Source code for torch_geometric.nn.conv.message_passing

import os
import re
import inspect
import os.path as osp
from uuid import uuid1
from itertools import chain
from inspect import Parameter
from typing import List, Optional, Set
from torch_geometric.typing import Adj, Size

import torch
from torch import Tensor
from jinja2 import Template
from torch_sparse import SparseTensor
from torch_scatter import gather_csr, scatter, segment_csr

from .utils.helpers import expand_left
from .utils.jit import class_from_module_repr
from .utils.typing import (sanitize, split_types_repr, parse_types,
from .utils.inspector import Inspector, func_header_repr, func_body_repr

[docs]class MessagePassing(torch.nn.Module): r"""Base class for creating message passing layers of the form .. math:: \mathbf{x}_i^{\prime} = \gamma_{\mathbf{\Theta}} \left( \mathbf{x}_i, \square_{j \in \mathcal{N}(i)} \, \phi_{\mathbf{\Theta}} \left(\mathbf{x}_i, \mathbf{x}_j,\mathbf{e}_{j,i}\right) \right), where :math:`\square` denotes a differentiable, permutation invariant function, *e.g.*, sum, mean or max, and :math:`\gamma_{\mathbf{\Theta}}` and :math:`\phi_{\mathbf{\Theta}}` denote differentiable functions such as MLPs. See `here < create_gnn.html>`__ for the accompanying tutorial. Args: aggr (string, optional): The aggregation scheme to use (:obj:`"add"`, :obj:`"mean"`, :obj:`"max"` or :obj:`None`). (default: :obj:`"add"`) flow (string, optional): The flow direction of message passing (:obj:`"source_to_target"` or :obj:`"target_to_source"`). (default: :obj:`"source_to_target"`) node_dim (int, optional): The axis along which to propagate. (default: :obj:`-2`) """ special_args: Set[str] = { 'edge_index', 'adj_t', 'edge_index_i', 'edge_index_j', 'size', 'size_i', 'size_j', 'ptr', 'index', 'dim_size' } def __init__(self, aggr: Optional[str] = "add", flow: str = "source_to_target", node_dim: int = -2): super(MessagePassing, self).__init__() self.aggr = aggr assert self.aggr in ['add', 'mean', 'max', None] self.flow = flow assert self.flow in ['source_to_target', 'target_to_source'] self.node_dim = node_dim self.inspector = Inspector(self) self.inspector.inspect(self.message) self.inspector.inspect(self.aggregate, pop_first=True) self.inspector.inspect(self.message_and_aggregate, pop_first=True) self.inspector.inspect(self.update, pop_first=True) self.__user_args__ = self.inspector.keys( ['message', 'aggregate', 'update']).difference(self.special_args) self.__fused_user_args__ = self.inspector.keys( ['message_and_aggregate', 'update']).difference(self.special_args) # Support for "fused" message passing. self.fuse = self.inspector.implements('message_and_aggregate') # Support for GNNExplainer. self.__explain__ = False self.__edge_mask__ = None def __check_input__(self, edge_index, size): the_size: List[Optional[int]] = [None, None] if isinstance(edge_index, Tensor): assert edge_index.dtype == torch.long assert edge_index.dim() == 2 assert edge_index.size(0) == 2 if size is not None: the_size[0] = size[0] the_size[1] = size[1] return the_size elif isinstance(edge_index, SparseTensor): if self.flow == 'target_to_source': raise ValueError( ('Flow direction "target_to_source" is invalid for ' 'message propagation via `torch_sparse.SparseTensor`. If ' 'you really want to make use of a reverse message ' 'passing flow, pass in the transposed sparse tensor to ' 'the message passing module, e.g., `adj_t.t()`.')) the_size[0] = edge_index.sparse_size(1) the_size[1] = edge_index.sparse_size(0) return the_size raise ValueError( ('`MessagePassing.propagate` only supports `torch.LongTensor` of ' 'shape `[2, num_messages]` or `torch_sparse.SparseTensor` for ' 'argument `edge_index`.')) def __set_size__(self, size: List[Optional[int]], dim: int, src: Tensor): the_size = size[dim] if the_size is None: size[dim] = src.size(self.node_dim) elif the_size != src.size(self.node_dim): raise ValueError( (f'Encountered tensor with size {src.size(self.node_dim)} in ' f'dimension {self.node_dim}, but expected size {the_size}.')) def __lift__(self, src, edge_index, dim): if isinstance(edge_index, Tensor): index = edge_index[dim] return src.index_select(self.node_dim, index) elif isinstance(edge_index, SparseTensor): if dim == 1: rowptr = rowptr = expand_left(rowptr, dim=self.node_dim, dims=src.dim()) return gather_csr(src, rowptr) elif dim == 0: col = return src.index_select(self.node_dim, col) raise ValueError def __collect__(self, args, edge_index, size, kwargs): i, j = (1, 0) if self.flow == 'source_to_target' else (0, 1) out = {} for arg in args: if arg[-2:] not in ['_i', '_j']: out[arg] = kwargs.get(arg, Parameter.empty) else: dim = 0 if arg[-2:] == '_j' else 1 data = kwargs.get(arg[:-2], Parameter.empty) if isinstance(data, (tuple, list)): assert len(data) == 2 if isinstance(data[1 - dim], Tensor): self.