nonadherence_concept_extraction/config.yaml at master · reneahlsdorf/nonadherence_concept_extraction · GitHub

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logger_enabled: true
debugging: true
njobs: 8 # Number of CPU cores to be used
overall_project_name: nonadherence_notes
generated_df_dir: generated_nonadherence

full_pipeline: ["catchall_label_filtering", "validation"]

google_setup:
  google_project_id: hst-953-2019

bigquery_mimic_lexicon_note_search:
  output_note_file: _filtered.parquet
  lexicon_dir: non_adherence_lexicons
  cohort_file: cohort_na.csv
  ignore_categories: [ECG, Echo, Radiology]
  debug_download: false
  use_bqstorage_api: true
  dump_all_notes: false

negex_negation_filter_dummy:
  input_note_file: _filtered.parquet
  output_note_file: _negated_dummy.parquet
  lexicon_dir: non_adherence_lexicons
  debug_check: false
  keep_categories: ['Consult', 'Case Management', 'Nursing', 'Discharge summary', 'Social Work', 'Nutrition', 'Rehab Services', 'Nursing/other', 'Respiratory ', 'Physician ', 'Pharmacy', 'General']

negex_negation_filter:
  input_note_file: _filtered.parquet
  output_note_file:  _negated.parquet
  negex_triggers: negex_triggers.txt
  lexicon_dir: non_adherence_lexicons
  debug_check: false
  use_only_positive_lexicons: false
  use_old_negation_scheme: false
  dump_all_matched_notes: true
  add_fullstop_after_newline_uppercase: false
  keep_categories: ['Consult', 'Case Management', 'Nursing', 'Discharge summary', 'Social Work', 'Nutrition', 'Rehab Services', 'Nursing/other', 'Respiratory ', 'Physician ', 'Pharmacy', 'General']


validation_compare_pipeline_results:
  validation_set_file: validationset_nonadherence_2019.csv
  file_prediction_a: _done_old.parquet
  file_prediction_b: _done.parquet
  file_sentence_info_a: _negated_old.parquet
  file_sentence_info_b: _negated.parquet
  get_examples_for_categories: ['Appointment_Nonadherence', 'Refusal_Against_Medical_Advise_Nonadherence', 'Nos_Nonadherence', 'Medication_Nonadherence', 'Dietary_Nonadherence']
  ignore_b: false


validation_table:
   validation_set_file: validationset_nonadherence_2019.csv
   input_note_files:
      - _all_out_catchall_label_filtering.parquet

validation:
  validation_set_file: validationset_nonadherence_2019.csv
  input_note_file: _all_out_catchall_label_filtering.parquet


word_distance_cohort_matcher:
  input_note_file: _negated.parquet
  output_note_file:  _corrected.parquet
  word_distance: 10
  word_filter_dir: nonadherence_diet_drugs_correction
  debug_check: false

catchall_label_filtering:
  input_note_file: _corrected.parquet
  output_note_file: _done.parquet
  catchall: nos_nonadherence