Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -28,6 +28,7 @@ _HOMEPAGE = "https://huggingface.co/datasets/thbndi/Mimic4Dataset"
 _CITATION = "https://proceedings.mlr.press/v193/gupta22a.html"
 _GIT_URL = "https://github.com/healthylaife/MIMIC-IV-Data-Pipeline"
 
+_ICD_CODE = f"{_BASE_URL}/icd10.txt"
 _DATA_GEN = f"{_BASE_URL}/data_generation_icu_modify.py"
 _DATA_GEN_HOSP= f"{_BASE_URL}/data_generation_modify.py"
 _DAY_INT= f"{_BASE_URL}/day_intervals_cohort_v22.py"
@@ -164,6 +165,10 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
 
         
         #####################downloads modules from hub
+        if not os.path.exists('./icd10.txt'):
+            file_path, head = urlretrieve(_ICD_CODE, "icd10.txt")
+            shutil.move(file_path, './')    
+                
         if not os.path.exists('./model/data_generation_icu_modify.py'):
             file_path, head = urlretrieve(_DATA_GEN, "data_generation_icu_modify.py")
             shutil.move(file_path, './model')
@@ -506,7 +511,39 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
                         'CHART/LAB': lab,
                         'OUT': out,
                         }          
-    
+ ######################################################text##############################################################
+    def _info_text(self):
+        features = datasets.Features(
+            {
+                "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
+                "COND" : datasets.Value(dtype='string', id=None),
+            }
+        )
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            homepage=_HOMEPAGE,
+            citation=_CITATION,
+        )
+
+    def _generate_examples_text(self, filepath):
+        icd = pd.read_csv('icd10.txt',names=['code','description'],sep='\t')
+        with open(filepath, 'rb') as fp:
+            dico = pickle.load(fp)
+        for key, data in dico.items():
+            conds = data['Cond']['fids']
+            text=[]
+            for code in conds:
+                desc = icd[icd['code']==code]
+                if not desc.empty:
+                    text.append(desc['description'].to_string(index=False))
+            template = 'The patient is diagnosed with {}.'
+            text = template.format('; '.join(text))
+            yield int(key),{
+                'label' : data['label'],
+                'COND': text,
+                }
+
 #############################################################################################################################
     def _info(self):
         self.path = self.init_cohort()
@@ -520,7 +557,6 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         else:
             return self._info_raw()
 
-
     def _split_generators(self, dl_manager):
         data_dir = "./data/dict/"+self.config.name.replace(" ","_")
         if self.val_size > 0 :