A data loader which merges data objects from a torch_geometric.data.Dataset to a mini-batch. Data objects can be either of type Data or HeteroData.
dataset (Dataset) – The dataset from which to load the data.
batch_size (int, optional) – How many samples per batch to load. (default: 1)
shuffle (bool, optional) – If set to True, the data will be reshuffled at every epoch. (default: False)
follow_batch (List[str], optional) – Creates assignment batch vectors for each key in the list. (default: None)
exclude_keys (List[str], optional) – Will exclude each key in the list. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader.
A data loader that performs mini-batch sampling from node information, using a generic BaseSampler implementation that defines a sample_from_nodes() function and is supported on the provided input data object.
data (Any) – A Data, HeteroData, or (FeatureStore, GraphStore) data object.
node_sampler (torch_geometric.sampler.BaseSampler) – The sampler implementation to be used with this loader. Needs to implement sample_from_nodes(). The sampler implementation must be compatible with the input data object.
input_nodes (torch.Tensor or str or Tuple[str, torch.Tensor]) – The indices of seed nodes to start sampling from. Needs to be either given as a torch.LongTensor or torch.BoolTensor. If set to None, all nodes will be considered. In heterogeneous graphs, needs to be passed as a tuple that holds the node type and node indices. (default: None)
input_time (torch.Tensor, optional) – Optional values to override the timestamp for the input nodes given in input_nodes. If not set, will use the timestamps in time_attr as default (if present). The time_attr needs to be set for this to work. (default: None)
transform (callable, optional) – A function/transform that takes in a sampled mini-batch and returns a transformed version. (default: None)
transform_sampler_output (callable, optional) – A function/transform that takes in a torch_geometric.sampler.SamplerOutput and returns a transformed version. (default: None)
filter_per_worker (bool, optional) – If set to True, will filter the returned data in each worker’s subprocess. If set to False, will filter the returned data in the main process. If set to None, will automatically infer the decision based on whether data partially lives on the GPU (filter_per_worker=True) or entirely on the CPU (filter_per_worker=False). There exists different trade-offs for setting this option. Specifically, setting this option to True for in-memory datasets will move all features to shared memory, which may result in too many open file handles. (default: None)
custom_cls (HeteroData, optional) – A custom HeteroData class to return for mini-batches in case of remote backends. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
Samples a subgraph from a batch of input nodes.
Joins the sampled nodes with their corresponding features, returning the resulting Data or HeteroData object to be used downstream.
A data loader that performs mini-batch sampling from link information, using a generic BaseSampler implementation that defines a sample_from_edges() function and is supported on the provided input data object.
Note
Negative sampling is currently implemented in an approximate way, i.e. negative edges may contain false negatives.
data (Any) – A Data, HeteroData, or (FeatureStore, GraphStore) data object.
link_sampler (torch_geometric.sampler.BaseSampler) – The sampler implementation to be used with this loader. Needs to implement sample_from_edges(). The sampler implementation must be compatible with the input data object.
edge_label_index (Tensor or EdgeType or Tuple[EdgeType, Tensor]) – The edge indices, holding source and destination nodes to start sampling from. If set to None, all edges will be considered. In heterogeneous graphs, needs to be passed as a tuple that holds the edge type and corresponding edge indices. (default: None)
edge_label (Tensor, optional) – The labels of edge indices from which to start sampling from. Must be the same length as the edge_label_index. (default: None)
edge_label_time (Tensor, optional) – The timestamps of edge indices from which to start sampling from. Must be the same length as edge_label_index. If set, temporal sampling will be used such that neighbors are guaranteed to fulfill temporal constraints, i.e., neighbors have an earlier timestamp than the output edge. The time_attr needs to be set for this to work. (default: None)
neg_sampling (NegativeSampling, optional) – The negative sampling configuration. For negative sampling mode "binary", samples can be accessed via the attributes edge_label_index and edge_label in the respective edge type of the returned mini-batch. In case edge_label does not exist, it will be automatically created and represents a binary classification task (0 = negative edge, 1 = positive edge). In case edge_label does exist, it has to be a categorical label from 0 to num_classes - 1. After negative sampling, label 0 represents negative edges, and labels 1 to num_classes represent the labels of positive edges. Note that returned labels are of type torch.float for binary classification (to facilitate the ease-of-use of F.binary_cross_entropy()) and of type torch.long for multi-class classification (to facilitate the ease-of-use of F.cross_entropy()). For negative sampling mode "triplet", samples can be accessed via the attributes src_index, dst_pos_index and dst_neg_index in the respective node types of the returned mini-batch. edge_label needs to be None for "triplet" negative sampling mode. If set to None, no negative sampling strategy is applied. (default: None)
neg_sampling_ratio (int or float, optional) – The ratio of sampled negative edges to the number of positive edges. Deprecated in favor of the neg_sampling argument. (default: None).
