Add scripts to run experiments.

main.py

@@ -165,7 +165,7 @@ def main(args):
  parser.add_argument('--data_dir', default='/ssd1/greg/NIH_CXR/images', type=str)
  parser.add_argument('--label_dir', default='labels/', type=str)
  parser.add_argument('--out_dir', default='results/', type=str, help="path to directory where results and model weights will be saved")
- parser.add_argument('--dataset', required=True, type=str, choices=['nih-lt', 'mimic-lt'])
+ parser.add_argument('--dataset', required=True, type=str, choices=['nih-lt', 'mimic-cxr-lt'])
  parser.add_argument('--loss', default='ce', type=str, choices=['ce', 'focal', 'ldam'])
  parser.add_argument('--drw', action='store_true', default=False)
  parser.add_argument('--rw_method', default='', choices=['', 'sklearn', 'cb'])

run_mimic-cxr-lt_experiments.sh

@@ -0,0 +1,146 @@
+#!/bin/bash
+
+echo "Training CE on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ce \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced CE on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ce \
+ --rw_method cb \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted CE on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ce \
+ --rw_method sklearn \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training focal loss on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss focal \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced focal loss on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss focal \
+ --rw_method cb \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted focal loss on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss focal \
+ --rw_method sklearn \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training LDAM loss on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ldam \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced LDAM loss on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ldam \
+ --rw_method cb \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced LDAM loss w/ DRW on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ldam \
+ --rw_method cb \
+ --drw \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted LDAM loss on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ldam \
+ --rw_method sklearn \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted LDAM loss w/ DRW on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ldam \
+ --rw_method sklearn \
+ --drw \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training mixup on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ce \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+ --mixup \
+ --mixup_alpha 0.2 \
+
+echo "Training balanced mixup on mimic-cxr-lt..."
+python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \
+ --out_dir mimic_results \
+ --dataset mimic-cxr-lt \
+ --loss ce \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+ --bal_mixup \
+ --mixup_alpha 0.2 \
+

run_nih-lt_experiments.sh

@@ -0,0 +1,146 @@
+#!/bin/bash
+
+echo "Training CE on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ce \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced CE on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ce \
+ --rw_method cb \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted CE on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ce \
+ --rw_method sklearn \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training focal loss on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss focal \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced focal loss on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss focal \
+ --rw_method cb \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted focal loss on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss focal \
+ --rw_method sklearn \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training LDAM loss on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ldam \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced LDAM loss on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ldam \
+ --rw_method cb \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training class-balanced LDAM loss w/ DRW on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ldam \
+ --rw_method cb \
+ --drw \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted LDAM loss on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ldam \
+ --rw_method sklearn \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training sklearn re-weighted LDAM loss w/ DRW on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ldam \
+ --rw_method sklearn \
+ --drw \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+
+echo "Training mixup on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ce \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+ --mixup \
+ --mixup_alpha 0.2 \
+
+echo "Training balanced mixup on NIH-LT..."
+python main.py --data_dir /ssd1/greg/NIH_CXR/images \
+ --out_dir nih_results \
+ --dataset nih-lt \
+ --loss ce \
+ --max_epochs 60 \
+ --patience 15 \
+ --batch_size 256 \
+ --lr 1e-4 \
+ --bal_mixup \
+ --mixup_alpha 0.2 \
+