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experiments_paper.sh
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experiments_paper.sh
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#!/bin/bash
group=paper_expts_2403
maybe_cluster="--cluster"
# # =================================================================================================
# # SEGMENTATION
# seed=0
# for fold in {0..4}; do
# for seed in {0..4}; do
# # simple brats
# python launcher.py --task train_seg --dataset simple_fets22_corrupted --fold $fold --seed $seed --backbone monai_unet_dropout --group $group $maybe_cluster
# # Prostate
# python launcher.py --task train_seg --dataset prostate_gonzalez --fold $fold --seed $seed --backbone dynamic_unet_dropout --group $group $maybe_cluster
# # MnMs
# python launcher.py --task train_seg --dataset mnms --fold $fold --seed $seed --backbone dynamic_unet_dropout --group $group $maybe_cluster
# # Covid
# python launcher.py --task train_seg --dataset covid_gonzalez --fold $fold --seed $seed --backbone dynamic_unet_dropout --group $group $maybe_cluster
# # KiTS
# python launcher.py --task train_seg --dataset kits23 --fold $fold --seed $seed --backbone dynamic_unet_dropout --group $group $maybe_cluster
# # BraTS 2019 (LGG vs HGG)
# python launcher.py --task train_seg --dataset brats19_lhgg --fold $fold --seed $seed --backbone dynamic_unet_dropout --group $group $maybe_cluster
# done
# done
# # =================================================================================================
# # CROSS-VALIDATION PIXEL CSF (prepare regression methods)
# # simple brats
# seed=0
# for fold in {0..4};
# do
# python launcher.py --task validate_pixel_csf --dataset simple_fets22_corrupted --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline \
# --group $group $maybe_cluster
# python launcher.py --task validate_pixel_csf --dataset simple_fets22_corrupted --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble \
# --group $group $maybe_cluster
# done
# # 3d datasets: mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg
# seed=0
# for dataset in mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg; do
# for fold in {0..4};
# do
# python launcher.py --task validate_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline \
# --group $group $maybe_cluster
# python launcher.py --task validate_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble \
# --group $group $maybe_cluster
# done
# done
# # =================================================================================================
# # PREPARE AUXDATA
# for dataset in simple_fets22_corrupted mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg; do
# python prepare_auxdata.py --expt_group $group --dataset $dataset $maybe_cluster
# done
# # =================================================================================================
# # STAGE 2 TRAINING
# # simple brats
# dataset=simple_fets22_corrupted
# seed=0
# for fold in {0..4}
# do
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_image mahalanobis_gonzalez \
# --group $group $maybe_cluster
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_image quality_regression --csf_pixel baseline \
# --group $group $maybe_cluster
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_image vae_mask_only --csf_pixel baseline \
# --group $group $maybe_cluster
# # aggregation
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# done
# # 3d data: mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg
# seed=0
# for dataset in mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg; do
# for fold in {0..4}; do
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_image mahalanobis_gonzalez \
# --group $group $maybe_cluster
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_image quality_regression \
# --group $group $maybe_cluster
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_image vae_mask_only \
# --group $group $maybe_cluster
# # aggregation
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task train_image_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# done
# done
# # =================================================================================================
# # INFERENCE PIXEL CSF
# dataset=simple_fets22_corrupted
# seed=0
# for fold in {0..4}
# do
# python launcher.py --task test_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline \
# --group $group $maybe_cluster
# python launcher.py --task test_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel mcdropout \
# --group $group $maybe_cluster
# python launcher.py --task test_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble \
# --group $group $maybe_cluster
# done
# seed=0
# for dataset in mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg; do
# for fold in {0..4}; do
# python launcher.py --task test_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline \
# --group $group $maybe_cluster
# python launcher.py --task test_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel mcdropout \
# --group $group $maybe_cluster
# python launcher.py --task test_pixel_csf --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble \
# --group $group $maybe_cluster
# done
# done
# # =================================================================================================
# # FAILURE DETECTION TESTING
# # Simple FeTS
# seed=0
# dataset=simple_fets22_corrupted
# for fold in {0..4}
# do
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline --csf_aggregation all_simple \
# --group $group --cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel mcdropout --csf_aggregation all_simple \
# --group $group --cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_aggregation all_simple \
# --group $group --cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_image mahalanobis_gonzalez \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline --csf_image quality_regression \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_image quality_regression \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_image vae_mask_only \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone monai_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# done
# # 3d datasets: mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg
# seed=0
# for dataset in mnms prostate_gonzalez kits23 covid_gonzalez brats19_lhgg; do
# for fold in {0..4}; do
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_aggregation all_simple \
# --group $group --cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel mcdropout --csf_aggregation all_simple \
# --group $group --cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_aggregation all_simple \
# --group $group --cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_image mahalanobis_gonzalez \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_image quality_regression \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_image quality_regression \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_image vae_mask_only \
# --group $group $maybe_cluster
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel baseline --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+radiomics \
# --group $group $maybe_cluster --cpu
# python launcher.py --task test_fd --dataset $dataset --fold $fold --seed $seed --backbone dynamic_unet_dropout --csf_pixel deep_ensemble --csf_aggregation predictive_entropy+heuristic \
# --group $group $maybe_cluster --cpu
# done
# done