set save_last default to false (#762)

kaiko-ai · Feb 13, 2025 · 2fea425 · 2fea425
1 parent c59d1e5
commit 2fea425
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diff --git a/configs/vision/pathology/offline/classification/bach.yaml b/configs/vision/pathology/offline/classification/bach.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/bracs.yaml b/configs/vision/pathology/offline/classification/bracs.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/breakhis.yaml b/configs/vision/pathology/offline/classification/breakhis.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/camelyon16.yaml b/configs/vision/pathology/offline/classification/camelyon16.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/BinaryBalancedAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/camelyon16_small.yaml b/configs/vision/pathology/offline/classification/camelyon16_small.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/BinaryBalancedAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/crc.yaml b/configs/vision/pathology/offline/classification/crc.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/gleason_arvaniti.yaml b/configs/vision/pathology/offline/classification/gleason_arvaniti.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/mhist.yaml b/configs/vision/pathology/offline/classification/mhist.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/BinaryBalancedAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/panda.yaml b/configs/vision/pathology/offline/classification/panda.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/panda_small.yaml b/configs/vision/pathology/offline/classification/panda_small.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/patch_camelyon.yaml b/configs/vision/pathology/offline/classification/patch_camelyon.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/BinaryBalancedAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/classification/unitopatho.yaml b/configs/vision/pathology/offline/classification/unitopatho.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/segmentation/bcss.yaml b/configs/vision/pathology/offline/segmentation/bcss.yaml
@@ -19,7 +19,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/segmentation/consep.yaml b/configs/vision/pathology/offline/segmentation/consep.yaml
@@ -19,7 +19,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/offline/segmentation/monusac.yaml b/configs/vision/pathology/offline/segmentation/monusac.yaml
@@ -22,7 +22,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/bach.yaml b/configs/vision/pathology/online/classification/bach.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/bracs.yaml b/configs/vision/pathology/online/classification/bracs.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/breakhis.yaml b/configs/vision/pathology/online/classification/breakhis.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/crc.yaml b/configs/vision/pathology/online/classification/crc.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/gleason_arvaniti.yaml b/configs/vision/pathology/online/classification/gleason_arvaniti.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/mhist.yaml b/configs/vision/pathology/online/classification/mhist.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/BinaryBalancedAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/patch_camelyon.yaml b/configs/vision/pathology/online/classification/patch_camelyon.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/BinaryBalancedAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/classification/unitopatho.yaml b/configs/vision/pathology/online/classification/unitopatho.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/MulticlassAccuracy}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/segmentation/bcss.yaml b/configs/vision/pathology/online/segmentation/bcss.yaml
@@ -20,7 +20,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/segmentation/consep.yaml b/configs/vision/pathology/online/segmentation/consep.yaml
@@ -20,7 +20,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/pathology/online/segmentation/monusac.yaml b/configs/vision/pathology/online/segmentation/monusac.yaml
@@ -20,7 +20,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/radiology/offline/segmentation/lits.yaml b/configs/vision/radiology/offline/segmentation/lits.yaml
@@ -17,7 +17,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/radiology/offline/segmentation/lits_balanced.yaml b/configs/vision/radiology/offline/segmentation/lits_balanced.yaml
@@ -18,7 +18,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/radiology/offline/segmentation/total_segmentator_2d.yaml b/configs/vision/radiology/offline/segmentation/total_segmentator_2d.yaml
@@ -19,7 +19,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/radiology/online/segmentation/lits.yaml b/configs/vision/radiology/online/segmentation/lits.yaml
@@ -20,7 +20,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/radiology/online/segmentation/lits_balanced.yaml b/configs/vision/radiology/online/segmentation/lits_balanced.yaml
@@ -20,7 +20,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/radiology/online/segmentation/total_segmentator_2d.yaml b/configs/vision/radiology/online/segmentation/total_segmentator_2d.yaml
@@ -19,7 +19,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: ${oc.env:SAVE_LAST, false}
           save_top_k: 1
           monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}

diff --git a/configs/vision/tests/offline/patch_camelyon.yaml b/configs/vision/tests/offline/patch_camelyon.yaml
@@ -28,7 +28,7 @@ trainer:
       - class_path: lightning.pytorch.callbacks.ModelCheckpoint
         init_args:
           filename: best
-          save_last: true
+          save_last: false
           save_top_k: 1
           monitor: &MONITOR_METRIC val/BinaryAccuracy
           mode: &MONITOR_METRIC_MODE max

diff --git a/docs/user-guide/advanced/replicate_evaluations.md b/docs/user-guide/advanced/replicate_evaluations.md
@@ -238,7 +238,7 @@ a proprietary dataset of 3.1M million slides, available for download on
 [HuggingFace](https://huggingface.co/paige-ai/Virchow2), run:
 
 ```
-MODEL_NAME=paige/virchow2 \
+MODEL_NAME=pathology/paige_virchow2 \
 NORMALIZE_MEAN="[0.485,0.456,0.406]" \
 NORMALIZE_STD="[0.229,0.224,0.225]" \
 IN_FEATURES=1280 \