transform (callable, optional) – A function/transform that takes in a sampled mini-batch and returns a transformed version. (default: None)
transform_sampler_output (callable, optional) – A function/transform that takes in a torch_geometric.sampler.SamplerOutput and returns a transformed version. (default: None)
filter_per_worker (bool, optional) – If set to True, will filter the returned data in each worker’s subprocess. If set to False, will filter the returned data in the main process. If set to None, will automatically infer the decision based on whether data partially lives on the GPU (filter_per_worker=True) or entirely on the CPU (filter_per_worker=False). There exists different trade-offs for setting this option. Specifically, setting this option to True for in-memory datasets will move all features to shared memory, which may result in too many open file handles. (default: None)
custom_cls (HeteroData, optional) – A custom HeteroData class to return for mini-batches in case of remote backends. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
Samples a subgraph from a batch of input edges.
Joins the sampled nodes with their corresponding features, returning the resulting Data or HeteroData object to be used downstream.
A data loader that performs neighbor sampling as introduced in the “Inductive Representation Learning on Large Graphs” paper. This loader allows for mini-batch training of GNNs on large-scale graphs where full-batch training is not feasible.
More specifically, num_neighbors denotes how many neighbors are sampled for each node in each iteration. NeighborLoader takes in this list of num_neighbors and iteratively samples num_neighbors[i] for each node involved in iteration i - 1.
Sampled nodes are sorted based on the order in which they were sampled. In particular, the first batch_size nodes represent the set of original mini-batch nodes.
from torch_geometric.datasets import Planetoid
from torch_geometric.loader import NeighborLoader
data = Planetoid(path, name='Cora')[0]
loader = NeighborLoader(
data,
# Sample 30 neighbors for each node for 2 iterations
num_neighbors=[30] * 2,
# Use a batch size of 128 for sampling training nodes
batch_size=128,
input_nodes=data.train_mask,
)
sampled_data = next(iter(loader))
print(sampled_data.batch_size)
>>> 128
By default, the data loader will only include the edges that were originally sampled (directed = True). This option should only be used in case the number of hops is equivalent to the number of GNN layers. In case the number of GNN layers is greater than the number of hops, consider setting directed = False, which will include all edges between all sampled nodes (but is slightly slower as a result).
Furthermore, NeighborLoader works for both homogeneous graphs stored via Data as well as heterogeneous graphs stored via HeteroData. When operating in heterogeneous graphs, up to num_neighbors neighbors will be sampled for each edge_type. However, more fine-grained control over the amount of sampled neighbors of individual edge types is possible:
from torch_geometric.datasets import OGB_MAG
from torch_geometric.loader import NeighborLoader
hetero_data = OGB_MAG(path)[0]
loader = NeighborLoader(
hetero_data,
# Sample 30 neighbors for each node and edge type for 2 iterations
num_neighbors={key: [30] * 2 for key in hetero_data.edge_types},
# Use a batch size of 128 for sampling training nodes of type paper
batch_size=128,
input_nodes=('paper', hetero_data['paper'].train_mask),
)
sampled_hetero_data = next(iter(loader))
print(sampled_hetero_data['paper'].batch_size)
>>> 128
The NeighborLoader will return subgraphs where global node indices are mapped to local indices corresponding to this specific subgraph. However, often times it is desired to map the nodes of the current subgraph back to the global node indices. The NeighborLoader will include this mapping as part of the data object:
loader = NeighborLoader(data, ...) sampled_data = next(iter(loader)) print(sampled_data.n_id) # Global node index of each node in batch.
