Upload 23 files
Browse files- milk10k_effb2_metadata/MILK10K_EFFB2_METADATA_CLI.md +20 -20
- milk10k_effb2_metadata/__pycache__/__init__.cpython-310.pyc +0 -0
- milk10k_effb2_metadata/__pycache__/cli.cpython-314.pyc +0 -0
- milk10k_effb2_metadata/__pycache__/data.cpython-314.pyc +0 -0
- milk10k_effb2_metadata/__pycache__/losses.cpython-310.pyc +0 -0
- milk10k_effb2_metadata/__pycache__/losses.cpython-314.pyc +0 -0
- milk10k_effb2_metadata/__pycache__/training.cpython-314.pyc +0 -0
- milk10k_effb2_metadata/cli.py +5 -6
- milk10k_effb2_metadata/losses.py +9 -16
- milk10k_effb2_metadata/training.py +2 -2
milk10k_effb2_metadata/MILK10K_EFFB2_METADATA_CLI.md
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@@ -86,7 +86,7 @@ python train_milk10k_effb2_dual_metadata.py \
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--output-dir milk10k_effb2_focal_sampler_p05
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```
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## 6.
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Recommended first run:
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--loss
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--weighted-sampler \
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--sampler-power 0.5 \
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-
--output-dir
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```
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Without sampler:
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@@ -106,25 +106,25 @@ Without sampler:
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--loss
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--output-dir
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```
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More conservative
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```bash
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--loss
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--
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--
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--weighted-sampler \
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--sampler-power 0.5 \
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--output-dir
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```
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Note: do not add `--class-weight` with `--loss
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## 7. K-Fold
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@@ -134,17 +134,17 @@ Note: do not add `--class-weight` with `--loss milk_lt`; `milk_lt` already uses
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--loss
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--weighted-sampler \
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--sampler-power 0.5 \
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--k-folds 5 \
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--output-dir
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```
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Outputs:
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```text
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-
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fold_00/
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fold_01/
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fold_02/
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--loss
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--weighted-sampler \
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--sampler-power 0.5 \
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--amp \
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--output-dir
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```
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## 9. Smoke Checks
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--freeze-epochs 0 \
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--finetune-epochs 0 \
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--loss
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--output-dir /tmp/milk10k_effb2_smoke_single
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```
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--freeze-epochs 0 \
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--finetune-epochs 0 \
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--loss
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--k-folds 2 \
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--output-dir /tmp/milk10k_effb2_smoke_kfold
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```
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```bash
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python predict_milk10k_effb2_dual_metadata.py \
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--checkpoint
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--data-dir /marimo/milk10k \
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--output milk10k_effb2_test_predictions.csv \
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--batch-size 16 \
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```bash
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python predict_milk10k_effb2_dual_metadata.py \
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--checkpoint
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--input-dir /path/to/MILK10k_Test_Input \
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--metadata-csv /path/to/MILK10k_Test_Metadata.csv \
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--output milk10k_effb2_test_predictions.csv \
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--output-dir milk10k_effb2_focal_sampler_p05
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```
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## 6. LDAM + DRW Loss
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Recommended first run:
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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+
--loss ldam \
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--weighted-sampler \
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--sampler-power 0.5 \
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--output-dir milk10k_effb2_ldam_sampler_p05
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```
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Without sampler:
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--loss ldam \
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--output-dir milk10k_effb2_ldam
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```
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More conservative LDAM margin with delayed DRW:
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```bash
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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+
--loss ldam \
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--ldam-max-margin 0.3 \
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--ldam-drw-start-epoch 8 \
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--weighted-sampler \
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--sampler-power 0.5 \
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--output-dir milk10k_effb2_ldam_conservative
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```
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Note: do not add `--class-weight` with `--loss ldam`; LDAM+DRW already uses effective-number alpha.
