-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathtrain.sh
181 lines (173 loc) · 5.77 KB
/
train.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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
data_path=pdbbind2020
################################################################################################
prompt_nf=8
python -c "from accelerate.utils import write_basic_config; write_basic_config(mixed_precision='no')"
accelerate launch promptbind/train_promptbind.py \
--batch_size 6 \
-d 0 \
-m 5 \
--data-path $data_path \
--label baseline \
--addNoise 5 \
--resultFolder ./results \
--tqdm-interval 60 \
--use-compound-com-cls \
--distmap-pred mlp \
--total-epochs 50 \
--exp-name new_prompt_$prompt_nf \
--coord-loss-weight 1.0 \
--pair-distance-loss-weight 1.0 \
--pair-distance-distill-loss-weight 1.0 \
--pocket-cls-loss-weight 1.0 \
--pocket-distance-loss-weight 0.05 \
--lr 1e-06 --lr-scheduler poly_decay \
--distmap-pred mlp \
--hidden-size 512 --pocket-pred-hidden-size 128 \
--n-iter 12 --mean-layers 4 \
--random-n-iter \
--refine refine_coord \
--coordinate-scale 5 \
--geometry-reg-step-size 0.001 \
--rm-layernorm --add-attn-pair-bias --explicit-pair-embed --add-cross-attn-layer \
--noise-for-predicted-pocket 0 \
--clip-grad \
--pocket-idx-no-noise \
--pocket-cls-loss-func bce \
--use-esm2-feat \
--pocket-pred-layers 1 \
--pocket-pred-n-iter 1 \
--center-dist-threshold 4 \
--mixed-precision no \
--pocket-prompt-nf $prompt_nf \
--complex-prompt-nf $prompt_nf \
--disable-validate \
--disable-tqdm
################################################################################################
prompt_nf=16
python -c "from accelerate.utils import write_basic_config; write_basic_config(mixed_precision='no')"
accelerate launch promptbind/train_promptbind.py \
--batch_size 6 \
-d 0 \
-m 5 \
--data-path $data_path \
--label baseline \
--addNoise 5 \
--resultFolder ./results \
--tqdm-interval 60 \
--use-compound-com-cls \
--distmap-pred mlp \
--total-epochs 50 \
--exp-name new_prompt_$prompt_nf \
--coord-loss-weight 1.0 \
--pair-distance-loss-weight 1.0 \
--pair-distance-distill-loss-weight 1.0 \
--pocket-cls-loss-weight 1.0 \
--pocket-distance-loss-weight 0.05 \
--lr 1e-06 --lr-scheduler poly_decay \
--distmap-pred mlp \
--hidden-size 512 --pocket-pred-hidden-size 128 \
--n-iter 12 --mean-layers 4 \
--random-n-iter \
--refine refine_coord \
--coordinate-scale 5 \
--geometry-reg-step-size 0.001 \
--rm-layernorm --add-attn-pair-bias --explicit-pair-embed --add-cross-attn-layer \
--noise-for-predicted-pocket 0 \
--clip-grad \
--pocket-idx-no-noise \
--pocket-cls-loss-func bce \
--use-esm2-feat \
--pocket-pred-layers 1 \
--pocket-pred-n-iter 1 \
--center-dist-threshold 4 \
--mixed-precision no \
--pocket-prompt-nf $prompt_nf \
--complex-prompt-nf $prompt_nf \
--disable-validate \
--disable-tqdm
################################################################################################
prompt_nf=32
python -c "from accelerate.utils import write_basic_config; write_basic_config(mixed_precision='no')"
accelerate launch promptbind/train_promptbind.py \
--batch_size 6 \
-d 0 \
-m 5 \
--data-path $data_path \
--label baseline \
--addNoise 5 \
--resultFolder ./results \
--tqdm-interval 60 \
--use-compound-com-cls \
--distmap-pred mlp \
--total-epochs 50 \
--exp-name new_prompt_$prompt_nf \
--coord-loss-weight 1.0 \
--pair-distance-loss-weight 1.0 \
--pair-distance-distill-loss-weight 1.0 \
--pocket-cls-loss-weight 1.0 \
--pocket-distance-loss-weight 0.05 \
--lr 1e-06 --lr-scheduler poly_decay \
--distmap-pred mlp \
--hidden-size 512 --pocket-pred-hidden-size 128 \
--n-iter 12 --mean-layers 4 \
--random-n-iter \
--refine refine_coord \
--coordinate-scale 5 \
--geometry-reg-step-size 0.001 \
--rm-layernorm --add-attn-pair-bias --explicit-pair-embed --add-cross-attn-layer \
--noise-for-predicted-pocket 0 \
--clip-grad \
--pocket-idx-no-noise \
--pocket-cls-loss-func bce \
--use-esm2-feat \
--pocket-pred-layers 1 \
--pocket-pred-n-iter 1 \
--center-dist-threshold 4 \
--mixed-precision no \
--pocket-prompt-nf $prompt_nf \
--complex-prompt-nf $prompt_nf \
--disable-validate \
--disable-tqdm
################################################################################################
prompt_nf=48
python -c "from accelerate.utils import write_basic_config; write_basic_config(mixed_precision='no')"
accelerate launch promptbind/train_promptbind.py \
--batch_size 6 \
-d 0 \
-m 5 \
--data-path $data_path \
--label baseline \
--addNoise 5 \
--resultFolder ./results \
--tqdm-interval 60 \
--use-compound-com-cls \
--distmap-pred mlp \
--total-epochs 50 \
--exp-name new_prompt_$prompt_nf \
--coord-loss-weight 1.0 \
--pair-distance-loss-weight 1.0 \
--pair-distance-distill-loss-weight 1.0 \
--pocket-cls-loss-weight 1.0 \
--pocket-distance-loss-weight 0.05 \
--lr 1e-06 --lr-scheduler poly_decay \
--distmap-pred mlp \
--hidden-size 512 --pocket-pred-hidden-size 128 \
--n-iter 12 --mean-layers 4 \
--random-n-iter \
--refine refine_coord \
--coordinate-scale 5 \
--geometry-reg-step-size 0.001 \
--rm-layernorm --add-attn-pair-bias --explicit-pair-embed --add-cross-attn-layer \
--noise-for-predicted-pocket 0 \
--clip-grad \
--pocket-idx-no-noise \
--pocket-cls-loss-func bce \
--use-esm2-feat \
--pocket-pred-layers 1 \
--pocket-pred-n-iter 1 \
--center-dist-threshold 4 \
--mixed-precision no \
--pocket-prompt-nf $prompt_nf \
--complex-prompt-nf $prompt_nf \
--disable-validate \
--disable-tqdm