In particular, the data loader will add the following attributes to the returned mini-batch:
batch_size The number of seed nodes (first nodes in the batch)
n_id The global node index for every sampled node
e_id The global edge index for every sampled edge
input_id: The global index of the input_nodes
num_sampled_nodes: The number of sampled nodes in each hop
num_sampled_edges: The number of sampled edges in each hop
data (Any) – A Data, HeteroData, or (FeatureStore, GraphStore) data object.
num_neighbors (List[int] or Dict[Tuple[str, str, str], List[int]]) – The number of neighbors to sample for each node in each iteration. If an entry is set to -1, all neighbors will be included. In heterogeneous graphs, may also take in a dictionary denoting the amount of neighbors to sample for each individual edge type.
input_nodes (torch.Tensor or str or Tuple[str, torch.Tensor]) – The indices of nodes for which neighbors are sampled to create mini-batches. Needs to be either given as a torch.LongTensor or torch.BoolTensor. If set to None, all nodes will be considered. In heterogeneous graphs, needs to be passed as a tuple that holds the node type and node indices. (default: None)
input_time (torch.Tensor, optional) – Optional values to override the timestamp for the input nodes given in input_nodes. If not set, will use the timestamps in time_attr as default (if present). The time_attr needs to be set for this to work. (default: None)
replace (bool, optional) – If set to True, will sample with replacement. (default: False)
subgraph_type (SubgraphType or str, optional) – The type of the returned subgraph. If set to "directional", the returned subgraph only holds the sampled (directed) edges which are necessary to compute representations for the sampled seed nodes. If set to "bidirectional", sampled edges are converted to bidirectional edges. If set to "induced", the returned subgraph contains the induced subgraph of all sampled nodes. (default: "directional")
disjoint (bool, optional) – If set to :obj: True, each seed node will create its own disjoint subgraph. If set to True, mini-batch outputs will have a batch vector holding the mapping of nodes to their respective subgraph. Will get automatically set to True in case of temporal sampling. (default: False)
temporal_strategy (str, optional) – The sampling strategy when using temporal sampling ("uniform", "last"). If set to "uniform", will sample uniformly across neighbors that fulfill temporal constraints. If set to "last", will sample the last num_neighbors that fulfill temporal constraints. (default: "uniform")
time_attr (str, optional) – The name of the attribute that denotes timestamps for either the nodes or edges in the graph. If set, temporal sampling will be used such that neighbors are guaranteed to fulfill temporal constraints, i.e. neighbors have an earlier or equal timestamp than the center node. (default: None)
weight_attr (str, optional) – The name of the attribute that denotes edge weights in the graph. If set, weighted/biased sampling will be used such that neighbors are more likely to get sampled the higher their edge weights are. Edge weights do not need to sum to one, but must be non-negative, finite and have a non-zero sum within local neighborhoods. (default: None)
transform (callable, optional) – A function/transform that takes in a sampled mini-batch and returns a transformed version. (default: None)
transform_sampler_output (callable, optional) – A function/transform that takes in a torch_geometric.sampler.SamplerOutput and returns a transformed version. (default: None)
is_sorted (bool, optional) – If set to True, assumes that edge_index is sorted by column. If time_attr is set, additionally requires that rows are sorted according to time within individual neighborhoods. This avoids internal re-sorting of the data and can improve runtime and memory efficiency. (default: False)
filter_per_worker (bool, optional) – If set to True, will filter the returned data in each worker’s subprocess. If set to False, will filter the returned data in the main process. If set to None, will automatically infer the decision based on whether data partially lives on the GPU (filter_per_worker=True) or entirely on the CPU (filter_per_worker=False). There exists different trade-offs for setting this option. Specifically, setting this option to True for in-memory datasets will move all features to shared memory, which may result in too many open file handles. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
A link-based data loader derived as an extension of the node-based torch_geometric.loader.NeighborLoader. This loader allows for mini-batch training of GNNs on large-scale graphs where full-batch training is not feasible.
More specifically, this loader first selects a sample of edges from the set of input edges edge_label_index (which may or not be edges in the original graph) and then constructs a subgraph from all the nodes present in this list by sampling num_neighbors neighbors in each iteration.
