Source code for torch_geometric.datasets.infection_dataset

from typing import Any, Callable, Dict, List, Optional, Union

import torch

from import InMemoryDataset
from torch_geometric.datasets.graph_generator import GraphGenerator
from torch_geometric.explain import Explanation
from torch_geometric.utils import k_hop_subgraph

[docs]class InfectionDataset(InMemoryDataset): r"""Generates a synthetic infection dataset for evaluating explainabilty algorithms, as described in the `"Explainability Techniques for Graph Convolutional Networks" <>`__ paper. The :class:`~torch_geometric.datasets.InfectionDataset` creates synthetic graphs coming from a :class:`~torch_geometric.datasets.graph_generator.GraphGenerator` with :obj:`num_infected` randomly assigned infected nodes. The dataset describes a node classification task of predicting the length of the shortest path to infected nodes, with corresponding ground-truth edge-level masks. For example, to generate a random Erdos-Renyi (ER) infection graph with :obj:`500` nodes and :obj:`0.004` edge probability, write: .. code-block:: python from torch_geometric.datasets import InfectionDataset from torch_geometric.datasets.graph_generator import ERGraph dataset = InfectionDataset( graph_generator=ERGraph(num_nodes=500, edge_prob=0.004), num_infected_nodes=50, max_path_length=3, ) Args: graph_generator (GraphGenerator or str): The graph generator to be used, *e.g.*, :class:`torch.geometric.datasets.graph_generator.BAGraph` (or any string that automatically resolves to it). num_infected_nodes (int or List[int]): The number of randomly selected infected nodes in the graph. If given as a list, will select a different number of infected nodes for different graphs. max_path_length (int, List[int]): The maximum shortest path length to determine whether a node will be infected. If given as a list, will apply different shortest path lengths for different graphs. (default: :obj:`5`) num_graphs (int, optional): The number of graphs to generate. The number of graphs will be automatically determined by :obj:`len(num_infected_nodes)` or :obj:`len(max_path_length)` in case either of them is given as a list, and should only be set in case one wants to create multiple graphs while :obj:`num_infected_nodes` and :obj:`max_path_length` are given as an integer. (default: :obj:`None`) graph_generator_kwargs (Dict[str, Any], optional): Arguments passed to the respective graph generator module in case it gets automatically resolved. (default: :obj:`None`) transform (callable, optional): A function/transform that takes in an :obj:`` object and returns a transformed version. The data object will be transformed before every access. (default: :obj:`None`) """ def __init__( self, graph_generator: Union[GraphGenerator, str], num_infected_nodes: Union[int, List[int]], max_path_length: Union[int, List[int]], num_graphs: Optional[int] = None, graph_generator_kwargs: Optional[Dict[str, Any]] = None, transform: Optional[Callable] = None, ): super().__init__(root=None, transform=transform) assert isinstance(num_infected_nodes, (int, list)) assert isinstance(max_path_length, (int, list)) if (num_graphs is None and isinstance(num_infected_nodes, int) and isinstance(max_path_length, int)): num_graphs = 1 if num_graphs is None and isinstance(num_infected_nodes, list): num_graphs = len(num_infected_nodes) if num_graphs is None and isinstance(max_path_length, list): num_graphs = len(max_path_length) assert num_graphs is not None self.graph_generator = GraphGenerator.resolve( graph_generator, **(graph_generator_kwargs or {}), ) self.num_infected_nodes = num_infected_nodes self.max_path_length = max_path_length self.num_graphs = num_graphs if isinstance(num_infected_nodes, int): num_infected_nodes = [num_infected_nodes] * num_graphs if isinstance(max_path_length, int): max_path_length = [max_path_length] * num_graphs if len(num_infected_nodes) != num_graphs: raise ValueError(f"The length of 'num_infected_nodes' " f"(got {len(num_infected_nodes)} does not match " f"with the number of graphs (got {num_graphs})") if len(max_path_length) != num_graphs: raise ValueError(f"The length of 'max_path_length' " f"(got {len(max_path_length)} does not match " f"with the number of graphs (got {num_graphs})") if any(num_infected_nodes) <= 0: raise ValueError(f"'num_infected_nodes' needs to be positive " f"(got {min(num_infected_nodes)})") if any(max_path_length) <= 0: raise ValueError(f"'max_path_length' needs to be positive " f"(got {min(max_path_length)})") data_list: List[Explanation] = [] for N, L in zip(num_infected_nodes, max_path_length): data_list.append(self.get_graph(N, L)), self.slices = self.collate(data_list) def get_graph(self, num_infected_nodes: int, max_path_length: int) -> Explanation: data = self.graph_generator() assert data.num_nodes is not None perm = torch.randperm(data.num_nodes) x = torch.zeros((data.num_nodes, 2)) x[perm[:num_infected_nodes], 1] = 1 # Infected x[perm[num_infected_nodes:], 0] = 1 # Healthy y = torch.empty(data.num_nodes, dtype=torch.long) y.fill_(max_path_length + 1) y[perm[:num_infected_nodes]] = 0 # Infected nodes have label `0`. assert data.edge_index is not None edge_mask = torch.zeros(data.num_edges, dtype=torch.bool) for num_hops in range(1, max_path_length + 1): sub_node_index, _, _, sub_edge_mask = k_hop_subgraph( perm[:num_infected_nodes], num_hops, data.edge_index, num_nodes=data.num_nodes, flow='target_to_source', directed=True) value = torch.full_like(sub_node_index, fill_value=num_hops) y[sub_node_index] = torch.min(y[sub_node_index], value) edge_mask |= sub_edge_mask return Explanation( x=x, edge_index=data.edge_index, y=y,, ) def __repr__(self) -> str: return (f'{self.__class__.__name__}({len(self)}, ' f'graph_generator={self.graph_generator}, ' f'num_infected_nodes={self.num_infected_nodes}, ' f'max_path_length={self.max_path_length})')