Merge pull request #77 from mallamanis/master

Implement scatter_logsumexp, scatter_softmax, scatter_log_softmax

README.md

@@ -34,6 +34,12 @@ The package consists of the following operations:
 * [**Scatter Std**](https://pytorch-scatter.readthedocs.io/en/latest/functions/std.html)
 * [**Scatter Min**](https://pytorch-scatter.readthedocs.io/en/latest/functions/min.html)
 * [**Scatter Max**](https://pytorch-scatter.readthedocs.io/en/latest/functions/max.html)
+* [**Scatter LogSumExp**](https://pytorch-scatter.readthedocs.io/en/latest/functions/logsumexp.html)
+
+In addition, we provide composite functions which make use of `scatter_*` operations under the hood:
+
+* [**Scatter Softmax**](https://pytorch-scatter.readthedocs.io/en/latest/composite/softmax.html#torch_scatter.composite.scatter_softmax)
+* [**Scatter LogSoftmax**](https://pytorch-scatter.readthedocs.io/en/latest/composite/softmax.html#torch_scatter.composite.scatter_log_softmax)
 
 All included operations are broadcastable, work on varying data types, and are implemented both for CPU and GPU with corresponding backward implementations.
 

docs/source/composite/softmax.rst

+Scatter Softmax
+===============
+
+.. automodule:: torch_scatter.composite
+   :noindex:
+
+.. autofunction:: scatter_softmax
+
+.. autofunction:: scatter_log_softmax

docs/source/functions/logsumexp.rst

+Scatter LogSumExp
+=================
+
+.. automodule:: torch_scatter
+   :noindex:
+
+.. autofunction:: scatter_logsumexp

docs/source/index.rst

@@ -14,6 +14,7 @@ All included operations are broadcastable, work on varying data types, and are i
    :caption: Package reference
 
    functions/*
+   composite/*
 
 Indices and tables
 ==================

test/composite/test_softmax.py

+from itertools import product
+
+import pytest
+import torch
+from torch_scatter.composite import scatter_log_softmax, scatter_softmax
+
+from test.utils import devices, tensor, grad_dtypes
+
+
+@pytest.mark.parametrize('dtype,device', product(grad_dtypes, devices))
+def test_softmax(dtype, device):
+    src = tensor([0.2, 0, 0.2, -2.1, 3.2, 7, -1, float('-inf')], dtype, device)
+    index = tensor([0, 1, 0, 1, 1, 2, 4, 4], torch.long, device)
+
+    out = scatter_softmax(src, index)
+
+    out0 = torch.softmax(torch.tensor([0.2, 0.2], dtype=dtype), dim=-1)
+    out1 = torch.softmax(torch.tensor([0, -2.1, 3.2], dtype=dtype), dim=-1)
+    out2 = torch.softmax(torch.tensor([7], dtype=dtype), dim=-1)
+    out4 = torch.softmax(torch.tensor([-1, float('-inf')], dtype=dtype),
+                         dim=-1)
+
+    expected = torch.stack([
+        out0[0], out1[0], out0[1], out1[1], out1[2], out2[0], out4[0], out4[1]
+    ], dim=0)
+
+    assert torch.allclose(out, expected)
+
+
+@pytest.mark.parametrize('dtype,device', product(grad_dtypes, devices))
+def test_log_softmax(dtype, device):
+    src = tensor([0.2, 0, 0.2, -2.1, 3.2, 7, -1, float('-inf')], dtype, device)
+    index = tensor([0, 1, 0, 1, 1, 2, 4, 4], torch.long, device)
+
+    out = scatter_log_softmax(src, index)
+
+    out0 = torch.log_softmax(torch.tensor([0.2, 0.2], dtype=dtype), dim=-1)
+    out1 = torch.log_softmax(torch.tensor([0, -2.1, 3.2], dtype=dtype), dim=-1)
+    out2 = torch.log_softmax(torch.tensor([7], dtype=dtype), dim=-1)
+    out4 = torch.log_softmax(torch.tensor([-1, float('-inf')], dtype=dtype),
+                             dim=-1)
+
+    expected = torch.stack([
+        out0[0], out1[0], out0[1], out1[1], out1[2], out2[0], out4[0], out4[1]
+    ], dim=0)
+
+    assert torch.allclose(out, expected)

