/prostate-cancer-prediction

Primary LanguagePython

prostate-cancer-prediction

BASELINES

MODELS 1: Time series with interpolation and discretization

MODELS 2: Irregular time series

FIRST STEP: Building database

PATIENTS WITH CANCER:

SELECT psaresults.ss_number_id,
(extract ( year from ambiguous_date) - extract ( year from ss_numbers.date_of_birth_15)) * 12 * 30 +
(extract ( month from ambiguous_date) - extract ( month from ss_numbers.date_of_birth_15)) * 30 +
(extract ( day from ambiguous_date) - extract ( day from ss_numbers.date_of_birth_15)) as days,
ambiguous_date, date_of_birth_15, result_numeric as psa, npcc_risk_class_group_1 as category

FROM ss_numbers, psaresults, kreftreg_data

WHERE diagnosis_date >= ambiguous_date and psaresults.ss_number_id = kreftreg_data.ss_number_id and
    ss_numbers.ss_number_id = psaresults.ss_number_id and (extract ( year from ambiguous_date) - extract ( year from ss_numbers.date_of_birth_15)) >= 30

PATIENTS WITHOUT CANCER:

SELECT psaresults.ss_number_id, 
(extract ( year from ambiguous_date) - extract ( year from ss_numbers.date_of_birth_15)) * 12 * 30 +
(extract ( month from ambiguous_date) - extract ( month from ss_numbers.date_of_birth_15)) * 30 +
(extract ( day from ambiguous_date) - extract ( day from ss_numbers.date_of_birth_15)) as days,
ambiguous_date, date_of_birth_15, result_numeric as psa

FROM (
SELECT distinct(psaresults.ss_number_id) as id

    FROM psaresults
    
    LEFT JOIN kreftreg_data
    
    ON psaresults.ss_number_id = kreftreg_data.ss_number_id
    
    WHERE kreftreg_data.ss_number_id is NULL) as tab, ss_numbers, psaresults

WHERE tab.id =  psaresults.ss_number_id and 
    ss_numbers.ss_number_id = psaresults.ss_number_id and (extract ( year from ambiguous_date) - extract ( year from ss_numbers.date_of_birth_15)) >= 30

SECOND STEP: Save the dataset

The datasets should be saved in the folder dataset with the names cancer.csv and nocancer.csv

THIRD STEP: Run the code

  1. CD prostate-cancer-prediction
  2. Launch the bash script commands.sh