About the visualization

[H-Q-N]

Missing parameters：

def create_embedding_model(args, mode='classification', config_dir='./configs'):
    """
    Create classification or survival models
    """
    config_path = os.path.join(config_dir, args.model_histo_config, 'config.json')
    assert os.path.exists(config_path), f"Config path {config_path} doesn't exist!"
    model_type = args.model_histo_type
    update_dict = {'in_dim': args.in_dim,
                   'out_size': args.n_proto,
                   'load_proto': args.load_proto,
                   'fix_proto': args.fix_proto,
                   'proto_path': args.proto_path}

_The "args.model_histo_config、args.model_histotype" used by this function is undefined.

def get_panther_encoder(in_dim, p, proto_path, config_dir='../'):
    parser = argparse.ArgumentParser()
    parser.add_argument('--model_type', type=str, default='PANTHER')
    parser.add_argument('--proto_model_type', type=str, default='PANTHER')
    parser.add_argument('--model_config', type=str, default='PANTHER_default')
    parser.add_argument('--in_dim', type=int, default=in_dim)
    parser.add_argument('--embed_dim', type=int, default=64)
    parser.add_argument('--n_proto', type=int, default=16)
    parser.add_argument('--n_classes', type=str, default=2)
    parser.add_argument('--out_size', type=int, default=p)
    parser.add_argument('--em_iter', type=int, default=1)
    parser.add_argument('--tau', type=float, default=1)
    parser.add_argument('--out_type', type=str, default='allcat')
    parser.add_argument('--n_fc_layers', type=int, default=0)
    parser.add_argument('--load_proto', type=int, default=1)
    parser.add_argument('--ot_eps', type=int, default=1)
    args = parser.parse_known_args()[0]
    args.fix_proto = 1
    args.proto_path = proto_path
    model = create_embedding_model(args, config_dir=config_dir)
    model.eval()
    return model

Could you provide the complete function definition for this part? Thank you very much!

[andrewsong90]

Hi @H-Q-N

I am currently traveling, but will get to this when I get chance - Thanks for your patience

[Richarizardd]

Hi @H-Q-N - see the most recent update to issue #3 , and let me know if this answers your questions!