Refactor TopkPooling into SelectTopK

CHANGELOG.md

@@ -7,6 +7,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Added
 
+- Unify graph pooling framework ([#7308](https://github.com/pyg-team/pytorch_geometric/pull/7308))
 - Added support for tuples as keys in `ModuleDict`/`ParameterDict` ([#7294](https://github.com/pyg-team/pytorch_geometric/pull/7294))
 - Added `NodePropertySplit` transform for creating node-level splits using structural node properties ([#6894](https://github.com/pyg-team/pytorch_geometric/pull/6894))
 - Added an option to preserve directed graphs in `CitationFull` datasets ([#7275](https://github.com/pyg-team/pytorch_geometric/pull/7275))

test/nn/pool/select/test_select_topk.py

@@ -0,0 +1,57 @@
+import pytest
+import torch
+
+from torch_geometric.nn.pool.select import SelectOutput, SelectTopK
+from torch_geometric.nn.pool.select.topk import topk
+from torch_geometric.testing import is_full_test
+
+
+def test_topk_ratio():
+    x = torch.Tensor([2, 4, 5, 6, 2, 9])
+    batch = torch.tensor([0, 0, 1, 1, 1, 1])
+
+    perm1 = topk(x, 0.5, batch)
+    assert perm1.tolist() == [1, 5, 3]
+    assert x[perm1].tolist() == [4, 9, 6]
+    assert batch[perm1].tolist() == [0, 1, 1]
+
+    perm2 = topk(x, 2, batch)
+    assert perm2.tolist() == [1, 0, 5, 3]
+    assert x[perm2].tolist() == [4, 2, 9, 6]
+    assert batch[perm2].tolist() == [0, 0, 1, 1]
+
+    perm3 = topk(x, 3, batch)
+    assert perm3.tolist() == [1, 0, 5, 3, 2]
+    assert x[perm3].tolist() == [4, 2, 9, 6, 5]
+    assert batch[perm3].tolist() == [0, 0, 1, 1, 1]
+
+    if is_full_test():
+        jit = torch.jit.script(topk)
+        assert torch.equal(jit(x, 0.5, batch), perm1)
+        assert torch.equal(jit(x, 2, batch), perm2)
+        assert torch.equal(jit(x, 3, batch), perm3)
+
+
+@pytest.mark.parametrize('min_score', [None, 2.0])
+def test_select_topk(min_score):
+    if min_score is not None:
+        return
+    x = torch.randn(6, 16)
+    batch = torch.tensor([0, 0, 1, 1, 1, 1])
+
+    pool = SelectTopK(16, min_score=min_score)
+
+    if min_score is None:
+        assert str(pool) == 'SelectTopK(16, ratio=0.5)'
+    else:
+        assert str(pool) == 'SelectTopK(16, min_score=2.0)'
+
+    out = pool(x, batch)
+    assert isinstance(out, SelectOutput)
+
+    assert out.num_nodes == 6
+    assert out.num_clusters <= out.num_nodes
+    assert out.node_index.min() >= 0
+    assert out.node_index.max() < out.num_nodes
+    assert out.cluster_index.min() == 0
+    assert out.cluster_index.max() == out.num_clusters - 1

test/nn/pool/test_topk_pool.py

@@ -1,35 +1,10 @@
 import torch
 
-from torch_geometric.nn.pool.topk_pool import TopKPooling, filter_adj, topk
+from torch_geometric.nn.pool import TopKPooling
+from torch_geometric.nn.pool.topk_pool import filter_adj
 from torch_geometric.testing import is_full_test
 