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## 7. K-Fold
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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+
--loss ldam \
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--weighted-sampler \
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--sampler-power 0.5 \
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--k-folds 5 \
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--output-dir milk10k_effb2_ldam_kfold5
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```
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Outputs:
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```text
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+
milk10k_effb2_ldam_kfold5/
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fold_00/
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fold_01/
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fold_02/
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python train_milk10k_effb2_dual_metadata.py \
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--clinical-checkpoint best_effnetb2_ufes_clinical.pth \
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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+
--loss ldam \
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--weighted-sampler \
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--sampler-power 0.5 \
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--amp \
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--output-dir milk10k_effb2_ldam_amp
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```
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## 9. Smoke Checks
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--freeze-epochs 0 \
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--finetune-epochs 0 \
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--loss ldam \
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--output-dir /tmp/milk10k_effb2_smoke_single
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```
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--dermoscopic-checkpoint efficientnet_b2_best_dermoscopic.pt \
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--freeze-epochs 0 \
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--finetune-epochs 0 \
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--loss ldam \
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--k-folds 2 \
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--output-dir /tmp/milk10k_effb2_smoke_kfold
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```
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```bash
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python predict_milk10k_effb2_dual_metadata.py \
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--checkpoint milk10k_effb2_ldam_sampler_p05/best.pt \
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--data-dir /marimo/milk10k \
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--output milk10k_effb2_test_predictions.csv \
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--batch-size 16 \
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```bash
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python predict_milk10k_effb2_dual_metadata.py \
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--checkpoint milk10k_effb2_ldam_sampler_p05/best.pt \
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--input-dir /path/to/MILK10k_Test_Input \
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--metadata-csv /path/to/MILK10k_Test_Metadata.csv \
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--output milk10k_effb2_test_predictions.csv \
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milk10k_effb2_metadata/__pycache__/__init__.cpython-310.pyc
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milk10k_effb2_metadata/__pycache__/training.cpython-314.pyc
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Binary files a/milk10k_effb2_metadata/__pycache__/training.cpython-314.pyc and b/milk10k_effb2_metadata/__pycache__/training.cpython-314.pyc differ
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milk10k_effb2_metadata/cli.py
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@@ -76,13 +76,12 @@ def parse_args() -> argparse.Namespace:
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parser.add_argument("--class-weight", action="store_true")
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parser.add_argument("--weighted-sampler", action="store_true")
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parser.add_argument("--sampler-power", type=float, default=1.0)
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-
parser.add_argument("--loss", choices=["ce", "focal", "
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parser.add_argument("--focal-gamma", type=float, default=2.0)
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-
parser.add_argument("--
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-
parser.add_argument("--
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-
parser.add_argument("--
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-
parser.add_argument("--
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-
parser.add_argument("--lt-alpha-max", type=float, default=10.0)
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parser.add_argument("--k-folds", type=int, default=1)
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parser.add_argument("--amp", action="store_true")
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parser.add_argument(
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parser.add_argument("--class-weight", action="store_true")
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parser.add_argument("--weighted-sampler", action="store_true")
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parser.add_argument("--sampler-power", type=float, default=1.0)
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+
parser.add_argument("--loss", choices=["ce", "focal", "ldam"], default="ce")
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parser.add_argument("--focal-gamma", type=float, default=2.0)
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+
parser.add_argument("--ldam-beta", type=float, default=0.9999)
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+
parser.add_argument("--ldam-max-margin", type=float, default=0.5)
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+
parser.add_argument("--ldam-drw-start-epoch", type=int, default=0)
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parser.add_argument("--ldam-alpha-max", type=float, default=10.0)
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parser.add_argument("--k-folds", type=int, default=1)
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parser.add_argument("--amp", action="store_true")
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parser.add_argument(
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milk10k_effb2_metadata/losses.py
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@@ -27,15 +27,14 @@ class FocalLoss(nn.Module):
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return loss.mean()
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-
class
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-
"""LDAM
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def __init__(
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self,
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class_counts: torch.Tensor,
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beta: float = 0.9999,
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max_margin: float = 0.5,
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-
logit_tau: float = 1.0,
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deferred_start_epoch: int = 0,
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alpha_max: float = 10.0,
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) -> None:
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@@ -43,15 +42,12 @@ class MILKLongTailLoss(nn.Module):
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counts = class_counts.float().clamp_min(1.0)
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margins = 1.0 / torch.sqrt(torch.sqrt(counts))
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margins = margins * (max_margin / margins.max().clamp_min(1e-12))
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-
priors = counts / counts.sum()
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alpha = effective_number_alpha(counts, beta)
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alpha = alpha.clamp(max=alpha_max)
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alpha = alpha * (counts.numel() / alpha.sum().clamp_min(1e-12))
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self.register_buffer("margins", margins)
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-
self.register_buffer("log_priors", priors.log())
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self.register_buffer("alpha", alpha)
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-
self.logit_tau = logit_tau
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self.deferred_start_epoch = deferred_start_epoch
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self.current_epoch = 0
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def forward(self, logits: torch.Tensor, labels: torch.Tensor) -> torch.Tensor:
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margins = self.margins.to(device=logits.device, dtype=logits.dtype)
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-
log_priors = self.log_priors.to(device=logits.device, dtype=logits.dtype)
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alpha = self.alpha.to(device=logits.device, dtype=logits.dtype)
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adjusted_logits = logits.clone()
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rows = torch.arange(labels.size(0), device=labels.device)
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adjusted_logits[rows, labels] = adjusted_logits[rows, labels] - margins[labels]
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-
adjusted_logits = adjusted_logits + self.logit_tau * log_priors
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loss = F.cross_entropy(adjusted_logits, labels, reduction="none")
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if self.current_epoch >= self.deferred_start_epoch:
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loss = loss * alpha[labels]
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if beta <= 0.0:
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return torch.ones_like(counts)
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if beta >= 1.0:
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-
raise ValueError("--
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beta_tensor = torch.tensor(beta, dtype=counts.dtype, device=counts.device)
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effective_num = 1.0 - torch.pow(beta_tensor, counts)
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alpha = (1.0 - beta_tensor) / effective_num.clamp_min(1e-12)
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def build_loss(train_df: pd.DataFrame, label_to_idx: dict[str, int], args: argparse.Namespace, device: torch.device) -> nn.Module:
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-
if args.loss == "
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counts = class_count_tensor(train_df, label_to_idx, device)
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-
return
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class_counts=counts,
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-
beta=args.
