ruoqi-liu / cure

CURE: A Pre-training Framework on Large-scale Patient Data for Treatment Effect Estimation

Introduction

Code for paper "A Pre-training Framework on Large-scale Patient Data for Treatment Effect Estimation".

In this paper, we propose a novel transformer-based pre-training and fine-tuning framework called CURE for TEE from observational data. CURE is pre-trained on large-scale unlabeled patient data to learn representative contextual patient representations, and then fine-tuned on labeled patient data for TEE.

We obtain and preprocess 3M large-scale observational data (MarketScan Research Databases) and 4 downstream TEE tasks (10-20K patient samples) for evaluating the comparative treatment effectiveness for patients with coronary artery disease (CAD).

Requirements

Install PyTorch==1.17.1 by following the instructions from the official website.

Install the remaining dependencies by running the script,

pip install -r requirements.txt

Dataset

The real world patient data used in this paper is MarketScan claims data.

Data flow chart

The data flow chart of MarketScan claims data.

Source: 2012 MarketScan® CCAE MDCR User Guide

Data files used

• Inpatient Admissions (I) : Admission summary records
• Outpatient Services (O): Individual outpatient claim records
• Outpatient Pharmaceutical Claims (D): Individual outpatient prescription drug claim records
• Population (P): Summarizes demographic information about the eligible population

Input data demo

The demo of the input data can be found in the data/demo

Cohort

The data structure for cohort table is as follows,

Column Name	Description	Note
ENROLID	Patient enroll ID	Unique identifier for each patient
Index_date	The date of first CAD encounter	i.e., min (ADMDATE [1st CAD admission date for the inpatient records],SVCDATE [1st CAD service date for the outpatient records])
DTSTART	Date of insurance enrollment start	M/D/Y, e.g., 03/25/2732
DTEND	Date of insurance enrollment end	M/D/Y, e.g., 03/25/2732

Drug table

The data structure for the drug table is as follows,

Column Name	Description	Note
ENROLID	Patient enroll ID	Unique identifier for each patient
NDCNUM	National drug code (NDC)	We map NDC to observational medical outcomes partnership (OMOP) ingredient concept ID, and obtain 1,353 unique drugs
SVCDATE	Date to take the prescription	M/D/Y, e.g., 03/25/2732
DAYSUPP	Days supply. The number of days of drug therapy covered by this prescription	Day, e.g., 28

Inpatient table

The data structure for the inpatient table is as follows,

Column Name	Description	Note
ENROLID	Patient enroll ID	Unique identifier for each patient
DX1-DX15	Diagnosis codes. International Classification of Diseases (ICD) codes	57,089 ICD-9/10 codes considered in the dataset. Dictionary for ICD-9 and ICD-10 codes.
DXVER	Flag to denote ICD-9/10 codes	“9” = ICD-9-CM and “0” = ICD-10-CM
ADMDATE	Admission date for this inpatient visit	M/D/Y, e.g., 03/25/2732
Days	The number of days stay in the inpatient hospital	Day, e.g., 28

Outpatient table

The data structure for the outpatient table is as follows,

Column Name	Description	Note
ENROLID	Patient enroll ID	Unique identifier for each patient
DX1-DX4	Diagnosis codes. International Classification of Diseases (ICD) codes	57,089 ICD-9/10 codes considered in the dataset. Dictionary for ICD-9 and ICD-10 codes.
DXVER	Flag to denote ICD-9/10 codes	“9” = ICD-9-CM and “0” = ICD-10-CM
SVCDATE	Service date for this outpatient visit	M/D/Y, e.g., 03/25/2732

Demographics

The data structure for demo table is as follows,

Column Name	Description	Note
ENROLID	Patient enroll ID	Unique identifier for each patient
DOBYR	birth year	Year, e.g., 2099
SEX	gender	1- male; 2- female

Pre-train CURE

python pretrain.py 
  --data_path data/preprocessed_data/cad/cohort 
  --vocab_file data/preprocessed_data/cad/vocab.txt 
  --do_train 
  --max_steps 100000 
  --learning_rate 1e-4 
  --overwrite_output_dir 
  --output_dir output/all_masked_prediction_cad_bertbase 
  --mask_prediction 
  --per_device_train_batch_size 24 
  --per_device_eval_batch_size 24 
  --validation_split_percentage 1 
  --logging_steps 100 
  --save_steps 5000 
  --max_seq_length 256 
  --baseline_window 360 
  --cache_dir cache/ 
  --time_embedding 
  --warmup_steps 10000

Fine-tune CURE for treatment effect estimation

python finetune_TEE.py 
  --model_name_or_path output/all_masked_prediction_cad_bertbase 
  --data_path data/preprocessed_data/cad/cohort 
  --target_drug Rivaroxaban.json 
  --compared_drug Aspirin.json 
  --vocab_file data/preprocessed_data/cad/vocab.txt 
  --do_train 
  --do_eval 
  --num_train_epoch 2 
  --learning_rate 5e-5 
  --overwrite_output_dir 
  --output_dir output/all_masked_prediction_cad_bertbase_finetuned_outcome_prediction_cad 
  --outcome_prediction 
  --per_device_train_batch_size 32 
  --per_device_eval_batch_size 32 
  --validation_split_percentage 10 
  --cache_dir cache/ 
  --logging_steps 50 
  --save_steps 10000 
  --max_seq_length 256 
  --baseline_window 360 
  --overwrite_cache 
  --time_embedding