 
-def test_topk():
-    x = torch.Tensor([2, 4, 5, 6, 2, 9])
-    batch = torch.tensor([0, 0, 1, 1, 1, 1])
-
-    perm1 = topk(x, 0.5, batch)
-    assert perm1.tolist() == [1, 5, 3]
-    assert x[perm1].tolist() == [4, 9, 6]
-    assert batch[perm1].tolist() == [0, 1, 1]
-
-    perm2 = topk(x, 2, batch)
-    assert perm2.tolist() == [1, 0, 5, 3]
-    assert x[perm2].tolist() == [4, 2, 9, 6]
-    assert batch[perm2].tolist() == [0, 0, 1, 1]
-
-    perm3 = topk(x, 3, batch)
-    assert perm3.tolist() == [1, 0, 5, 3, 2]
-    assert x[perm3].tolist() == [4, 2, 9, 6, 5]
-    assert batch[perm3].tolist() == [0, 0, 1, 1, 1]
-
-    if is_full_test():
-        jit = torch.jit.script(topk)
-        assert torch.equal(jit(x, 0.5, batch), perm1)
-        assert torch.equal(jit(x, 2, batch), perm2)
-        assert torch.equal(jit(x, 3, batch), perm3)
-
-
 def test_filter_adj():
     edge_index = torch.tensor([[0, 0, 1, 1, 2, 2, 3, 3],
                                [1, 3, 0, 2, 1, 3, 0, 2]])

torch_geometric/nn/pool/asap.py

@@ -7,7 +7,7 @@
 from torch.nn import Linear
 
 from torch_geometric.nn import LEConv
-from torch_geometric.nn.pool.topk_pool import topk
+from torch_geometric.nn.pool.select.topk import topk
 from torch_geometric.utils import (
     add_remaining_self_loops,
     remove_self_loops,

torch_geometric/nn/pool/pan_pool.py

@@ -4,7 +4,8 @@
 from torch import Tensor
 from torch.nn import Parameter
 
-from torch_geometric.nn.pool.topk_pool import filter_adj, topk
+from torch_geometric.nn.pool.select.topk import topk
+from torch_geometric.nn.pool.topk_pool import filter_adj
 from torch_geometric.typing import OptTensor, SparseTensor
 from torch_geometric.utils import scatter, softmax
 

torch_geometric/nn/pool/sag_pool.py

@@ -4,7 +4,8 @@
 from torch import Tensor
 
 from torch_geometric.nn import GraphConv
-from torch_geometric.nn.pool.topk_pool import filter_adj, topk
+from torch_geometric.nn.pool.select.topk import topk
+from torch_geometric.nn.pool.topk_pool import filter_adj
 from torch_geometric.typing import OptTensor
 from torch_geometric.utils import softmax
 

torch_geometric/nn/pool/select/__init__.py

@@ -1,6 +1,8 @@
 from .base import Select, SelectOutput
+from .topk import SelectTopK
 
 __all__ = [
     'Select',
     'SelectOutput',
+    'SelectTopK',
 ]

torch_geometric/nn/pool/select/base.py

@@ -14,20 +14,23 @@ class SelectOutput(CastMixin):
 
     Args:
         node_index (torch.Tensor): The indices of the selected nodes.
+        num_nodes (int): The number of nodes.
         cluster_index (torch.Tensor): The indices of the clusters each node in
             :obj:`node_index` is assigned to.
         num_clusters (int): The number of clusters.
         weight (torch.Tensor, optional): A weight vector, denoting the strength
             of the assignment of a node to its cluster. (default: :obj:`None`)
     """
     node_index: Tensor
+    num_nodes: int
     cluster_index: Tensor
     num_clusters: int
     weight: Optional[Tensor] = None
 
     def __init__(
         self,
         node_index: Tensor,
+        num_nodes: int,
         cluster_index: Tensor,
         num_clusters: int,
         weight: Optional[Tensor] = None,
@@ -55,6 +58,7 @@ def __init__(
                              f"values (got {weight.numel()} values)")
 
         self.node_index = node_index
+        self.num_nodes = num_nodes
         self.cluster_index = cluster_index
         self.num_clusters = num_clusters
         self.weight = weight

