Update dataset_utils.py

dataset_utils.py

@@ -1,580 +1,402 @@
-import os
 import pandas as pd
-import datasets
-import sys
 import pickle
-import subprocess
-import shutil
-from urllib.request import urlretrieve
-from sklearn.model_selection import train_test_split
-from sklearn.preprocessing import LabelEncoder
-import yaml
 import numpy as np
-from .dataset_utils import vocab, concat_data, generate_deep, generate_ml, generate_text, open_dict
-from .task_cohort import create_cohort
-
-
-
-_DESCRIPTION = """\
-Dataset for mimic4 data, by default for the Mortality task.
-Available tasks are: Mortality, Length of Stay, Readmission, Phenotype.
-The data is extracted from the mimic4 database using this pipeline: 'https://github.com/healthylaife/MIMIC-IV-Data-Pipeline/tree/main'
-mimic path should have this form : "path/to/mimic4data/from/username/mimiciv/2.2"
-If you choose a Custom task provide a configuration file for the Time series.
-Currently working with Mimic-IV version 1 and 2
-"""
-_BASE_URL = "https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main"
-_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"
-_CONFIG_URLS = {'los' : f"{_BASE_URL}/config/los.config",
-                'mortality' : f"{_BASE_URL}/config/mortality.config",
-                'phenotype' : f"{_BASE_URL}/config/phenotype.config",
-                'readmission' : f"{_BASE_URL}/config/readmission.config"
-        }
-
-
-class Mimic4DatasetConfig(datasets.BuilderConfig):
-    """BuilderConfig for Mimic4Dataset."""
-
-    def __init__(
-        self,
-        **kwargs,
-    ):
-        super().__init__(**kwargs)
-
-
-class Mimic4Dataset(datasets.GeneratorBasedBuilder):
-    """Create Mimic4Dataset dataset from Mimic-IV data stored in user machine."""
-    VERSION = datasets.Version("1.0.0")
-
-    def __init__(self, **kwargs):
-        self.mimic_path = kwargs.pop("mimic_path", None)
-        self.encoding = kwargs.pop("encoding",'concat')
-        self.config_path = kwargs.pop("config_path",None)
-        self.test_size = kwargs.pop("test_size",0.2)
-        self.val_size = kwargs.pop("val_size",0.1)
-        self.generate_cohort = kwargs.pop("generate_cohort",True)
-
-        if self.encoding == 'concat':
-            self.concat = True
-        else:
-            self.concat = False
-            
-        super().__init__(**kwargs)
+import torch
+
+
+def create_vocab(file,task):
+    with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+        condVocab = pickle.load(fp)
+    condVocabDict={}
+    condVocabDict[0]=0
+    for val in range(len(condVocab)):
+        condVocabDict[condVocab[val]]= val+1    
+
+    return condVocabDict
+
+def gender_vocab():
+    genderVocabDict={}
+    genderVocabDict['<PAD>']=0
+    genderVocabDict['M']=1
+    genderVocabDict['F']=2
+
+    return genderVocabDict
+
+def vocab(task,diag_flag,proc_flag,out_flag,chart_flag,med_flag,lab_flag):
+        condVocabDict={}
+        procVocabDict={}
+        medVocabDict={}
+        outVocabDict={}
+        chartVocabDict={}
+        labVocabDict={}
+        ethVocabDict={}
+        ageVocabDict={}
+        genderVocabDict={}
+        insVocabDict={}
         
+        ethVocabDict=create_vocab('ethVocab',task)
+        with open('./data/dict/'+task+'/ethVocabDict', 'wb') as fp:
+            pickle.dump(ethVocabDict, fp)
+            
+        ageVocabDict=create_vocab('ageVocab',task)
+        with open('./data/dict/'+task+'/ageVocabDict', 'wb') as fp:
+            pickle.dump(ageVocabDict, fp)
         
-    BUILDER_CONFIGS = [
-        Mimic4DatasetConfig(
-            name="Phenotype",
-            version=VERSION,
-            description="Dataset for mimic4 Phenotype task"
-        ),
-        Mimic4DatasetConfig(
-            name="Readmission",
-            version=VERSION,
-            description="Dataset for mimic4 Readmission task"
-        ),
-        Mimic4DatasetConfig(
-            name="Length of Stay",
-            version=VERSION,
-            description="Dataset for mimic4 Length of Stay task"
-        ),
-        Mimic4DatasetConfig(
-            name="Mortality",
-            version=VERSION,
-            description="Dataset for mimic4 Mortality task"
-        ),
-    ]
-    
-    DEFAULT_CONFIG_NAME = "Mortality"
+        genderVocabDict=gender_vocab()
+        with open('./data/dict/'+task+'/genderVocabDict', 'wb') as fp:
+            pickle.dump(genderVocabDict, fp)
+            
+        insVocabDict=create_vocab('insVocab',task)
+        with open('./data/dict/'+task+'/insVocabDict', 'wb') as fp:
+            pickle.dump(insVocabDict, fp)
         
