Source code for dgl.data.adapter

"""Dataset adapters for re-purposing a dataset for a different kind of training task."""

import os
import json
import numpy as np

from .. import backend as F
from ..convert import graph as create_dgl_graph
from ..sampling.negative import _calc_redundancy
from .dgl_dataset import DGLDataset
from . import utils
from ..base import DGLError
from .. import backend as F

__all__ = ['AsNodePredDataset', 'AsLinkPredDataset', 'AsGraphPredDataset']


[docs]class AsNodePredDataset(DGLDataset): """Repurpose a dataset for a standard semi-supervised transductive node prediction task. The class converts a given dataset into a new dataset object such that: - Contains only one graph, accessible from ``dataset[0]``. - The graph stores: - Node labels in ``g.ndata['label']``. - Train/val/test masks in ``g.ndata['train_mask']``, ``g.ndata['val_mask']``, and ``g.ndata['test_mask']`` respectively. - In addition, the dataset contains the following attributes: - ``num_classes``, the number of classes to predict. - ``train_idx``, ``val_idx``, ``test_idx``, train/val/test indexes. If the input dataset contains heterogeneous graphs, users need to specify the ``target_ntype`` argument to indicate which node type to make predictions for. In this case: - Node labels are stored in ``g.nodes[target_ntype].data['label']``. - Training masks are stored in ``g.nodes[target_ntype].data['train_mask']``. So do validation and test masks. The class will keep only the first graph in the provided dataset and generate train/val/test masks according to the given split ratio. The generated masks will be cached to disk for fast re-loading. If the provided split ratio differs from the cached one, it will re-process the dataset properly. Parameters ---------- dataset : DGLDataset The dataset to be converted. split_ratio : (float, float, float), optional Split ratios for training, validation and test sets. They must sum to one. target_ntype : str, optional The node type to add split mask for. Attributes ---------- num_classes : int Number of classes to predict. train_idx : Tensor An 1-D integer tensor of training node IDs. val_idx : Tensor An 1-D integer tensor of validation node IDs. test_idx : Tensor An 1-D integer tensor of test node IDs. Examples -------- >>> ds = dgl.data.AmazonCoBuyComputerDataset() >>> print(ds) Dataset("amazon_co_buy_computer", num_graphs=1, save_path=...) >>> new_ds = dgl.data.AsNodePredDataset(ds, [0.8, 0.1, 0.1]) >>> print(new_ds) Dataset("amazon_co_buy_computer-as-nodepred", num_graphs=1, save_path=...) >>> print('train_mask' in new_ds[0].ndata) True """ def __init__(self, dataset, split_ratio=None, target_ntype=None, **kwargs): self.dataset = dataset self.split_ratio = split_ratio self.target_ntype = target_ntype super().__init__(self.dataset.name + '-as-nodepred', hash_key=(split_ratio, target_ntype, dataset.name, 'nodepred'), **kwargs) def process(self): is_ogb = hasattr(self.dataset, 'get_idx_split') if is_ogb: g, label = self.dataset[0] self.g = g.clone() self.g.ndata['label'] = F.reshape(label, (g.num_nodes(),)) else: self.g = self.dataset[0].clone() if 'label' not in self.g.nodes[self.target_ntype].data: raise ValueError("Missing node labels. Make sure labels are stored " "under name 'label'.") if self.split_ratio is None: if is_ogb: split = self.dataset.get_idx_split() train_idx, val_idx, test_idx = split['train'], split['valid'], split['test'] n = self.g.num_nodes() train_mask = utils.generate_mask_tensor(utils.idx2mask(train_idx, n)) val_mask = utils.generate_mask_tensor(utils.idx2mask(val_idx, n)) test_mask = utils.generate_mask_tensor(utils.idx2mask(test_idx, n)) self.g.ndata['train_mask'] = train_mask