2. task

pyhealth/tasks/__init__.py

@@ -39,5 +39,4 @@
  sleep_staging_isruc_fn,
  sleep_staging_shhs_fn,
 )
-
-
+from .patient_linkage import patient_linkage_mimic3_fn

pyhealth/tasks/patient_linkage.py

@@ -0,0 +1,71 @@
+from pyhealth.data import Patient
+
+
+def patient_linkage_mimic3_fn(patient: Patient):
+ """ Patient linkage task for the mimic3 dataset. """
+
+ # exclude patients with less than two visits
+ if len(patient) < 2:
+ return []
+
+ samples = []
+ q_visit = patient.get_visit_by_index(len(patient) - 1)
+ d_visit = patient.get_visit_by_index(len(patient) - 2)
+
+ q_age = (q_visit.encounter_time - patient.birth_datetime).days // 365.25
+ d_age = (d_visit.encounter_time - patient.birth_datetime).days // 365.25
+
+ # exclude patients under 18
+ if (q_age < 18) or (d_age < 18):
+ return []
+
+ q_conditions = q_visit.get_code_list(table="DIAGNOSES_ICD")
+ d_conditions = d_visit.get_code_list(table="DIAGNOSES_ICD")
+
+ # exclude patients without conditions
+ if len(q_conditions) * len(d_conditions) == 0:
+ return []
+
+ # identifiers
+ gender = patient.gender
+ insurance = q_visit.attr_dict["insurance"]
+ language = q_visit.attr_dict["language"]
+ religion = q_visit.attr_dict["religion"]
+ marital_status = q_visit.attr_dict["marital_status"]
+ ethnicity = q_visit.attr_dict["ethnicity"]
+ insurance = "" if insurance != insurance else insurance
+ language = "" if language != language else language
+ religion = "" if religion != religion else religion
+ marital_status = "" if marital_status != marital_status else marital_status
+ ethnicity = "" if ethnicity != ethnicity else ethnicity
+ q_identifiers = "+".join(
+ [gender, insurance, language, religion, marital_status, ethnicity]
+ )
+
+ insurance = d_visit.attr_dict["insurance"]
+ language = d_visit.attr_dict["language"]
+ religion = d_visit.attr_dict["religion"]
+ marital_status = d_visit.attr_dict["marital_status"]
+ ethnicity = d_visit.attr_dict["ethnicity"]
+ insurance = "" if insurance != insurance else insurance
+ language = "" if language != language else language
+ religion = "" if religion != religion else religion
+ marital_status = "" if marital_status != marital_status else marital_status
+ ethnicity = "" if ethnicity != ethnicity else ethnicity
+ d_identifiers = "+".join(
+ [gender, insurance, language, religion, marital_status, ethnicity]
+ )
+
+ samples.append({
+ "patient_id": patient.patient_id,
+ "visit_id": q_visit.visit_id,
+ "conditions": ["<cls>"] + q_conditions,
+ "age": q_age,
+ "identifiers": q_identifiers,
+ "d_visit_id": d_visit.visit_id,
+ "d_conditions": ["<cls>"] + d_conditions,
+ "d_age": d_age,
+ "d_identifiers": d_identifiers,
+ })
+
+ return samples