from torch_geometric.datasets import Planetoid
from torch_geometric.loader import LinkNeighborLoader
data = Planetoid(path, name='Cora')[0]
loader = LinkNeighborLoader(
data,
# Sample 30 neighbors for each node for 2 iterations
num_neighbors=[30] * 2,
# Use a batch size of 128 for sampling training nodes
batch_size=128,
edge_label_index=data.edge_index,
)
sampled_data = next(iter(loader))
print(sampled_data)
>>> Data(x=[1368, 1433], edge_index=[2, 3103], y=[1368],
train_mask=[1368], val_mask=[1368], test_mask=[1368],
edge_label_index=[2, 128])
It is additionally possible to provide edge labels for sampled edges, which are then added to the batch:
loader = LinkNeighborLoader(
data,
num_neighbors=[30] * 2,
batch_size=128,
edge_label_index=data.edge_index,
edge_label=torch.ones(data.edge_index.size(1))
)
sampled_data = next(iter(loader))
print(sampled_data)
>>> Data(x=[1368, 1433], edge_index=[2, 3103], y=[1368],
train_mask=[1368], val_mask=[1368], test_mask=[1368],
edge_label_index=[2, 128], edge_label=[128])
The rest of the functionality mirrors that of NeighborLoader, including support for heterogeneous graphs. In particular, the data loader will add the following attributes to the returned mini-batch:
n_id The global node index for every sampled node
e_id The global edge index for every sampled edge
input_id: The global index of the edge_label_index
num_sampled_nodes: The number of sampled nodes in each hop
num_sampled_edges: The number of sampled edges in each hop
Note
Negative sampling is currently implemented in an approximate way, i.e. negative edges may contain false negatives.
Warning
Note that the sampling scheme is independent from the edge we are making a prediction for. That is, by default supervision edges in edge_label_index will not get masked out during sampling. In case there exists an overlap between message passing edges in data.edge_index and supervision edges in edge_label_index, you might end up sampling an edge you are making a prediction for. You can generally avoid this behavior (if desired) by making data.edge_index and edge_label_index two disjoint sets of edges, e.g., via the RandomLinkSplit transformation and its disjoint_train_ratio argument.
data (Any) – A Data, HeteroData, or (FeatureStore, GraphStore) data object.
num_neighbors (List[int] or Dict[Tuple[str, str, str], List[int]]) – The number of neighbors to sample for each node in each iteration. If an entry is set to -1, all neighbors will be included. In heterogeneous graphs, may also take in a dictionary denoting the amount of neighbors to sample for each individual edge type.
edge_label_index (Tensor or EdgeType or Tuple[EdgeType, Tensor]) – The edge indices for which neighbors are sampled to create mini-batches. If set to None, all edges will be considered. In heterogeneous graphs, needs to be passed as a tuple that holds the edge type and corresponding edge indices. (default: None)
edge_label (Tensor, optional) – The labels of edge indices for which neighbors are sampled. Must be the same length as the edge_label_index. If set to None its set to torch.zeros(…) internally. (default: None)
edge_label_time (Tensor, optional) – The timestamps for edge indices for which neighbors are sampled. Must be the same length as edge_label_index. If set, temporal sampling will be used such that neighbors are guaranteed to fulfill temporal constraints, i.e., neighbors have an earlier timestamp than the output edge. The time_attr needs to be set for this to work. (default: None)
replace (bool, optional) – If set to True, will sample with replacement. (default: False)
subgraph_type (SubgraphType or str, optional) – The type of the returned subgraph. If set to "directional", the returned subgraph only holds the sampled (directed) edges which are necessary to compute representations for the sampled seed nodes. If set to "bidirectional", sampled edges are converted to bidirectional edges. If set to "induced", the returned subgraph contains the induced subgraph of all sampled nodes. (default: "directional")
disjoint (bool, optional) – If set to :obj: True, each seed node will create its own disjoint subgraph. If set to True, mini-batch outputs will have a batch vector holding the mapping of nodes to their respective subgraph. Will get automatically set to True in case of temporal sampling. (default: False)
temporal_strategy (str, optional) – The sampling strategy when using temporal sampling ("uniform", "last"). If set to "uniform", will sample uniformly across neighbors that fulfill temporal constraints. If set to "last", will sample the last num_neighbors that fulfill temporal constraints. (default: "uniform")
neg_sampling (NegativeSampling, optional) – The negative sampling configuration. For negative sampling mode "binary", samples can be accessed via the attributes edge_label_index and edge_label in the respective edge type of the returned mini-batch. In case edge_label does not exist, it will be automatically created and represents a binary classification task (0 = negative edge, 1 = positive edge). In case edge_label does exist, it has to be a categorical label from 0 to num_classes - 1. After negative sampling, label 0 represents negative edges, and labels 1 to num_classes represent the labels of positive edges. Note that returned labels are of type torch.float for binary classification (to facilitate the ease-of-use of F.binary_cross_entropy()) and of type torch.long for multi-class classification (to facilitate the ease-of-use of F.cross_entropy()). For negative sampling mode "triplet", samples can be accessed via the attributes src_index, dst_pos_index and dst_neg_index in the respective node types of the returned mini-batch. edge_label needs to be None for "triplet" negative sampling mode. If set to None, no negative sampling strategy is applied. (default: None)