self.g.ndata['val_mask'] = val_mask self.g.ndata['test_mask'] = test_mask else: assert "train_mask" in self.g.nodes[self.target_ntype].data, \ "train_mask is not provided, please specify split_ratio to generate the masks" assert "val_mask" in self.g.nodes[self.target_ntype].data, \ "val_mask is not provided, please specify split_ratio to generate the masks" assert "test_mask" in self.g.nodes[self.target_ntype].data, \ "test_mask is not provided, please specify split_ratio to generate the masks" else: if self.verbose: print('Generating train/val/test masks...') utils.add_nodepred_split(self, self.split_ratio, self.target_ntype) self._set_split_index() self.num_classes = getattr(self.dataset, 'num_classes', None) if self.num_classes is None: self.num_classes = len(F.unique(self.g.nodes[self.target_ntype].data['label'])) def has_cache(self): return os.path.isfile(os.path.join(self.save_path, 'graph_{}.bin'.format(self.hash))) def load(self): with open(os.path.join(self.save_path, 'info_{}.json'.format(self.hash)), 'r') as f: info = json.load(f) if (info['split_ratio'] != self.split_ratio or info['target_ntype'] != self.target_ntype): raise ValueError('Provided split ratio is different from the cached file. ' 'Re-process the dataset.') self.split_ratio = info['split_ratio'] self.target_ntype = info['target_ntype'] self.num_classes = info['num_classes'] gs, _ = utils.load_graphs(os.path.join(self.save_path, 'graph_{}.bin'.format(self.hash))) self.g = gs[0] self._set_split_index() def save(self): utils.save_graphs(os.path.join(self.save_path, 'graph_{}.bin'.format(self.hash)), [self.g]) with open(os.path.join(self.save_path, 'info_{}.json'.format(self.hash)), 'w') as f: json.dump({ 'split_ratio': self.split_ratio, 'target_ntype': self.target_ntype, 'num_classes': self.num_classes}, f)
[docs] def __getitem__(self, idx): return self.g
[docs] def __len__(self): return 1
def _set_split_index(self): """Add train_idx/val_idx/test_idx as dataset attributes according to corresponding mask.""" ndata = self.g.nodes[self.target_ntype].data self.train_idx = F.nonzero_1d(ndata['train_mask']) self.val_idx = F.nonzero_1d(ndata['val_mask']) self.test_idx = F.nonzero_1d(ndata['test_mask'])
def negative_sample(g, num_samples): """Random sample negative edges from graph, excluding self-loops, the result samples might be less than num_samples """ num_nodes = g.num_nodes() redundancy = _calc_redundancy( num_samples, g.num_edges(), num_nodes ** 2) sample_size = int(num_samples*(1+redundancy)) edges = np.random.randint(0, num_nodes, size=(2, sample_size)) edges = np.unique(edges, axis=1) # remove self loop mask_self_loop = edges[0] == edges[1] # remove existing edges has_edges = F.asnumpy(g.has_edges_between(edges[0], edges[1])) mask = ~(np.logical_or(mask_self_loop, has_edges)) edges = edges[:, mask] if edges.shape[1] >= num_samples: edges = edges[:, :num_samples] return edges
[docs]class AsLinkPredDataset(DGLDataset): """Repurpose a dataset for link prediction task. The created dataset will include data needed for link prediction. Currently it only supports homogeneous graphs. It will keep only the first graph in the provided dataset and generate train/val/test edges according to the given split ratio, and the correspondent negative edges based on the neg_ratio. The generated edges will be cached to disk for fast re-loading. If the provided split ratio differs from the cached one, it will re-process the dataset properly. Parameters ---------- dataset : DGLDataset The dataset to be converted. split_ratio : (float, float, float), optional Split ratios for training, validation and