nichecompass.nn.OneHopGCNNormNodeLabelAggregator

class nichecompass.nn.OneHopGCNNormNodeLabelAggregator(modality)

One-hop GCN Norm Node Label Aggregator class that uses a symmetrically normalized sum of the omics feature vector of a node’s 1-hop neighbors to build an aggregated neighbor omics feature vector for a node. It returns a concatenation of the node’s own omics feature vector and the gcn-norm aggregated neighbor omics feature vector as node labels for the omics reconstruction task.

modality:

Omics modality that is aggregated. Can be either rna or atac.

Methods table

forward(x, edge_index[, return_agg_weights])

Forward pass of the One-hop GCN Norm Node Label Aggregator.

Methods

OneHopGCNNormNodeLabelAggregator.forward(x, edge_index, return_agg_weights=False)

Forward pass of the One-hop GCN Norm Node Label Aggregator.

Parameters:

• x (Tensor) – Tensor containing the omics features of the nodes in the current node batch including sampled neighbors. (Size: n_nodes_batch_and_sampled_neighbors x n_node_features)

• edge_index (Tensor) – Tensor containing the node indices of edges in the current node batch including sampled neighbors. (Size: 2 x n_edges_batch_and_sampled_neighbors)

• return_agg_weights (bool (default: False)) – If ´True´, also return the aggregation weights (norm weights).

Return type:

Tensor

Returns:

x_neighbors:

Tensor containing the node labels of the nodes in the current node batch. These labels are used for the omics reconstruction task. (Size: n_nodes_batch x (2 x n_node_features))

alpha:

Neighbor aggregation weights.