Updated configs for abnormal lab prediction tasks

src/MEDS_DEV/tasks/criteria/abnormal_lab/blood_chemistry/elevated_creatinine/first_24h.yaml

@@ -0,0 +1,61 @@
+description: >-
+  This task predicts whether the patient will have elevated _creatinine_ values within the next 24
+  hours, given the first 24 hours of their admission to the _hospital_. To be included, 1) patients
+  must have at least one measurement for _creatinine_ within the next 24 hours after their
+  admission to the hospital, 2) patients must not have shown elevated _creatinine_ values
+  previously, and 3) their length of stay in the hospital must be at least 48 hours.
+
+predicates:
+  hospital_admission: ???
+  hospital_discharge: ???
+  birth: ???
+  death: ???
+  discharge_or_death:
+    expr: or(death, hospital_discharge)
+
+  # Plain predicates
+  creatinine:
+    code: ???
+  abnormally_high_creatinine:
+    code: ???
+    value_min: 1.3 # mg/dL
+    value_min_inclusive: False
+    value_max: null
+
+trigger: hospital_admission
+
+windows:
+  input:
+    start: null
+    end: trigger + 24h
+    start_inclusive: True
+    end_inclusive: True
+    index_timestamp: end
+    # do not allow to have shown elevated creatinine values previously
+    has:
+      abnormally_high_creatinine: (None, 0)
+  # do not allow hospital discharge to happen within the input + target window
+  no_discharge:
+    start: trigger
+    end: start + 48h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      hospital_admission: (None, 0)
+      discharge_or_death: (None, 0)
+  # do not allow to include children (age <= 18) patients
+  no_children:
+    start: end - 6570d # 18 years = 365 * 18 days
+    end: trigger
+    start_inclusive: True
+    end_inclusive: True
+    has:
+      birth: (None, 0)
+  target:
+    start: input.end
+    end: start + 24h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      creatinine: (1, None)
+    label: abnormally_high_creatinine

src/MEDS_DEV/tasks/criteria/abnormal_lab/blood_chemistry/hyponatremia/first_24h.yaml

@@ -0,0 +1,61 @@
+description: >-
+  This task predicts whether the patient will have low _sodium_ values (hyponatremia) within the
+  next 24 hours, given the first 24 hours of their admission to the _hospital_. To be included,
+  1) patients must have at least one measurement for _sodium_ within the next 24 hours after their
+  admission to the hospital, 2) patients must not have shown low _sodium_ values previously, and
+  3) their length of stay in the hospital must be at least 48 hours.
+
+predicates:
+  hospital_admission: ???
+  hospital_discharge: ???
+  birth: ???
+  death: ???
+  discharge_or_death:
+    expr: or(death, hospital_discharge)
+
+  # Plain predicates
+  sodium:
+    code: ???
+  abnormally_low_sodium:
+    code: ???
+    value_min: null
+    value_max: 135 # mEq/L
+    value_max_inclusive: False
+
+trigger: hospital_admission
+
+windows:
+  input:
+    start: null
+    end: trigger + 24h
+    start_inclusive: True
+    end_inclusive: True
+    index_timestamp: end
+    # do not allow to have shown low sodium values previously
+    has:
+      abnormally_low_sodium: (None, 0)
+  # do not allow hospital discharge to happen within the input + target window
+  no_discharge:
+    start: trigger
+    end: start + 48h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      hospital_admission: (None, 0)
+      discharge_or_death: (None, 0)
+  # do not allow to include children (age <= 18) patients
+  no_children:
+    start: end - 6570d # 18 years = 365 * 18 days
+    end: trigger
+    start_inclusive: True
+    end_inclusive: True
+    has:
+      birth: (None, 0)
+  target:
+    start: input.end
+    end: start + 24h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      sodium: (1, None)
+    label: abnormally_low_sodium

src/MEDS_DEV/tasks/criteria/abnormal_lab/in_icu/blood_chemistry/metabolic_acidosis/first_24h.yaml → src/MEDS_DEV/tasks/criteria/abnormal_lab/blood_chemistry/metabolic_acidosis/first_24h.yaml

