-
Notifications
You must be signed in to change notification settings - Fork 0
/
binary_rxrx2_predictions.yaml
56 lines (56 loc) · 1.69 KB
/
binary_rxrx2_predictions.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
ckpt_path: /path/to/deep-paint/results/models/binary_rxrx2.ckpt # update path to the trained model
model:
class_path: deep_paint.lightning.DeepLightningModule
data:
class_path: deep_paint.lightning.DeepLightningDataModule
init_args:
data_dir: /path/to/rxrx2 # update path to the rxrx2 dataset
metadata_path: /path/to/rxrx2_binary.csv # update path to the binary metadata
image_ext: .png
path_col: directory
label_col: label
stratify_col: label
group_col: null
channels: true
channel_map:
DNA: _w1
ER: _w2
Actin: _w3
RNA: _w4
Mitochondria: _w5
Golgi: _w6
sizes: [0.7, 0.15, 0.15]
predict_metadata: test
test_transforms:
class_path: torchvision.transforms.Compose
init_args:
transforms:
- class_path: torchvision.transforms.ToTensor
- class_path: torchvision.transforms.Normalize
init_args:
mean: [0.0140, 0.0617, 0.0316, 0.0348, 0.0072, 0.0444]
std: [0.0237, 0.0550, 0.0150, 0.0287, 0.0068, 0.0250]
batch_size: 16
num_workers: 16 # update to equal the number of CPU cores
seed: 42
trainer:
accelerator: gpu
devices: 1
max_epochs: 1
deterministic: true
logger:
class_path: lightning.pytorch.loggers.TensorBoardLogger
init_args:
save_dir: /path/to/save_dir # update path to your save directory
name: logs
callbacks:
- class_path: deep_paint.lightning.PlotConfusionMatrix
init_args:
plot_every_n_epochs: 1
backend: matplotlib
label_col: label
class_col: class
save: false
- class_path: lightning.pytorch.callbacks.RichModelSummary
init_args:
max_depth: 2