test/test_logsumexp.py

+from itertools import product
+
+import torch
+import pytest
+from torch_scatter import scatter_logsumexp
+
+from .utils import devices, tensor, grad_dtypes
+
+
+@pytest.mark.parametrize('dtype,device', product(grad_dtypes, devices))
+def test_logsumexp(dtype, device):
+    src = tensor([0.5, 0, 0.5, -2.1, 3.2, 7, -1, float('-inf')], dtype, device)
+    index = tensor([0, 1, 0, 1, 1, 2, 4, 4], torch.long, device)
+
+    out = scatter_logsumexp(src, index)
+
+    out0 = torch.logsumexp(torch.tensor([0.5, 0.5], dtype=dtype), dim=-1)
+    out1 = torch.logsumexp(torch.tensor([0, -2.1, 3.2], dtype=dtype), dim=-1)
+    out2 = torch.logsumexp(torch.tensor(7, dtype=dtype), dim=-1)
+    out3 = torch.tensor(torch.finfo(dtype).min, dtype=dtype)
+    out4 = torch.tensor(-1, dtype=dtype)
+
+    expected = torch.stack([out0, out1, out2, out3, out4], dim=0)
+    assert torch.allclose(out, expected)

torch_scatter/__init__.py

@@ -6,6 +6,8 @@ from .mean import scatter_mean
 from .std import scatter_std
 from .max import scatter_max
 from .min import scatter_min
+from .logsumexp import scatter_logsumexp
+import torch_scatter.composite
 
 __version__ = '1.3.2'
 
@@ -18,5 +20,7 @@ __all__ = [
     'scatter_std',
     'scatter_max',
     'scatter_min',
+    'scatter_logsumexp',
+    'torch_scatter',
     '__version__',
 ]

torch_scatter/composite/__init__.py

+from .softmax import scatter_log_softmax, scatter_softmax
+
+__all__ = [
+    'scatter_softmax',
+    'scatter_log_softmax',
+]

torch_scatter/composite/softmax.py

+import torch
+
+from torch_scatter import scatter_add, scatter_max
+
+
+def scatter_softmax(src, index, dim=-1, eps=1e-12):
+    r"""
+    Softmax operation over all values in :attr:`src` tensor that share indices
+    specified in the :attr:`index` tensor along a given axis :attr:`dim`.
+
+    For one-dimensional tensors, the operation computes
+
+    .. math::
+        \mathrm{out}_i = {\textrm{softmax}(\mathrm{src})}_i =
+        \frac{\exp(\mathrm{src}_i)}{\sum_j \exp(\mathrm{src}_j)}
+
+    where :math:`\sum_j` is over :math:`j` such that
+    :math:`\mathrm{index}_j = i`.
+
+    Args:
+        src (Tensor): The source tensor.
+        index (LongTensor): The indices of elements to scatter.
+        dim (int, optional): The axis along which to index.
+            (default: :obj:`-1`)
+        eps (float, optional): Small value to ensure numerical stability.
+            (default: :obj:`1e-12`)
+
+    :rtype: :class:`Tensor`
+    """
+    if not torch.is_floating_point(src):
+        raise ValueError('`scatter_softmax` can only be computed over tensors '
+                         'with floating point data types.')
+
+    max_value_per_index, _ = scatter_max(src, index, dim=dim, fill_value=0)
+    max_per_src_element = max_value_per_index.gather(dim, index)
+
+    recentered_scores = src - max_per_src_element
+    recentered_scores_exp = recentered_scores.exp()
+
+    sum_per_index = scatter_add(recentered_scores_exp, index, dim=dim)
+    normalizing_constants = (sum_per_index + eps).gather(dim, index)
+
+    return recentered_scores_exp / normalizing_constants
+
+
+def scatter_log_softmax(src, index, dim=-1, eps=1e-12):
+    r"""
+    Log-softmax operation over all values in :attr:`src` tensor that share
+    indices specified in the :attr:`index` tensor along a given axis
+    :attr:`dim`.
+
+    For one-dimensional tensors, the operation computes
+
+    .. math::
+        \mathrm{out}_i = {\textrm{log_softmax}(\mathrm{src})}_i =
+        \log \left( \frac{\exp(\mathrm{src}_i)}{\sum_j \exp(\mathrm{src}_j)}
+        \right)
+
+    where :math:`\sum_j` is over :math:`j` such that
+    :math:`\mathrm{index}_j = i`.
+
+    Args:
+        src (Tensor): The source tensor.
+        index (LongTensor): The indices of elements to scatter.
+        dim (int, optional): The axis along which to index.
+            (default: :obj:`-1`)
+        eps (float, optional): Small value to ensure numerical stability.
+            (default: :obj:`1e-12`)
+
+    :rtype: :class:`Tensor`
+    """
+    if not torch.is_floating_point(src):
+        raise ValueError('`scatter_log_softmax` can only be computed over '
+                         'tensors with floating point data types.')
+
+    max_value_per_index, _ = scatter_max(src, index, dim=dim, fill_value=0)
+    max_per_src_element = max_value_per_index.gather(dim, index)
+
+    recentered_scores = src - max_per_src_element
+
+    sum_per_index = scatter_add(src=recentered_scores.exp(), index=index,
+                                dim=dim)
+
+    normalizing_constants = torch.log(sum_per_index + eps).gather(dim, index)
+
+    return recentered_scores - normalizing_constants