test sets. Must sum to one. neg_ratio : int, optional Indicate how much negative samples to be sampled The number of the negative samples will be equal or less than neg_ratio * num_positive_edges. Attributes ------- feat_size: int The size of the feature dimension in the graph train_graph: DGLGraph The DGLGraph for training val_edges: Tuple[Tuple[Tensor, Tensor], Tuple[Tensor, Tensor]] The validation set edges, encoded as ((positive_edge_src, positive_edge_dst), (negative_edge_src, negative_edge_dst)) test_edges: Tuple[Tuple[Tensor, Tensor], Tuple[Tensor, Tensor]] The test set edges, encoded as ((positive_edge_src, positive_edge_dst), (negative_edge_src, negative_edge_dst)) Examples -------- >>> ds = dgl.data.CoraGraphDataset() >>> print(ds) Dataset("cora_v2", num_graphs=1, save_path=...) >>> new_ds = dgl.data.AsLinkPredDataset(ds, [0.8, 0.1, 0.1]) >>> print(new_ds) Dataset("cora_v2-as-linkpred", num_graphs=1, save_path=/home/ubuntu/.dgl/cora_v2-as-linkpred) >>> print(hasattr(new_ds, "test_edges")) True """ def __init__(self, dataset, split_ratio=None, neg_ratio=3, **kwargs): self.g = dataset[0] self.num_nodes = self.g.num_nodes() self.dataset = dataset self.split_ratio = split_ratio self.neg_ratio = neg_ratio super().__init__(dataset.name + '-as-linkpred', hash_key=(neg_ratio, split_ratio, dataset.name, 'linkpred'), **kwargs) def process(self): if self.split_ratio is None: # Handle logics for OGB link prediction dataset assert hasattr(self.dataset, "get_edge_split"), \ "dataset doesn't have get_edge_split method, please specify split_ratio and neg_ratio to generate the split" # This is likely to be an ogb dataset self.edge_split = self.dataset.get_edge_split() self._train_graph = self.g if 'source_node' in self.edge_split["test"]: # Probably ogbl-citation2 pos_e = (self.edge_split["valid"]["source_node"], self.edge_split["valid"]["target_node"]) neg_e_size = self.edge_split["valid"]['target_node_neg'].shape[-1] neg_e_src = np.repeat(self.edge_split['valid']['source_node'], neg_e_size) neg_e_dst = np.reshape(self.edge_split["valid"]["target_node_neg"], -1) self._val_edges = pos_e, (neg_e_src, neg_e_dst) pos_e = (self.edge_split["test"]["source_node"], self.edge_split["test"]["target_node"]) neg_e_size = self.edge_split["test"]['target_node_neg'].shape[-1] neg_e_src = np.repeat(self.edge_split['test']['source_node'], neg_e_size) neg_e_dst = np.reshape(self.edge_split["test"]["target_node_neg"], -1) self._test_edges = pos_e, (neg_e_src, neg_e_dst) elif 'edge' in self.edge_split["test"]: # Probably ogbl-collab pos_e_tensor, neg_e_tensor = self.edge_split["valid"][ "edge"], self.edge_split["valid"]["edge_neg"] pos_e = (pos_e_tensor[:, 0], pos_e_tensor[:, 1]) neg_e = (neg_e_tensor[:, 0], neg_e_tensor[:, 1]) self._val_edges = pos_e, neg_e pos_e_tensor, neg_e_tensor = self.edge_split["test"][ "edge"], self.edge_split["test"]["edge_neg"] pos_e = (pos_e_tensor[:, 0], pos_e_tensor[:, 1]) neg_e = (neg_e_tensor[:, 0], neg_e_tensor[:, 1]) self._test_edges = pos_e, neg_e # delete edge split to save memory self.edge_split = None else: assert self.split_ratio is not None, "Need to specify split_ratio" assert self.neg_ratio is not None, "Need to specify neg_ratio" ratio = self.split_ratio graph = self.dataset[0] n = graph.num_edges() src, dst = graph.edges() src, dst = F.asnumpy(src), F.asnumpy(dst) n_train, n_val, n_test = int( n * ratio[0]), int(n * ratio[1]), int(n * ratio[2]) idx = np.random.permutation(n) train_pos_idx = idx[:n_train] val_pos_idx = idx[n_train:n_train+n_val] test_pos_idx = idx[n_train+n_val:] neg_src, neg_dst = negative_sample( graph, self.neg_ratio*(n_val+n_test)) neg_n_val, neg_n_test = self.neg_ratio * n_val, self.neg_ratio * n_test neg_val_src, neg_val_dst = neg_src[:neg_n_val], neg_dst[:neg_n_val] neg_test_src, neg_test_dst = neg_src[neg_n_val:], neg_dst[neg_n_val:] self._val_edges = (F.tensor(src[val_pos_idx]), F.tensor(dst[val_pos_idx]) ), (F.tensor(neg_val_src), F.tensor(neg_val_dst)) self._test_edges = (F.tensor(src[test_pos_idx]), F.tensor(dst[test_pos_idx])), (F.tensor(neg_test_src), F.tensor(neg_test_dst)) self._train_graph = create_dgl_graph( (src[train_pos_idx], dst[train_pos_idx]), num_nodes=self.num_nodes) self._train_graph.ndata["feat"] = graph.ndata["feat"] def has_cache(self): return os.path.isfile(os.path.join(self.save_path, 'graph_{}.bin'.format(self.hash))) def load(self): gs, tensor_dict = utils.load_graphs( os.path.join(self.save_path, 'graph_{}.bin'.format(self.hash))) self.g = gs[0] self._train_graph = self.g self._val_edges = (tensor_dict["val_pos_src"], tensor_dict["val_pos_dst"]), ( tensor_dict["val_neg_src"], tensor_dict["val_neg_dst"]) self._test_edges = (tensor_dict["test_pos_src"], tensor_dict["test_pos_dst"]), ( tensor_dict["test_neg_src"], tensor_dict["test_neg_dst"]) with open(os.path.join(self.save_path, 'info_{}.json'.format(self.hash)), 'r') as f: info = json.load(f) self.split_ratio = info["split_ratio"] self.neg_ratio = info["neg_ratio"] def save(self): tensor_dict = { "val_pos_src": self._val_edges[0][0], "val_pos_dst": self._val_edges[0][1], "val_neg_src": self._val_edges[1][0], "val_neg_dst": self._val_edges[1][1], "test_pos_src": self._test_edges[0][0], "test_pos_dst": self._test_edges[0][1], "test_neg_src": self._test_edges[1][0], "test_neg_dst": self._test_edges[1][1], } utils.save_graphs(os.path.join(self.save_path, 'graph_{}.bin'.format(self.hash)), [ self._train_graph], tensor_dict) with open(os.path.join(self.save_path, 'info_{}.json'.format(self.hash)), 'w') as f: json.dump({ 'split_ratio': self.split_ratio, 'neg_ratio': self.neg_ratio}, f) @property def feat_size(self): return self._train_graph.ndata["feat"].shape[-1] @property def train_graph(self): return self._train_graph @property def val_edges(self): return self._val_edges @property def test_edges(self): return self._test_edges
[docs] def __getitem__(self, idx): return self.g
[docs] def __len__(self): return 1
[docs]class AsGraphPredDataset(DGLDataset): """Repurpose a dataset for standard graph property prediction task. The created dataset will include data needed for graph property prediction. Currently it only supports homogeneous graphs. The class converts a given dataset into a new dataset object such that: - It stores ``len(dataset)`` graphs. - The i-th graph and its label is accessible from ``dataset[i]``. The class will generate a train/val/test split if :attr:`split_ratio` is provided. The generated split will be cached to disk for fast re-loading. If the provided split ratio differs from the cached one, it will re-process the dataset properly. Parameters ---------- dataset : DGLDataset The dataset to be converted. split_ratio : (float, float, float), optional Split ratios for training, validation and test sets. They must sum to one. Attributes ---------- num_tasks : int Number of tasks to predict. num_classes : int Number of classes to predict per task, None for regression datasets. train_idx : Tensor An 1-D integer tensor of training node IDs. val_idx : Tensor An 1-D integer tensor of validation node IDs. test_idx : Tensor An 1-D integer tensor of test node IDs. node_feat_size : int Input node feature size, None if not applicable. edge_feat_size : int Input edge feature size, None if not applicable. Examples -------- >>> from dgl.data import