active-learning-pub/config.example at master · AMCeScience/active-learning-pub · GitHub

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import os

CWD = os.getcwd()

DB_FILE = CWD + '/Database/miner_database.db'

DEBUG = False

### Pubmed API config:
PUBMED_EMAIL = 'aj.vanaltena@amsterdamumc.nl'
DB_INSERT_LIMIT = 100

### CLEF specific config
STORE_LOCATION = CWD + '/Pubmed results/'
TRAIN_QREL_LOCATION = CWD + '/Database/CLEF_data/qrel_abs_train'
TEST_QREL_LOCATION = CWD + '/Database/CLEF_data/qrel_abs_test'
DOC_COLLECTION = CWD + '/Text_data/document_collection.pickle'

TEXT_DATA_LOCATION = CWD + '/Text_data'
RESULTS_LOCATION = CWD + '/Results'
PLOT_LOCATION = CWD + '/Plots/'

### Preprocessing
EXTRA_STOPWORDS = []
KEEP_DASHES = False
KEEP_NUMBERS = False

MIN_DOCFREQ = 2
MAX_DOCFREQ = 0.95
MATRIX_COLLECTION = CWD + '/Text_data/matrix_collection.pickle'

### Parallel computing
POOL_PROCESSES = 6
NUM_ITERATIONS = 50

SIMILARITY_STEPS = [0, 1, 2, 3, 4, 5, 7, 9, 10, 15, 30]

SINGLE_REVIEWS = ['CD009647', 'CD008054', 'CD010438', 'CD009185', 'CD008691', 'CD008081', 'CD010023', 'CD009591', 'CD009372', 'CD008803', 'CD012019', 'CD008760']
GROUP_REVIEWS = ['CD007427', 'CD010542', 'CD010705', 'CD009593', 'CD009551', 'CD007394', 'CD009135', 'CD009579', 'CD010173', 'CD010276', 'CD009944', 'CD011134', 'CD009323', 'CD009519', 'CD010409', 'CD009786', 'CD010386', 'CD010632', 'CD008782', 'CD010772', 'CD010771', 'CD011145', 'CD010653', 'CD010860', 'CD010775', 'CD010783', 'CD010633', 'CD010896', 'CD011549', 'CD011548', 'CD010339', 'CD007431', 'CD008686', 'CD011984', 'CD009925', 'CD011975', 'CD008643', 'CD009020']

# Review groups, grouped by manually assigned ICD-10 codes
GROUPS = {
  'tuberculosis': ['CD009593', 'CD010705'],
  'aspergillosis': ['CD007394', 'CD009135', 'CD009551', 'CD009579'],
  'cancer': ['CD009944', 'CD011134', 'CD009323', 'CD010409', 'CD009519', 'CD010276', 'CD010173', 'CD009786'],
  'dementia': ['CD010771', 'CD010632', 'CD008782', 'CD010775', 'CD010653', 'CD010896', 'CD010772', 'CD011145', 'CD010633', 'CD010386', 'CD010783', 'CD010860'],
  'liver and bile duct': ['CD011549', 'CD011548', 'CD010339', 'CD010542'],
  'joint pain': ['CD008643', 'CD007427', 'CD008686', 'CD009020', 'CD007431'],
  'down syndrome': ['CD011984', 'CD011975', 'CD009925'],
  'singles': ['CD010438', 'CD008054', 'CD009591', 'CD008691', 'CD008803', 'CD009647', 'CD008760', 'CD009372', 'CD012019', 'CD008081', 'CD009185', 'CD010023'],
}

EXCLUDE_REVIEWS = True

REMOVED_REVIEWS = GROUPS['singles']