Added bipartite pooling operator from `"DeepTreeGANv2: Iterative Pool…

…ing of Point Clouds" <https://arxiv.org/abs/2312.00042>`.

CHANGELOG.md

@@ -7,6 +7,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Added
 
+- Added bipartite pooling operator from `"DeepTreeGANv2: Iterative Pooling of Point Clouds" <https://arxiv.org/abs/2312.00042>`.
 - Added the `GRetriever` model ([#9480](https://github.com/pyg-team/pytorch_geometric/pull/9480))
 - Added the `ClusterPooling` layer ([#9627](https://github.com/pyg-team/pytorch_geometric/pull/9627))
 - Added the `LinkPredMRR` metric ([#9632](https://github.com/pyg-team/pytorch_geometric/pull/9632))

test/nn/pool/test_bipartite_pool.py

@@ -0,0 +1,54 @@
+import torch
+
+from torch_geometric import nn
+
+
+def test_bipartite_pooling():
+    num_nodes = 100
+    ratio = 10
+    in_channels = 5
+    out_channels = 8
+    num_graphs = 4
+    kw = dict(in_channels=in_channels, out_channels=out_channels)
+
+    gnnlist = [
+        nn.GINConv(torch.nn.Linear(in_channels, out_channels)),
+        # nn.GENConv(**kw), # gradient test breaks
+        nn.GeneralConv(**kw),
+        nn.GraphConv(**kw),
+        nn.MFConv(**kw),
+        # nn.SimpleConv(), # gradient test breaks
+        nn.SAGEConv(**kw),
+        nn.WLConvContinuous(),
+        nn.GATv2Conv(add_self_loops=False, **kw),
+        nn.GATConv(add_self_loops=False, **kw),
+    ]
+    batch = torch.arange(num_graphs).repeat_interleave(num_nodes)
+    for gnn in gnnlist:
+
+        pool = nn.BipartitePooling(in_channels, ratio=ratio, gnn=gnn)
+
+        x = torch.randn((num_graphs * num_nodes, in_channels)).requires_grad_()
+        x.retain_grad()
+        out, new_batchidx = pool(x, batch)
+
+        if isinstance(gnn, (nn.SimpleConv, nn.WLConvContinuous)):
+            assert out.shape == torch.Size([num_graphs * ratio, in_channels])
+        else:
+            assert out.shape == torch.Size([num_graphs * ratio, out_channels])
+
+        for grad_graph in range(num_graphs):
+
+            out[new_batchidx == grad_graph].sum().backward(retain_graph=True)
+            # only graph igraph gets a gradient
+            for check_graph in range(num_graphs):
+                grad_grap_i = x.grad[batch == check_graph].abs().sum(1)
+                if grad_graph == check_graph:
+                    assert (grad_grap_i > 0).all()
+                else:
+                    assert (grad_grap_i == 0).all()
+
+            x.grad.zero_()
+            # all seed nodes get a gradient
+            assert (pool.seed_nodes.grad.abs().sum(1) > 0).all()
+            pool.seed_nodes.grad.zero_()

torch_geometric/nn/pool/__init__.py

@@ -15,6 +15,7 @@
 from .max_pool import max_pool, max_pool_neighbor_x, max_pool_x
 from .topk_pool import TopKPooling
 from .sag_pool import SAGPooling
+from .bipartite_pool import BipartitePooling
 from .edge_pool import EdgePooling
 from .cluster_pool import ClusterPooling
 from .asap import ASAPooling
@@ -344,6 +345,7 @@ def nearest(
     'ApproxMIPSKNNIndex',
     'TopKPooling',
     'SAGPooling',
+    'BipartitePooling',
     'EdgePooling',
     'ClusterPooling',
     'ASAPooling',

