-
Notifications
You must be signed in to change notification settings - Fork 4
/
config.yaml
158 lines (158 loc) · 2.79 KB
/
config.yaml
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
CUDA_VISIBLE_DEVICES: 3
logging:
log_dir: /data5/ziweicui/cellvit256-unireplknet-n
mode: online
project: Cell-Segmentation
notes: CellViT-256
log_comment: CellViT-256-resnet50-tiny
tags:
- Fold-1
- ViT256
wandb_dir: /data5/ziweicui/UniRepLKNet-optimizerconfig-unetdecoder-inputconv/results
level: Debug
group: CellViT256
run_id: anifw9ux
wandb_file: anifw9ux
random_seed: 19
gpu: 0
data:
dataset: PanNuke
dataset_path: /data5/ziweicui/cellvit-png
train_folds:
- 0
val_folds:
- 1
test_folds:
- 2
num_nuclei_classes: 6
num_tissue_classes: 19
model:
backbone: default
pretrained_encoder: /data5/ziweicui/semi_supervised_resnet50-08389792.pth
shared_skip_connections: true
loss:
nuclei_binary_map:
focaltverskyloss:
loss_fn: FocalTverskyLoss
weight: 1
dice:
loss_fn: dice_loss
weight: 1
hv_map:
mse:
loss_fn: mse_loss_maps
weight: 2.5
msge:
loss_fn: msge_loss_maps
weight: 8
nuclei_type_map:
bce:
loss_fn: xentropy_loss
weight: 0.5
dice:
loss_fn: dice_loss
weight: 0.2
mcfocaltverskyloss:
loss_fn: MCFocalTverskyLoss
weight: 0.5
args:
num_classes: 6
tissue_types:
ce:
loss_fn: CrossEntropyLoss
weight: 0.1
training:
drop_rate: 0
attn_drop_rate: 0.1
drop_path_rate: 0.1
batch_size: 32
epochs: 130
optimizer: AdamW
early_stopping_patience: 130
scheduler:
scheduler_type: cosine
hyperparameters:
#gamma: 0.85
eta_min: 1e-5
optimizer_hyperparameter:
# betas:
# - 0.85
# - 0.95
#lr: 0.004
opt_lower: 'AdamW'
lr: 0.0008
opt_betas: [0.85,0.95]
weight_decay: 0.05
opt_eps: 0.00000008
unfreeze_epoch: 25
sampling_gamma: 0.85
sampling_strategy: cell+tissue
mixed_precision: true
transformations:
randomrotate90:
p: 0.5
horizontalflip:
p: 0.5
verticalflip:
p: 0.5
downscale:
p: 0.15
scale: 0.5
blur:
p: 0.2
blur_limit: 10
gaussnoise:
p: 0.25
var_limit: 50
colorjitter:
p: 0.2
scale_setting: 0.25
scale_color: 0.1
superpixels:
p: 0.1
zoomblur:
p: 0.1
randomsizedcrop:
p: 0.1
elastictransform:
p: 0.2
normalize:
mean:
- 0.5
- 0.5
- 0.5
std:
- 0.5
- 0.5
- 0.5
eval_checkpoint: latest_checkpoint.pth
dataset_config:
tissue_types:
Adrenal_gland: 0
Bile-duct: 1
Bladder: 2
Breast: 3
Cervix: 4
Colon: 5
Esophagus: 6
HeadNeck: 7
Kidney: 8
Liver: 9
Lung: 10
Ovarian: 11
Pancreatic: 12
Prostate: 13
Skin: 14
Stomach: 15
Testis: 16
Thyroid: 17
Uterus: 18
nuclei_types:
Background: 0
Neoplastic: 1
Inflammatory: 2
Connective: 3
Dead: 4
Epithelial: 5
run_sweep: false
agent: null