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dvc.yaml
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stages:
ogt_protein_classifier_data_prep:
cmd: python pipeline/ogt_protein_classifier_data_prep.py
deps:
- ./data/database
- ./l2tml_utils/data_utils.py
- ./l2tml_utils/dataset_deduplication.py
- ./pipeline/ogt_protein_classifier_data_prep.py
outs:
- ./data/ogt_protein_classifier/data
params:
- ogt_protein_classifier_data_prep.data_batch_size
- ogt_protein_classifier_data_prep.deduplication
- ogt_protein_classifier_data_prep.dev_keep_columns
- ogt_protein_classifier_data_prep.dev_sample_init_data
- ogt_protein_classifier_data_prep.max_protein_len
- ogt_protein_classifier_data_prep.max_upsampling
- ogt_protein_classifier_data_prep.min_balance
- ogt_protein_classifier_data_prep.ogt_window
- ogt_protein_classifier_data_prep.split_type
- ogt_protein_classifier_data_prep.train_test_frac
metrics:
- ./data/ogt_protein_classifier/data_metrics.yaml:
cache: false
frozen: true
ogt_protein_classifier_train_evaluate:
cmd: torchrun --nproc_per_node gpu pipeline/ogt_protein_classifier_train_evaluate.py
deps:
- ./data/ogt_protein_classifier/data
- ./l2tml_utils/model_utils.py
- ./pipeline/ogt_protein_classifier_train_evaluate.py
outs:
- ./data/ogt_protein_classifier/dvclive/report.md:
cache: false
persist: true
- ./data/ogt_protein_classifier/model:
checkpoint: true
params:
- ogt_protein_classifier_train_evaluate.batch_size
- ogt_protein_classifier_train_evaluate.dev_subsample_data
- ogt_protein_classifier_train_evaluate.dropout
- ogt_protein_classifier_train_evaluate.epochs
- ogt_protein_classifier_train_evaluate.fp16
- ogt_protein_classifier_train_evaluate.grad_accum
- ogt_protein_classifier_train_evaluate.grad_checkpointing
- ogt_protein_classifier_train_evaluate.lr
- ogt_protein_classifier_train_evaluate.lr_scheduler
- ogt_protein_classifier_train_evaluate.model
- ogt_protein_classifier_train_evaluate.n_save_per_epoch
- ogt_protein_classifier_train_evaluate.protocol
- ogt_protein_classifier_train_evaluate.push
metrics:
- ./data/ogt_protein_classifier/dvclive/metrics.json:
cache: false
persist: true
- ./data/ogt_protein_classifier/model_metrics.yaml:
cache: false
plots:
- ./data/ogt_protein_classifier/dvclive/plots:
cache: false
persist: true
frozen: true
ogt_protein_regressor_data_prep:
cmd: python pipeline/ogt_protein_regressor_data_prep.py
deps:
- ./pipeline/ogt_protein_regressor_data_prep.py
- ./data/database
- ./l2tml_utils/data_utils.py
- ./l2tml_utils/dataset_deduplication.py
outs:
- ./data/ogt_protein_regressor/data
params:
- ogt_protein_regressor_data_prep.split_type
- ogt_protein_regressor_data_prep.train_test_frac
- ogt_protein_regressor_data_prep.max_protein_len
- ogt_protein_regressor_data_prep.min_protein_len
- ogt_protein_regressor_data_prep.balancing
- ogt_protein_regressor_data_prep.deduplication
- ogt_protein_regressor_data_prep.data_batch_size
- ogt_protein_regressor_data_prep.dev_keep_columns
- ogt_protein_regressor_data_prep.dev_sample_init_data
metrics:
- ./data/ogt_protein_regressor/data_metrics.yaml:
cache: false
ogt_protein_regressor_train_evaluate:
cmd: torchrun --nproc_per_node gpu pipeline/ogt_protein_regressor_train_evaluate.py
deps:
- ./pipeline/ogt_protein_regressor_train_evaluate.py
- ./l2tml_utils/model_utils.py
- ./data/ogt_protein_regressor/data
outs:
- ./data/ogt_protein_regressor/model:
checkpoint: true
- ./data/ogt_protein_regressor/dvclive/report.md:
cache: false
persist: true
params:
- ogt_protein_regressor_train_evaluate.model
- ogt_protein_regressor_train_evaluate.protocol
- ogt_protein_regressor_train_evaluate.batch_size
- ogt_protein_regressor_train_evaluate.epochs
- ogt_protein_regressor_train_evaluate.n_save_per_epoch
- ogt_protein_regressor_train_evaluate.dropout
- ogt_protein_regressor_train_evaluate.lr_scheduler
- ogt_protein_regressor_train_evaluate.lr
- ogt_protein_regressor_train_evaluate.grad_accum
- ogt_protein_regressor_train_evaluate.grad_checkpointing
- ogt_protein_regressor_train_evaluate.fp16
- ogt_protein_regressor_train_evaluate.dev_subsample_data
metrics:
- ./data/ogt_protein_regressor/model_metrics.yaml:
cache: false
- ./data/ogt_protein_regressor/dvclive/metrics.json:
cache: false
persist: true
plots:
- ./data/ogt_protein_regressor/dvclive/plots:
cache: false
persist: true
ogt_protein_regressor_predict:
cmd: python ./pipeline/ogt_protein_regressor_predict.py
deps:
- ./data/ogt_protein_regressor/model
- ./data/ogt_protein_regressor/data
- ./pipeline/ogt_protein_regressor_predict.py
plots:
- ./data/ogt_protein_regressor/prediction_dist.png:
cache: false
persist: true
- ./data/ogt_protein_regressor/prediction_scatter.png:
cache: false
persist: true
- ./data/ogt_protein_regressor/error_dist.png:
cache: false
persist: true
- ./data/ogt_protein_regressor/error_bins.png:
cache: false
persist: true
- ./data/ogt_protein_regressor/error_confidence.png:
cache: false
persist: true
- ./data/ogt_protein_regressor/error_bounds.png:
cache: false
persist: true