torch_scatter/logsumexp.py

+import torch
+
+from . import scatter_add, scatter_max
+
+
+def scatter_logsumexp(src, index, dim=-1, out=None, dim_size=None,
+                      fill_value=None, eps=1e-12):
+    r"""Fills :attr:`out` with the log of summed exponentials of all values
+    from the :attr:`src` tensor at the indices specified in the :attr:`index`
+    tensor along a given axis :attr:`dim`.
+    If multiple indices reference the same location, their
+    **exponential contributions add**
+    (`cf.` :meth:`~torch_scatter.scatter_add`).
+
+    For one-dimensional tensors, the operation computes
+
+    .. math::
+        \mathrm{out}_i = \log \, \left( \exp(\mathrm{out}_i) + \sum_j
+        \exp(\mathrm{src}_j) \right)
+
+    where :math:`\sum_j` is over :math:`j` such that
+    :math:`\mathrm{index}_j = i`.
+
+    Args:
+        src (Tensor): The source tensor.
+        index (LongTensor): The indices of elements to scatter.
+        dim (int, optional): The axis along which to index.
+            (default: :obj:`-1`)
+        out (Tensor, optional): The destination tensor. (default: :obj:`None`)
+        dim_size (int, optional): If :attr:`out` is not given, automatically
+            create output with size :attr:`dim_size` at dimension :attr:`dim`.
+            If :attr:`dim_size` is not given, a minimal sized output tensor is
+            returned. (default: :obj:`None`)
+        fill_value (int, optional): If :attr:`out` is not given, automatically
+            fill output tensor with :attr:`fill_value`. (default: :obj:`None`)
+        eps (float, optional): Small value to ensure numerical stability.
+            (default: :obj:`1e-12`)
+
+    :rtype: :class:`Tensor`
+    """
+    if not torch.is_floating_point(src):
+        raise ValueError('`scatter_logsumexp` can only be computed over '
+                         'tensors with floating point data types.')
+
+    max_value_per_index, _ = scatter_max(src, index, dim, out, dim_size,
+                                         fill_value)
+    max_per_src_element = max_value_per_index.gather(dim, index)
+    recentered_scores = src - max_per_src_element
+    out = (out - max_per_src_element).exp() if out is not None else None
+
+    sum_per_index = scatter_add(recentered_scores.exp(), index, dim, out,
+                                dim_size, fill_value=0)
+
+    return torch.log(sum_per_index + eps) + max_value_per_index