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Update job commands to sweep cls_token, ordinal_mode and `contras…
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…tive_loss_weight` cfg options
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@nathanpainchaud
nathanpainchaud committed Jul 2, 2024
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24 changes: 12 additions & 12 deletions didactic/scripts/experiments.sh
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# xtab-finetune
# tabular data only
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-xtab-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=xtab-finetune trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.cls_token=True,False task.ordinal_mode=True,False ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tabular-only.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-xtab-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=xtab-finetune trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.contrastive_loss_weight=0,0.2 task.cls_token=False,True task.ordinal_mode=False,True ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tabular-only.log 2>&1
# tabular + time-series data
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-xtab-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=8 +experiment=xtab-finetune trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=True,False task.ordinal_mode=True,False ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tabular+ts.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-xtab-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=8 +experiment=xtab-finetune trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task.contrastive_loss_weight=0,0.2 task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=False,True task.ordinal_mode=False,True ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tabular+ts.log 2>&1

# bidirectional-xtab
# tabular + time-series data
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-bidirectional-xtab didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=8 +experiment=bidirectional-xtab trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=True,False task.ordinal_mode=True,False ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt '+trial=range(10)' >>$HOME/data/didactic/results/bidirectional-xtab,data=tabular+ts.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-bidirectional-xtab didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=8 +experiment=bidirectional-xtab trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task.contrastive_loss_weight=0,0.2 task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=False,True task.ordinal_mode=False,True ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt '+trial=range(10)' >>$HOME/data/didactic/results/bidirectional-xtab,data=tabular+ts.log 2>&1

# random
# tabular data only
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-random didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=random trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.cls_token=True task.ordinal_mode=True '+trial=range(10)' >>$HOME/data/didactic/results/random,data=tabular-only.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-random didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=random trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.contrastive_loss_weight=0,0.2 task.cls_token=False,True task.ordinal_mode=False,True '+trial=range(10)' >>$HOME/data/didactic/results/random,data=tabular-only.log 2>&1
# tabular + time-series data
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-random didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=random trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=True task.ordinal_mode=True '+trial=range(10)' >>$HOME/data/didactic/results/random,data=tabular+ts.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-random didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=random trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task.contrastive_loss_weight=0,0.2 task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=False,True task.ordinal_mode=False,True '+trial=range(10)' >>$HOME/data/didactic/results/random,data=tabular+ts.log 2>&1

# pretrain
# tabular data only
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=pretrain trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.cls_token=True '+trial=range(10)' >>$HOME/data/didactic/results/pretrain,data=tabular-only.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=pretrain trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.cls_token=False,True '+trial=range(10)' >>$HOME/data/didactic/results/pretrain,data=tabular-only.log 2>&1
# tabular + time-series data
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=pretrain trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=True '+trial=range(10)' >>$HOME/data/didactic/results/pretrain,data=tabular+ts.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=pretrain trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=False,True '+trial=range(10)' >>$HOME/data/didactic/results/pretrain,data=tabular+ts.log 2>&1

# finetune
# tabular data only
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=finetune trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.cls_token=True task.ordinal_mode=True '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/multirun/cardiac-multimodal-representation/pretrain/data=${hydra:runtime.choices.task/data}/encoder=cardinal-ft-transformer,cross_blocks=${oc.select:task.model.encoder.n_bidirectional_blocks,0},time_series_tokenizer=${hydra:runtime.choices.task/time_series_tokenizer/model}/cls_token=${task.cls_token}/+${trial}.ckpt' >>$HOME/data/didactic/results/finetune,data=tabular-only.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=finetune trainer.enable_progress_bar=False task/data=tab-selec,tab-no-echo-data,tab-all task.contrastive_loss_weight=0,0.2 task.cls_token=False,True task.ordinal_mode=False,True '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/multirun/cardiac-multimodal-representation/pretrain/data=${hydra:runtime.choices.task/data}/encoder=cardinal-ft-transformer,cross_blocks=${oc.select:task.model.encoder.n_bidirectional_blocks,0},time_series_tokenizer=${hydra:runtime.choices.task/time_series_tokenizer/model}/cls_token=${task.cls_token}/+${trial}.ckpt' >>$HOME/data/didactic/results/finetune,data=tabular-only.log 2>&1
# tabular + time-series data
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=finetune trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=True task.ordinal_mode=True '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/multirun/cardiac-multimodal-representation/pretrain/data=${hydra:runtime.choices.task/data}/encoder=cardinal-ft-transformer,cross_blocks=${oc.select:task.model.encoder.n_bidirectional_blocks,0},time_series_tokenizer=${hydra:runtime.choices.task/time_series_tokenizer/model}/cls_token=${task.cls_token}/+${trial}.ckpt' >>$HOME/data/didactic/results/finetune,data=tabular+ts.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=finetune trainer.enable_progress_bar=False task/data=tab-selec+ts,tab-no-echo-data+ts,tab-all+ts task.contrastive_loss_weight=0,0.2 task/time_series_tokenizer/model=linear-embedding,transformer task.cls_token=False,True task.ordinal_mode=False,True '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/multirun/cardiac-multimodal-representation/pretrain/data=${hydra:runtime.choices.task/data}/encoder=cardinal-ft-transformer,cross_blocks=${oc.select:task.model.encoder.n_bidirectional_blocks,0},time_series_tokenizer=${hydra:runtime.choices.task/time_series_tokenizer/model}/cls_token=${task.cls_token}/+${trial}.ckpt' >>$HOME/data/didactic/results/finetune,data=tabular+ts.log 2>&1

# records-xgb
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-records-stratification python ~/remote/didactic/didactic/tasks/cardiac_records_stratification.py -m hydra/launcher=joblib hydra.launcher.n_jobs=10 task/data=tab-selec,tab-no-echo-data,tab-all ~task.time_series_attrs task.target_attr=ht_severity '+trial=range(10)' >>$HOME/data/didactic/results/records-xgb.log 2>&1
Expand Down Expand Up @@ -62,12 +62,12 @@ target_path=$HOME/data/didactic/results/compiled_results
# Compile the prediction scores over the different trials of each config
for task in "${!tasks_data[@]}"; do
for data in ${tasks_data[${task}]}; do
for contrastive in 0; do
for contrastive in 0 0.2; do
for cross_blocks in ${cross_blocks[${task}]}; do
for time_series_tokenizer in ${time_series_tokenizers[${data}]}; do
for cls_token in True; do
for cls_token in False True; do

for ordinal_mode in True; do
for ordinal_mode in False True; do
run_path="$task/data=$data/contrastive=$contrastive/cross_blocks=$cross_blocks,time_series_tokenizer=$time_series_tokenizer/cls_token=$cls_token/ordinal_mode=$ordinal_mode"

# Copy model checkpoints to target directory
Expand Down

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