neg_sampling_ratio (int or float, optional) – The ratio of sampled negative edges to the number of positive edges. Deprecated in favor of the neg_sampling argument. (default: None)
time_attr (str, optional) – The name of the attribute that denotes timestamps for either the nodes or edges in the graph. If set, temporal sampling will be used such that neighbors are guaranteed to fulfill temporal constraints, i.e. neighbors have an earlier or equal timestamp than the center node. Only used if edge_label_time is set. (default: None)
weight_attr (str, optional) – The name of the attribute that denotes edge weights in the graph. If set, weighted/biased sampling will be used such that neighbors are more likely to get sampled the higher their edge weights are. Edge weights do not need to sum to one, but must be non-negative, finite and have a non-zero sum within local neighborhoods. (default: None)
transform (callable, optional) – A function/transform that takes in a sampled mini-batch and returns a transformed version. (default: None)
transform_sampler_output (callable, optional) – A function/transform that takes in a torch_geometric.sampler.SamplerOutput and returns a transformed version. (default: None)
is_sorted (bool, optional) – If set to True, assumes that edge_index is sorted by column. If time_attr is set, additionally requires that rows are sorted according to time within individual neighborhoods. This avoids internal re-sorting of the data and can improve runtime and memory efficiency. (default: False)
filter_per_worker (bool, optional) – If set to True, will filter the returned data in each worker’s subprocess. If set to False, will filter the returned data in the main process. If set to None, will automatically infer the decision based on whether data partially lives on the GPU (filter_per_worker=True) or entirely on the CPU (filter_per_worker=False). There exists different trade-offs for setting this option. Specifically, setting this option to True for in-memory datasets will move all features to shared memory, which may result in too many open file handles. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
The Heterogeneous Graph Sampler from the “Heterogeneous Graph Transformer” paper. This loader allows for mini-batch training of GNNs on large-scale graphs where full-batch training is not feasible.
HGTLoader tries to (1) keep a similar number of nodes and edges for each type and (2) keep the sampled sub-graph dense to minimize the information loss and reduce the sample variance.
Methodically, HGTLoader keeps track of a node budget for each node type, which is then used to determine the sampling probability of a node. In particular, the probability of sampling a node is determined by the number of connections to already sampled nodes and their node degrees. With this, HGTLoader will sample a fixed amount of neighbors for each node type in each iteration, as given by the num_samples argument.
Sampled nodes are sorted based on the order in which they were sampled. In particular, the first batch_size nodes represent the set of original mini-batch nodes.
from torch_geometric.loader import HGTLoader
from torch_geometric.datasets import OGB_MAG
hetero_data = OGB_MAG(path)[0]
loader = HGTLoader(
hetero_data,
# Sample 512 nodes per type and per iteration for 4 iterations
num_samples={key: [512] * 4 for key in hetero_data.node_types},
# Use a batch size of 128 for sampling training nodes of type paper
batch_size=128,
input_nodes=('paper', hetero_data['paper'].train_mask),
)
sampled_hetero_data = next(iter(loader))
print(sampled_data.batch_size)
>>> 128
data (Any) – A Data, HeteroData, or (FeatureStore, GraphStore) data object.
num_samples (List[int] or Dict[str, List[int]]) – The number of nodes to sample in each iteration and for each node type. If given as a list, will sample the same amount of nodes for each node type.
input_nodes (str or Tuple[str, torch.Tensor]) – The indices of nodes for which neighbors are sampled to create mini-batches. Needs to be passed as a tuple that holds the node type and corresponding node indices. Node indices need to be either given as a torch.LongTensor or torch.BoolTensor. If node indices are set to None, all nodes of this specific type will be considered.
transform (callable, optional) – A function/transform that takes in an a sampled mini-batch and returns a transformed version. (default: None)
transform_sampler_output (callable, optional) – A function/transform that takes in a torch_geometric.sampler.SamplerOutput and returns a transformed version. (default: None)
is_sorted (bool, optional) – If set to True, assumes that edge_index is sorted by column. This avoids internal re-sorting of the data and can improve runtime and memory efficiency. (default: False)
filter_per_worker (bool, optional) – If set to True, will filter the returned data in each worker’s subprocess. If set to False, will filter the returned data in the main process. If set to None, will automatically infer the decision based on whether data partially lives on the GPU (filter_per_worker=True) or entirely on the CPU (filter_per_worker=False). There exists different trade-offs for setting this option. Specifically, setting this option to True for in-memory datasets will move all features to shared memory, which may result in too many open file handles. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
Clusters/partitions a graph data object into multiple subgraphs, as motivated by the “Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks” paper.
