Add HeteroData support to RemoveIsolatedNodes (#4479)

* hetero isolated support

* update

* typo

Co-authored-by: rusty1s <matthias.fey@tu-dortmund.de>

test/transforms/test_remove_isolated_nodes.py

@@ -1,18 +1,51 @@
 import torch
 
-from torch_geometric.data import Data
+from torch_geometric.data import Data, HeteroData
 from torch_geometric.transforms import RemoveIsolatedNodes
 
 
 def test_remove_isolated_nodes():
-    assert RemoveIsolatedNodes().__repr__() == 'RemoveIsolatedNodes()'
+    assert str(RemoveIsolatedNodes()) == 'RemoveIsolatedNodes()'
+
+    data = Data()
+    data.x = torch.arange(3)
+    data.edge_index = torch.tensor([[0, 2], [2, 0]])
+    data.edge_attr = torch.arange(2)
 
-    edge_index = torch.tensor([[0, 2, 1, 0], [2, 0, 1, 0]])
-    edge_attr = torch.tensor([1, 2, 3, 4])
-    x = torch.tensor([[1], [2], [3]])
-    data = Data(edge_index=edge_index, edge_attr=edge_attr, x=x)
     data = RemoveIsolatedNodes()(data)
+
     assert len(data) == 3
-    assert data.edge_index.tolist() == [[0, 1, 0], [1, 0, 0]]
-    assert data.edge_attr.tolist() == [1, 2, 4]
-    assert data.x.tolist() == [[1], [3]]
+    assert data.x.tolist() == [0, 2]
+    assert data.edge_index.tolist() == [[0, 1], [1, 0]]
+    assert data.edge_attr.tolist() == [0, 1]
+
+
+def test_remove_isolated_nodes_in_hetero_data():
+    data = HeteroData()
+
+    data['p'].x = torch.arange(6)
+    data['a'].x = torch.arange(6)
+    data['i'].num_nodes = 4
+
+    # isolated paper nodes: {4}
+    # isolated author nodes: {3, 4, 5}
+    # isolated institution nodes: {0, 1, 2, 3}
+    data['p', '1', 'p'].edge_index = torch.tensor([[0, 1, 2], [0, 1, 3]])
+    data['p', '2', 'a'].edge_index = torch.tensor([[1, 3, 5], [0, 1, 2]])
+    data['p', '2', 'a'].edge_attr = torch.arange(3)
+    data['p', '3', 'a'].edge_index = torch.tensor([[5], [2]])
+
+    data = RemoveIsolatedNodes()(data)
+
+    assert len(data) == 4
+    assert data['p'].num_nodes == 5
+    assert data['a'].num_nodes == 3
+    assert data['i'].num_nodes == 0
+
+    assert data['p'].x.tolist() == [0, 1, 2, 3, 5]
+    assert data['a'].x.tolist() == [0, 1, 2]
+
+    assert data['1'].edge_index.tolist() == [[0, 1, 2], [0, 1, 3]]
+    assert data['2'].edge_index.tolist() == [[1, 3, 4], [0, 1, 2]]
+    assert data['2'].edge_attr.tolist() == [0, 1, 2]
+    assert data['3'].edge_index.tolist() == [[4], [2]]

torch_geometric/transforms/remove_isolated_nodes.py

@@ -1,28 +1,63 @@
-import re
+from collections import defaultdict
+from typing import Union
 
 import torch
 
+from torch_geometric.data import Data, HeteroData
 from torch_geometric.data.datapipes import functional_transform
 from torch_geometric.transforms import BaseTransform
-from torch_geometric.utils import remove_isolated_nodes
 
 
 @functional_transform('remove_isolated_nodes')
 class RemoveIsolatedNodes(BaseTransform):
     r"""Removes isolated nodes from the graph
     (functional name: :obj:`remove_isolated_nodes`)."""
-    def __call__(self, data):
-        num_nodes = data.num_nodes
-        out = remove_isolated_nodes(data.edge_index, data.edge_attr, num_nodes)
-        data.edge_index, data.edge_attr, mask = out
+    def __call__(self, data: Union[Data, HeteroData]):
+        # Gather all nodes that occur in at least one edge (across all types):
+        n_id_dict = defaultdict(list)
+        for store in data.edge_stores:
+            if 'edge_index' not in store:
+                continue
+
+            if store._key is None:
+                src = dst = None
+            else:
+                src, _, dst = store._key
+
+            n_id_dict[src].append(store.edge_index[0])
+            n_id_dict[dst].append(store.edge_index[1])
+
+        n_id_dict = {k: torch.cat(v).unique() for k, v in n_id_dict.items()}
+
+        n_map_dict = {}
+        for store in data.node_stores:
+            if store._key not in n_id_dict:
+                n_id_dict[store._key] = torch.empty((0, ), dtype=torch.long)
 
-        if hasattr(data, '__num_nodes__'):
-            data.num_nodes = int(mask.sum())
+            idx = n_id_dict[store._key]
+            mapping = idx.new_zeros(data.num_nodes)
+            mapping[idx] = torch.arange(idx.numel(), device=mapping.device)
+            n_map_dict[store._key] = mapping
 
-        for key, item in data:
-            if bool(re.search('edge', key)):
+        for store in data.edge_stores:
+            if 'edge_index' not in store:
                 continue
-            if torch.is_tensor(item) and item.size(0) == num_nodes:
-                data[key] = item[mask]
+
+            if store._key is None:
+                src = dst = None
+            else:
+                src, _, dst = store._key
+
+            row = n_map_dict[src][store.edge_index[0]]
+            col = n_map_dict[dst][store.edge_index[1]]
+            store.edge_index = torch.stack([row, col], dim=0)
+
+        for store in data.node_stores:
+            for key, value in store.items():
+                if key == 'num_nodes':
+                    store.num_nodes = n_id_dict[store._key].numel()
+
+                elif store.is_node_attr(key):
+                    store[key] = value[n_id_dict[store._key]]
 
         return data