Add R57 repeat checkpoint and update model zoo
Browse files
configs/finetune_cremi_real_unetr_aniso_em_mse_maws_publicem_r16_seed777_long20k_r57q.yaml
ADDED
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| 1 |
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seed: 777
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| 2 |
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device: cuda
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output_dir: /volume/med-train/users/dchen02/code/dbMiM/outputs/finetune_cremi_real_unetr_aniso_em_mse_maws_publicem_r16_seed777_long20k_r57q
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pretrained: /volume/med-train/users/dchen02/code/dbMiM/outputs/pretrain_public_em_membrane_dbmim_r16/pretrained_latest.pt
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data:
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synthetic: false
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image_paths:
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- /volume/med-train/users/dchen02/code/dbMiM/data/CREMI
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label_paths:
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- /volume/med-train/users/dchen02/code/dbMiM/data/CREMI
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image_keys:
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- volumes/raw
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- raw
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- main
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label_keys:
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- volumes/labels/neuron_ids
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- labels
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- label
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- gt
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volume_size:
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- 32
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- 160
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- 160
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length_multiplier: 2048
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augment: true
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widen_border: true
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widen_border_radius: 1
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augment_rotate_xy: true
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augment_gamma: true
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augment_gamma_range:
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- 0.7
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- 1.5
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augment_noise_std: 0.035
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model:
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architecture: unetr_aniso_em
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in_channels: 1
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out_channels: 3
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volume_size:
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- 32
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- 160
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- 160
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patch_size:
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- 4
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- 16
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- 16
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embed_dim: 192
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depth: 6
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num_heads: 6
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feature_size: 32
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dropout: 0.05
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em_refine_depth: 2
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channel_bias_init:
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- -0.2
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- 0.0
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- 0.0
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train:
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batch_size: 2
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epochs: 200
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max_steps: 20000
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num_workers: 8
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lr: 8.0e-05
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weight_decay: 0.01
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amp: true
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log_every: 20
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eval_every: 0
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eval_max_batches: 0
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save_every: 0
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save_steps: 1000
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val_fraction: 0.0
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clip_grad: 1.0
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replicate_affinity_boundary: true
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loss:
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loss_type: mse
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bce_weight: 1.0
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dice_weight: 0.0
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boundary_dice_weight: 0.0
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bcar_weight: 0.0
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bcar_calibration_weight: 0.0
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membrane_weight: 0.75
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membrane_axis_weights:
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- 0.25
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- 1.0
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- 1.0
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membrane_clip: 4.0
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membrane_normalize: true
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channel_weights:
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- 1.35
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- 1.0
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- 1.0
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encoder_lr: 1.0e-05
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encoder_param_prefixes:
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- pos_embed
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- patch_embed
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- encoder_blocks
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- norm
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