Note
The underlying METIS algorithm requires undirected graphs as input.
data (torch_geometric.data.Data) – The graph data object.
num_parts (int) – The number of partitions.
recursive (bool, optional) – If set to True, will use multilevel recursive bisection instead of multilevel k-way partitioning. (default: False)
save_dir (str, optional) – If set, will save the partitioned data to the save_dir directory for faster re-use. (default: None)
filename (str, optional) – Name of the stored partitioned file. (default: None)
log (bool, optional) – If set to False, will not log any progress. (default: True)
keep_inter_cluster_edges (bool, optional) – If set to True, will keep inter-cluster edge connections. (default: False)
sparse_format (str, optional) – The sparse format to use for computing partitions. (default: "csr")
The data loader scheme from the “Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks” paper which merges partioned subgraphs and their between-cluster links from a large-scale graph data object to form a mini-batch.
cluster_data (torch_geometric.loader.ClusterData) – The already partioned data object.
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
The GraphSAINT sampler base class from the “GraphSAINT: Graph Sampling Based Inductive Learning Method” paper. Given a graph in a data object, this class samples nodes and constructs subgraphs that can be processed in a mini-batch fashion. Normalization coefficients for each mini-batch are given via node_norm and edge_norm data attributes.
data (torch_geometric.data.Data) – The graph data object.
batch_size (int) – The approximate number of samples per batch.
num_steps (int, optional) – The number of iterations per epoch. (default: 1)
sample_coverage (int) – How many samples per node should be used to compute normalization statistics. (default: 0)
save_dir (str, optional) – If set, will save normalization statistics to the save_dir directory for faster re-use. (default: None)
log (bool, optional) – If set to False, will not log any pre-processing progress. (default: True)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size or num_workers.
The GraphSAINT node sampler class (see GraphSAINTSampler).
The GraphSAINT edge sampler class (see GraphSAINTSampler).
The GraphSAINT random walk sampler class (see GraphSAINTSampler).
walk_length (int) – The length of each random walk.
The ShaDow \(k\)-hop sampler from the “Decoupling the Depth and Scope of Graph Neural Networks” paper. Given a graph in a data object, the sampler will create shallow, localized subgraphs. A deep GNN on this local graph then smooths the informative local signals.
data (torch_geometric.data.Data) – The graph data object.
depth (int) – The depth/number of hops of the localized subgraph.
num_neighbors (int) – The number of neighbors to sample for each node in each hop.
node_idx (LongTensor or BoolTensor, optional) – The nodes that should be considered for creating mini-batches. If set to None, all nodes will be considered.
replace (bool, optional) – If set to True, will sample neighbors with replacement. (default: False)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size or num_workers.
A data loader that randomly samples nodes within a graph and returns their induced subgraph.
data (torch_geometric.data.Data or torch_geometric.data.HeteroData) – The Data or HeteroData graph object.
num_parts (int) – The number of partitions.
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as num_workers.
A loader that returns a tuple of data objects by sampling from multiple NodeLoader or LinkLoader instances.
loaders (List[NodeLoader] or List[LinkLoader]) – The loader instances.
filter_per_worker (bool, optional) – If set to True, will filter the returned data in each worker’s subprocess. If set to False, will filter the returned data in the main process. If set to None, will automatically infer the decision based on whether data partially lives on the GPU (filter_per_worker=True) or entirely on the CPU (filter_per_worker=False). There exists different trade-offs for setting this option. Specifically, setting this option to True for in-memory datasets will move all features to shared memory, which may result in too many open file handles. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
A data loader which batches data objects from a torch_geometric.data.dataset to a Python list. Data objects can be either of type Data or HeteroData.
Note
This data loader should be used for multi-GPU support via torch_geometric.nn.DataParallel.
dataset (Dataset) – The dataset from which to load the data.
batch_size (int, optional) – How many samples per batch to load. (default: 1)
shuffle (bool, optional) – If set to True, the data will be reshuffled at every epoch. (default: False)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as drop_last or num_workers.
