-
Notifications
You must be signed in to change notification settings - Fork 12
/
classifier_fine_tune_b2.sh
136 lines (114 loc) · 5.03 KB
/
classifier_fine_tune_b2.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
#!/bin/sh
#SBATCH --output=/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/psc_logs/b2_cls_ft_%j.out
pwd
hostname
date
CURRENT=$(date +"%Y-%m-%d_%T")
echo $CURRENT
slurm_output_train_mass=/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/psc_logs/b2_cls_ft_mass_$CURRENT.out
slurm_output_train_calc=/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/psc_logs/b2_cls_ft_calc_$CURRENT.out
slurm_output_train_density=/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/psc_logs/b2_cls_ft_density_$CURRENT.out
slurm_output_train_cancer=/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/psc_logs/b2_cls_ft_cancer_$CURRENT.out
echo "Mammo-clip b2"
source /ocean/projects/asc170022p/shg121/anaconda3/etc/profile.d/conda.sh
conda activate breast_clip_rtx_6000
# Mass (VinDr)
python ./src/codebase/train_classifier.py \
--img-dir 'External/Vindr/vindr-mammo-a-large-scale-benchmark-dataset-for-computer-aided-detection-and-diagnosis-in-full-field-digital-mammography-1.0.0/images_png' \
--csv-file 'External/Vindr/vindr-mammo-a-large-scale-benchmark-dataset-for-computer-aided-detection-and-diagnosis-in-full-field-digital-mammography-1.0.0/vindr_detection_v1_folds.csv' \
--clip_chk_pt_path "/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/codebase/outputs/upmc_clip/b2_detector_period_n/checkpoints/fold_0/b2-model-best-epoch-10.tar" \
--data_frac 1.0 \
--dataset 'ViNDr' \
--arch 'upmc_breast_clip_det_b2_period_n_ft' \
--label "Mass" \
--epochs 30 \
--batch-size 8 \
--num-workers 0 \
--print-freq 10000 \
--log-freq 500 \
--running-interactive 'n' \
--n_folds 1 \
--lr 5.0e-5 \
--weighted-BCE 'y' \
--balanced-dataloader 'n' >$slurm_output_train_mass
# Suspicious_Calcification (VinDr)
python ./src/codebase/train_classifier.py \
--img-dir 'External/Vindr/vindr-mammo-a-large-scale-benchmark-dataset-for-computer-aided-detection-and-diagnosis-in-full-field-digital-mammography-1.0.0/images_png' \
--csv-file 'External/Vindr/vindr-mammo-a-large-scale-benchmark-dataset-for-computer-aided-detection-and-diagnosis-in-full-field-digital-mammography-1.0.0/vindr_detection_v1_folds.csv' \
--clip_chk_pt_path "/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/codebase/outputs/upmc_clip/b2_detector_period_n/checkpoints/fold_0/b2-model-best-epoch-10.tar" \
--data_frac 1.0 \
--dataset 'ViNDr' \
--arch 'upmc_breast_clip_det_b2_period_n_ft' \
--label "Suspicious_Calcification" \
--epochs 30 \
--batch-size 8 \
--num-workers 0 \
--print-freq 10000 \
--log-freq 500 \
--running-interactive 'n' \
--n_folds 1 \
--lr 5.0e-5 \
--weighted-BCE 'y' \
--balanced-dataloader 'n'>$slurm_output_train_calc
# Density (VinDr)
python ./src/codebase/train_classifier.py \
--img-dir 'External/Vindr/vindr-mammo-a-large-scale-benchmark-dataset-for-computer-aided-detection-and-diagnosis-in-full-field-digital-mammography-1.0.0/images_png' \
--csv-file 'External/Vindr/vindr-mammo-a-large-scale-benchmark-dataset-for-computer-aided-detection-and-diagnosis-in-full-field-digital-mammography-1.0.0/vindr_detection_v1_folds.csv' \
--clip_chk_pt_path "/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/codebase/outputs/upmc_clip/b2_detector_period_n/checkpoints/fold_0/b2-model-best-epoch-10.tar" \
--data_frac 1.0 \
--dataset 'ViNDr' \
--arch 'upmc_breast_clip_det_b2_period_n_ft' \
--label "density" \
--epochs 30 \
--batch-size 8 \
--num-workers 0 \
--print-freq 10000 \
--log-freq 500 \
--running-interactive 'n' \
--n_folds 1 \
--lr 5.0e-5 \
--weighted-BCE 'y' \
--balanced-dataloader 'n'>$slurm_output_train_density
# Cancer (RSNA)
python ./src/codebase/train_classifier.py \
--img-dir 'RSNA_Cancer_Detection/train_images_png' \
--csv-file 'RSNA_Cancer_Detection/train_folds.csv' \
--clip_chk_pt_path "/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/codebase/outputs/upmc_clip/b2_detector_period_n/checkpoints/fold_0/b2-model-best-epoch-10.tar" \
--dataset 'RSNA' \
--data_frac 1.0 \
--label "cancer" \
--n_folds 1 \
--lr 5e-5 \
--weight-decay 1e-4 \
--warmup-epochs 1 \
--arch 'upmc_breast_clip_det_b2_period_n_ft' \
--epochs 20 \
--batch-size 6 \
--num-workers 0 \
--print-freq 10000 \
--log-freq 500 \
--running-interactive 'n' \
--lr 5.0e-5 \
--weighted-BCE 'y' \
--balanced-dataloader 'n'>$slurm_output_train_cancer
python ./src/codebase/train_classifier.py \
--img-dir 'RSNA_Cancer_Detection/train_images_png' \
--csv-file 'RSNA_Cancer_Detection/train_folds.csv' \
--clip_chk_pt_path "/restricted/projectnb/batmanlab/shawn24/PhD/Mammo-CLIP/src/codebase/outputs/upmc_clip/b2_detector_period_n/checkpoints/fold_0/b2-model-best-epoch-10.tar" \
--dataset 'RSNA' \
--data_frac 1.0 \
--label "cancer" \
--n_folds 1 \
--lr 5e-5 \
--weight-decay 1e-4 \
--warmup-epochs 1 \
--arch 'upmc_breast_clip_det_b2_period_n_ft' \
--epochs 20 \
--batch-size 6 \
--num-workers 0 \
--print-freq 10000 \
--log-freq 500 \
--running-interactive 'y' \
--lr 5.0e-5 \
--weighted-BCE 'y' \
--balanced-dataloader 'n'