Add Mean Validation Dice 0.6123 + validation_summary.json (per-case results from checkpoint_best)
Browse files- README.md +16 -13
- validation_summary.json +1962 -0
README.md
CHANGED
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@@ -37,8 +37,8 @@ This is a single-fold pretrain checkpoint, intended as a starting point for down
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| **Loss** | Dice + Cross-Entropy (nnU-Net default), `batch_dice=True` |
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| **Schedule** | 1000 epochs, polynomial LR decay 0.01 → 0, batch size 2, patch `[80, 192, 160]` |
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| **Hardware** | 1× NVIDIA H100 80GB, ~7h wall-time |
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| **Generalization** | No measurable overfitting — train/val loss curves overlap throughout |
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## Files in this repo
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@@ -144,24 +144,27 @@ Input images should be CT volumes named with the nnU-Net channel suffix: `<case_
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## Evaluation
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The training plot (`progress.png`) shows:
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1. **Smooth Pseudo Dice climb** from 0 → 0.55 in the first ~50 epochs, then 0.55 → 0.77 over epochs 50–870. Slow continuous improvement throughout, with diminishing returns past epoch ~600.
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2. **Train/val loss curves overlap nearly perfectly** end-to-end. With 483 training cases, the model has enough data variety that it cannot memorize specifics
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- 33-institution / 4-scanner variability adds domain shift that hurts pooled-voxel Dice but improves transfer.
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- LDCT is noisier than diagnostic CT.
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## Why this checkpoint matters
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| **Loss** | Dice + Cross-Entropy (nnU-Net default), `batch_dice=True` |
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| **Schedule** | 1000 epochs, polynomial LR decay 0.01 → 0, batch size 2, patch `[80, 192, 160]` |
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| **Hardware** | 1× NVIDIA H100 80GB, ~7h wall-time |
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| **Mean Validation Dice** (per-case, sliding-window) | **0.6123** |
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| **Best EMA Pseudo Dice** (in-training proxy) | 0.7663 (epoch ~870) |
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| **Generalization** | No measurable overfitting — train/val loss curves overlap throughout |
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## Files in this repo
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## Evaluation
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Two complementary Dice metrics, both honest, computed on the 121 fold-0 validation cases:
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| Metric | Value | What it measures |
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|--------|-------|------------------|
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| **Mean Validation Dice** (per-case, sliding-window) | **0.6123** | Per-case Dice from full-volume `nnUNetv2_predict` inference, averaged across 121 val cases. **Case-weighted** — every scan counts equally regardless of tumor size. *This is the metric most papers report.* |
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| **Best EMA Pseudo Dice** (in-training) | 0.7663 | Voxel-pooled Dice across validation patches during training. **Voxel-weighted** — large lesions dominate. Used by nnU-Net to select `checkpoint_best.pth`. |
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| Pseudo Dice raw (jagged) range | 0.45–0.85 | (peak per-epoch readings during training) |
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| Train/val loss gap (final epoch) | ~0 | No measurable overfitting throughout. |
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The **0.15 gap** between Pseudo Dice (0.7663) and Mean Validation Dice (0.6123) is wider than the gap on uniform-tumor datasets like MSD Task06 (~0.10 gap there). NLSTseg has lesion volumes spanning 0.03 → 372 cm³ (median 1.37 cm³, long-tailed), so voxel-pooled Dice is dominated by the few large lesions while per-case Dice gives equal weight to many small-lesion cases that are individually harder. The voxel-pool vs case-average disagreement reflects this distribution honestly.
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The training plot (`progress.png`) shows:
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1. **Smooth Pseudo Dice climb** from 0 → 0.55 in the first ~50 epochs, then 0.55 → 0.77 over epochs 50–870. Slow continuous improvement throughout, with diminishing returns past epoch ~600.
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2. **Train/val loss curves overlap nearly perfectly** end-to-end. With 483 training cases (10× MSD-only's 50), the model has enough data variety that it cannot memorize specifics. This translates into clean generalization — no overfitting to manage.
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For comparisons against other methods, **cite the Mean Validation Dice (0.6123)**. Pseudo Dice is useful as an in-training monitoring signal but not for cross-method comparison.
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Per-case validation results are available in `validation_summary.json` (Dice, IoU, TP/FP/FN counts per case).
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The 0.6123 figure reflects the difficulty of small-lesion segmentation in heterogeneous, multi-institutional LDCT. It is the model's honest performance on its native validation distribution.
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## Why this checkpoint matters
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validation_summary.json
ADDED
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@@ -0,0 +1,1962 @@
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| 1948 |
+
"Dice": 0.4976374322922669,
|
| 1949 |
+
"FN": 220,
|
| 1950 |
+
"FP": 4139,
|
| 1951 |
+
"IoU": 0.3312365756366984,
|
| 1952 |
+
"TN": 65005194,
|
| 1953 |
+
"TP": 2159,
|
| 1954 |
+
"n_pred": 6298,
|
| 1955 |
+
"n_ref": 2379
|
| 1956 |
+
}
|
| 1957 |
+
},
|
| 1958 |
+
"prediction_file": "/proj/rasool_lab_projects/Maaz/cln-segmenter/data/nlstseg_nnunet/nnunet_results/Dataset503_NLSTseg/nnUNetTrainer__nnUNetPlans__3d_fullres/fold_0/validation/nlst_0605.nii.gz",
|
| 1959 |
+
"reference_file": "/proj/rasool_lab_projects/Maaz/cln-segmenter/data/nlstseg_nnunet/nnunet_preprocessed/Dataset503_NLSTseg/gt_segmentations/nlst_0605.nii.gz"
|
| 1960 |
+
}
|
| 1961 |
+
]
|
| 1962 |
+
}
|