-    def init_cohort(self):
-        if self.config_path==None:
-            if self.config.name == 'Phenotype' : self.config_path = _CONFIG_URLS['phenotype'] 
-            if self.config.name == 'Readmission' : self.config_path = _CONFIG_URLS['readmission'] 
-            if self.config.name == 'Length of Stay' : self.config_path = _CONFIG_URLS['los'] 
-            if self.config.name == 'Mortality' : self.config_path = _CONFIG_URLS['mortality']
+        if diag_flag:
+            file='condVocab'
+            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+                condVocabDict = pickle.load(fp)
+        if proc_flag:
+            file='procVocab'
+            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+                procVocabDict = pickle.load(fp)
+        if med_flag:
+            file='medVocab'
+            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+                medVocabDict = pickle.load(fp)
+        if out_flag:
+            file='outVocab'
+            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+                outVocabDict = pickle.load(fp)
+        if chart_flag:
+            file='chartVocab'
+            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+                chartVocabDict = pickle.load(fp)
+        if lab_flag:
+            file='labsVocab'
+            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
+                labVocabDict = pickle.load(fp)
         
-        version = self.mimic_path.split('/')[-1]
-        mimic_folder= self.mimic_path.split('/')[-2]
-        mimic_complete_path='/'+mimic_folder+'/'+version
-
-        current_directory = os.getcwd()
-        if os.path.exists(os.path.dirname(current_directory)+'/MIMIC-IV-Data-Pipeline-main'):
-            dir =os.path.dirname(current_directory) 
-            os.chdir(dir)
+        return len(condVocabDict),len(procVocabDict),len(medVocabDict),len(outVocabDict),len(chartVocabDict),len(labVocabDict),ethVocabDict,genderVocabDict,ageVocabDict,insVocabDict
+
+def open_dict(task,cond, proc, out, chart, lab, med):
+    if cond:
+        with open("./data/dict/"+task+"/condVocab", 'rb') as fp:
+            condDict = pickle.load(fp)
+    else:
+        condDict = None
+    if proc:
+        with open("./data/dict/"+task+"/procVocab", 'rb') as fp:
+            procDict = pickle.load(fp)
+    else:
+        procDict = None
+    if out:
+        with open("./data/dict/"+task+"/outVocab", 'rb') as fp:
+            outDict = pickle.load(fp)
+    else:
+        outDict = None
+    if chart:
+        with open("./data/dict/"+task+"/chartVocab", 'rb') as fp:
+            chartDict = pickle.load(fp)
+    elif lab:
+        with open("./data/dict/"+task+"/labsVocab", 'rb') as fp:
+            chartDict = pickle.load(fp)
+    else:
+        chartDict = None
+    if med:
+        with open("./data/dict/"+task+"/medVocab", 'rb') as fp:
+            medDict = pickle.load(fp)
+    else:
+        medDict = None
+    
+    return condDict, procDict, outDict, chartDict, medDict
+
+def concat_data(data,task,feat_cond,feat_proc,feat_out,feat_chart,feat_meds,feat_lab,condDict, procDict, outDict, chartDict, medDict):
+    meds=data['Med']
+    proc = data['Proc']
+    out = data['Out']
+    chart = data['Chart']
+    cond= data['Cond']['fids']
+
+    cond_df=pd.DataFrame()
+    proc_df=pd.DataFrame()
+    out_df=pd.DataFrame()
+    chart_df=pd.DataFrame()
+    meds_df=pd.DataFrame()
+
+    #demographic
+    demo=pd.DataFrame(columns=['Age','gender','ethnicity','label','insurance'])
+    new_row = {'Age': data['age'], 'gender': data['gender'], 'ethnicity': data['ethnicity'], 'label': data['label'], 'insurance': data['insurance']}
+    demo = demo.append(new_row, ignore_index=True)
+
+    ##########COND#########
+    if (feat_cond):
+        conds=pd.DataFrame(condDict,columns=['COND'])
+        features=pd.DataFrame(np.zeros([1,len(conds)]),columns=conds['COND'])
+
+        #onehot encode
+        if(cond ==[]):
+            cond_df=pd.DataFrame(np.zeros([1,len(features)]),columns=features['COND'])
+            cond_df=cond_df.fillna(0)
         else:
-            #move to parent directory of mimic data
-            dir = self.mimic_path.replace(mimic_complete_path,'')
-            print('dir : ',dir)
-            if dir[-1]!='/':
-                dir=dir+'/'
-            elif dir=='':
-                dir="./"
-            parent_dir = os.path.dirname(self.mimic_path)
-            os.chdir(parent_dir)
-
-        #####################clone git repo if doesnt exists
-        repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
-        if os.path.exists('MIMIC-IV-Data-Pipeline-main'):
-            path_bench = './MIMIC-IV-Data-Pipeline-main'
+            cond_df=pd.DataFrame(cond,columns=['COND'])
+            cond_df['val']=1
+            cond_df=(cond_df.drop_duplicates()).pivot(columns='COND',values='val').reset_index(drop=True)
+            cond_df=cond_df.fillna(0)
+            oneh = cond_df.sum().to_frame().T
+            combined_df = pd.concat([features,oneh],ignore_index=True).fillna(0)
+            combined_oneh=combined_df.sum().to_frame().T
+            cond_df=combined_oneh
+            for c in cond_df.columns :
+                if c not in features: 
+                    cond_df=cond_df.drop(columns=[c])
+
+    ##########PROC#########
+    if (feat_proc):
+        if proc :
+            feat=proc.keys()
+            proc_val=[proc[key] for key in feat]
+            procedures=pd.DataFrame(procDict,columns=['PROC'])
+            features=pd.DataFrame(np.zeros([1,len(procedures)]),columns=procedures['PROC'])
+            procs=pd.DataFrame(columns=feat)
+            for p,v in zip(feat,proc_val):
+                procs[p]=v
+            features=features.drop(columns=procs.columns.to_list())
+            proc_df = pd.concat([features,procs],axis=1).fillna(0)
+            proc_df.columns=pd.MultiIndex.from_product([["PROC"], proc_df.columns])
         else:
-            path_bench ='./MIMIC-IV-Data-Pipeline-main'