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-
max_margin=args.
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-
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-
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-
alpha_max=args.lt_alpha_max,
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)
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weight = None
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return loss.mean()
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+
class LDAMLoss(nn.Module):
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+
"""LDAM with deferred effective-number reweighting."""
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def __init__(
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self,
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class_counts: torch.Tensor,
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beta: float = 0.9999,
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max_margin: float = 0.5,
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deferred_start_epoch: int = 0,
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alpha_max: float = 10.0,
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) -> None:
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counts = class_counts.float().clamp_min(1.0)
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margins = 1.0 / torch.sqrt(torch.sqrt(counts))
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margins = margins * (max_margin / margins.max().clamp_min(1e-12))
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alpha = effective_number_alpha(counts, beta)
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alpha = alpha.clamp(max=alpha_max)
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alpha = alpha * (counts.numel() / alpha.sum().clamp_min(1e-12))
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self.register_buffer("margins", margins)
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self.register_buffer("alpha", alpha)
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self.deferred_start_epoch = deferred_start_epoch
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self.current_epoch = 0
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def forward(self, logits: torch.Tensor, labels: torch.Tensor) -> torch.Tensor:
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margins = self.margins.to(device=logits.device, dtype=logits.dtype)
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alpha = self.alpha.to(device=logits.device, dtype=logits.dtype)
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adjusted_logits = logits.clone()
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rows = torch.arange(labels.size(0), device=labels.device)
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adjusted_logits[rows, labels] = adjusted_logits[rows, labels] - margins[labels]
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loss = F.cross_entropy(adjusted_logits, labels, reduction="none")
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| 64 |
if self.current_epoch >= self.deferred_start_epoch:
|
| 65 |
loss = loss * alpha[labels]
|
|
|
|
| 70 |
if beta <= 0.0:
|
| 71 |
return torch.ones_like(counts)
|
| 72 |
if beta >= 1.0:
|
| 73 |
+
raise ValueError("--ldam-beta must be less than 1.0")
|
| 74 |
beta_tensor = torch.tensor(beta, dtype=counts.dtype, device=counts.device)
|
| 75 |
effective_num = 1.0 - torch.pow(beta_tensor, counts)
|
| 76 |
alpha = (1.0 - beta_tensor) / effective_num.clamp_min(1e-12)
|
|
|
|
| 87 |
|
| 88 |
|
| 89 |
def build_loss(train_df: pd.DataFrame, label_to_idx: dict[str, int], args: argparse.Namespace, device: torch.device) -> nn.Module:
|
| 90 |
+
if args.loss == "ldam":
|
| 91 |
counts = class_count_tensor(train_df, label_to_idx, device)
|
| 92 |
+
return LDAMLoss(
|
| 93 |
class_counts=counts,
|
| 94 |
+
beta=args.ldam_beta,
|
| 95 |
+
max_margin=args.ldam_max_margin,
|
| 96 |
+
deferred_start_epoch=args.ldam_drw_start_epoch,
|
| 97 |
+
alpha_max=args.ldam_alpha_max,
|
|
|
|
| 98 |
)
|
| 99 |
|
| 100 |
weight = None
|
milk10k_effb2_metadata/training.py
CHANGED
|
@@ -416,8 +416,8 @@ def run_training_split(
|
|
| 416 |
f"freeze_metadata_head={args.freeze_metadata_head}, metadata_lr={args.metadata_lr}"
|
| 417 |
)
|
| 418 |
print(f"Loss: {args.loss}, class_weight={args.class_weight}, weighted_sampler={args.weighted_sampler}")
|
| 419 |
-
if args.loss == "
|
| 420 |
-
print("Note: --class-weight is ignored for --loss
|
| 421 |
|
| 422 |
history: list[dict[str, Any]] = []
|
| 423 |
history_path = output_dir / "history.csv"
|
|
|
|
| 416 |
f"freeze_metadata_head={args.freeze_metadata_head}, metadata_lr={args.metadata_lr}"
|
| 417 |
)
|
| 418 |
print(f"Loss: {args.loss}, class_weight={args.class_weight}, weighted_sampler={args.weighted_sampler}")
|
| 419 |
+
if args.loss == "ldam" and args.class_weight:
|
| 420 |
+
print("Note: --class-weight is ignored for --loss ldam because LDAM+DRW uses effective-number alpha.")
|
| 421 |
|
| 422 |
history: list[dict[str, Any]] = []
|
| 423 |
history_path = output_dir / "history.csv"
|