Source code for torch_geometric.data.hetero_data

import copy
import re
from collections import defaultdict, namedtuple
from collections.abc import Mapping
from itertools import chain
from typing import Any, Dict, List, NamedTuple, Optional, Tuple, Union

import torch
from torch import Tensor
from torch_sparse import SparseTensor

from torch_geometric.data.data import BaseData, Data, size_repr
from torch_geometric.data.storage import BaseStorage, EdgeStorage, NodeStorage
from torch_geometric.typing import EdgeType, NodeType, QueryType
from torch_geometric.utils import bipartite_subgraph, is_undirected

NodeOrEdgeType = Union[NodeType, EdgeType]
NodeOrEdgeStorage = Union[NodeStorage, EdgeStorage]


[docs]class HeteroData(BaseData): r"""A data object describing a heterogeneous graph, holding multiple node and/or edge types in disjunct storage objects. Storage objects can hold either node-level, link-level or graph-level attributes. In general, :class:`~torch_geometric.data.HeteroData` tries to mimic the behaviour of a regular **nested** Python dictionary. In addition, it provides useful functionality for analyzing graph structures, and provides basic PyTorch tensor functionalities. .. code-block:: from torch_geometric.data import HeteroData data = HeteroData() # Create two node types "paper" and "author" holding a feature matrix: data['paper'].x = torch.randn(num_papers, num_paper_features) data['author'].x = torch.randn(num_authors, num_authors_features) # Create an edge type "(author, writes, paper)" and building the # graph connectivity: data['author', 'writes', 'paper'].edge_index = ... # [2, num_edges] data['paper'].num_nodes >>> 23 data['author', 'writes', 'paper'].num_edges >>> 52 # PyTorch tensor functionality: data = data.pin_memory() data = data.to('cuda:0', non_blocking=True) Note that there exists multiple ways to create a heterogeneous graph data, *e.g.*: * To initialize a node of type :obj:`"paper"` holding a node feature matrix :obj:`x_paper` named :obj:`x`: .. code-block:: python from torch_geometric.data import HeteroData data = HeteroData() data['paper'].x = x_paper data = HeteroData(paper={ 'x': x_paper }) data = HeteroData({'paper': { 'x': x_paper }}) * To initialize an edge from source node type :obj:`"author"` to destination node type :obj:`"paper"` with relation type :obj:`"writes"` holding a graph connectivity matrix :obj:`edge_index_author_paper` named :obj:`edge_index`: .. code-block:: python data = HeteroData() data['author', 'writes', 'paper'].edge_index = edge_index_author_paper data = HeteroData(author__writes__paper={ 'edge_index': edge_index_author_paper }) data = HeteroData({ ('author', 'writes', 'paper'): { 'edge_index': edge_index_author_paper } }) """ DEFAULT_REL = 'to' def __init__(self, _mapping: Optional[Dict[str, Any]] = None, **kwargs): self.__dict__['_global_store'] = BaseStorage(_parent=self) self.__dict__['_node_store_dict'] = {} self.__dict__['_edge_store_dict'] = {} for key, value in chain((_mapping or {}).items(), kwargs.items()): if '__' in key and isinstance(value, Mapping): key = tuple(key.split('__')) if isinstance(value, Mapping): self[key].update(value) else: setattr(self, key, value) def __getattr__(self, key: str) -> Any: # `data.*_dict` => Link to node and edge stores. # `data.*` => Link to the `_global_store`. # Using `data.*_dict` is the same as using `collect()` for collecting # nodes and edges features. if hasattr(self._global_store, key): return getattr(self._global_store, key) elif bool(re.search('_dict$', key)): return self.collect(key[:-5]) raise AttributeError(f"'{self.__class__.