-            subprocess.run(["git", "clone", repo_url, path_bench])
-            os.makedirs(path_bench+'/'+'mimic-iv')
-            shutil.move(version,path_bench+'/'+'mimic-iv')
-
-        os.chdir(path_bench)
-        self.mimic_path = './'+'mimic-iv'+'/'+version
-
-        ####################Get configurations param
-        #download config file if not custom
-        if self.config_path[0:4] == 'http':
-            c = self.config_path.split('/')[-1]
-            file_path, head = urlretrieve(self.config_path,c)
-        else :
-            file_path = self.config_path
-        if not os.path.exists('./config'):
-            os.makedirs('config')
-        
-        #save config file in config folder
-        self.conf='./config/'+file_path.split('/')[-1]
-        if not os.path.exists(self.conf):
-            shutil.move(file_path,'./config')
-        with open(self.conf) as f:
-            config = yaml.safe_load(f)
-
-            
-        timeW = config['timeWindow']
-        self.timeW=int(timeW.split()[1])
-        self.bucket = config['timebucket']
-        self.predW = config['predW']
-
-        self.data_icu = config['icu_no_icu']=='ICU'
-        
-        if self.data_icu:
-            self.feat_cond, self.feat_chart, self.feat_proc, self.feat_meds, self.feat_out, self.feat_lab = config['diagnosis'], config['chart'], config['proc'],  config['meds'], config['output'], False
+            procedures=pd.DataFrame(procDict,columns=['PROC'])
+            features=pd.DataFrame(np.zeros([1,len(procedures)]),columns=procedures['PROC'])
+            features.columns=pd.MultiIndex.from_product([["PROC"], features.columns])
+            proc_df=features.fillna(0)
+
+    ##########OUT#########
+    if (feat_out):
+        if out :
+            feat=out.keys()
+            out_val=[out[key] for key in feat]
+            outputs=pd.DataFrame(outDict,columns=['OUT'])
+            features=pd.DataFrame(np.zeros([1,len(outputs)]),columns=outputs['OUT'])
+            outs=pd.DataFrame(columns=feat)
+            for o,v in zip(feat,out_val):
+                outs[o]=v
+            features=features.drop(columns=outs.columns.to_list())
+            out_df = pd.concat([features,outs],axis=1).fillna(0)
+            out_df.columns=pd.MultiIndex.from_product([["OUT"], out_df.columns])
         else:
-            self.feat_cond, self.feat_lab, self.feat_proc, self.feat_meds, self.feat_chart, self.feat_out = config['diagnosis'], config['lab'], config['proc'],  config['meds'], False, False
-
-        
-        #####################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')
-
-        if not os.path.exists('./model/data_generation_modify.py'):
-            file_path, head = urlretrieve(_DATA_GEN_HOSP, "data_generation_modify.py")
-            shutil.move(file_path, './model')
+            outputs=pd.DataFrame(outDict,columns=['OUT'])
+            features=pd.DataFrame(np.zeros([1,len(outputs)]),columns=outputs['OUT'])
+            features.columns=pd.MultiIndex.from_product([["OUT"], features.columns])
+            out_df=features.fillna(0)
+
+    ##########CHART#########
+    if (feat_chart):
+        if chart:
+            charts=chart['val']
+            feat=charts.keys()
+            chart_val=[charts[key] for key in feat]
+            charts=pd.DataFrame(chartDict,columns=['CHART'])
+            features=pd.DataFrame(np.zeros([1,len(charts)]),columns=charts['CHART'])
+            chart=pd.DataFrame(columns=feat)
+            for c,v in zip(feat,chart_val):
+                chart[c]=v
+            features=features.drop(columns=chart.columns.to_list())
+            chart_df = pd.concat([features,chart],axis=1).fillna(0)
+            chart_df.columns=pd.MultiIndex.from_product([["CHART"], chart_df.columns])
+        else:
+            charts=pd.DataFrame(chartDict,columns=['CHART'])
+            features=pd.DataFrame(np.zeros([1,len(charts)]),columns=charts['CHART'])
+            features.columns=pd.MultiIndex.from_product([["CHART"], features.columns])
+            chart_df=features.fillna(0)
+        ##########LAB#########
+    
+    if (feat_lab):
+        if chart:
+            charts=chart['val']
+            feat=charts.keys()
+            chart_val=[charts[key] for key in feat]
+            charts=pd.DataFrame(chartDict,columns=['LAB'])
+            features=pd.DataFrame(np.zeros([1,len(charts)]),columns=charts['LAB'])
+            chart=pd.DataFrame(columns=feat)
+            for c,v in zip(feat,chart_val):
+                chart[c]=v
+            features=features.drop(columns=chart.columns.to_list())
+            chart.columns=pd.MultiIndex.from_product([["LAB"], chart.columns])
+            chart_df = pd.concat([features,chart],axis=1).fillna(0)
+            chart_df.columns=pd.MultiIndex.from_product([["LAB"], chart_df.columns])
+        else:
+            charts=pd.DataFrame(chartDict,columns=['LAB'])
+            features=pd.DataFrame(np.zeros([1,len(charts)]),columns=charts['LAB'])
+            features.columns=pd.MultiIndex.from_product([["LAB"], features.columns])
+            chart_df=features.fillna(0)
+    
+    ###MEDS
+    if (feat_meds):
+        if meds:
+            feat=meds['signal'].keys()
+            med_val=[meds['amount'][key] for key in feat]
+            meds=pd.DataFrame(medDict,columns=['MEDS'])
+            features=pd.DataFrame(np.zeros([1,len(meds)]),columns=meds['MEDS'])
+            med=pd.DataFrame(columns=feat)
+            for m,v in zip(feat,med_val):
+                med[m]=v
+            features=features.drop(columns=med.columns.to_list())
+            meds_df = pd.concat([features,med],axis=1).fillna(0)
+            meds_df.columns=pd.MultiIndex.from_product([["MEDS"], meds_df.columns])
+        else:
+            meds=pd.DataFrame(medDict,columns=['MEDS'])
+            features=pd.DataFrame(np.zeros([1,len(meds)]),columns=meds['MEDS'])
+            features.columns=pd.MultiIndex.from_product([["MEDS"], features.columns])
+            meds_df=features.fillna(0)
 