__set_size__(size, 1 - dim, data[1 - dim]) data = data[dim] if isinstance(data, Tensor): self.__set_size__(size, dim, data) data = self.__lift__(data, edge_index, j if arg[-2:] == '_j' else i) out[arg] = data if isinstance(edge_index, Tensor): out['adj_t'] = None out['edge_index'] = edge_index out['edge_index_i'] = edge_index[i] out['edge_index_j'] = edge_index[j] out['ptr'] = None elif isinstance(edge_index, SparseTensor): out['adj_t'] = edge_index out['edge_index'] = None out['edge_index_i'] = out['edge_index_j'] = out['ptr'] = out['edge_weight'] = out['edge_attr'] = out['edge_type'] = out['index'] = out['edge_index_i'] out['size'] = size out['size_i'] = size[1] or size[0] out['size_j'] = size[0] or size[1] out['dim_size'] = out['size_i'] return out
[docs] def propagate(self, edge_index: Adj, size: Size = None, **kwargs): r"""The initial call to start propagating messages. Args: edge_index (Tensor or SparseTensor): A :obj:`torch.LongTensor` or a :obj:`torch_sparse.SparseTensor` that defines the underlying graph connectivity/message passing flow. :obj:`edge_index` holds the indices of a general (sparse) assignment matrix of shape :obj:`[N, M]`. If :obj:`edge_index` is of type :obj:`torch.LongTensor`, its shape must be defined as :obj:`[2, num_messages]`, where messages from nodes in :obj:`edge_index[0]` are sent to nodes in :obj:`edge_index[1]` (in case :obj:`flow="source_to_target"`). If :obj:`edge_index` is of type :obj:`torch_sparse.SparseTensor`, its sparse indices :obj:`(row, col)` should relate to :obj:`row = edge_index[1]` and :obj:`col = edge_index[0]`. The major difference between both formats is that we need to input the *transposed* sparse adjacency matrix into :func:`propagate`. size (tuple, optional): The size :obj:`(N, M)` of the assignment matrix in case :obj:`edge_index` is a :obj:`LongTensor`. If set to :obj:`None`, the size will be automatically inferred and assumed to be quadratic. This argument is ignored in case :obj:`edge_index` is a :obj:`torch_sparse.SparseTensor`. (default: :obj:`None`) **kwargs: Any additional data which is needed to construct and aggregate messages, and to update node embeddings. """ size = self.__check_input__(edge_index, size) # Run "fused" message and aggregation (if applicable). if (isinstance(edge_index, SparseTensor) and self.fuse and not self.__explain__): coll_dict = self.__collect__(self.__fused_user_args__, edge_index, size, kwargs) msg_aggr_kwargs = self.inspector.distribute( 'message_and_aggregate', coll_dict) out = self.message_and_aggregate(edge_index, **msg_aggr_kwargs) update_kwargs = self.inspector.distribute('update', coll_dict) return self.update(out, **update_kwargs) # Otherwise, run both functions in separation. elif isinstance(edge_index, Tensor) or not self.fuse: coll_dict = self.__collect__(self.__user_args__, edge_index, size, kwargs) msg_kwargs = self.inspector.distribute('message', coll_dict) out = self.message(**msg_kwargs) # For `GNNExplainer`, we require a separate message and aggregate # procedure since this allows us to inject the `edge_mask` into the # message passing computation scheme. if self.__explain__: edge_mask = self.__edge_mask__.sigmoid() # Some ops add self-loops to `edge_index`. We need to do the # same for `edge_mask` (but do not train those). if out.size(self.node_dim) != edge_mask.size(0): loop = edge_mask.new_ones(size[0]) edge_mask =[edge_mask, loop], dim=0) assert out.size(self.node_dim) == edge_mask.size(0) out = out * edge_mask.view([-1] + [1] * (out.dim() - 1)) aggr_kwargs = self.inspector.distribute('aggregate', coll_dict) out = self.aggregate(out, **aggr_kwargs) update_kwargs = self.inspector.distribute('update', coll_dict) return self.update(out, **update_kwargs)
[docs] def message(self, x_j: Tensor) -> Tensor: r"""Constructs messages from node :math:`j` to node :math:`i` in analogy to :math:`\phi_{\mathbf{\Theta}}` for each edge in :obj:`edge_index`. This function can take any argument as input which was initially passed to :meth:`propagate`. Furthermore, tensors passed to :meth:`propagate` can be mapped to the respective nodes :math:`i` and :math:`j` by appending :obj:`_i` or :obj:`_j` to the variable name, *.e.g.* :obj:`x_i` and :obj:`x_j`. """ return x_j