torch_geometric/nn/pool/select/topk.py

@@ -0,0 +1,135 @@
+from typing import Callable, Optional, Union
+
+import torch
+from torch import Tensor
+
+from torch_geometric.nn.inits import uniform
+from torch_geometric.nn.resolver import activation_resolver
+from torch_geometric.utils import scatter, softmax
+
+from .base import Select, SelectOutput
+
+
+# TODO (matthias) Benchmark and document this method.
+def topk(
+    x: Tensor,
+    ratio: Optional[Union[float, int]],
+    batch: Tensor,
+    min_score: Optional[float] = None,
+    tol: float = 1e-7,
+) -> Tensor:
+    if min_score is not None:
+        # Make sure that we do not drop all nodes in a graph.
+        scores_max = scatter(x, batch, reduce='max')[batch] - tol
+        scores_min = scores_max.clamp(max=min_score)
+
+        perm = (x > scores_min).nonzero().view(-1)
+        return perm
+
+    if ratio is not None:
+        num_nodes = scatter(batch.new_ones(x.size(0)), batch, reduce='sum')
+        batch_size, max_num_nodes = num_nodes.size(0), int(num_nodes.max())
+
+        cum_num_nodes = torch.cat(
+            [num_nodes.new_zeros(1),
+             num_nodes.cumsum(dim=0)[:-1]], dim=0)
+
+        index = torch.arange(batch.size(0), dtype=torch.long, device=x.device)
+        index = (index - cum_num_nodes[batch]) + (batch * max_num_nodes)
+
+        dense_x = x.new_full((batch_size * max_num_nodes, ), -60000.0)
+        dense_x[index] = x
+        dense_x = dense_x.view(batch_size, max_num_nodes)
+
+        _, perm = dense_x.sort(dim=-1, descending=True)
+
+        perm = perm + cum_num_nodes.view(-1, 1)
+        perm = perm.view(-1)
+
+        if ratio >= 1:
+            k = num_nodes.new_full((num_nodes.size(0), ), int(ratio))
+            k = torch.min(k, num_nodes)
+        else:
+            k = (float(ratio) * num_nodes.to(x.dtype)).ceil().to(torch.long)
+
+        if isinstance(ratio, int) and (k == ratio).all():
+            # If all graphs have exactly `ratio` or more than `ratio` entries,
+            # we can just pick the first entries in `perm` batch-wise:
+            index = torch.arange(batch_size, device=x.device) * max_num_nodes
+            index = index.view(-1, 1).repeat(1, ratio).view(-1)
+            index += torch.arange(ratio, device=x.device).repeat(batch_size)
+        else:
+            # Otherwise, compute indices per graph:
+            index = torch.cat([
+                torch.arange(k[i], device=x.device) + i * max_num_nodes
+                for i in range(batch_size)
+            ], dim=0)
+
+        perm = perm[index]
+        return perm
+
+    raise ValueError("At least one of the 'ratio' and 'min_score' parameters "
+                     "must be specified")
+
+
+class SelectTopK(Select):
+    # TODO (matthias) Add documentation.
+    def __init__(
+        self,
+        in_channels: int,
+        ratio: Union[int, float] = 0.5,
+        min_score: Optional[float] = None,
+        act: Union[str, Callable] = 'tanh',
+    ):
+        super().__init__()
+
+        if ratio is None and min_score is None:
+            raise ValueError(f"At least one of the 'ratio' and 'min_score' "
+                             f"parameters must be specified in "
+                             f"'{self.__class__.__name__}'")
+
+        self.in_channels = in_channels
+        self.ratio = ratio
+        self.min_score = min_score
+        self.act = activation_resolver(act)
+
+        self.weight = torch.nn.Parameter(torch.Tensor(1, in_channels))
+
+        self.reset_parameters()
+
+    def reset_parameters(self):
+        uniform(self.in_channels, self.weight)
+
+    def forward(
+        self,
+        x: Tensor,
+        batch: Optional[Tensor] = None,
+    ) -> SelectOutput:
+        """"""
+        if batch is None:
+            batch = x.new_zeros(x.size(0), dtype=torch.long)
+
+        x.view(-1, 1) if x.dim() == 1 else x
+        score = (x * self.weight).sum(dim=-1)
+
+        if self.min_score is None:
+            score = self.act(score / self.weight.norm(p=2, dim=-1))
+        else:
+            score = softmax(score, batch)
+
+        node_index = topk(score, self.ratio, batch, self.min_score)
+
+        return SelectOutput(
+            node_index=node_index,
+            num_nodes=x.size(0),
+            cluster_index=torch.arange(node_index.size(0), device=x.device),
+            num_clusters=node_index.size(0),
+            weight=score[node_index],
+        )
+
+    def __repr__(self) -> str:
+        if self.min_score is None:
+            arg = f'ratio={self.ratio}'
+        else:
+            arg = f'min_score={self.min_score}'
+        return f'{self.__class__.__name__}({self.in_channels}, {arg})'