-
Notifications
You must be signed in to change notification settings - Fork 1
/
config.json
97 lines (96 loc) · 2.63 KB
/
config.json
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
{
"CPU_LIMIT": 5,
"TIMEKEEP":true,
"ignore": {
"cord_loader": true,
"downloader": false,
"text_loader":true,
"pubmed_bulk_loader":true,
"splitter": false,
"ner": false,
"analysis": false,
"merger": true,
"metrics":true,
"nel":true,
"result_inspection":true
},
"downloader": {
"input_path": "data/Lund-Autophagy-1.txt",
"output_path": "results/dataloader/text.json",
"batch_size": 100
},
"cord_loader": {
"input_path": "data/metadata.csv",
"output_path": "results/dataloader/text.json",
"subset":false,
"subset_file": ""
},
"text_loader": {
"input_path": "data/freetext.txt",
"output_path": "results/dataloader/text.json",
"prefix": "freetext"
},
"pubmed_bulk_loader": {
"output_path": "data/pubmed/",
"baseline": "24",
"subset": true,
"subset_range":[0,3],
"get_nightly_update_files": false,
"update_file_range":[0,0],
"count_articles": true,
"raw_download_path": ""
},
"splitter": {
"input_path": "results/dataloader/text.json",
"output_folder": "results/splitter/",
"output_file_prefix": "sentences",
"pubmed_bulk": false,
"file_limit":[0,100],
"tokenizer": "spacy",
"model_name": "en_core_web_sm",
"batch_size": 100
},
"ner": {
"input_path": "results/splitter/",
"output_path": "results/ner/",
"output_file_prefix": "ner_chemical",
"model_type": "biobert_finetuned",
"model_folder": "aitslab",
"model_name": "biobert_huner_chemical_v1",
"vocab_path": "",
"store_tokens":"no",
"labels": "",
"clear_old_results": true,
"article_limit": [-1,90000],
"entity_type": "chemical",
"multiprocessing":true
},
"analysis": {
"input_path": "results/ner/",
"output_path": "results/analysis/",
"entity_type":"chemical",
"plot_top_n":50
},
"merger": {
"paths": ["results/ner/model-1/", "results/ner/model-2/", "results/ner/model-3/"],
"entities": ["model-1_entity", "model-2_entity","model-3_entity"],
"output_path": "results/merged/path/to/merged-folder/",
"output_prefix": "merged"
},
"metrics": {
"predictions_file":"path/to/predictions/file.txt",
"true_file":"path/to/true/annotated/file.txt",
"output_file":"results/metrics/path/to/metrics_file.txt",
"pred_sep": " ",
"true_sep":" "
},
"nel":{
"input_path": "results/text-ner-Lund-Autophagy-1_species/",
"output_path": "results/text-nel_Lund_Autophagy-1_species.json"
},
"result_inspection":{
"input_folder": "results/ner/",
"output_file": "results/ner_search.txt",
"entities": ["tsc", "mtor", "cell", "cells", "rapamycin"]
}
}