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Add config to include data from health records only + update experime…
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…nt commands to include new data config
nathanpainchaud committed Nov 23, 2023

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37 changes: 37 additions & 0 deletions didactic/config/task/data/records.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
# @package _global_

task:
tabular_attrs:
# Attributes from patient records unrelated to echocardiogram exams
- age
- sex
- bmi
- hf
- cad
- pad
- stroke
- tobacco
- diabetes
- dyslipidemia
- etiology
- ddd
- bradycardic
- ace_inhibitor
- arb
- tz_diuretic
- central_acting
- beta_blocker
- spironolactone
- alpha_blocker
- ccb
- sbp_24
- dbp_24
- pp_24
- ht_severity
- ht_grade
- creat
- gfr
- nt_probnp
- nt_probnp_group

time_series_attrs: []
14 changes: 10 additions & 4 deletions didactic/scripts/experiments.sh
Original file line number Diff line number Diff line change
@@ -4,25 +4,27 @@ CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/resu
# w/ time-series data + w/ ordinal constraint
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=5 +experiment=cardinal/xtab-finetune trainer.enable_progress_bar=False task/data=tab-13+time-series,tabular+time-series task.contrastive_loss_weight=0,0.2,1 task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt ~callbacks.learning_rate_finder '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tab-13+ts,tab+ts,ordinal=True.log 2>&1
# w/o time-series data + w/o ordinal constraint
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=cardinal/xtab-finetune trainer.enable_progress_bar=False task/data=tab-13,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt ~callbacks.learning_rate_finder '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tab-13,tab,ordinal=False.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=cardinal/xtab-finetune trainer.enable_progress_bar=False task/data=tab-13,records,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt ~callbacks.learning_rate_finder '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tab-13,tab,ordinal=False.log 2>&1
# w/o time-series data + w/ ordinal constraint
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=cardinal/xtab-finetune trainer.enable_progress_bar=False task/data=tab-13,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt ~callbacks.learning_rate_finder '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tab-13,tab,ordinal=True.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=cardinal/xtab-finetune trainer.enable_progress_bar=False task/data=tab-13,records,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt ~callbacks.learning_rate_finder '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tab-13,tab,ordinal=True.log 2>&1

# scratch
# w/ time-series data + w/o ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13+time-series,tabular+time-series task.contrastive_loss_weight=0,0.2,1 task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13+ts,tab+ts,ordinal=False.log 2>&1
# w/ time-series data + w/ ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13+time-series,tabular+time-series task.contrastive_loss_weight=0,0.2,1 task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13+ts,tab+ts,ordinal=True.log 2>&1
# w/o time-series data + w/o ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13,tab,ordinal=False.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13,records,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13,tab,ordinal=False.log 2>&1
# w/o time-series data + w/ ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13,tab,ordinal=True.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13,records,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13,tab,ordinal=True.log 2>&1

# pretrain
# tab-13
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-pretrain trainer.enable_progress_bar=False task/data=tab-13 '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab-13.log 2>&1
# tab-13+time-series
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-pretrain trainer.enable_progress_bar=False task/data=tab-13+time-series task/time_series_tokenizer/model=linear-embedding,transformer '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab-13+ts.log 2>&1
# records
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-pretrain trainer.enable_progress_bar=False task/data=records exclude_tabular_attrs=[ht_severity,ht_grade] '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=records.log 2>&1
# tabular
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-pretrain trainer.enable_progress_bar=False task/data=tabular exclude_tabular_attrs=[ht_severity,ht_grade] '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab.log 2>&1
# tabular+time-series
@@ -37,6 +39,10 @@ CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/resu
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-finetune trainer.enable_progress_bar=False task/data=tab-13+time-series task.contrastive_loss_weight=0,0.2,1 task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/results/cardiac-multimodal-representation/pretrain/${hydra:runtime.choices.task/data}/${hydra:runtime.choices.task/time_series_tokenizer/model}/${trial}.ckpt' >>$HOME/data/didactic/results/multimodal-xformer-finetune,data=tab-13+ts,ordinal=False.log 2>&1
# tab-13+time-series + w/ ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-finetune trainer.enable_progress_bar=False task/data=tab-13+time-series task.contrastive_loss_weight=0,0.2,1 task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/results/cardiac-multimodal-representation/pretrain/${hydra:runtime.choices.task/data}/${hydra:runtime.choices.task/time_series_tokenizer/model}/${trial}.ckpt' >>$HOME/data/didactic/results/multimodal-xformer-finetune,data=tab-13+ts,ordinal=True.log 2>&1
# records + w/o ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-finetune trainer.enable_progress_bar=False task/data=records task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/results/cardiac-multimodal-representation/pretrain/${hydra:runtime.choices.task/data}/None/ht_severity/${trial}.ckpt' >>$HOME/data/didactic/results/multimodal-xformer-finetune,data=records,ordinal=False.log 2>&1
# records + w/ ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-finetune trainer.enable_progress_bar=False task/data=records task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/results/cardiac-multimodal-representation/pretrain/${hydra:runtime.choices.task/data}/None/ht_severity/${trial}.ckpt' >>$HOME/data/didactic/results/multimodal-xformer-finetune,data=records,ordinal=True.log 2>&1
# tabular + w/o ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-finetune trainer.enable_progress_bar=False task/data=tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=False '+trial=range(10)' 'ckpt=/home/local/USHERBROOKE/pain5474/data/didactic/results/cardiac-multimodal-representation/pretrain/${hydra:runtime.choices.task/data}/None/ht_severity/${trial}.ckpt' >>$HOME/data/didactic/results/multimodal-xformer-finetune,data=tab,ordinal=False.log 2>&1
# tabular + w/ ordinal constraint

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