diff --git a/README.md b/README.md index 4e0ba701..eb335ea8 100644 --- a/README.md +++ b/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 diff --git a/sample_configs/imminent_mortality.yaml b/sample_configs/imminent_mortality.yaml index 3901ba0f..8c9a934d 100644 --- a/sample_configs/imminent_mortality.yaml +++ b/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 diff --git a/sample_configs/inhospital_mortality.yaml b/sample_configs/inhospital_mortality.yaml index a8f7eae5..68758f75 100644 --- a/sample_configs/inhospital_mortality.yaml +++ b/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) diff --git a/sample_configs/intervention_weaning.yaml b/sample_configs/intervention_weaning.yaml index 683b6848..d3f63abb 100644 --- a/sample_configs/intervention_weaning.yaml +++ b/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: diff --git a/sample_configs/long_term_recurrence.yaml b/sample_configs/long_term_recurrence.yaml index 79da7620..71f6f995 100644 --- a/sample_configs/long_term_recurrence.yaml +++ b/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: diff --git a/sample_configs/readmission_risk.yaml b/sample_configs/readmission_risk.yaml index 0d9f81aa..c77e68b7 100644 --- a/sample_configs/readmission_risk.yaml +++ b/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