genomicBERT: Train a deep learning classifier

This explains the use of train.py. Use this if you already know what hyperparameters are needed. Otherwise use sweep.py. For conventional machine learning, the sweep, train and cross validation steps are combined in one operation.

Source data

Source data is a HuggingFace dataset object as a csv, json or parquet file. Specify --format accordingly.

Results

Note

Entry points are available if this is installed using the automated conda method. You can then use the command line argument directly, for example: create_dataset_bio. If not, you will need to use the script directly, which follows the same naming pattern, for example: python create_dataset_bio.py.

Running the code as below:

python train_model.py <TRAIN_DATA> <FORMAT> <TOKENISER_PATH> --test TEST_DATA --valid VALIDATION_DATA --hyperparameter_file PARAMS.JSON --entity_name WANDB_ENTITY_NAME --project_name WANDB_PROJECT_NAME --group_name WANDB_GROUP_NAME --sweep_count N --metric_opt [ eval/accuracy | eval/validation | eval/loss | eval/precision | eval/recall ] --output_dir OUTPUT_DIR --label_names labels

Note

Remember to provide the --label_names argument! This is labels by default (if this wasn’t changed in any previous part of the pipeline).

You will obtain a json file with weights for each token. Any special tokens you add will also be present. This will be used in the next step of creating a HuggingFace compatible dataset object.

Notes

The original documentation to specify training arguments is available here.

Usage

The full list of arguments is truncated, and only arguments added by this package are shown. These are available on the corresponding HuggingFace transformers.TrainingArguments documentation shown above.

python train.py -h

Take HuggingFace dataset and train. Arguments match that of
TrainingArguments, with the addition of [ train, test, valid, tokeniser_path,
vocab_size, model, device, entity_name, project_name, group_name,
config_from_run, metric_opt, hyperparameter_file, no_shuffle, wandb_off,
override_output_dir ]. See: https://huggingface.co/docs/transformers/v4.19.4/
en/main_classes/trainer#transformers.TrainingArguments

positional arguments:
  train                 path to [ csv | csv.gz | json | parquet ] file
  format                specify input file type [ csv | json | parquet ]
  tokeniser_path        path to tokeniser.json file to load data from

options:
  -h, --help            show this help message and exit
  --output_dir OUTPUT_DIR
                        The output directory where the model predictions and
                        checkpoints will be written. (default: None)
  --overwrite_output_dir [OVERWRITE_OUTPUT_DIR]
                        Overwrite the content of the output directory. Use
                        this to continue training if output_dir points to a
                        checkpoint directory. (default: False)
  -t TEST, --test TEST  path to [ csv | csv.gz | json | parquet ] file
                        (default: None)
  -v VALID, --valid VALID
                        path to [ csv | csv.gz | json | parquet ] file
                        (default: None)
  -m MODEL, --model MODEL
                        choose model [ distilbert | longformer ] distilbert
                        handles shorter sequences up to 512 tokens longformer
                        handles longer sequences up to 4096 tokens (DEFAULT:
                        distilbert) (default: distilbert)
  -d DEVICE, --device DEVICE
                        choose device [ cpu | cuda:0 ] (DEFAULT: detect)
                        (default: None)
  -s VOCAB_SIZE, --vocab_size VOCAB_SIZE
                        vocabulary size for model configuration (default:
                        32000)
  -f HYPERPARAMETER_FILE, --hyperparameter_file HYPERPARAMETER_FILE
                        provide training_args.bin or json file of hyperparameters.
                        NOTE: if given, this overrides all
                        HfTrainingArguments! This is overridden by
                        --config_from_run! (default: )
  -e ENTITY_NAME, --entity_name ENTITY_NAME
                        provide wandb team name (if available). NOTE: has no
                        effect if wandb is disabled. (default: )
  -p PROJECT_NAME, --project_name PROJECT_NAME
                        provide wandb project name (if available). NOTE: has
                        no effect if wandb is disabled. (default: )
  -g GROUP_NAME, --group_name GROUP_NAME
                        provide wandb group name (if desired). (default:
                        train)
  -c CONFIG_FROM_RUN, --config_from_run CONFIG_FROM_RUN
                        load arguments from existing wandb run. NOTE: if
                        given, this overrides --hyperparameter_file!
                        (default: None)
  METRIC_OPT, --metric_opt METRIC_OPT
                        score to maximise [ eval/accuracy | eval/validation |
                        eval/loss | eval/precision | eval/recall ] (DEFAULT:
                        eval/f1) (default: eval/f1)
  --override_output_dir
                        override output directory (DEFAULT: OFF) (default:
                        False)
  --no_shuffle          turn off random shuffling (DEFAULT: SHUFFLE)
                        (default: True)
  --wandb_off           log training in real time online (DEFAULT: ON)
                        (default: True)

  [ADDITIONAL ARGUMENTS TRUNCATED]