A data loader which batches data objects from a torch_geometric.data.dataset to a torch_geometric.data.Batch object by stacking all attributes in a new dimension.
Note
To make use of this data loader, all graph attributes in the dataset need to have the same shape. In particular, this data loader should only be used when working with dense adjacency matrices.
dataset (Dataset) – The dataset from which to load the data.
batch_size (int, optional) – How many samples per batch to load. (default: 1)
shuffle (bool, optional) – If set to True, the data will be reshuffled at every epoch. (default: False)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as drop_last or num_workers.
A data loader which merges successive events of a torch_geometric.data.TemporalData to a mini-batch.
data (TemporalData) – The TemporalData from which to load the data.
batch_size (int, optional) – How many samples per batch to load. (default: 1)
neg_sampling_ratio (float, optional) – The ratio of sampled negative destination nodes to the number of positive destination nodes. (default: 0.0)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader.
The neighbor sampler from the “Inductive Representation Learning on Large Graphs” paper, which allows for mini-batch training of GNNs on large-scale graphs where full-batch training is not feasible.
Given a GNN with \(L\) layers and a specific mini-batch of nodes node_idx for which we want to compute embeddings, this module iteratively samples neighbors and constructs bipartite graphs that simulate the actual computation flow of GNNs.
More specifically, sizes denotes how much neighbors we want to sample for each node in each layer. This module then takes in these sizes and iteratively samples sizes[l] for each node involved in layer l. In the next layer, sampling is repeated for the union of nodes that were already encountered. The actual computation graphs are then returned in reverse-mode, meaning that we pass messages from a larger set of nodes to a smaller one, until we reach the nodes for which we originally wanted to compute embeddings.
Hence, an item returned by NeighborSampler holds the current batch_size, the IDs n_id of all nodes involved in the computation, and a list of bipartite graph objects via the tuple (edge_index, e_id, size), where edge_index represents the bipartite edges between source and target nodes, e_id denotes the IDs of original edges in the full graph, and size holds the shape of the bipartite graph. For each bipartite graph, target nodes are also included at the beginning of the list of source nodes so that one can easily apply skip-connections or add self-loops.
edge_index (Tensor or SparseTensor) – A torch.LongTensor or a torch_sparse.SparseTensor that defines the underlying graph connectivity/message passing flow. edge_index holds the indices of a (sparse) symmetric adjacency matrix. If edge_index is of type torch.LongTensor, its shape must be defined as [2, num_edges], where messages from nodes edge_index[0] are sent to nodes in edge_index[1] (in case flow="source_to_target"). If edge_index is of type torch_sparse.SparseTensor, its sparse indices (row, col) should relate to row = edge_index[1] and col = edge_index[0]. The major difference between both formats is that we need to input the transposed sparse adjacency matrix.
sizes ([int]) – The number of neighbors to sample for each node in each layer. If set to sizes[l] = -1, all neighbors are included in layer l.
node_idx (LongTensor, optional) – The nodes that should be considered for creating mini-batches. If set to None, all nodes will be considered.
num_nodes (int, optional) – The number of nodes in the graph. (default: None)
return_e_id (bool, optional) – If set to False, will not return original edge indices of sampled edges. This is only useful in case when operating on graphs without edge features to save memory. (default: True)
transform (callable, optional) – A function/transform that takes in a sampled mini-batch and returns a transformed version. (default: None)
**kwargs (optional) – Additional arguments of torch.utils.data.DataLoader, such as batch_size, shuffle, drop_last or num_workers.
A weighted random sampler that randomly samples elements according to class distribution. As such, it will either remove samples from the majority class (under-sampling) or add more examples from the minority class (over-sampling).
Graph-level sampling:
from torch_geometric.loader import DataLoader, ImbalancedSampler sampler = ImbalancedSampler(dataset) loader = DataLoader(dataset, batch_size=64, sampler=sampler, ...)
Node-level sampling:
from torch_geometric.loader import NeighborLoader, ImbalancedSampler
sampler = ImbalancedSampler(data, input_nodes=data.train_mask)
loader = NeighborLoader(data, input_nodes=data.train_mask,
batch_size=64, num_neighbors=[-1, -1],
sampler=sampler, ...)
