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CELL-E_2_HPA_Finetuned_480

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PyTorch
Transformers
biology
microscopy
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Emaad commited on
Commit
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Files changed (2) hide show
  1. nucleus_vqgan.yaml +45 -0
  2. threshold_vqgan.yaml +46 -0
nucleus_vqgan.yaml ADDED
@@ -0,0 +1,45 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ model:
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+ base_learning_rate: 4.5e-06
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+ target: taming.models.vqgan.VQModel
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+ params:
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+ image_key: nucleus
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+ monitor: val/rec_loss
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+ ckpt_path:
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+ embed_dim: 256
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+ n_embed: 512
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+ ddconfig:
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+ double_z: false
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+ z_channels: 256
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+ resolution: 256
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+ in_channels: 1
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+ out_ch: 1
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+ ch: 128
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+ ch_mult:
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+ - 1
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+ - 1
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+ - 2
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+ - 2
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+ - 4
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+ num_res_blocks: 2
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+ attn_resolutions:
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+ - 16
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+ dropout: 0.0
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+ lossconfig:
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+ target: taming.modules.losses.vqperceptual.VQLPIPSWithDiscriminator
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+ params:
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+ disc_conditional: false
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+ disc_in_channels: 1
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+ disc_start: 50000
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+ disc_weight: 0.2
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+ codebook_weight: 1.0
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+
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+ data:
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+ target: celle_main.CellDataModule
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+ params:
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+ data_csv: /data/HPA/train_test_split_50_pct_cluster.csv
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+ dataset: HPA
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+ text_seq_len: 0
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+ crop_size: 256
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+ resize: 600
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+ batch_size: 7
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+ num_workers: 8
threshold_vqgan.yaml ADDED
@@ -0,0 +1,46 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ model:
2
+ base_learning_rate: 4.5e-05
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+ target: taming.models.vqgan.VQModel
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+ params:
5
+ image_key: threshold
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+ monitor: val/rec_loss
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+ ckpt_path:
8
+ embed_dim: 256
9
+ n_embed: 512
10
+ ddconfig:
11
+ double_z: false
12
+ z_channels: 256
13
+ resolution: 256
14
+ in_channels: 1
15
+ out_ch: 1
16
+ ch: 128
17
+ ch_mult:
18
+ - 1
19
+ - 1
20
+ - 2
21
+ - 2
22
+ - 4
23
+ num_res_blocks: 2
24
+ attn_resolutions:
25
+ - 16
26
+ dropout: 0.0
27
+ lossconfig:
28
+ target: taming.modules.losses.vqperceptual.VQLPIPSWithDiscriminator
29
+ params:
30
+ disc_conditional: false
31
+ disc_in_channels: 1
32
+ disc_start: 100000
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+ disc_weight: 0.2
34
+ codebook_weight: 1.0
35
+
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+ data:
37
+ target: celle_main.CellDataModule
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+ params:
39
+ data_csv: data/HPA/train_test_split_50_pct_cluster.csv
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+ dataset: HPA
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+ text_seq_len: 0
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+ threshold: median
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+ crop_size: 256
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+ resize: 600
45
+ batch_size: 7
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+ num_workers: 8