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Erva Ulusoy commited on
Commit
b9adca5
·
1 Parent(s): 301ba09

updated configs

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Files changed (3) hide show
  1. data/models/prothgt-config-biological-process.yaml +17 -45
  2. data/models/prothgt-config-cellular-component.yaml +17 -45
  3. data/models/prothgt-config-molecular-function.yaml +17 -46
data/models/prothgt-config-biological-process.yaml CHANGED
@@ -1,45 +1,17 @@
1
- lr:
2
- desc: null
3
- value: 0.001
4
- wd:
5
- desc: null
6
- value: 5.0e-05
7
- epochs:
8
- desc: null
9
- value: 100
10
- tr_batch_size:
11
- desc: null
12
- value: 1024
13
- hidden_channels:
14
- desc: null
15
- value:
16
- - 128
17
- - - 256
18
- - 128
19
- - 64
20
- - 1
21
- num_heads:
22
- desc: null
23
- value: 8
24
- num_layers:
25
- desc: null
26
- value: 2
27
- num_neighbors:
28
- desc: null
29
- value:
30
- - 256
31
- mlp_dropout:
32
- desc: null
33
- value: 0.4
34
- mlp_lr:
35
- desc: null
36
- value: 0.005
37
- mlp_wd:
38
- desc: null
39
- value: 0.0001
40
- neg_sample_ratio:
41
- desc: null
42
- value: 100
43
- pos_weight:
44
- desc: null
45
- value: 100
 
1
+ {
2
+ "lr": 0.001,
3
+ "wd": 5e-5,
4
+ "epochs": 100,
5
+ "tr_batch_size": 1024,
6
+ "hidden_channels": [128, [256, 128, 64, 1]],
7
+ "num_heads": 8,
8
+ "num_layers": 2,
9
+ "num_neighbors": [256],
10
+
11
+ "mlp_dropout" : 0.4,
12
+ "mlp_lr": 0.005,
13
+ "mlp_wd": 0.0001,
14
+
15
+ "neg_sample_ratio": 100,
16
+ "pos_weight": 100,
17
+ }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
data/models/prothgt-config-cellular-component.yaml CHANGED
@@ -1,45 +1,17 @@
1
- lr:
2
- desc: null
3
- value: 0.005
4
- wd:
5
- desc: null
6
- value: 0
7
- epochs:
8
- desc: null
9
- value: 100
10
- tr_batch_size:
11
- desc: null
12
- value: 2048
13
- hidden_channels:
14
- desc: null
15
- value:
16
- - 32
17
- - - 64
18
- - 32
19
- - 16
20
- - 1
21
- num_heads:
22
- desc: null
23
- value: 16
24
- num_layers:
25
- desc: null
26
- value: 3
27
- num_neighbors:
28
- desc: null
29
- value:
30
- - 256
31
- mlp_dropout:
32
- desc: null
33
- value: 0.2
34
- mlp_lr:
35
- desc: null
36
- value: 0.01
37
- mlp_wd:
38
- desc: null
39
- value: 0
40
- neg_sample_ratio:
41
- desc: null
42
- value: 100
43
- pos_weight:
44
- desc: null
45
- value: 100
 
1
+ {
2
+ "lr": 0.005,
3
+ "wd": 0,
4
+ "epochs": 100,
5
+ "tr_batch_size": 2048,
6
+ "hidden_channels": [32, [64, 32, 16, 1]],
7
+ "num_heads": 16,
8
+ "num_layers": 3,
9
+ "num_neighbors": [256],
10
+
11
+ "mlp_dropout" : 0.2,
12
+ "mlp_lr": 0.01,
13
+ "mlp_wd": 0,
14
+
15
+ "neg_sample_ratio": 100,
16
+ "pos_weight": 100,
17
+ }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
data/models/prothgt-config-molecular-function.yaml CHANGED
@@ -1,46 +1,17 @@
1
- lr:
2
- desc: null
3
- value: 0.005
4
- wd:
5
- desc: null
6
- value: 0
7
- epochs:
8
- desc: null
9
- value: 100
10
- tr_batch_size:
11
- desc: null
12
- value: 512
13
- hidden_channels:
14
- desc: null
15
- value:
16
- - 32
17
- - - 64
18
- - 32
19
- - 16
20
- - 8
21
- - 1
22
- num_heads:
23
- desc: null
24
- value: 2
25
- num_layers:
26
- desc: null
27
- value: 2
28
- num_neighbors:
29
- desc: null
30
- value:
31
- - 32
32
- mlp_dropout:
33
- desc: null
34
- value: 0.4
35
- mlp_lr:
36
- desc: null
37
- value: 0.01
38
- mlp_wd:
39
- desc: null
40
- value: 1.0e-05
41
- neg_sample_ratio:
42
- desc: null
43
- value: 100
44
- pos_weight:
45
- desc: null
46
- value: 100
 
1
+ {
2
+ "lr": 0.005,
3
+ "wd": 0,
4
+ "epochs": 100,
5
+ "tr_batch_size": 512,
6
+ "hidden_channels": [32, [64, 32, 16, 8, 1]],
7
+ "num_heads": 2,
8
+ "num_layers": 2,
9
+ "num_neighbors": [32],
10
+
11
+ "mlp_dropout" : 0.4,
12
+ "mlp_lr": 0.01,
13
+ "mlp_wd": 0.00001,
14
+
15
+ "neg_sample_ratio": 100,
16
+ "pos_weight": 100,
17
+ }