@@ -1,8 +1,9 @@
 description: >-
   This task predicts whether the patient will have low _bicarbonate_ values (metabolic acidosis)
-  within the next 24 hours, given the first 24 hours of their admission to the ICU. To be included,
-  patients must have at least one measurement for _bicarbonate_ within the next 24 hours after
-  their admission to ICU, and their length of stay in ICU should be at least 24 hours.
+  within the next 24 hours, given the first 24 hours of their admission to the hospital. To be
+  included, 1) patients must have at least one measurement for _bicarbonate_ within the next 24
+  hours after their admission to the hospital, 2) patients must not have shown low _bicarbonate_
+  values previously, and 3) their length of stay in the hospital must be at least 48 hours.
 
 predicates:
   icu_admission: ???
@@ -18,9 +19,10 @@ predicates:
   abnormally_low_bicarbonate:
     code: ???
     value_min: null
-    value_max: ???
+    value_max: 22 # mEq/L
+    value_max_inclusive: False
 
-trigger: icu_admission
+trigger: hospital_admission
 
 windows:
   input:
@@ -29,15 +31,26 @@ windows:
     start_inclusive: True
     end_inclusive: True
     index_timestamp: end
-  # do not allow icu discharge to happen within the input + target window.
+    # do not allow to have shown low bicarbonate values previously
+    has:
+      abnormally_low_bicarbonate: (None, 0)
+  # do not allow hospital discharge to happen within the input + target window
   no_discharge:
     start: trigger
     end: start + 48h
     start_inclusive: False
     end_inclusive: True
     has:
-      icu_admission: (None, 0)
+      hospital_admission: (None, 0)
       discharge_or_death: (None, 0)
+  # do not allow to include children (age <= 18) patients
+  no_children:
+    start: end - 6570d # 18 years = 365 * 18 days
+    end: trigger
+    start_inclusive: True
+    end_inclusive: True
+    has:
+      birth: (None, 0)
   target:
     start: input.end
     end: start + 24h

src/MEDS_DEV/tasks/criteria/abnormal_lab/cbc/anemia/first_24h.yaml

@@ -0,0 +1,61 @@
+description: >-
+  This task predicts whether the patient will have low _hemoglobin_ values (anemia) within the next
+  24 hours, given the first 24 hours of their admission to the _hospital_. To be included,
+  1) patients must have at least one measurement for _hemoglobin_ within the next 24 hours after
+  their admission to the hospital, 2) patients must not have shown low _hemoglobin_ values
+  previously, and 3) their length of stay in the hospital must be at least 48 hours.
+
+predicates:
+  hospital_admission: ???
+  hospital_discharge: ???
+  birth: ???
+  death: ???
+  discharge_or_death:
+    expr: or(death, hospital_discharge)
+
+  # Plain predicates
+  hemoglobin:
+    code: ???
+  abnormally_low_hemoglobin:
+    code: ???
+    value_min: null
+    value_max: 13 # g/dL
+    value_max_inclusive: False
+
+trigger: hospital_admission
+
+windows:
+  input:
+    start: null
+    end: trigger + 24h
+    start_inclusive: True
+    end_inclusive: True
+    index_timestamp: end
+    # do not allow to have shown low hemoglobin values previously
+    has:
+      abnormally_low_hemoglobin: (None, 0)
+  # do not allow hospital discharge to happen within the input + target window
+  no_discharge:
+    start: trigger
+    end: start + 48h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      hospital_admission: (None, 0)
+      discharge_or_death: (None, 0)
+  # do not allow to include children (age <= 18) patients
+  no_children:
+    start: end - 6570d # 18 years = 365 * 18 days
+    end: trigger
+    start_inclusive: True
+    end_inclusive: True
+    has:
+      birth: (None, 0)
+  target:
+    start: input.end
+    end: start + 24h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      hemoglobin: (1, None)
+    label: abnormally_low_hemoglobin

