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dvc.yaml
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dvc.yaml
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stages:
convert_baseline:
cmd: python3 scripts/convert_sas_to_feather.py --input_filename data/raw_data/merged_baseline.sas7bdat
--output_filename data/raw_data/baseline.feather
deps:
- data/raw_data/merged_baseline.sas7bdat
- scripts/convert_sas_to_feather.py
outs:
- data/raw_data/baseline.feather
convert_inr:
cmd: python3 scripts/convert_sas_to_feather.py --input_filename data/raw_data/merged_inr.sas7bdat
--output_filename data/raw_data/inr.feather
deps:
- data/raw_data/merged_inr.sas7bdat
- scripts/convert_sas_to_feather.py
outs:
- data/raw_data/inr.feather
convert_events:
cmd: python3 scripts/convert_sas_to_feather.py --input_filename data/raw_data/merged_events.sas7bdat
--output_filename data/raw_data/events.feather
deps:
- data/raw_data/merged_events.sas7bdat
- scripts/convert_sas_to_feather.py
outs:
- data/raw_data/events.feather
preprocess:
cmd: python3 scripts/preprocess_combine_af.py --baseline_path data/raw_data/baseline.feather
--inr_path data/raw_data/inr.feather --events_path data/raw_data/events.feather
--output_directory data/clean_data
params:
- preprocess
- data
deps:
- data/raw_data/baseline.feather
- data/raw_data/events.feather
- data/raw_data/inr.feather
- scripts/preprocess_combine_af.py
outs:
- data/clean_data/baseline.feather
- data/clean_data/inr.feather
- data/clean_data/events.feather
- data/clean_data/merged.feather
- data/clean_data/train_data.feather
- data/clean_data/val_data.feather
- data/clean_data/test_data.feather
- data/auditing/impute_inr_and_dose.feather
- data/auditing/merge_inr_baseline.feather
- data/auditing/merge_inr_events.feather
- data/auditing/merge_trials_and_remove_outlying_doses.feather
- data/auditing/preprocess_all_baseline.feather
- data/auditing/preprocess_all_events.feather
- data/auditing/preprocess_all_inr.feather
- data/auditing/preprocess_aristotle.feather
- data/auditing/preprocess_engage_rocket.feather
- data/auditing/preprocess_rely.feather
- data/auditing/remove_short_trajectories.feather
- data/auditing/split_data_test.feather
- data/auditing/split_data_train.feather
- data/auditing/split_data_val.feather
- data/auditing/split_trajectories_at_events.feather
- data/auditing/split_trajectories_at_gaps.feather
audit_preprocess:
cmd: python3 scripts/audit_combine_preprocessing.py > output/combine_preprocess_audit.txt
deps:
- data/auditing/impute_inr_and_dose.feather
- data/auditing/merge_inr_baseline.feather
- data/auditing/merge_inr_events.feather
- data/auditing/merge_trials_and_remove_outlying_doses.feather
- data/auditing/preprocess_all_baseline.feather
- data/auditing/preprocess_all_events.feather
- data/auditing/preprocess_all_inr.feather
- data/auditing/preprocess_aristotle.feather
- data/auditing/preprocess_engage_rocket.feather
- data/auditing/preprocess_rely.feather
- data/auditing/remove_short_trajectories.feather
- data/auditing/split_data_test.feather
- data/auditing/split_data_train.feather
- data/auditing/split_data_val.feather
- data/auditing/split_trajectories_at_events.feather
- data/auditing/split_trajectories_at_gaps.feather
- data/clean_data/baseline.feather
- data/clean_data/inr.feather
- data/clean_data/events.feather
- data/clean_data/merged.feather
- data/clean_data/train_data.feather
- data/clean_data/val_data.feather
- data/clean_data/test_data.feather
- scripts/audit_combine_preprocessing.py
params:
- preprocess
- data
outs:
- output/combine_preprocess_audit.txt:
cache: false
- data/auditing/inr_dose_change_tile.png:
cache: false
- data/auditing/dose_change_inr_change_tile.png:
cache: false
tune_behavior_cloner:
cmd: python3 scripts/tune_bc.py
deps:
- data/clean_data/train_data.feather
- data/clean_data/val_data.feather
- scripts/tune_bc.py
params:
- data.events_to_keep
- data.events_to_split
- data.min_train_trajectory_length
- data.state_columns
- replay_buffer.init.time_varying
- replay_buffer.init.include_dose_time_varying
- behavior_cloner
outs:
- ray_logs/bc
select_behavior_cloner_wis:
cmd: python3 scripts/choose_bc.py --target_metric "val/calibration_error" --target_mode min
deps:
- ray_logs/bc
- data/clean_data/train_data.feather
- data/clean_data/val_data.feather
- scripts/choose_bc.py
params:
- behavior_cloner
outs:
- output/behavior_cloner_wis
select_behavior_cloner_generative_init:
cmd: python3 scripts/choose_bc.py --target_metric "val/multi_f1_0.3" --target_mode max --output_prefix ./output/behavior_cloner_generative_init
deps:
- ray_logs/bc
- data/clean_data/train_data.feather
- data/clean_data/val_data.feather
- scripts/choose_bc.py
params:
- behavior_cloner
outs:
- output/behavior_cloner_generative_init
tune_dsbcq:
cmd: python3 scripts/tune_smdp_dbcq.py --feasibility_behavior_policy `pwd`/output/behavior_cloner_generative_init/checkpoint.pt
deps:
- output/behavior_cloner_wis
- output/behavior_cloner_generative_init
- data/clean_data/train_data.feather
- data/clean_data/val_data.feather
- scripts/tune_smdp_dbcq.py
params:
- data.events_to_keep
- data.events_to_split
- data.min_train_trajectory_length
- data.state_columns
- replay_buffer.init.time_varying
- replay_buffer.init.include_dose_time_varying
- dsbcq
outs:
- ray_logs/dbcq
evaluate:
cmd: bash scripts/evaluate.sh
deps:
- data/combine_test_ids.txt
- data/raw_data/rely_subjids.sas7bdat
- data/raw_data/ittr_baseline.csv
- data/raw_data/sas_libs
- data/raw_data/drugs_rely.csv
- data/clean_data/train_data.feather
- data/clean_data/test_data.feather
- data/clean_data/events.feather
- ray_logs/dbcq
- scripts/evaluate.sh
- scripts/evaluate_best_model.py
- scripts/format_metrics.py
- scripts/link_rely_subj_ids.py
- scripts/process_model_inputs.py
- scripts/estimate_agreement_models.R
params:
- replay_buffer.init.time_varying
- replay_buffer.init.include_dose_time_varying
- dsbcq
outs:
- output/rely_test_evaluation