torch_geometric/nn/pool/bipartite_pool.py

@@ -0,0 +1,105 @@
+from typing import Tuple
+
+import torch
+from torch import Tensor
+
+from torch_geometric.typing import OptTensor
+
+
+class BipartitePooling(torch.nn.Module):
+    r"""The bipartite pooling operator from the `"DeepTreeGANv2: Iterative
+    Pooling of Point Clouds" <https://arxiv.org/abs/2312.00042>`_ paper.
+
+    The Pooling layer constructs a dense bipartite graph between the input
+    nodes and the "Seed" nodes that are trainable parameters of the layer.
+
+    Args:
+        in_channels (int): Size of each input sample.
+        ratio (int): Number of seed nodes
+        gnn (torch.nn.Module): A graph neural network layer that
+            implements the bipartite messages passing methode, such as
+            :class:`torch_geometric.nn.conv.GATv2Conv`,
+            :class:`torch_geometric.nn.conv.GATConv`.
+            :class:`torch_geometric.nn.conv.GINConv`,
+            :class:`torch_geometric.nn.conv.GeneralConv`,
+            :class:`torch_geometric.nn.conv.GraphConv`,
+            :class:`torch_geometric.nn.conv.MFConv`,
+            :class:`torch_geometric.nn.conv.SAGEConv`,
+            :class:`torch_geometric.nn.conv.WLConvContinuous`,
+            Recommended: `:class:`torch_geometric.nn.conv.GATv2Conv`
+             with `add_self_loops=False`.
+    Shapes:
+        - **inputs:**
+            node features :math:`(|\mathcal{V}|, F_{in})`,
+            batch :math:`(|\mathcal{V}|)`
+        - **outputs:**
+            node features (`ratio`, :math:`F_{out}`)
+            batch (`"ratio"`)
+    """
+    def __init__(
+        self,
+        in_channels: int,
+        ratio: int,
+        gnn: torch.nn.Module,
+        **kwargs,
+    ):
+        super().__init__()
+
+        self.in_channels = in_channels
+        self.ratio = ratio
+
+        self.seed_nodes = torch.nn.Parameter(
+            torch.empty(size=(self.ratio, self.in_channels)))
+        self.gnn = gnn
+
+        self.reset_parameters()
+
+    def reset_parameters(self):
+        r"""Resets all learnable parameters of the module."""
+        self.gnn.reset_parameters()
+        self.seed_nodes.data.normal_()
+
+    def forward(
+        self,
+        x: Tensor,
+        batch: OptTensor = None,
+    ) -> Tuple[Tensor, Tensor]:
+        r"""Forward pass.
+
+        Args:
+            x (torch.Tensor): The node feature matrix.
+
+            batch (torch.Tensor, optional): The batch vector
+                :math:`\mathbf{b} \in {\{ 0, \ldots, B-1\}}^N`, which assigns
+                each node to a specific example. (default: :obj:`None`)
+        """
+        if batch is None:
+            batch = torch.zeros((x.size(0)), dtype=torch.long).to(x.device)
+        batch_size = batch.max() + 1
+
+        x_aggrs = self.seed_nodes.repeat(batch_size, 1)
+
+        source_graph_size = len(x)
+
+        source = torch.arange(source_graph_size, device=x.device,
+                              dtype=torch.long).repeat_interleave(self.ratio)
+
+        target = torch.arange(self.ratio, device=x.device,
+                              dtype=torch.long).repeat(source_graph_size)
+        target += batch.repeat_interleave(self.ratio) * self.ratio
+
+        out = self.gnn(
+            x=(x, x_aggrs),
+            edge_index=torch.vstack([source, target]),
+            # size=(len(x), self.ratio * int(batch_size)),
+        )
+
+        new_batchidx = torch.arange(batch_size, dtype=torch.long,
+                                    device=x.device).repeat_interleave(
+                                        self.ratio)
+
+        return (out, new_batchidx)
+
+    def __repr__(self) -> str:
+        return (f'{self.__class__.__name__}({self.gnn.__class__.__name__}, '
+                f'{self.in_channels}, {self.ratio})')