mindspore_gl.dataset.PPI

class mindspore_gl.dataset.PPI(root)

PPI Dataset, a source dataset for reading and parsing PPI dataset.

About PPI dataset:

protein roles in various protein-protein interaction (PPI) graphs, with each graph corresponding to a different human tissue. positional gene sets are used, motif gene sets and immunological signatures as features and gene ontology sets as labels (121 in total), collected from the Molecular Signatures Database. The average graph contains 2373 nodes, with an average degree of 28.8.

Statistics:

• Graphs: 24

• Nodes: ~2245.3

• Edges: ~61,318.4

• Number of Classes: 121

• Label split:

  • Train examples: 20

  • Valid examples: 2

  • Test examples: 2

Dataset can be download here: PPI.

You can organize the dataset files into the following directory structure and read.

.
└── ppi
    ├── valid_feats.npy
    ├── valid_labels.npy
    ├── valid_graph_id.npy
    ├── valid_graph.json
    ├── train_feats.npy
    ├── train_labels.npy
    ├── train_graph_id.npy
    ├── train_graph.json
    ├── test_feats.npy
    ├── test_labels.npy
    ├── test_graph_id.npy
    └── test_graph.json

Parameters

root (str) – path to the root directory that contains ppi_with_mask.npz.

Raises

• TypeError – if root is not a str.

• RuntimeError – if root does not contain data files.

Examples

>>> from mindspore_gl.dataset.ppi import PPI
>>> root = "path/to/ppi"
>>> dataset = PPI(root)

property graph_count

Total graph numbers.

Returns

• int, numbers of graph.

Examples

>>> #dataset is an instance object of Dataset
>>> graph_count = dataset.graph_count

property graph_edges

Accumulative graph edges count.

Returns

• numpy.ndarray, array of accumulative edges.

Examples

>>> #dataset is an instance object of Dataset
>>> val_mask = dataset.graph_edges

graph_node_feat(graph_idx)

Graph features.

Parameters

graph_idx (int) – index of graph.

Returns

• numpy.ndarray, node feature of graph.

Examples

>>> #dataset is an instance object of Dataset
>>> graph_node_feat = dataset.graph_node_feat(graph_idx)

graph_node_label(graph_idx)

Graph Node label.

Parameters

graph_idx (int) – index of graph.

Returns

• numpy.ndarray, node label of graph.

Examples

>>> #dataset is an instance object of Dataset
>>> graph_node_label = dataset.graph_node_label(graph_idx)

property graph_nodes

Accumulative graph nodes count.

Returns

• numpy.ndarray, array of accumulative nodes.

Examples

>>> #dataset is an instance object of Dataset
>>> val_mask = dataset.graph_nodes

property node_feat

Node features.

Returns

• numpy.ndarray, array of node feature.

Examples

>>> #dataset is an instance object of Dataset
>>> node_feat = dataset.node_feat

property node_feat_size

Feature size of each node.

Returns

• int, the number of feature size.

Examples

>>> #dataset is an instance object of Dataset
>>> node_feat_size = dataset.node_feat_size

property node_label

Ground truth labels of each node.

Returns

• numpy.ndarray, array of node label.

Examples

>>> #dataset is an instance object of Dataset
>>> node_label = dataset.node_label

property num_classes

Number of label classes.

Returns

• int, the number of classes.

Examples

>>> #dataset is an instance object of Dataset
>>> num_classes = dataset.num_classes

property test_graphs

Test graph ID.

Returns

• numpy.ndarray, array of test graph ID.

Examples

>>> #dataset is an instance object of Dataset
>>> test_graphs = dataset.test_graphs

property test_mask

Mask of test nodes.

Returns

• numpy.ndarray, array of mask.

Examples

>>> #dataset is an instance object of Dataset
>>> test_mask = dataset.test_mask

property train_graphs

Train graph ID.

Returns

• numpy.ndarray, array of train graph ID.

Examples

>>> #dataset is an instance object of Dataset
>>> train_graphs = dataset.train_graphs

property train_mask

Mask of training nodes.

Returns

• numpy.ndarray, array of mask.

Examples

>>> #dataset is an instance object of Dataset
>>> train_mask = dataset.train_mask

property val_graphs

Valid graph ID.

Returns

• numpy.ndarray, array of valid graph ID.

Examples

>>> #dataset is an instance object of Dataset
>>> val_graphs = dataset.val_graphs

property val_mask

Mask of validation nodes.

Returns

• numpy.ndarray, array of mask.

Examples

>>> #dataset is an instance object of Dataset
>>> val_mask = dataset.val_mask