-        if not os.path.exists('./preprocessing/day_intervals_preproc/day_intervals_cohort_v22.py'):
-            file_path, head = urlretrieve(_DAY_INT, "day_intervals_cohort_v22.py")
-            shutil.move(file_path, './preprocessing/day_intervals_preproc')
-            
-        data_dir = "./data/dict/"+self.config.name.replace(" ","_")+"/dataDic"
-        sys.path.append(path_bench)
-        config = self.config_path.split('/')[-1]
+    dyn_df = pd.concat([meds_df,proc_df,out_df,chart_df], axis=1)
+    return dyn_df,cond_df,demo
 
-        #####################create task cohort
-        if self.generate_cohort:
-            create_cohort(self.config.name.replace(" ","_"),self.mimic_path,config)
 
-        #####################Split data into train, test and val
-        with open(data_dir, 'rb') as fp:
-            dataDic = pickle.load(fp)
-        data = pd.DataFrame.from_dict(dataDic)
 
-        dict_dir = "./data/dict/"+self.config.name.replace(" ","_")
-        
-        data=data.T
-        train_data, test_data = train_test_split(data, test_size=self.test_size, random_state=42)
-        if self.val_size > 0 :
-            train_data, val_data = train_test_split(train_data, test_size=self.val_size, random_state=42)
-            val_dic = val_data.to_dict('index')
-            val_path = dict_dir+'/val_data.pkl'
-            with open(val_path, 'wb') as f:
-                pickle.dump(val_dic, f)
-        
-        train_dic = train_data.to_dict('index')
-        test_dic = test_data.to_dict('index')
+def generate_deep(data,task,feat_cond,feat_proc,feat_out,feat_chart,feat_meds,feat_lab,condDict, procDict, outDict, chartDict, medDict):
+    meds = []
+    charts = []
+    proc = []
+    out = []
+    lab = []
+    stat = []
+    demo = []
     
