`medcat.utils.model_creator`

Module Contents

`create_cdb`(concept_csv_file, medcat_config)	Create concept database from csv.
`create_vocab`(cdb, training_data_list, medcat_config, ...)	Create vocabulary for word embeddings and spell check from list of training documents and CDB.
`train_unsupervised`(cdb, vocab, config, output_dir, ...)	Perform unsupervised training and save updated CDB.
`create_models`(config_file)	Create MedCAT CDB and Vocabulary models.
`main`(config_file)

medcat.utils.model_creator.create_cdb(concept_csv_file, medcat_config)

Create concept database from csv.

Parameters:

concept_csv_file (Path) – Path to CSV file containing all concepts and synonyms.
medcat_config (Config) – MedCAT configuration file.

Returns:

CDB – MedCAT concept database containing list of entities and synonyms, without context embeddings.

Return type:

medcat.cdb.CDB

medcat.utils.model_creator.create_vocab(cdb, training_data_list, medcat_config, output_dir, unigram_table_size)

Create vocabulary for word embeddings and spell check from list of training documents and CDB.

Parameters:

cdb (medcat.cdb.CDB) – MedCAT concept database containing list of entities and synonyms.
training_data_list (list) – List of example documents.
medcat_config (medcat.config.Config) – MedCAT configuration file.
output_dir (pathlib.Path) – Output directory to write vocabulary and data.txt (required to create vocabulary) to.
unigram_table_size (int) – Size of unigram table to be initialized before creating vocabulary.

Returns:

medcat.vocab.Vocab – MedCAT vocabulary created from CDB and training documents.

medcat.utils.model_creator.train_unsupervised(cdb, vocab, config, output_dir, training_data_list)

Perform unsupervised training and save updated CDB.

Although not returned explicitly in this function, the CDB will be updated with context embeddings.

Parameters:

cdb (medcat.cdb.CDB) – MedCAT concept database containing list of entities and synonyms.
vocab (medcat.vocab.Vocab) – MedCAT vocabulary created from CDB and training documents.
config (medcat.config.Config) – MedCAT configuration file.
output_dir (pathlib.Path) – Output directory to write updated CDB to.
training_data_list (list) – List of example documents.

Returns:

medcat.cdb.CDB – MedCAT concept database containing list of entities and synonyms, as well as context embeddings.

medcat.utils.model_creator.create_models(config_file)

Create MedCAT CDB and Vocabulary models.

Parameters:: config_file (pathlib.Path) – Location of model creator configuration file to specify input, output and MedCAT configuration.
Returns:: medcat.cat.CAT – Containing CDB, Vocab and Config.