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lucidtronix Oct 10, 2025
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label file optional in test
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83 changes: 69 additions & 14 deletions ml4h/arguments.py
Original file line number Diff line number Diff line change
Expand Up @@ -106,12 +106,47 @@ def parse_args():
'Note that setting this argument has the effect of linking the first input_tensors'
'argument to the TensorMap made from this file.',
)
parser.add_argument(
'--latent_dimensions', default=256, type=int, help='Dimensionality (size) of latent space',
)
parser.add_argument(
'--latent_dimensions_start', default=0, type=int, help='Starting dimension of latent space',
)
parser.add_argument(
'--latent_output_files', nargs='*', default=[], help=
'Path to a file containing latent space values from which an input TensorMap will be made.'
'Note that setting this argument has the effect of linking the first output_tensors'
'argument to the TensorMap made from this file.',
)
parser.add_argument(
'--input_numeric_columns', nargs='*', default=[], help=
'List of columns with continuous numeric values to use as Transformer inputs.'
)
parser.add_argument(
'--input_categorical_columns', nargs='*', default=[], help=
'List of columns with categorical values to learn an embed as input into Transformer.'
)
parser.add_argument(
'--target_regression_columns', nargs='*', default=[], help=
'List of columns with continuous numeric values to predict.'
)
parser.add_argument(
'--target_binary_columns', nargs='*', default=[], help=
'List of columns with binary values to predict.'
)
parser.add_argument(
'--group_column', default=None, help='Column to group on for embedding transformer.'
)
parser.add_argument(
'--sort_column', default=None, help='Column to sort on for embedding transformer.'
)
parser.add_argument(
'--sort_column_ascend', default=False, action='store_true', help='Sort on for embedding transformer.',
)
parser.add_argument(
'--merge_columns', nargs='*', default=['mrn', 'view'], help=
'List of columns to merge on for input and labels Transformer.'
)
parser.add_argument(
'--categorical_field_ids', nargs='*', default=[], type=int,
help='List of field ids from which input features will be collected.',
Expand Down Expand Up @@ -260,12 +295,32 @@ def parse_args():
parser.add_argument('--interpolate_step', type=float, default =1.0,
help='Diffusion model synthetic interpolation step size continuous condition')


parser.add_argument(
'--transformer_input_file', help='File with latent space input for transformers',
)
parser.add_argument(
'--transformer_label_file', help='File with target labels for transformers',
)
parser.add_argument(
'--transformer_size', default=32, type=int,
help='Number of output neurons in Transformer encoders and decoders, '
'the number of internal neurons and the number of layers are set by the --dense_layers',
)
parser.add_argument(
'--transformer_layers', default=4, type=int, help='Number of residual attention layers in transformers',
)
parser.add_argument(
'--transformer_max_size', default=128, type=int, help='Maximum number of input positions for longitudinal/embedding transformers',
)
parser.add_argument(
'--transformer_categorical_embed', default=4, type=int, help='Size of embedding of input categorical data',
)
parser.add_argument(
'--transformer_token_embed', default=32, type=int, help='Size of embedding of transformer input tokens',
)
parser.add_argument(
'--transformer_dropout_rate', default=0.1, type=float, help='Dropout rate for the longitudinal/embedding transformer.',
)
parser.add_argument('--pretrain_trainable', default=False, action='store_true', help='If set, do not freeze pretrained layers.')

# Training and Hyper-Parameter Optimization Parameters
Expand Down Expand Up @@ -554,14 +609,14 @@ def _process_args(args):
args.tensor_maps_in.append(input_map)
args.tensor_maps_out.append(output_map)

if len(args.latent_input_files) > 0:
new_pairs = []
for lif in args.latent_input_files:
tm = generate_latent_tensor_map_from_file(lif, args.input_tensors.pop(0))
args.tensor_maps_in.append(tm)
new_pairs.append(tm)
if len(args.pairs) > 0:
args.pairs = [new_pairs]
# if len(args.latent_input_files) > 0:
# new_pairs = []
# for lif in args.latent_input_files:
# tm = generate_latent_tensor_map_from_file(lif, args.input_tensors.pop(0))
# args.tensor_maps_in.append(tm)
# new_pairs.append(tm)
# if len(args.pairs) > 0:
# args.pairs = [new_pairs]

args.tensor_maps_in.extend([tensormap_lookup(it, args.tensormap_prefix) for it in args.input_tensors])

Expand All @@ -588,11 +643,11 @@ def _process_args(args):
),
)

if len(args.latent_output_files) > 0:
for lof in args.latent_output_files:
args.tensor_maps_out.append(
generate_latent_tensor_map_from_file(lof, args.output_tensors.pop(0)),
)
# if len(args.latent_output_files) > 0:
# for lof in args.latent_output_files:
# args.tensor_maps_out.append(
# generate_latent_tensor_map_from_file(lof, args.output_tensors.pop(0)),
# )

args.tensor_maps_out.extend([tensormap_lookup(ot, args.tensormap_prefix) for ot in args.output_tensors])
args.tensor_maps_out = parent_sort(args.tensor_maps_out)
Expand Down
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