[docs] def aggregate(self, inputs: Tensor, index: Tensor, ptr: Optional[Tensor] = None, dim_size: Optional[int] = None) -> Tensor: r"""Aggregates messages from neighbors as :math:`\square_{j \in \mathcal{N}(i)}`. Takes in the output of message computation as first argument and any argument which was initially passed to :meth:`propagate`. By default, this function will delegate its call to scatter functions that support "add", "mean" and "max" operations as specified in :meth:`__init__` by the :obj:`aggr` argument. """ if ptr is not None: ptr = expand_left(ptr, dim=self.node_dim, dims=inputs.dim()) return segment_csr(inputs, ptr, reduce=self.aggr) else: return scatter(inputs, index, dim=self.node_dim, dim_size=dim_size, reduce=self.aggr)
[docs] def message_and_aggregate(self, adj_t: SparseTensor) -> Tensor: r"""Fuses computations of :func:`message` and :func:`aggregate` into a single function. If applicable, this saves both time and memory since messages do not explicitly need to be materialized. This function will only gets called in case it is implemented and propagation takes place based on a :obj:`torch_sparse.SparseTensor`. """ raise NotImplementedError
[docs] def update(self, inputs: Tensor) -> Tensor: r"""Updates node embeddings in analogy to :math:`\gamma_{\mathbf{\Theta}}` for each node :math:`i \in \mathcal{V}`. Takes in the output of aggregation as first argument and any argument which was initially passed to :meth:`propagate`. """ return inputs
[docs] @torch.jit.unused def jittable(self, typing: Optional[str] = None): r"""Analyzes the :class:`MessagePassing` instance and produces a new jittable module. Args: typing (string, optional): If given, will generate a concrete instance with :meth:`forward` types based on :obj:`typing`, *e.g.*: :obj:`"(Tensor, Optional[Tensor]) -> Tensor"`. """ # Find and parse `propagate()` types to format `{arg1: type1, ...}`. if hasattr(self, 'propagate_type'): prop_types = { k: sanitize(str(v)) for k, v in self.propagate_type.items() } else: source = inspect.getsource(self.__class__) match ='#\s*propagate_type:\s*\((.*)\)', source) if match is None: raise TypeError( 'TorchScript support requires the definition of the types ' 'passed to `propagate()`. Please specificy them via\n\n' 'propagate_type = {"arg1": type1, "arg2": type2, ... }\n\n' 'or via\n\n' '# propagate_type: (arg1: type1, arg2: type2, ...)\n\n' 'inside the `MessagePassing` module.') prop_types = split_types_repr( prop_types = dict([re.split(r'\s*:\s*', t) for t in prop_types]) # Parse `__collect__()` types to format `{arg:1, type1, ...}`. collect_types = self.inspector.types( ['message', 'aggregate', 'update']) # Collect `forward()` header, body and @overload types. forward_types = parse_types(self.forward) forward_types = [resolve_types(*types) for types in forward_types] forward_types = list(chain.from_iterable(forward_types)) keep_annotation = len(forward_types) < 2 forward_header = func_header_repr(self.forward, keep_annotation) forward_body = func_body_repr(self.forward, keep_annotation) if keep_annotation: forward_types = [] elif typing is not None: forward_types = [] forward_body = 8 * ' ' + f'# type: {typing}\n{forward_body}' root = os.path.dirname(osp.realpath(__file__)) with open(osp.join(root, 'message_passing.jinja'), 'r') as f: template = Template( uid = uuid1().hex[:6] cls_name = f'{self.__class__.__name__}Jittable_{uid}' jit_module_repr = template.render( uid=uid, module=str(self.__class__.__module__), cls_name=cls_name, parent_cls_name=self.__class__.__name__, prop_types=prop_types, collect_types=collect_types, user_args=self.__user_args__, forward_header=forward_header, forward_types=forward_types, forward_body=forward_body, msg_args=self.inspector.keys(['message']), aggr_args=self.inspector.keys(['aggregate']), msg_and_aggr_args=self.inspector.keys(['message_and_aggregate']), update_args=self.inspector.keys(['update']), check_input=inspect.getsource(self.__check_input__)[:-1], lift=inspect.getsource(self.__lift__)[:-1], ) # Instantiate a class from the rendered JIT module representation. cls = class_from_module_repr(cls_name, jit_module_repr) module = cls.__new__(cls) module.__dict__ = self.__dict__.copy() module.jittable = None return module