Default to MEDS predicates for shipping with repo

README.md

@@ -178,7 +178,7 @@ windows:
   ...
 ```
 
-Sample task configuration files for 6 common tasks are provided in `sample_configs/`. All task configurations can be directly extracted using `'direct'` mode on `sample_data/sample_data.csv` as this predicates dataframe was designed specifically to capture concepts needed for all tasks. However, only `inhospital_mortality.yaml` and `imminent-mortality.yaml` would be able to be extracted on `sample_data/esgpt_sample` and `sample_data/meds_sample` due to a lack of required concepts in the datasets.
+Sample task configuration files for 6 common tasks are provided in `sample_configs/`. All task configurations can be directly extracted using `'direct'` mode on `sample_data/sample_data.csv` as this predicates dataframe was designed specifically to capture concepts needed for all tasks. However, only `inhospital_mortality.yaml` and `imminent-mortality.yaml` would be able to be extracted on `sample_data/esgpt_sample` and `sample_data/meds_sample` due to a lack of required concepts in the datasets (predicates are defined as per the MEDS sample data by default; modifications will be needed for ESGPT).
 
 ### Predicates
 

sample_configs/imminent_mortality.yaml

@@ -1,7 +1,7 @@
 # Task: 24-hour Imminent Mortality Prediction
 predicates:
   death:
-    code: event_type//DEATH
+    code: DEATH
 
 trigger: _ANY_EVENT
 

sample_configs/inhospital_mortality.yaml

@@ -1,11 +1,11 @@
 # Task: 24-hour In-hospital Mortality Prediction
 predicates:
   admission:
-    code: event_type//ADMISSION
+    code: { regex: "ADMISSION//.*" }
   discharge:
-    code: event_type//DISCHARGE
+    code: { regex: "DISCHARGE//.*" }
   death:
-    code: event_type//DEATH
+    code: DEATH
   discharge_or_death:
     expr: or(discharge, death)
 

sample_configs/intervention_weaning.yaml

@@ -1,9 +1,9 @@
 # Task: Ventilation Weaning Prediction
 predicates:
   procedure_start:
-    code: event_type//PROCEDURE_START
+    code: PROCEDURE_START
   procedure_end:
-    code: event_type//PROCEDURE_END
+    code: PROCEDURE_END
   ventilation:
     code: procedure//Invasive Ventilation
   ventilation_start:

sample_configs/long_term_recurrence.yaml

@@ -1,9 +1,9 @@
 # Task: Long-term (3 Years) MI Recurrence Prediction
 predicates:
   admission:
-    code: event_type//ADMISSION
+    code: { regex: "ADMISSION//.*" }
   discharge:
-    code: event_type//DISCHARGE
+    code: { regex: "DISCHARGE//.*" }
   diagnosis_ICD9CM_41071:
     code: diagnosis//ICD9CM_41071
   diagnosis_ICD10CM_I214:

sample_configs/readmission_risk.yaml

@@ -1,9 +1,9 @@
 # Task: 30-day Readmission Risk Prediction
 predicates:
   admission:
-    code: event_type//ADMISSION
+    code: { regex: "ADMISSION//.*" }
   discharge:
-    code: event_type//DISCHARGE
+    code: { regex: "DISCHARGE//.*" }
 
 trigger: admission