__name__}' has no " f"attribute '{key}'") def __setattr__(self, key: str, value: Any): # NOTE: We aim to prevent duplicates in node or edge types. if key in self.node_types: raise AttributeError(f"'{key}' is already present as a node type") elif key in self.edge_types: raise AttributeError(f"'{key}' is already present as an edge type") setattr(self._global_store, key, value) def __delattr__(self, key: str): delattr(self._global_store, key) def __getitem__(self, *args: Tuple[QueryType]) -> Any: # `data[*]` => Link to either `_global_store`, _node_store_dict` or # `_edge_store_dict`. # If neither is present, we create a new `Storage` object for the given # node/edge-type. key = self._to_canonical(*args) out = self._global_store.get(key, None) if out is not None: return out if isinstance(key, tuple): return self.get_edge_store(*key) else: return self.get_node_store(key) def __setitem__(self, key: str, value: Any): if key in self.node_types: raise AttributeError(f"'{key}' is already present as a node type") elif key in self.edge_types: raise AttributeError(f"'{key}' is already present as an edge type") self._global_store[key] = value def __delitem__(self, *args: Tuple[QueryType]): # `del data[*]` => Link to `_node_store_dict` or `_edge_store_dict`. key = self._to_canonical(*args) if key in self.edge_types: del self._edge_store_dict[key] elif key in self.node_types: del self._node_store_dict[key] else: del self._global_store[key] def __copy__(self): out = self.__class__.__new__(self.__class__) for key, value in self.__dict__.items(): out.__dict__[key] = value out.__dict__['_global_store'] = copy.copy(self._global_store) out._global_store._parent = out out.__dict__['_node_store_dict'] = {} for key, store in self._node_store_dict.items(): out._node_store_dict[key] = copy.copy(store) out._node_store_dict[key]._parent = out out.__dict__['_edge_store_dict'] = {} for key, store in self._edge_store_dict.items(): out._edge_store_dict[key] = copy.copy(store) out._edge_store_dict[key]._parent = out return out def __deepcopy__(self, memo): out = self.__class__.__new__(self.__class__) for key, value in self.__dict__.items(): out.__dict__[key] = copy.deepcopy(value, memo) out._global_store._parent = out for key in self._node_store_dict.keys(): out._node_store_dict[key]._parent = out for key in out._edge_store_dict.keys(): out._edge_store_dict[key]._parent = out return out def __repr__(self) -> str: info1 = [size_repr(k, v, 2) for k, v in self._global_store.items()] info2 = [size_repr(k, v, 2) for k, v in self._node_store_dict.items()] info3 = [size_repr(k, v, 2) for k, v in self._edge_store_dict.items()] info = ',\n'.join(info1 + info2 + info3) info = f'\n{info}\n' if len(info) > 0 else info return f'{self.__class__.__name__}({info})' def stores_as(self, data: 'HeteroData'): for node_type in data.node_types: self.get_node_store(node_type) for edge_type in data.edge_types: self.get_edge_store(*edge_type) return self @property def stores(self) -> List[BaseStorage]: r"""Returns a list of all storages of the graph.""" return ([self._global_store] + list(self.node_stores) + list(self.edge_stores)) @property def node_types(self) -> List[NodeType]: r"""Returns a list of all node types of the graph.""" return list(self._node_store_dict.keys()) @property def node_stores(self) -> List[NodeStorage]: r"""Returns a list of all node storages of the graph.""" return list(self._node_store_dict.values()) @property def edge_types(self) -> List[EdgeType]: r"""Returns a list of all edge types of the graph.""" return list(self._edge_store_dict.keys()) @property def edge_stores(self) -> List[EdgeStorage]: r"""Returns a list of all edge storages of the graph.""" return list(self._edge_store_dict.values())
[docs] def node_items(self) -> List[Tuple[NodeType, NodeStorage]]: r"""Returns a list of node type and node storage pairs.""" return list(self._node_store_dict.items())
[docs] def edge_items(self) -> List[Tuple[EdgeType, EdgeStorage]]: r"""Returns a list of edge type and edge storage pairs.""" return list(self._edge_store_dict.items())
[docs] def to_dict(self) -> Dict[str, Any]: out = self._global_store.to_dict() for key, store in chain(self._node_store_dict.items(), self._edge_store_dict.items()): out[key] = store.to_dict() return out
[docs] def to_namedtuple(self) -> NamedTuple: field_names = list(self._global_store.keys()) field_values = list(self._global_store.values()) field_names += [ '__'.join(key) if isinstance(key, tuple) else key for key in self.node_types + self.edge_types ] field_values += [ store.to_namedtuple() for store in self.node_stores + self.edge_stores ] DataTuple = namedtuple('DataTuple', field_names) return DataTuple(*field_values)