-        train_path = dict_dir+'/train_data.pkl'
-        test_path = dict_dir+'/test_data.pkl'
-        
-        with open(train_path, 'wb') as f:
-            pickle.dump(train_dic, f)
-        with open(test_path, 'wb') as f:
-            pickle.dump(test_dic, f)
-        return dict_dir
+    size_cond, size_proc, size_meds, size_out, size_chart, size_lab, eth_vocab,gender_vocab,age_vocab,ins_vocab=vocab(task.replace(" ","_"),feat_cond,feat_proc,feat_out,feat_chart,feat_meds,False)
+    dyn,cond_df,demo=concat_data(data,task.replace(" ","_"),feat_cond,feat_proc,feat_out,feat_chart,feat_meds,feat_lab,condDict, procDict, outDict, chartDict, medDict)
+    if feat_chart:
+        charts = dyn['CHART'].fillna(0).values
+    if feat_meds:
+        meds = dyn['MEDS'].fillna(0).values
+    if feat_proc:
+        proc = dyn['PROC'].fillna(0).values
+    if feat_out:
+        out = dyn['OUT'].fillna(0).values
+    if feat_lab:
+        lab = dyn['LAB'].fillna(0).values
+    if feat_cond:
+        stat=cond_df.values[0]
+    y = int(demo['label'])
     
+    demo["gender"].replace(gender_vocab, inplace=True)
+    demo["ethnicity"].replace(eth_vocab, inplace=True)
+    demo["insurance"].replace(ins_vocab, inplace=True)
+    demo["Age"].replace(age_vocab, inplace=True)
+    demo=demo[["gender","ethnicity","insurance","Age"]]
+    demo = demo.values[0]
+    return stat, demo, meds, charts, out, proc, lab, y
 
-    def verif_dim_tensor(self, proc, out, chart, meds, lab):
-        interv = (self.timeW//self.bucket)
-        verif=True
-        if self.feat_proc:
-            if (len(proc)!= interv):
-                verif=False
-        if self.feat_out:
-            if (len(out)!=interv):
-                verif=False
-        if self.feat_chart:
-            if (len(chart)!=interv):
-                verif=False
-        if self.feat_meds:
-            if (len(meds)!=interv):
-                verif=False
-        if self.feat_lab:
-            if (len(lab)!=interv):
-                verif=False
-        return verif
-    
-###########################################################RAW##################################################################
-
-    def _info_raw(self):
-        features = datasets.Features(
-            {
-                "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
-                "gender": datasets.Value("string"),
-                "ethnicity": datasets.Value("string"),
-                "insurance": datasets.Value("string"),
-                "age": datasets.Value("int32"),
-                "COND": datasets.Sequence(datasets.Value("string")),
-                "MEDS": {
-                            "signal": 
-                                {
-                                    "id": datasets.Sequence(datasets.Value("int32")),
-                                    "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                }
-                            ,
-                            "rate": 
-                                {
-                                    "id": datasets.Sequence(datasets.Value("int32")),
-                                    "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                }
-                            ,
-                            "amount": 
-                                {
-                                    "id": datasets.Sequence(datasets.Value("int32")),
-                                    "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                }
-                            
-                        },
-                "PROC":  {
-                            "id": datasets.Sequence(datasets.Value("int32")),
-                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                },
-                "CHART/LAB":
-                    {
-                        "signal" : {
-                            "id": datasets.Sequence(datasets.Value("int32")),
-                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                },
-                        "val" : {
-                            "id": datasets.Sequence(datasets.Value("int32")),
-                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                },
-                    },
-                "OUT":  {
-                            "id": datasets.Sequence(datasets.Value("int32")),
-                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
-                                },
-                
-            }
-        )
-        return datasets.DatasetInfo(
-            description=_DESCRIPTION,
-            features=features,
-            homepage=_HOMEPAGE,
-            citation=_CITATION,
-        )
-
-    def _generate_examples_raw(self, filepath):
-        with open(filepath, 'rb') as fp:
-            dataDic = pickle.load(fp)
-        for hid, data in dataDic.items():
-            proc_features = data['Proc']
-            meds_features = data['Med']
-            out_features = data['Out']
-            cond_features = data['Cond']['fids']
-            eth= data['ethnicity']
-            age = data['age']
-            gender = data['gender']
-            label = data['label']
-            insurance=data['insurance']
-            
-            items = list(proc_features.keys())
-            values =[proc_features[i] for i in items ]
-            procs = {"id" : items,
-                  "value": values}
-            
-            items_outs = list(out_features.keys())
-            values_outs =[out_features[i] for i in items_outs ]
-            outs = {"id" : items_outs,
-                  "value": values_outs}
 