src/MEDS_DEV/tasks/criteria/abnormal_lab/cbc/leukocytosis/first_24h.yaml

@@ -0,0 +1,61 @@
+description: >-
+  This task predicts whether the patient will have high _WBC_ values (leukocytosis) within the next
+  24 hours, given the first 24 hours of their admission to the _hospital_. To be included,
+  1) patients must have at least one measurement for _WBC_ within the next 24 hours after their
+  admission to the hospital, 2) patients must not have shown high _WBC_ values previously, and
+  3) their length of stay in the hospital must be at least 48 hours.
+
+predicates:
+  hospital_admission: ???
+  hospital_discharge: ???
+  birth: ???
+  death: ???
+  discharge_or_death:
+    expr: or(death, hospital_discharge)
+
+  # Plain predicates
+  wbc:
+    code: ???
+  abnormally_high_wbc:
+    code: ???
+    value_min: 11 # K/uL
+    value_min_inclusive: False
+    value_max: null
+
+trigger: hospital_admission
+
+windows:
+  input:
+    start: null
+    end: trigger + 24h
+    start_inclusive: True
+    end_inclusive: True
+    index_timestamp: end
+    # do not allow to have shown high WBC values previously
+    has:
+      abnormally_high_wbc: (None, 0)
+  # do not allow hospital discharge to happen within the input + target window
+  no_discharge:
+    start: trigger
+    end: start + 48h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      hospital_admission: (None, 0)
+      discharge_or_death: (None, 0)
+  # do not allow to include children (age <= 18) patients
+  no_children:
+    start: end - 6570d # 18 years = 365 * 18 days
+    end: trigger
+    start_inclusive: True
+    end_inclusive: True
+    has:
+      birth: (None, 0)
+  target:
+    start: input.end
+    end: start + 24h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      wbc: (1, None)
+    label: abnormally_high_wbc

src/MEDS_DEV/tasks/criteria/abnormal_lab/cbc/thrombocytopenia/first_24h.yaml

@@ -0,0 +1,61 @@
+description: >-
+  This task predicts whether the patient will have low _platelets_ values (thrombocytopenia) within
+  the next 24 hours, given the first 24 hours of their admission to the hospital. To be included,
+  1) patients must have at least one measurement for _platelets_ within the next 24 hours after
+  their admission to the hospital, 2) patients must not have shown low _platelets_ values
+  previously, and 3) their length of stay in the hospital must be at least 48 hours.
+
+predicates:
+  hospital_admission: ???
+  hospital_discharge: ???
+  birth: ???
+  death: ???
+  discharge_or_death:
+    expr: or(death, hospital_discharge)
+
+  # Plain predicates
+  platelets:
+    code: ???
+  abnormally_low_platelets:
+    code: ???
+    value_min: null
+    value_max: 150 # K/uL
+    value_max_inclusive: False
+
+trigger: hospital_admission
+
+windows:
+  input:
+    start: null
+    end: trigger + 24h
+    start_inclusive: True
+    end_inclusive: True
+    index_timestamp: end
+    # do not allow to have shown low platelets values previously
+    has:
+      abnormally_low_platelets: (None, 0)
+  # do not allow hospital discharge to happen within the input + target window
+  no_discharge:
+    start: trigger
+    end: start + 48h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      hospital_admission: (None, 0)
+      discharge_or_death: (None, 0)
+  # do not allow to include children (age <= 18) patients
+  no_children:
+    start: end - 6570d # 18 years = 365 * 18 days
+    end: trigger
+    start_inclusive: True
+    end_inclusive: True
+    has:
+      birth: (None, 0)
+  target:
+    start: input.end
+    end: start + 24h
+    start_inclusive: False
+    end_inclusive: True
+    has:
+      platelets: (1, None)
+    label: abnormally_low_platelets