-
Notifications
You must be signed in to change notification settings - Fork 10
/
run.sh
133 lines (103 loc) · 5.16 KB
/
run.sh
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
# fd means: fudan's CMDD dataset
# cy means: ours chunyu dataset
# the number following dis means: the id of target disease
# notice that there are three modes: train / fine-tune / evaluate
# Pretrain-Only setting (Multi-task learning): train + evaluate directly
# Fine-tuning setting: train + fine-tuning + evaluate
# Meta-learning setting: meta-train (w/o graph-evolving) + fine-tuning + evaluate
# GEML setting: meta-train + fine-tuning + evaluate
# geml: our method
# kgr: our ablated method (w/o graph-evolving)
# nkd: NKD
# poks: POKS
# Follwing commands are what we used mostly:
CUDA_VISIBLE_DEVICES=1 allennlp train -s /data3/linshuai/gen/save_fd/geml/geml_hidden_dis17_test1 \
our.json \
--include-package our_geml_fd
CUDA_VISIBLE_DEVICES=1 allennlp train -s /data3/linshuai/gen/save_fd/geml/geml_hidden_test1 \
our.json \
--include-package our_geml_cy
CUDA_VISIBLE_DEVICES=3 allennlp train -s /data3/linshuai/gen/save_fd/pretrain/nkd_dis9_test1 \
NKD.json \
--include-package NKD
#meta
CUDA_VISIBLE_DEVICES=5 allennlp train -s /data3/linshuai/gen/save_fd/meta/kgr_dis17_test1 \
our.json \
--include-package our_meta_fd
CUDA_VISIBLE_DEVICES=5 allennlp train -s /data3/linshuai/gen/save_fd/meta/kgr_dis17_test1 \
our.json \
--include-package our_meta_fd
CUDA_VISIBLE_DEVICES=4 allennlp train -s /data3/linshuai/gen/save_fd/meta/poks_dis9_test1 \
poks.json \
--include-package poks
CUDA_VISIBLE_DEVICES=5 allennlp train -s /data3/linshuai/gen/save_fd/geml/geml_dis9_test1 \
our.json \
--include-package our_old_fd
CUDA_VISIBLE_DEVICES=4 allennlp evaluate /data3/linshuai/gen/save/ours_ft_fulldata1_dis73_0.1 \
cy/dis_pk_dir/test_cy_73.pk \
--include-package our_old\
--output-file /data3/linshuai/gen/save/ours_ft_fulldata1_dis73_0.1.txt
CUDA_VISIBLE_DEVICES=4 allennlp fine-tune -m /data3/linshuai/gen/save/ours_fulldata_1 \
-c our_ft.json \
--include-package our_old \
-s /data3/linshuai/gen/save/ours_ft_fulldata1_dis73_0.1
CUDA_VISIBLE_DEVICES=3 allennlp evaluate /data3/linshuai/gen/save/ft/geml_lr0.01_3 \
cy/dis_pk_dir/meta_test/test_cy_52.pk \
--include-package our_eval \
--output-file /data3/linshuai/gen/save/ft/geml_ft_lr0.01_3
CUDA_VISIBLE_DEVICES=3 allennlp evaluate /data3/linshuai/gen/save/pretrain/poks_dis9_test1 \
cy/dis_pk_dir/meta_test/test_cy_46.pk \
--include-package poks \
--output-file /data3/linshuai/gen/save/ztpoks_zt_pret_dis46_1
CUDA_VISIBLE_DEVICES=3 allennlp evaluate /data3/linshuai/gen/save/ft/kgr_meta_dis46_4 \
cy/dis_pk_dir/meta_test/test_cy_46.pk \
--include-package our_eval \
--output-file /data3/linshuai/gen/save/ft/kgr_ft_meta_dis46_4
CUDA_VISIBLE_DEVICES=3 allennlp fine-tune -m /data3/linshuai/gen/save/meta/kgr_test1 \
-c our_ft.json \
--include-package our_old \
-s /data3/linshuai/gen/save/ft/kgr_meta_dis46_4
CUDA_VISIBLE_DEVICES=0 allennlp fine-tune -m /data3/linshuai/gen/save/geml/geml_hidden_1 \
-c our_ft.json \
--include-package our_old \
-s /data3/linshuai/gen/save/ft/geml_dis52_1
CUDA_VISIBLE_DEVICES=1 allennlp evaluate /data3/linshuai/gen/save/geml/geml5 \
cy/dis_pk_dir/meta_test/test_cy_73.pk \
--include-package our_eval \
--output-file /data3/linshuai/gen/save/zt/geml5
CUDA_VISIBLE_DEVICES=1 allennlp evaluate /data3/linshuai/gen/save/discussion/geml_dis52_30_1 \
cy/dis_pk_dir/meta_test/test_cy_52.pk \
--include-package our_eval \
--output-file /data3/linshuai/gen/save/zt/geml_dis52_30_1
CUDA_VISIBLE_DEVICES=0 allennlp train -s /data3/linshuai/gen/save/geml/geml_hidden_1 \
our.json \
--include-package our_geml_cy
#zs
CUDA_VISIBLE_DEVICES=1 allennlp evaluate /data3/linshuai/gen/save_fd/discussion/geml_hidden_dis9_100_test2 \
fd/dis_pk_dir/meta_test/test_fd_9.pk \
--include-package our_geml_eval_fd \
--output-file /data3/linshuai/gen/save_fd/discussion/geml_hidden_dis9_100_test2_human
CUDA_VISIBLE_DEVICES=6 allennlp evaluate /data3/linshuai/gen/save/discussion/geml_hidden_dis9_50_test2 \
cy/dis_pk_dir/meta_test/test_cy_73.pk \
--include-package poks_cy \
--output-file /data3/linshuai/gen/save/pret/poks_pret_eval_dis73_1
CUDA_VISIBLE_DEVICES=0 allennlp fine-tune -m /data3/linshuai/gen/save_fd/geml/geml_hidden_dis9_test2 \
-c our_ft.json \
--include-package our_geml_fd \
-s /data3/linshuai/gen/save_fd/discussion/geml_hidden_dis9_100_test2
CUDA_VISIBLE_DEVICES=1 allennlp fine-tune -m /data3/linshuai/gen/save_fd/meta/kgr_dis9_test1 \
-c our_ft.json \
--include-package our_old_fd \
-s /data3/linshuai/gen/save_fd/ft/kgr_pret_dis9_test1
CUDA_VISIBLE_DEVICES=0 allennlp fine-tune -m /data3/linshuai/gen/save_fd/geml/geml_dis9_test1 \
-c our_ft.json \
--include-package our_geml_fd \
-s /data3/linshuai/gen/save_fd/zt/geml_hidden_dis9_test2
CUDA_VISIBLE_DEVICES=6 allennlp fine-tune -m /data3/linshuai/gen/save_fd/pretrain/kgr_dis9_test1 \
-c our_ft.json \
--include-package poks \
-s /data3/linshuai/gen/save_fd/ft/poks_meta_dis9_test1
CUDA_VISIBLE_DEVICES=7 allennlp evaluate /data3/linshuai/gen/save_fd/ft/poks_meta_dis17_test1 \
fd/dis_pk_dir/meta_test_old/test_fd_17.pk \
--include-package poks \
--output-file /data3/linshuai/gen/save_fd/ft/poks_meta_eval_dis17_test1