-            if self.data_icu:
-                chart_features = data['Chart']
-            else:
-                chart_features = data['Lab']
-
-            #chart signal
-            if ('signal' in chart_features):
-                items_chart_sig = list(chart_features['signal'].keys())
-                values_chart_sig =[chart_features['signal'][i] for i in items_chart_sig ]
-                chart_sig = {"id" : items_chart_sig,
-                        "value": values_chart_sig}
-            else:
-                chart_sig = {"id" : [],
-                        "value": []}
-            #chart val
-            if ('val' in chart_features):
-                items_chart_val = list(chart_features['val'].keys())
-                values_chart_val =[chart_features['val'][i] for i in items_chart_val ]
-                chart_val = {"id" : items_chart_val,
-                        "value": values_chart_val}
+def generate_ml(dyn, stat, demo, concat_cols, concat):
+    X_df = pd.DataFrame()
+    
+    if concat:
+        dyna=dyn.copy()
+        dyna.columns=dyna.columns.droplevel(0)
+        dyna=dyna.to_numpy()
+        dyna=np.nan_to_num(dyna, copy=False)
+        dyna=dyna.reshape(1,-1)
+        dyn_df=pd.DataFrame(data=dyna,columns=concat_cols)
+    else:
+        dyn_df=pd.DataFrame()
+        for key in dyn.columns.levels[0]:     
+            dyn_temp=dyn[key]
+            if ((key=="CHART") or (key=="MEDS")):
+                agg=dyn_temp.aggregate("mean")
+                agg=agg.reset_index()
             else:
-                chart_val = {"id" : [],
-                        "value": []}
-                
-            charts = {"signal" : chart_sig,
-                    "val" : chart_val}
+                agg=dyn_temp.aggregate("max")
+                agg=agg.reset_index()
 