[docs] def __cat_dim__(self, key: str, value: Any, store: Optional[NodeOrEdgeStorage] = None, *args, **kwargs) -> Any: if isinstance(value, SparseTensor) and 'adj' in key: return (0, 1) elif 'index' in key or 'face' in key: return -1 return 0
[docs] def __inc__(self, key: str, value: Any, store: Optional[NodeOrEdgeStorage] = None, *args, **kwargs) -> Any: if 'batch' in key: return int(value.max()) + 1 elif isinstance(store, EdgeStorage) and 'index' in key: return torch.tensor(store.size()).view(2, 1) else: return 0
@property def num_nodes(self) -> Optional[int]: r"""Returns the number of nodes in the graph.""" return super().num_nodes @property def num_node_features(self) -> Dict[NodeType, int]: r"""Returns the number of features per node type in the graph.""" return { key: store.num_node_features for key, store in self._node_store_dict.items() } @property def num_features(self) -> Dict[NodeType, int]: r"""Returns the number of features per node type in the graph. Alias for :py:attr:`~num_node_features`.""" return self.num_node_features @property def num_edge_features(self) -> Dict[EdgeType, int]: r"""Returns the number of features per edge type in the graph.""" return { key: store.num_edge_features for key, store in self._edge_store_dict.items() }
[docs] def is_undirected(self) -> bool: r"""Returns :obj:`True` if graph edges are undirected.""" edge_index, _, _ = to_homogeneous_edge_index(self) return is_undirected(edge_index, num_nodes=self.num_nodes)
def debug(self): pass # TODO ########################################################################### def _to_canonical(self, *args: Tuple[QueryType]) -> NodeOrEdgeType: # Converts a given `QueryType` to its "canonical type": # 1. `relation_type` will get mapped to the unique # `(src_node_type, relation_type, dst_node_type)` tuple. # 2. `(src_node_type, dst_node_type)` will get mapped to the unique # `(src_node_type, *, dst_node_type)` tuple, and # `(src_node_type, 'to', dst_node_type)` otherwise. if len(args) == 1: args = args[0] if isinstance(args, str): node_types = [key for key in self.node_types if key == args] if len(node_types) == 1: args = node_types[0] return args # Try to map to edge type based on unique relation type: edge_types = [key for key in self.edge_types if key[1] == args] if len(edge_types) == 1: args = edge_types[0] return args elif len(args) == 2: # Try to find the unique source/destination node tuple: edge_types = [ key for key in self.edge_types if key[0] == args[0] and key[-1] == args[-1] ] if len(edge_types) == 1: args = edge_types[0] return args else: args = (args[0], self.DEFAULT_REL, args[1]) return args return args
[docs] def metadata(self) -> Tuple[List[NodeType], List[EdgeType]]: r"""Returns the heterogeneous meta-data, *i.e.* its node and edge types. .. code-block:: python data = HeteroData() data['paper'].x = ... data['author'].x = ... data['author', 'writes', 'paper'].edge_index = ... print(data.metadata()) >>> (['paper', 'author'], [('author', 'writes', 'paper')]) """ return self.node_types, self.edge_types
[docs] def collect(self, key: str) -> Dict[NodeOrEdgeType, Any]: r"""Collects the attribute :attr:`key` from all node and edge types. .. code-block:: python data = HeteroData() data['paper'].x = ... data['author'].x = ... print(data.collect('x')) >>> { 'paper': ..., 'author': ...} .. note:: This is equivalent to writing :obj:`data.x_dict`. """ mapping = {} for subtype, store in chain(self._node_store_dict.items(), self._edge_store_dict.items()): if hasattr(store, key): mapping[subtype] = getattr(store, key) return mapping
[docs] def get_node_store(self, key: NodeType) -> NodeStorage: r"""Gets the :class:`~torch_geometric.data.storage.NodeStorage` object of a particular node type :attr:`key`. If the storage is not present yet, will create a new :class:`torch_geometric.data.storage.NodeStorage` object for the given node type. .. code-block:: python data = HeteroData() node_storage = data.get_node_store('paper') """ out = self._node_store_dict.get(key, None) if out is None: out = NodeStorage(_parent=self, _key=key) self._node_store_dict[key] = out return out
