diff --git a/run_mimic-cxr-lt_experiments.sh b/run_mimic-cxr-lt_experiments.sh index 07ba085..49f89ab 100644 --- a/run_mimic-cxr-lt_experiments.sh +++ b/run_mimic-cxr-lt_experiments.sh @@ -1,7 +1,7 @@ #!/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 \ +python src/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 \ @@ -11,7 +11,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -22,7 +22,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -33,7 +33,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -43,7 +43,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -54,7 +54,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -65,7 +65,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -75,7 +75,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -86,7 +86,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -98,7 +98,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -109,7 +109,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -121,7 +121,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ @@ -133,7 +133,7 @@ python main.py --data_dir /ssd1/greg/physionet.org/files/mimic-cxr-jpg/2.0.0 \ --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 \ +python src/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 \ diff --git a/run_nih-lt_experiments.sh b/run_nih-lt_experiments.sh index 4bc5c9d..262ed79 100644 --- a/run_nih-lt_experiments.sh +++ b/run_nih-lt_experiments.sh @@ -1,7 +1,7 @@ #!/bin/bash echo "Training CE on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ce \ @@ -11,7 +11,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training class-balanced CE on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ce \ @@ -22,7 +22,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training sklearn re-weighted CE on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ce \ @@ -33,7 +33,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training focal loss on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss focal \ @@ -43,7 +43,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training class-balanced focal loss on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss focal \ @@ -54,7 +54,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training sklearn re-weighted focal loss on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss focal \ @@ -65,7 +65,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training LDAM loss on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ldam \ @@ -75,7 +75,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training class-balanced LDAM loss on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ldam \ @@ -86,7 +86,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training class-balanced LDAM loss w/ DRW on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ldam \ @@ -98,7 +98,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training sklearn re-weighted LDAM loss on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ldam \ @@ -109,7 +109,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --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 \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ldam \ @@ -121,7 +121,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --lr 1e-4 \ echo "Training mixup on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ce \ @@ -133,7 +133,7 @@ python main.py --data_dir /ssd1/greg/NIH_CXR/images \ --mixup_alpha 0.2 \ echo "Training balanced mixup on NIH-LT..." -python main.py --data_dir /ssd1/greg/NIH_CXR/images \ +python src/main.py --data_dir /ssd1/greg/NIH_CXR/images \ --out_dir nih_results \ --dataset nih-lt \ --loss ce \ diff --git a/datasets.py b/src/datasets.py similarity index 100% rename from datasets.py rename to src/datasets.py diff --git a/losses.py b/src/losses.py similarity index 100% rename from losses.py rename to src/losses.py diff --git a/main.py b/src/main.py similarity index 100% rename from main.py rename to src/main.py diff --git a/utils.py b/src/utils.py similarity index 100% rename from utils.py rename to src/utils.py