Upload 15 files

checkpoints/checkpoint_epoch_579.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:44a2d223c90828fe19858511c02f980222b61b67debb1efd910daf7a23ccc329
+size 172060937

config.toml

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+experiment_name = "unet_dec_21"
+base_dir = "/exports/csce/eddie/eng/groups/DunnGroup/matthew/models_gelgenie"
+
+[processing]
+base_hardware = "EDDIE"
+device = "GPU"
+pe = 1
+memory = 64
+
+[data]
+n_channels = 1
+batch_size = 2
+num_workers = 1
+val_percent = 10
+dir_train_mask = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/quantitation_ladder_gels/masks",]
+dir_train_img = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/quantitation_ladder_gels/images",]
+dir_val_img = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/quantitation_ladder_gels/val_images",]
+dir_val_mask = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/quantitation_ladder_gels/val_masks",]
+split_training_dataset = false
+apply_augmentations = true
+padding = true
+individual_padding = false
+weak_augmentations = false
+minmax_norm = false
+
+[model]
+model_name = "smp_unet"
+classes = 2
+in_channels = 1
+encoder_name = "resnet18"
+
+[training]
+loss = [ "dice", "crossentropy",]
+loss_component_weighting = [ 1, 1,]
+class_loss_weighting = false
+class_loss_weight_damper = [ 1.0, 1.0,]
+lr = 0.0001
+epochs = 600
+grad_scaler = true
+load_checkpoint = false
+optimizer_type = "adam"
+scheduler_type = "CosineAnnealingWarmRestarts"
+save_checkpoint = true
+checkpoint_frequency = 1
+wandb_track = true
+model_cleanup_frequency = 20
+wandb_id = "2eoqe1dp"
+
+[training.scheduler_specs]
+restart_period = 100