[docs] def get_edge_store(self, src: str, rel: str, dst: str) -> EdgeStorage: r"""Gets the :class:`~torch_geometric.data.storage.EdgeStorage` object of a particular edge type given by the tuple :obj:`(src, rel, dst)`. If the storage is not present yet, will create a new :class:`torch_geometric.data.storage.EdgeStorage` object for the given edge type. .. code-block:: python data = HeteroData() edge_storage = data.get_edge_store('author', 'writes', 'paper') """ key = (src, rel, dst) out = self._edge_store_dict.get(key, None) if out is None: out = EdgeStorage(_parent=self, _key=key) self._edge_store_dict[key] = out return out
[docs] def rename(self, name: NodeType, new_name: NodeType) -> 'HeteroData': r"""Renames the node type :obj:`name` to :obj:`new_name` in-place.""" node_store = self._node_store_dict.pop(name) node_store._key = new_name self._node_store_dict[new_name] = node_store for edge_type in self.edge_types: src, rel, dst = edge_type if src == name or dst == name: edge_store = self._edge_store_dict.pop(edge_type) src = new_name if src == name else src dst = new_name if dst == name else dst edge_type = (src, rel, dst) edge_store._key = edge_type self._edge_store_dict[edge_type] = edge_store return self
[docs] def subgraph(self, subset_dict: Dict[NodeType, Tensor]) -> 'HeteroData': r"""Returns the induced subgraph containing the node types and corresponding nodes in :obj:`subset_dict`. .. code-block:: python data = HeteroData() data['paper'].x = ... data['author'].x = ... data['conference'].x = ... data['paper', 'cites', 'paper'].edge_index = ... data['author', 'paper'].edge_index = ... data['paper', 'conference'].edge_index = ... print(data) >>> HeteroData( paper={ x=[10, 16] }, author={ x=[5, 32] }, conference={ x=[5, 8] }, (paper, cites, paper)={ edge_index=[2, 50] }, (author, to, paper)={ edge_index=[2, 30] }, (paper, to, conference)={ edge_index=[2, 25] } ) subset_dict = { 'paper': torch.tensor([3, 4, 5, 6]), 'author': torch.tensor([0, 2]), } print(data.subgraph(subset_dict)) >>> HeteroData( paper={ x=[4, 16] }, author={ x=[2, 32] }, (paper, cites, paper)={ edge_index=[2, 24] }, (author, to, paper)={ edge_index=[2, 5] } ) Args: subset_dict (Dict[str, LongTensor or BoolTensor]): A dictonary holding the nodes to keep for each node type. """ data = self.__class__(self._global_store) for node_type, subset in subset_dict.items(): for key, value in self[node_type].items(): if key == 'num_nodes': if subset.dtype == torch.bool: data[node_type].num_nodes = int(subset.sum()) else: data[node_type].num_nodes = subset.size(0) elif self[node_type].is_node_attr(key): data[node_type][key] = value[subset] else: data[node_type][key] = value for edge_type in self.edge_types: src, _, dst = edge_type if src not in subset_dict or dst not in subset_dict: continue edge_index, _, edge_mask = bipartite_subgraph( (subset_dict[src], subset_dict[dst]), self[edge_type].edge_index, relabel_nodes=True, size=(self[src].num_nodes, self[dst].num_nodes), return_edge_mask=True, ) for key, value in self[edge_type].items(): if key == 'edge_index': data[edge_type].edge_index = edge_index elif self[edge_type].is_edge_attr(key): data[edge_type][key] = value[edge_mask] else: data[edge_type][key] = value return data
[docs] def to_homogeneous(self, node_attrs: Optional[List[str]] = None, edge_attrs: Optional[List[str]] = None, add_node_type: bool = True, add_edge_type: bool = True) -> Data: """Converts a :class:`~torch_geometric.data.HeteroData` object to a homogeneous :class:`~torch_geometric.data.Data` object. By default, all features with same feature dimensionality across different types will be merged into a single representation, unless otherwise specified via the :obj:`node_attrs` and :obj:`edge_attrs` arguments. Furthermore, attributes named :obj:`node_type` and :obj:`edge_type` will be added to the returned :class:`~torch_geometric.data.Data` object, denoting node-level and edge-level vectors holding the node and edge type as integers, respectively. Args: node_attrs (List[str], optional): The node