You can also pass in the class labels directly as a torch.Tensor:
from torch_geometric.loader import NeighborLoader, ImbalancedSampler
sampler = ImbalancedSampler(data.y)
loader = NeighborLoader(data, input_nodes=data.train_mask,
batch_size=64, num_neighbors=[-1, -1],
sampler=sampler, ...)
dataset (Dataset or Data or Tensor) – The dataset or class distribution from which to sample the data, given either as a Dataset, Data, or torch.Tensor object.
input_nodes (Tensor, optional) – The indices of nodes that are used by the corresponding loader, e.g., by NeighborLoader. If set to None, all nodes will be considered. This argument should only be set for node-level loaders and does not have any effect when operating on a set of graphs as given by Dataset. (default: None)
num_samples (int, optional) – The number of samples to draw for a single epoch. If set to None, will sample as much elements as there exists in the underlying data. (default: None)
Dynamically adds samples to a mini-batch up to a maximum size (either based on number of nodes or number of edges). When data samples have a wide range in sizes, specifying a mini-batch size in terms of number of samples is not ideal and can cause CUDA OOM errors.
Within the DynamicBatchSampler, the number of steps per epoch is ambiguous, depending on the order of the samples. By default the __len__() will be undefined. This is fine for most cases but progress bars will be infinite. Alternatively, num_steps can be supplied to cap the number of mini-batches produced by the sampler.
from torch_geometric.loader import DataLoader, DynamicBatchSampler sampler = DynamicBatchSampler(dataset, max_num=10000, mode="node") loader = DataLoader(dataset, batch_sampler=sampler, ...)
dataset (Dataset) – Dataset to sample from.
max_num (int) – Size of mini-batch to aim for in number of nodes or edges.
mode (str, optional) – "node" or "edge" to measure batch size. (default: "node")
shuffle (bool, optional) – If set to True, will have the data reshuffled at every epoch. (default: False)
skip_too_big (bool, optional) – If set to True, skip samples which cannot fit in a batch by itself. (default: False)
num_steps (int, optional) – The number of mini-batches to draw for a single epoch. If set to None, will iterate through all the underlying examples, but __len__() will be None since it is ambiguous. (default: None)
A GPU prefetcher class for asynchronously transferring data of a torch.utils.data.DataLoader from host memory to device memory.
loader (torch.utils.data.DataLoader) – The data loader.
device (torch.device, optional) – The device to load the data to. (default: None)
A loader to cache mini-batch outputs, e.g., obtained during NeighborLoader iterations.
loader (torch.utils.data.DataLoader) – The data loader.
device (torch.device, optional) – The device to load the data to. (default: None)
transform (callable, optional) – A function/transform that takes in a sampled mini-batch and returns a transformed version. (default: None)
Clears the cache.
A context manager to enable CPU affinity for data loader workers (only used when running on CPU devices).
Affinitization places data loader workers threads on specific CPU cores. In effect, it allows for more efficient local memory allocation and reduces remote memory calls. Every time a process or thread moves from one core to another, registers and caches need to be flushed and reloaded. This can become very costly if it happens often, and our threads may also no longer be close to their data, or be able to share data in a cache.
See here for the accompanying tutorial.
Warning
To correctly affinitize compute threads (i.e. with KMP_AFFINITY), please make sure that you exclude loader_cores from the list of cores available for the main process. This will cause core oversubsription and exacerbate performance.
loader = NeigborLoader(data, num_workers=3)
with loader.enable_cpu_affinity(loader_cores=[0, 1, 2]):
for batch in loader:
pass
Enables CPU affinity.
loader_cores ([int], optional) – List of CPU cores to which data loader workers should affinitize to. By default, it will affinitize to numa0 cores. If used with "spawn" multiprocessing context, it will automatically enable multithreading and use multiple cores per each worker.
Loader meant for making RAG queries from a remote backend.
Retrieve a subgraph associated with the query with all its feature attributes.
Feature store template for remote GNN RAG backend.
Makes a comparison between the query and all the nodes to get all the closest nodes. Return the indices of the nodes that are to be seeds for the RAG Sampler.
Makes a comparison between the query and all the edges to get all the closest nodes. Returns the edge indices that are to be the seeds for the RAG Sampler.
Combines sampled subgraph output with features in a Data object.
Graph store template for remote GNN RAG backend.
Sample a subgraph using the seeded nodes and edges.
Register a feature store to be used with the sampler. Samplers need info from the feature store in order to work properly on HeteroGraphs.
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