-            #meds signal
-            if ('signal' in meds_features):
-                items_meds_sig = list(meds_features['signal'].keys())
-                values_meds_sig =[meds_features['signal'][i] for i in items_meds_sig ]
-                meds_sig = {"id" : items_meds_sig,
-                    "value": values_meds_sig}
-            else:
-                meds_sig = {"id" : [],
-                    "value": []}
-            #meds rate
-            if ('rate' in meds_features):
-                items_meds_rate = list(meds_features['rate'].keys())
-                values_meds_rate =[meds_features['rate'][i] for i in items_meds_rate ]
-                meds_rate = {"id" : items_meds_rate,
-                        "value": values_meds_rate}
+            if dyn_df.empty:
+                dyn_df=agg
             else:
-                meds_rate = {"id" : [],
-                        "value": []}
-            #meds amount
-            if ('amount' in meds_features):
-                items_meds_amount = list(meds_features['amount'].keys())
-                values_meds_amount =[meds_features['amount'][i] for i in items_meds_amount ]
-                meds_amount = {"id" : items_meds_amount,
-                        "value": values_meds_amount}
-            else:
-                meds_amount = {"id" : [],
-                        "value": []}
-            
-            meds = {"signal" : meds_sig,
-                    "rate" : meds_rate,
-                    "amount" : meds_amount}
-            
-
-            yield int(hid), {
-                "label" : label,
-                "gender" : gender,
-                "ethnicity" : eth,
-                "insurance" : insurance,
-                "age" : age,
-                "COND" : cond_features,
-                "PROC" : procs,
-                "CHART/LAB" : charts,
-                "OUT" : outs,
-                "MEDS" : meds
-            }
-
-
-
-###########################################################ENCODED##################################################################
-        
-    def _info_encoded(self):
-        features = datasets.Features(
-            {
-                "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
-                "features" : datasets.Sequence(datasets.Value("float32")),
-            }
-        )
-        return datasets.DatasetInfo(
-            description=_DESCRIPTION,
-            features=features,
-            homepage=_HOMEPAGE,
-            citation=_CITATION,
-        )
-
-    def _generate_examples_encoded(self, filepath):
-        path= './data/dict/'+self.config.name.replace(" ","_")+'/ethVocab'
-        with open(path, 'rb') as fp:
-            ethVocab = pickle.load(fp)
-
-        path= './data/dict/'+self.config.name.replace(" ","_")+'/insVocab'
-        with open(path, 'rb') as fp:
-            insVocab = pickle.load(fp)
-
-        genVocab = ['<PAD>', 'M', 'F']
-        gen_encoder = LabelEncoder()
-        eth_encoder = LabelEncoder()
-        ins_encoder = LabelEncoder()
-        gen_encoder.fit(genVocab)
-        eth_encoder.fit(ethVocab)
-        ins_encoder.fit(insVocab)
-        with open(filepath, 'rb') as fp:
-            dico = pickle.load(fp)
-
-        df = pd.DataFrame.from_dict(dico, orient='index')
-        for i, data in df.iterrows():
-            dyn_df,cond_df,demo=concat_data(data,self.config.name.replace(" ","_"),self.feat_cond,self.feat_proc,self.feat_out, self.feat_chart, self.feat_meds,self.feat_lab,self.condDict, self.procDict, self.outDict, self.chartDict, self.medDict)
-            dyn=dyn_df.copy()
-            dyn.columns=dyn.columns.droplevel(0)
-            concat_cols = [f"{col}_{t}" for t in range(dyn.shape[0]) for col in dyn.columns]
-            demo['gender']=gen_encoder.transform(demo['gender'])
-            demo['ethnicity']=eth_encoder.transform(demo['ethnicity'])
-            demo['insurance']=ins_encoder.transform(demo['insurance'])
-            label = data['label']
-            demo=demo.drop(['label'],axis=1)
-            X= generate_ml(dyn_df,cond_df,demo,concat_cols,self.concat)
-            X=X.values[0]
-            
-            interv = (self.timeW//self.bucket)
-            size_concat = self.size_cond+ self.size_proc * interv + self.size_meds * interv+ self.size_out * interv+ self.size_chart *interv+ self.size_lab * interv + 4
-            size_aggreg = self.size_cond+ self.size_proc + self.size_meds+ self.size_out+ self.size_chart+ self.size_lab + 4
-
-            if ((self.concat and len(X)==size_concat) or ((not self.concat) and len(X)==size_aggreg)):
-                yield int(i), {
-                    "label": label,
-                    "features": X,
-                }
-
-######################################################DEEP###############################################################
-    def _info_deep(self):
-        features = datasets.Features(
-            {
-                "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
-                "DEMO": datasets.Sequence(datasets.Value("int64")),
-                "COND" : datasets.Sequence(datasets.Value("int64")),
-                "MEDS" : datasets.Array2D(shape=(None, self.size_meds), dtype='int64') ,
-                "PROC" : datasets.Array2D(shape=(None, self.size_proc), dtype='int64') ,
-                "CHART/LAB" : datasets.Array2D(shape=(None, self.size_chart), dtype='int64') ,
-                "OUT" : datasets.Array2D(shape=(None, self.size_out), dtype='int64') ,
-                
-            }
-        )
-        return datasets.DatasetInfo(
-            description=_DESCRIPTION,
-            features=features,
-            homepage=_HOMEPAGE,
-            citation=_CITATION,
-        )
-
-    
-    def _generate_examples_deep(self, filepath):
-        with open(filepath, 'rb') as fp:
-            dico = pickle.load(fp)
-
-        for key, data in dico.items():   
-            stat, demo, meds, chart, out, proc, lab, y = generate_deep(data, self.config.name.replace(" ","_"), self.feat_cond,  self.feat_proc,  self.feat_out,  self.feat_chart, self.feat_meds,self.feat_lab,self.condDict, self.procDict, self.outDict, self.chartDict, self.medDict)
-            if self.verif_dim_tensor(proc, out, chart, meds, lab):
-                if self.data_icu:
-                    yield int(key), {
-                        'label': y,
-                        'DEMO': demo,
-                        'COND': stat,
-                        'MEDS': meds,
-                        'PROC': proc,
-                        'CHART/LAB': chart,
-                        'OUT': out,
-                        }
-                else:
-                    yield int(key), {
-                        'label': y,
-                        'DEMO': demo,
-                        'COND': stat,
-                        'MEDS': meds,
-                        'PROC': proc,
-                        'CHART/LAB': lab,
-                        'OUT': out,
-                        }          
- ######################################################text##############################################################
-    def _info_text(self):
-        features = datasets.Features(
-            {
-                "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
-                "text" : 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(self.mimic_path+'/hosp/d_icd_diagnoses.csv.gz',compression='gzip', header=0)
-        items= pd.read_csv(self.mimic_path+'/icu/d_items.csv.gz',compression='gzip', header=0)
-        with open(filepath, 'rb') as fp:
-            dico = pickle.load(fp)
-            
-        for key, data in dico.items():
-            demo_text,cond_text,chart_text,meds_text,proc_text,out_text = generate_text(data,icd,items, self.feat_cond, self.feat_chart, self.feat_meds, self.feat_proc, self.feat_out)
-                
-            yield int(key),{
-                'label' : data['label'],
-                'text': demo_text+cond_text+chart_text+meds_text+proc_text+out_text
-            }
-
-#############################################################################################################################
-    def _info(self):
-        self.path = self.init_cohort()
-        self.size_cond, self.size_proc, self.size_meds, self.size_out, self.size_chart, self.size_lab, eth_vocab,gender_vocab,age_vocab,ins_vocab=vocab(self.config.name.replace(" ","_"),self.feat_cond,self.feat_proc,self.feat_out,self.feat_chart,self.feat_meds,self.feat_lab)
-        self.condDict, self.procDict, self.outDict, self.chartDict, self.medDict = open_dict(self.config.name.replace(" ","_"),self.feat_cond,self.feat_proc,self.feat_out,self.feat_chart,self.feat_lab,self.feat_meds)
-        if (self.encoding == 'concat' or self.encoding =='aggreg'):
-            return self._info_encoded()
+                dyn_df=pd.concat([dyn_df,agg],axis=0)
+        dyn_df=dyn_df.T
+        dyn_df.columns = dyn_df.iloc[0]
+        dyn_df=dyn_df.iloc[1:,:]
         
