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Update commands to launch experiments in bash script (part 2/?)
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@nathanpainchaud
nathanpainchaud committed Nov 14, 2023
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33 changes: 31 additions & 2 deletions didactic/scripts/experiments.sh
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# 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-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=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+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-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.ordinal_head.distribution=poisson,binomial task.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
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
# 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

# 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)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13+ts,tab+ts,ordinal=False.log 2>&1
# w/ time-series data + w/ ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-xtab-finetune didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/xtab-finetune trainer.enable_progress_bar=False task/data=tab-13,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.ordinal_head.distribution=poisson,binomial task.ordinal_head.tau_mode=learn_sigm,learn_fn ckpt=$HOME/data/models/xtab/iter_2k_patch.ckpt ~callbacks.learning_rate_finder '+trial=range(10)' >>$HOME/data/didactic/results/xtab-finetune,data=tab-13,tab,ordinal=True.log 2>&1
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13+time-series,tabular+time-series task.contrastive_loss_weight=0,0.2,1 task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' >>$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)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13,tab,ordinal=False.log 2>&1
# w/o time-series data + w/ ordinal constraint
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-scratch didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-scratch trainer.enable_progress_bar=False task/data=tab-13,tabular task.contrastive_loss_weight=0,0.2,1 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] task.ordinal_mode=True task.model.ordinal_head.distribution=poisson,binomial task.model.ordinal_head.tau_mode=learn_sigm,learn_fn '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-scratch,data=tab-13,tab,ordinal=True.log 2>&1

# 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 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab-13.log 2>&1
# tab-13+time-series
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-pretrain trainer.enable_progress_bar=False task/data=tab-13+time-series task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab-13+ts.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 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab.log 2>&1
# tabular+time-series
CARDIAC_MULTIMODAL_REPR_PATH=/home/local/USHERBROOKE/pain5474/data/didactic/results/multirun/cardiac-multimodal-representation COMET_PROJECT_NAME=didactic-multimodal-xformer-pretrain didactic-runner -m hydra/launcher=joblib hydra.launcher.n_jobs=10 +experiment=cardinal/multimodal-xformer-pretrain trainer.enable_progress_bar=False task/data=tabular+time-series task/time_series_tokenizer/model=linear-embedding,transformer 'task.predict_losses={ht_severity:{_target_:torch.nn.CrossEntropyLoss}}' exclude_tabular_attrs=[ht_severity,ht_grade] '+trial=range(10)' >>$HOME/data/didactic/results/multimodal-xformer-pretrain,data=tab+ts.log 2>&1

# finetune
# w/ time-series data + w/o ordinal constraint

# w/ time-series data + w/ ordinal constraint

# w/o time-series data + w/o ordinal constraint

# w/o time-series data + w/ ordinal constraint


# Plot 2D embeddings of the transformer encoder representations
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