Open justaddcoffee opened 3 years ago
Need to decide how this would work. Right now it's BYOH (bring your own holdouts), and they are supplied like this:
graph_data: graph: node_path: tests/resources/test_graphs/pos_train_nodes.tsv edge_path: tests/resources/test_graphs/pos_train_edges.tsv pos_validation: edge_path: tests/resources/test_graphs/pos_valid_edges.tsv neg_training: edge_path: tests/resources/test_graphs/neg_train_edges.tsv neg_validation: edge_path: tests/resources/test_graphs/neg_valid_edges.tsv
One way to support either BYOH or having NEAT make holdouts:
graph_data: graph: node_path: tests/resources/test_graphs/pos_train_nodes.tsv edge_path: tests/resources/test_graphs/pos_train_edges.tsv holdout: make_holdouts: type: connected_holdout # only option at the moment random_state: 42 # seed train_size: 0.8 # fraction edge_types: # optional - biolink:interacts_with - biolink:has_gene_product verbose: bool existing_holdouts: # this OR make_holdouts (not both) pos_validation: edge_path: tests/resources/test_graphs/pos_valid_edges.tsv neg_training: edge_path: tests/resources/test_graphs/neg_train_edges.tsv neg_validation: edge_path: tests/resources/test_graphs/neg_valid_edges.tsv
(note to self - I've already implemented this, essentially just need to expose the code to the YAML)
Need to decide how this would work. Right now it's BYOH (bring your own holdouts), and they are supplied like this:
One way to support either BYOH or having NEAT make holdouts: