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2DCNN/src/shell/table3.sh
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| 1 | +#!/usr/bin/env sh | ||
| 2 | + | ||
| 3 | +# DEFINE | ||
| 4 | +DATA_ROOT_PATH="" | ||
| 5 | +DEVICE="cuda" | ||
| 6 | + | ||
| 7 | +############################## Table 3 ######################################### | ||
| 8 | +#### This commands Assumes that you have computed the best models for the architecture | ||
| 9 | +#### or table 1 commands are already run | ||
| 10 | +#### We show commands for k=2, | ||
| 11 | +#### for other values of k just modify the frame_keep_fraction parameter | ||
| 12 | +#### k=2 -> 0.5 | ||
| 13 | +#### k=4 -> 0.25 | ||
| 14 | +#### k=5 -> 0.2 | ||
| 15 | +#### k=10 -> 0.1 | ||
| 16 | +################################################################################ | ||
| 17 | + | ||
| 18 | +# 3d cnn with 50% frames (k=2), with imputation | ||
| 19 | +python3 -m src.scripts.main -c config/config.py \ | ||
| 20 | + --exp_name 3d_cnn_eval_k=2_imputed \ | ||
| 21 | + -r /tmp \ | ||
| 22 | + --mode test \ | ||
| 23 | + --device $DEVICE --wandb.use 0 \ | ||
| 24 | + --model.arch.file src/arch/brain_age_3d.py \ | ||
| 25 | + --data.root_path "$DATA_ROOT_PATH" \ | ||
| 26 | + --data.frame_keep_style random --data.frame_keep_fraction 0.5 \ | ||
| 27 | + --data.impute fill \ | ||
| 28 | + --statefile result/3d_cnn/run_0001/best_model.pt | ||
| 29 | + | ||
| 30 | +# 2d lstm with 50% frames (k=2), without imputation | ||
| 31 | +python3 -m src.scripts.main -c config/config.py \ | ||
| 32 | + --exp_name 2d_slice_lstm_eval_k=2 \ | ||
| 33 | + -r /tmp \ | ||
| 34 | + --mode test \ | ||
| 35 | + --device $DEVICE --wandb.use 0 \ | ||
| 36 | + --model.arch.file src/arch/brain_age_slice_lstm.py \ | ||
| 37 | + --data.root_path "$DATA_ROOT_PATH" \ | ||
| 38 | + --data.frame_keep_style random --data.frame_keep_fraction 0.5 \ | ||
| 39 | + --data.impute drop \ | ||
| 40 | + --statefile result/2d_slice_lstm/run_0001/best_model.pt | ||
| 41 | + | ||
| 42 | +# 2d lstm with 50% frames (k=2), with imputation | ||
| 43 | +python3 -m src.scripts.main -c config/config.py \ | ||
| 44 | + --exp_name 2d_slice_lstm_eval_k=2_imputed \ | ||
| 45 | + -r /tmp \ | ||
| 46 | + --mode test \ | ||
| 47 | + --device $DEVICE --wandb.use 0 \ | ||
| 48 | + --model.arch.file src/arch/brain_age_slice_lstm.py \ | ||
| 49 | + --data.root_path "$DATA_ROOT_PATH" \ | ||
| 50 | + --data.frame_keep_style random --data.frame_keep_fraction 0.5 \ | ||
| 51 | + --data.impute fill \ | ||
| 52 | + --statefile result/2d_slice_lstm/run_0001/best_model.pt | ||
| 53 | + | ||
| 54 | +# 2D-slice-attention with 50% frames (k=2), without imputation | ||
| 55 | +python3 -m src.scripts.main -c config/config.py \ | ||
| 56 | + --exp_name 2d_slice_attention_eval_k=2 \ | ||
| 57 | + -r /tmp \ | ||
| 58 | + --mode test \ | ||
| 59 | + --device $DEVICE --wandb.use 0 \ | ||
| 60 | + --model.arch.file src/arch/brain_age_slice_set.py \ | ||
| 61 | + --model.arch.attn_dim 32 --model.arch.attn_num_heads 1 \ | ||
| 62 | + --model.arch.attn_drop 1 --model.arch.agg_fn "attention" \ | ||
| 63 | + --data.root_path "$DATA_ROOT_PATH" \ | ||
| 64 | + --data.frame_keep_style random --data.frame_keep_fraction 0.5 \ | ||
| 65 | + --data.impute drop \ | ||
| 66 | + --statefile result/2d_slice_attention/run_0001/best_model.pt | ||
| 67 | + | ||
| 68 | +# 2D-slice-mean with 50% frames (k=2), without imputation | ||
| 69 | +python3 -m src.scripts.main -c config/config.py \ | ||
| 70 | + --exp_name 2d_slice_mean_eval_k=2 \ | ||
| 71 | + -r /tmp \ | ||
| 72 | + --mode test \ | ||
| 73 | + --device $DEVICE --wandb.use 0 \ | ||
| 74 | + --model.arch.file src/arch/brain_age_slice_set.py \ | ||
| 75 | + --model.arch.attn_dim 32 --model.arch.attn_num_heads 1 \ | ||
| 76 | + --model.arch.attn_drop 1 --model.arch.agg_fn "mean" \ | ||
| 77 | + --data.root_path "$DATA_ROOT_PATH" \ | ||
| 78 | + --data.frame_keep_style random --data.frame_keep_fraction 0.5 \ | ||
| 79 | + --data.impute drop \ | ||
| 80 | + --statefile result/2d_slice_attention/run_0001/best_model.pt | ||
| 81 | + | ||
| 82 | +# 2D-slice-max with 50% frames (k=2), without imputation | ||
| 83 | +python3 -m src.scripts.main -c config/config.py \ | ||
| 84 | + --exp_name 2d_slice_max_eval_k=2 \ | ||
| 85 | + -r /tmp \ | ||
| 86 | + --mode test \ | ||
| 87 | + --device $DEVICE --wandb.use 0 \ | ||
| 88 | + --model.arch.file src/arch/brain_age_slice_set.py \ | ||
| 89 | + --model.arch.attn_dim 32 --model.arch.attn_num_heads 1 \ | ||
| 90 | + --model.arch.attn_drop 1 --model.arch.agg_fn "max" \ | ||
| 91 | + --data.root_path "$DATA_ROOT_PATH" \ | ||
| 92 | + --data.frame_keep_style random --data.frame_keep_fraction 0.5 \ | ||
| 93 | + --data.impute drop \ | ||
| 94 | + --statefile result/2d_slice_attention/run_0001/best_model.pt |
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