features to combine across all node types. These node features need to be of the same feature dimensionality. If set to :obj:`None`, will automatically determine which node features to combine. (default: :obj:`None`) edge_attrs (List[str], optional): The edge features to combine across all edge types. These edge features need to be of the same feature dimensionality. If set to :obj:`None`, will automatically determine which edge features to combine. (default: :obj:`None`) add_node_type (bool, optional): If set to :obj:`False`, will not add the node-level vector :obj:`node_type` to the returned :class:`~torch_geometric.data.Data` object. (default: :obj:`True`) add_edge_type (bool, optional): If set to :obj:`False`, will not add the edge-level vector :obj:`edge_type` to the returned :class:`~torch_geometric.data.Data` object. (default: :obj:`True`) """ def _consistent_size(stores: List[BaseStorage]) -> List[str]: sizes_dict = defaultdict(list) for store in stores: for key, value in store.items(): if key in ['edge_index', 'adj_t']: continue if isinstance(value, Tensor): dim = self.__cat_dim__(key, value, store) size = value.size()[:dim] + value.size()[dim + 1:] sizes_dict[key].append(tuple(size)) return [ k for k, sizes in sizes_dict.items() if len(sizes) == len(stores) and len(set(sizes)) == 1 ] edge_index, node_slices, edge_slices = to_homogeneous_edge_index(self) device = edge_index.device if edge_index is not None else None data = Data(**self._global_store.to_dict()) if edge_index is not None: data.edge_index = edge_index data._node_type_names = list(node_slices.keys()) data._edge_type_names = list(edge_slices.keys()) # Combine node attributes into a single tensor: if node_attrs is None: node_attrs = _consistent_size(self.node_stores) for key in node_attrs: values = [store[key] for store in self.node_stores] dim = self.__cat_dim__(key, values[0], self.node_stores[0]) value = torch.cat(values, dim) if len(values) > 1 else values[0] data[key] = value if not data.can_infer_num_nodes: data.num_nodes = list(node_slices.values())[-1][1] # Combine edge attributes into a single tensor: if edge_attrs is None: edge_attrs = _consistent_size(self.edge_stores) for key in edge_attrs: values = [store[key] for store in self.edge_stores] dim = self.__cat_dim__(key, values[0], self.edge_stores[0]) value = torch.cat(values, dim) if len(values) > 1 else values[0] data[key] = value if add_node_type: sizes = [offset[1] - offset[0] for offset in node_slices.values()] sizes = torch.tensor(sizes, dtype=torch.long, device=device) node_type = torch.arange(len(sizes), device=device) data.node_type = node_type.repeat_interleave(sizes) if add_edge_type and edge_index is not None: sizes = [offset[1] - offset[0] for offset in edge_slices.values()] sizes = torch.tensor(sizes, dtype=torch.long, device=device) edge_type = torch.arange(len(sizes), device=device) data.edge_type = edge_type.repeat_interleave(sizes) return data
# Helper functions ############################################################ def to_homogeneous_edge_index( data: HeteroData, ) -> Tuple[Optional[Tensor], Dict[NodeType, Any], Dict[EdgeType, Any]]: # Record slice information per node type: cumsum = 0 node_slices: Dict[NodeType, Tuple[int, int]] = {} for node_type, store in data._node_store_dict.items(): num_nodes = store.num_nodes node_slices[node_type] = (cumsum, cumsum + num_nodes) cumsum += num_nodes # Record edge indices and slice information per edge type: cumsum = 0 edge_indices: List[Tensor] = [] edge_slices: Dict[EdgeType, Tuple[int, int]] = {} for edge_type, store in data._edge_store_dict.items(): src, _, dst = edge_type offset = [[node_slices[src][0]], [node_slices[dst][0]]] offset = torch.tensor(offset, device=store.edge_index.device) edge_indices.append(store.edge_index + offset) num_edges = store.num_edges edge_slices[edge_type] = (cumsum, cumsum + num_edges) cumsum += num_edges edge_index = None if len(edge_indices) == 1: # Memory-efficient `torch.cat`: edge_index = edge_indices[0] elif len(edge_indices) > 0: edge_index = torch.cat(edge_indices, dim=-1) return edge_index, node_slices, edge_slices