+    Returns
+    -------
+    out: tensor_variable
+        The discrete linear convolution of in1 with in2.
+
+    """
+    in1 = as_tensor_variable(in1)
+    in2 = as_tensor_variable(in2)
+
+    if mode == "same":
+        # We implement "same" as "valid" with padded `in1`.
+        in1_batch_shape = tuple(in1.shape)[:-1]
+        zeros_left = in2.shape[0] // 2
+        zeros_right = (in2.shape[0] - 1) // 2
+        in1 = join(
+            -1,
+            zeros((*in1_batch_shape, zeros_left), dtype=in2.dtype),
+            in1,
+            zeros((*in1_batch_shape, zeros_right), dtype=in2.dtype),
+        )
+        mode = "valid"
+
+    return cast(TensorVariable, Blockwise(Conv1d(mode=mode))(in1, in2))

tests/link/jax/signal/__init__.py

@@ -0,0 +1,18 @@
+import numpy as np
+import pytest
+
+from pytensor.tensor import dmatrix
+from pytensor.tensor.signal import convolve1d
+from tests.link.jax.test_basic import compare_jax_and_py
+
+
+@pytest.mark.parametrize("mode", ["full", "valid", "same"])
+def test_convolve1d(mode):
+    x = dmatrix("x")
+    y = dmatrix("y")
+    out = convolve1d(x[None], y[:, None], mode=mode)
+
+    rng = np.random.default_rng()
+    test_x = rng.normal(size=(3, 5))
+    test_y = rng.normal(size=(7, 11))
+    compare_jax_and_py([x, y], out, [test_x, test_y])

tests/link/jax/signal/test_conv.py

@@ -0,0 +1,22 @@
+import numpy as np
+import pytest
+
+from pytensor.tensor import dmatrix
+from pytensor.tensor.signal import convolve1d
+from tests.link.numba.test_basic import compare_numba_and_py
+
+
+pytestmark = pytest.mark.filterwarnings("error")
+
+
+@pytest.mark.parametrize("mode", ["full", "valid", "same"])
+def test_convolve1d(mode):
+    x = dmatrix("x")
+    y = dmatrix("y")
+    out = convolve1d(x[None], y[:, None], mode=mode)
+
+    rng = np.random.default_rng()
+    test_x = rng.normal(size=(3, 5))
+    test_y = rng.normal(size=(7, 11))
+    # Blockwise dispatch for numba can't be run on object mode
+    compare_numba_and_py([x, y], out, [test_x, test_y], eval_obj_mode=False)

tests/link/numba/signal/test_conv.py

@@ -0,0 +1,49 @@
+from functools import partial
+
+import numpy as np
+import pytest
+from scipy.signal import convolve as scipy_convolve
+
+from pytensor import config, function
+from pytensor.tensor import matrix, vector
+from pytensor.tensor.signal.conv import convolve1d
+from tests import unittest_tools as utt
+
+
+@pytest.mark.parametrize("kernel_shape", [3, 5, 8], ids=lambda x: f"kernel_shape={x}")
+@pytest.mark.parametrize("data_shape", [3, 5, 8], ids=lambda x: f"data_shape={x}")
+@pytest.mark.parametrize("mode", ["full", "valid", "same"])
+def test_convolve1d(mode, data_shape, kernel_shape):
+    data = vector("data")
+    kernel = vector("kernel")
+    op = partial(convolve1d, mode=mode)
+
+    rng = np.random.default_rng((26, kernel_shape, data_shape, sum(map(ord, mode))))
+    data_val = rng.normal(size=data_shape).astype(data.dtype)
+    kernel_val = rng.normal(size=kernel_shape).astype(kernel.dtype)
+
+    fn = function([data, kernel], op(data, kernel))
+    np.testing.assert_allclose(
+        fn(data_val, kernel_val),
+        scipy_convolve(data_val, kernel_val, mode=mode),
+        rtol=1e-6 if config.floatX == "float32" else 1e-15,
+    )
+    utt.verify_grad(op=lambda x: op(x, kernel_val), pt=[data_val])
+
+
+def test_convolve1d_batch():
+    x = matrix("data")
+    y = matrix("kernel")
+    out = convolve1d(x, y)
+
+    rng = np.random.default_rng(38)
+    x_test = rng.normal(size=(2, 8)).astype(x.dtype)
+    y_test = x_test[::-1]
+
+    res = out.eval({x: x_test, y: y_test})
+    # Second entry of x, y are just y, x respectively,
+    # so res[0] and res[1] should be identical.
+    rtol = 1e-6 if config.floatX == "float32" else 1e-15
+    res_np = np.convolve(x_test[0], y_test[0])
+    np.testing.assert_allclose(res[0], res_np, rtol=rtol)
+    np.testing.assert_allclose(res[1], res_np, rtol=rtol)