Update model zoo metadata
Browse files
configs/finetune_cremi_real_unetr_aniso_em_mse_maws_publicem_r16_seed309_long20k_r48q.yaml
ADDED
|
@@ -0,0 +1,95 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
seed: 309
|
| 2 |
+
device: cuda
|
| 3 |
+
output_dir: /volume/med-train/users/dchen02/code/dbMiM/outputs/finetune_cremi_real_unetr_aniso_em_mse_maws_publicem_r16_seed309_long20k_r48q
|
| 4 |
+
pretrained: /volume/med-train/users/dchen02/code/dbMiM/outputs/pretrain_public_em_membrane_dbmim_r16/pretrained_latest.pt
|
| 5 |
+
data:
|
| 6 |
+
synthetic: false
|
| 7 |
+
image_paths:
|
| 8 |
+
- /volume/med-train/users/dchen02/code/dbMiM/data/CREMI
|
| 9 |
+
label_paths:
|
| 10 |
+
- /volume/med-train/users/dchen02/code/dbMiM/data/CREMI
|
| 11 |
+
image_keys:
|
| 12 |
+
- volumes/raw
|
| 13 |
+
- raw
|
| 14 |
+
- main
|
| 15 |
+
label_keys:
|
| 16 |
+
- volumes/labels/neuron_ids
|
| 17 |
+
- labels
|
| 18 |
+
- label
|
| 19 |
+
- gt
|
| 20 |
+
volume_size:
|
| 21 |
+
- 32
|
| 22 |
+
- 160
|
| 23 |
+
- 160
|
| 24 |
+
length_multiplier: 2048
|
| 25 |
+
augment: true
|
| 26 |
+
widen_border: true
|
| 27 |
+
widen_border_radius: 1
|
| 28 |
+
augment_rotate_xy: true
|
| 29 |
+
augment_gamma: true
|
| 30 |
+
augment_gamma_range:
|
| 31 |
+
- 0.7
|
| 32 |
+
- 1.5
|
| 33 |
+
augment_noise_std: 0.035
|
| 34 |
+
model:
|
| 35 |
+
architecture: unetr_aniso_em
|
| 36 |
+
in_channels: 1
|
| 37 |
+
out_channels: 3
|
| 38 |
+
volume_size:
|
| 39 |
+
- 32
|
| 40 |
+
- 160
|
| 41 |
+
- 160
|
| 42 |
+
patch_size:
|
| 43 |
+
- 4
|
| 44 |
+
- 16
|
| 45 |
+
- 16
|
| 46 |
+
embed_dim: 192
|
| 47 |
+
depth: 6
|
| 48 |
+
num_heads: 6
|
| 49 |
+
feature_size: 32
|
| 50 |
+
dropout: 0.05
|
| 51 |
+
em_refine_depth: 2
|
| 52 |
+
channel_bias_init:
|
| 53 |
+
- -0.2
|
| 54 |
+
- 0.0
|
| 55 |
+
- 0.0
|
| 56 |
+
train:
|
| 57 |
+
batch_size: 2
|
| 58 |
+
epochs: 200
|
| 59 |
+
max_steps: 20000
|
| 60 |
+
num_workers: 8
|
| 61 |
+
lr: 8.0e-05
|
| 62 |
+
weight_decay: 0.01
|
| 63 |
+
amp: true
|
| 64 |
+
log_every: 20
|
| 65 |
+
eval_every: 0
|
| 66 |
+
eval_max_batches: 0
|
| 67 |
+
save_every: 0
|
| 68 |
+
save_steps: 1000
|
| 69 |
+
val_fraction: 0.0
|
| 70 |
+
clip_grad: 1.0
|
| 71 |
+
replicate_affinity_boundary: true
|
| 72 |
+
loss:
|
| 73 |
+
loss_type: mse
|
| 74 |
+
bce_weight: 1.0
|
| 75 |
+
dice_weight: 0.0
|
| 76 |
+
boundary_dice_weight: 0.0
|
| 77 |
+
bcar_weight: 0.0
|
| 78 |
+
bcar_calibration_weight: 0.0
|
| 79 |
+
membrane_weight: 0.75
|
| 80 |
+
membrane_axis_weights:
|
| 81 |
+
- 0.25
|
| 82 |
+
- 1.0
|
| 83 |
+
- 1.0
|
| 84 |
+
membrane_clip: 4.0
|
| 85 |
+
membrane_normalize: true
|
| 86 |
+
channel_weights:
|
| 87 |
+
- 1.35
|
| 88 |
+
- 1.0
|
| 89 |
+
- 1.0
|
| 90 |
+
encoder_lr: 1.0e-05
|
| 91 |
+
encoder_param_prefixes:
|
| 92 |
+
- pos_embed
|
| 93 |
+
- patch_embed
|
| 94 |
+
- encoder_blocks
|
| 95 |
+
- norm
|