AsGraphPredDataset >>> from ogb.graphproppred import DglGraphPropPredDataset >>> dataset = DglGraphPropPredDataset(name='ogbg-molhiv') >>> new_dataset = AsGraphPredDataset(dataset) >>> print(new_dataset) Dataset("ogbg-molhiv-as-graphpred", num_graphs=41127, save_path=...) >>> print(len(new_dataset)) 41127 >>> print(new_dataset[0]) (Graph(num_nodes=19, num_edges=40, ndata_schemes={'feat': Scheme(shape=(9,), dtype=torch.int64)} edata_schemes={'feat': Scheme(shape=(3,), dtype=torch.int64)}), tensor([0])) """ def __init__(self, dataset, split_ratio=None, **kwargs): self.dataset = dataset self.split_ratio = split_ratio super().__init__(dataset.name + '-as-graphpred', hash_key=(split_ratio, dataset.name, 'graphpred'), **kwargs) def process(self): is_ogb = hasattr(self.dataset, 'get_idx_split') if self.split_ratio is None: if is_ogb: split = self.dataset.get_idx_split() self.train_idx = split['train'] self.val_idx = split['valid'] self.test_idx = split['test'] else: # Handle FakeNewsDataset try: self.train_idx = F.nonzero_1d(self.dataset.train_mask) self.val_idx = F.nonzero_1d(self.dataset.val_mask) self.test_idx = F.nonzero_1d(self.dataset.test_mask) except: raise DGLError('The input dataset does not have default train/val/test\ split. Please specify split_ratio to generate the split.') else: if self.verbose: print('Generating train/val/test split...') train_ratio, val_ratio, _ = self.split_ratio num_graphs = len(self.dataset) num_train = int(num_graphs * train_ratio) num_val = int(num_graphs * val_ratio) idx = np.random.permutation(num_graphs) self.train_idx = F.tensor(idx[:num_train]) self.val_idx = F.tensor(idx[num_train: num_train + num_val]) self.test_idx = F.tensor(idx[num_train + num_val:]) if hasattr(self.dataset, 'num_classes'): # GINDataset, MiniGCDataset, FakeNewsDataset, TUDataset, # LegacyTUDataset, BA2MotifDataset self.num_classes = self.dataset.num_classes else: # None for multi-label classification and regression self.num_classes = None if hasattr(self.dataset, 'num_tasks'): # OGB datasets self.num_tasks = self.dataset.num_tasks else: self.num_tasks = 1 def has_cache(self): return os.path.isfile(os.path.join(self.save_path, 'info_{}.json'.format(self.hash))) def load(self): with open(os.path.join(self.save_path, 'info_{}.json'.format(self.hash)), 'r') as f: info = json.load(f) if info['split_ratio'] != self.split_ratio: raise ValueError('Provided split ratio is different from the cached file. ' 'Re-process the dataset.') self.split_ratio = info['split_ratio'] self.num_tasks = info['num_tasks'] self.num_classes = info['num_classes'] split = np.load(os.path.join(self.save_path, 'split_{}.npz'.format(self.hash))) self.train_idx = F.zerocopy_from_numpy(split['train_idx']) self.val_idx = F.zerocopy_from_numpy(split['val_idx']) self.test_idx = F.zerocopy_from_numpy(split['test_idx']) def save(self): if not os.path.exists(self.save_path): os.makedirs(self.save_path) with open(os.path.join(self.save_path, 'info_{}.json'.format(self.hash)), 'w') as f: json.dump({ 'split_ratio': self.split_ratio, 'num_tasks': self.num_tasks, 'num_classes': self.num_classes}, f) np.savez(os.path.join(self.save_path, 'split_{}.npz'.format(self.hash)), train_idx=F.zerocopy_to_numpy(self.train_idx), val_idx=F.zerocopy_to_numpy(self.val_idx), test_idx=F.zerocopy_to_numpy(self.test_idx))
[docs] def __getitem__(self, idx): return self.dataset[idx]
[docs] def __len__(self): return len(self.dataset)
@property def node_feat_size(self): g = self[0][0] return g.ndata['feat'].shape[-1] if 'feat' in g.ndata else None @property def edge_feat_size(self): g = self[0][0] return g.edata['feat'].shape[-1] if 'feat' in g.edata else None