model_structure.txt

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+======================================================================
+Layer (type:depth-idx)                        Param #
+======================================================================
+smp_UNet                                      --
+├─ResNetEncoder: 1-1                          --
+│    └─Conv2d: 2-1                            3,136
+│    └─BatchNorm2d: 2-2                       128
+│    └─ReLU: 2-3                              --
+│    └─MaxPool2d: 2-4                         --
+│    └─Sequential: 2-5                        --
+│    │    └─BasicBlock: 3-1                   --
+│    │    │    └─Conv2d: 4-1                  36,864
+│    │    │    └─BatchNorm2d: 4-2             128
+│    │    │    └─ReLU: 4-3                    --
+│    │    │    └─Conv2d: 4-4                  36,864
+│    │    │    └─BatchNorm2d: 4-5             128
+│    │    └─BasicBlock: 3-2                   --
+│    │    │    └─Conv2d: 4-6                  36,864
+│    │    │    └─BatchNorm2d: 4-7             128
+│    │    │    └─ReLU: 4-8                    --
+│    │    │    └─Conv2d: 4-9                  36,864
+│    │    │    └─BatchNorm2d: 4-10            128
+│    └─Sequential: 2-6                        --
+│    │    └─BasicBlock: 3-3                   --
+│    │    │    └─Conv2d: 4-11                 73,728
+│    │    │    └─BatchNorm2d: 4-12            256
+│    │    │    └─ReLU: 4-13                   --
+│    │    │    └─Conv2d: 4-14                 147,456
+│    │    │    └─BatchNorm2d: 4-15            256
+│    │    │    └─Sequential: 4-16             --
+│    │    │    │    └─Conv2d: 5-1             8,192
+│    │    │    │    └─BatchNorm2d: 5-2        256
+│    │    └─BasicBlock: 3-4                   --
+│    │    │    └─Conv2d: 4-17                 147,456
+│    │    │    └─BatchNorm2d: 4-18            256
+│    │    │    └─ReLU: 4-19                   --
+│    │    │    └─Conv2d: 4-20                 147,456
+│    │    │    └─BatchNorm2d: 4-21            256
+│    └─Sequential: 2-7                        --
+│    │    └─BasicBlock: 3-5                   --
+│    │    │    └─Conv2d: 4-22                 294,912
+│    │    │    └─BatchNorm2d: 4-23            512
+│    │    │    └─ReLU: 4-24                   --
+│    │    │    └─Conv2d: 4-25                 589,824
+│    │    │    └─BatchNorm2d: 4-26            512
+│    │    │    └─Sequential: 4-27             --
+│    │    │    │    └─Conv2d: 5-3             32,768
+│    │    │    │    └─BatchNorm2d: 5-4        512
+│    │    └─BasicBlock: 3-6                   --
+│    │    │    └─Conv2d: 4-28                 589,824
+│    │    │    └─BatchNorm2d: 4-29            512
+│    │    │    └─ReLU: 4-30                   --
+│    │    │    └─Conv2d: 4-31                 589,824
+│    │    │    └─BatchNorm2d: 4-32            512
+│    └─Sequential: 2-8                        --
+│    │    └─BasicBlock: 3-7                   --
+│    │    │    └─Conv2d: 4-33                 1,179,648
+│    │    │    └─BatchNorm2d: 4-34            1,024
+│    │    │    └─ReLU: 4-35                   --
+│    │    │    └─Conv2d: 4-36                 2,359,296
+│    │    │    └─BatchNorm2d: 4-37            1,024
+│    │    │    └─Sequential: 4-38             --
+│    │    │    │    └─Conv2d: 5-5             131,072
+│    │    │    │    └─BatchNorm2d: 5-6        1,024
+│    │    └─BasicBlock: 3-8                   --
+│    │    │    └─Conv2d: 4-39                 2,359,296
+│    │    │    └─BatchNorm2d: 4-40            1,024
+│    │    │    └─ReLU: 4-41                   --
+│    │    │    └─Conv2d: 4-42                 2,359,296
+│    │    │    └─BatchNorm2d: 4-43            1,024
+├─UnetDecoder: 1-2                            --
+│    └─Identity: 2-9                          --
+│    └─ModuleList: 2-10                       --
+│    │    └─DecoderBlock: 3-9                 --
+│    │    │    └─Conv2dReLU: 4-44             --
+│    │    │    │    └─Conv2d: 5-7             1,769,472
+│    │    │    │    └─BatchNorm2d: 5-8        512
+│    │    │    │    └─ReLU: 5-9               --
+│    │    │    └─Attention: 4-45              --
+│    │    │    │    └─Identity: 5-10          --
+│    │    │    └─Conv2dReLU: 4-46             --
+│    │    │    │    └─Conv2d: 5-11            589,824
+│    │    │    │    └─BatchNorm2d: 5-12       512
+│    │    ��    │    └─ReLU: 5-13              --
+│    │    │    └─Attention: 4-47              --
+│    │    │    │    └─Identity: 5-14          --
+│    │    └─DecoderBlock: 3-10                --
+│    │    │    └─Conv2dReLU: 4-48             --
+│    │    │    │    └─Conv2d: 5-15            442,368
+│    │    │    │    └─BatchNorm2d: 5-16       256
+│    │    │    │    └─ReLU: 5-17              --
+│    │    │    └─Attention: 4-49              --
+│    │    │    │    └─Identity: 5-18          --
+│    │    │    └─Conv2dReLU: 4-50             --
+│    │    │    │    └─Conv2d: 5-19            147,456
+│    │    │    │    └─BatchNorm2d: 5-20       256
+│    │    │    │    └─ReLU: 5-21              --
+│    │    │    └─Attention: 4-51              --
+│    │    │    │    └─Identity: 5-22          --
+│    │    └─DecoderBlock: 3-11                --
+│    │    │    └─Conv2dReLU: 4-52             --
+│    │    │    │    └─Conv2d: 5-23            110,592
+│    │    │    │    └─BatchNorm2d: 5-24       128
+│    │    │    │    └─ReLU: 5-25              --
+│    │    │    └─Attention: 4-53              --
+│    │    │    │    └─Identity: 5-26          --
+│    │    │    └─Conv2dReLU: 4-54             --
+│    │    │    │    └─Conv2d: 5-27            36,864
+│    │    │    │    └─BatchNorm2d: 5-28       128
+│    │    │    │    └─ReLU: 5-29              --
+│    │    │    └─Attention: 4-55              --
+│    │    │    │    └─Identity: 5-30          --
+│    │    └─DecoderBlock: 3-12                --
+│    │    │    └─Conv2dReLU: 4-56             --
+│    │    │    │    └─Conv2d: 5-31            36,864
+│    │    │    │    └─BatchNorm2d: 5-32       64
+│    │    │    │    └─ReLU: 5-33              --
+│    │    │    └─Attention: 4-57              --
+│    │    │    │    └─Identity: 5-34          --
+│    │    │    └─Conv2dReLU: 4-58             --
+│    │    │    │    └─Conv2d: 5-35            9,216
+│    │    │    │    └─BatchNorm2d: 5-36       64
+│    │    │    │    └─ReLU: 5-37              --
+│    │    │    └─Attention: 4-59              --
+│    │    │    │    └─Identity: 5-38          --
+│    │    └─DecoderBlock: 3-13                --
+│    │    │    └─Conv2dReLU: 4-60             --
+│    │    │    │    └─Conv2d: 5-39            4,608
+│    │    │    │    └─BatchNorm2d: 5-40       32
+│    │    │    │    └─ReLU: 5-41              --
+│    │    │    └─Attention: 4-61              --
+│    │    │    │    └─Identity: 5-42          --
+│    │    │    └─Conv2dReLU: 4-62             --
+│    │    │    │    └─Conv2d: 5-43            2,304
+│    │    │    │    └─BatchNorm2d: 5-44       32
+│    │    │    │    └─ReLU: 5-45              --
+│    │    │    └─Attention: 4-63              --
+│    │    │    │    └─Identity: 5-46          --
+├─SegmentationHead: 1-3                       --
+│    └─Conv2d: 2-11                           290
+│    └─Identity: 2-12                         --
+│    └─Activation: 2-13                       --
+│    │    └─Identity: 3-14                    --
+======================================================================
+Total params: 14,322,082
+Trainable params: 14,322,082
+Non-trainable params: 0
+======================================================================

model_summary.txt

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+           Model Summary           
+┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━┓
+┃      Parameter       ┃  Value   ┃
+┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━┩
+│       Network        │ smp_unet │
+│ Trainable Parameters │ 14322082 │
+│   Output channels    │    2     │
+└──────────────────────┴──────────┘

onnx_checkpoints/unet_dec_21_epoch_579.onnx

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+size 57279486

time_log.txt

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+Time initiated first training run: 2023_12_21_23;13;51
+Time resumed training run: 2023_12_22_23;20;40

torchscript_checkpoints/unet_dec_21_epoch_579.pt

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+oid sha256:fcdca2fc286b1f00b9656fcd023756754d40cd4c62b1de83cbf3341bf0f7dfeb
+size 57594684

training_logs/training_stats.csv

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