NetTIME/NetTIME_evaluate.py at master · ryi06/NetTIME · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
import argparse

from NetTIME import EvaluateWorkflow

######## User Input ########
parser = argparse.ArgumentParser("Evaluating a trained NetTIME model.")

# Evaluation parameters
parser.add_argument(
    "--batch_size",
    type=int,
    default=2700,
    help="Evaluation batch size. Default: 2700",
)
parser.add_argument(
    "--num_workers",
    type=int,
    default=10,
    help="Number of workers used to perform multi-process data loading. "
    "Default: 10",
)
parser.add_argument(
    "--seed", type=int, default=1111, help="Random seed. Default: 1111"
)
parser.add_argument(
    "--model_config",
    type=str,
    default=None,
    help="Specify an alternative path to model .config file.",
)
parser.add_argument(
    "--ckpt_dir",
    type=str,
    default=None,
    help="Specify an alternative location to find checkpoints to be evaluated.",
)

# Data
parser.add_argument(
    "--output_key",
    type=str,
    default=["output_conserved"],
    nargs="+",
    help="A list of keys specifying the types of target labels to use for "
    "evaluation. Default: output_conserved",
)
parser.add_argument(
    "--dataset",
    type=str,
    default="data/datasets/training_example/validation_minOverlap200_maxUnion600.h5",
    help="Path to evaluation data. Default: "
    "data/datasets/training_example/validation_minOverlap200_maxUnion600.h5",
)
parser.add_argument(
    "--dtype",
    type=str,
    default="VALIDATION",
    help="Dataset type. Default: VALIDATION.",
)
parser.add_argument(
    "--index_file",
    type=str,
    default="data/embeddings/example.pkl",
    help="Path to a pickle file containing indices for TF and cell type labels."
    "Default: data/embeddings/example.pkl",
)
parser.add_argument(
    "--exclude_groups",
    type=str,
    default=None,
    nargs="+",
    help="List of group names to be excluded from evaluation. "
    "Default: None, all conditions in DATASET are included during evaluation.",
)
parser.add_argument(
    "--include_groups",
    type=str,
    default=None,
    nargs="+",
    help="List of group names to be included for evaluation."
    "Default: None, all conditions in DATASET are included during evaluation.",
)

# Save
parser.add_argument(
    "--output_dir",
    type=str,
    default="experiments/",
    help="Root directory for saving experiment results."
    "Default: experiments/",
)
parser.add_argument(
    "--experiment_name",
    type=str,
    default="training_example",
    help="experiment name.",
)
parser.add_argument(
    "--result_dir",
    type=str,
    default=None,
    help="Specify an alternative location to save checkpoint evaluation files.",
)

args = parser.parse_args()

######## Configure workflow ########
workflow = EvaluateWorkflow()

# Evaluation parameters
workflow.batch_size = args.batch_size
workflow.num_workers = args.num_workers
workflow.seed = args.seed
workflow.model_config = args.model_config
workflow.ckpt_dir = args.ckpt_dir

# Data
workflow.output_key = args.output_key
workflow.dataset = args.dataset
workflow.dtype = args.dtype
workflow.index_file = args.index_file
workflow.exclude_groups = args.exclude_groups
workflow.include_groups = args.include_groups

# Save
workflow.output_dir = args.output_dir
workflow.experiment_name = args.experiment_name
workflow.result_dir = args.result_dir

# Args
workflow.args = args

######## Model Run ########
workflow.run()