-        elif self.encoding == 'tensor' :
-            return self._info_deep()
-
-        elif self.encoding == 'text' :
-            return self._info_text()
+    X_df = pd.concat([dyn_df, stat, demo], axis=1)
+    return X_df 
+
+
+def generate_text(data,icd,items,feat_cond,feat_chart,feat_meds, feat_proc, feat_out):
+    #Demographics
+    age = data['age']
+    gender = data['gender']
+    if gender=='F':
+        gender='female'
+    elif gender=='M':
+        gender='male'
+    else:
+        gender='unknown'
+    ethn=data['ethnicity'].lower()
+    ins=data['insurance']
+
+    #Diagnosis
+    if feat_cond:
+        conds = data.get('Cond', {}).get('fids', [])
+        conds=[icd[icd['icd_code'] == code]['long_title'].to_string(index=False) for code in conds if not icd[icd['icd_code'] == code].empty]
+        cond_text = '; '.join(conds)
+        cond_text = f"The patient {ethn} {gender}, {age} years old, covered by {ins} was diagnosed with {cond_text}. " if cond_text else ''
+    else:
+        cond_text = ''
             
+    #chart
+    if feat_chart:
+        chart = data.get('Chart', {})
+        if chart:
+            charts = chart.get('val', {})
+            feat = charts.keys()
+            chart_val = [charts[key] for key in feat]
+            chart_mean = [round(np.mean(c), 3) for c in chart_val]
+            feat_text = [(items[items['itemid'] == f]['label']).to_string(index=False) for f in feat]
+            chart_text = '; '.join(f"{mean_val} for {feat_label}" for mean_val, feat_label in zip(chart_mean, feat_text))
+            chart_text = f"The chart events measured were: {chart_text}. "
         else:
-            return self._info_raw()
-
-    def _split_generators(self, dl_manager):
-        data_dir = "./data/dict/"+self.config.name.replace(" ","_")
-        if self.val_size > 0 :
-            return [
-                datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir+'/train_data.pkl'}),
-                datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": data_dir+'/val_data.pkl'}),
-                datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_dir+'/test_data.pkl'}),
-            ]
-        else : 
-            return [
-                datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir+'/train_data.pkl'}),
-                datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_dir+'/test_data.pkl'}),
-            ]
+            chart_text = 'No chart events were measured. '
+    else:
+        chart_text = ''
         
-    def _generate_examples(self, filepath):
-        if (self.encoding == 'concat' or self.encoding == 'aggreg'):
-            yield from self._generate_examples_encoded(filepath)
         
-        elif self.encoding == 'tensor' :
-            yield from self._generate_examples_deep(filepath)
+    #meds
+    if feat_meds:
+        meds = data.get('Med', {})
+        if meds:
+            feat = meds['signal'].keys()
+            meds_val = [meds['amount'][key] for key in feat]
+            meds_mean = [round(np.mean(c), 3) for c in meds_val]
+            feat_text = [(items[items['itemid'] == f]['label']).to_string(index=False) for f in feat]
+            meds_text = '; '.join(f"{mean_val} of {feat_label}" for mean_val, feat_label in zip(meds_mean, feat_text))
+            meds_text = f"The mean amounts of medications administered during the episode were: {meds_text}. "
+        else:
+            meds_text = 'No medications were administered. '
+    else:
+        meds_text = ''
+
+    #proc
+    if feat_proc:  
+        proc = data['Proc']
+        if proc:
+            feat=proc.keys()
+            feat_text = [(items[items['itemid']==f]['label']).to_string(index=False) for f in feat]
+            template = 'The procedures performed were: {}. '
+            proc_text= template.format('; '.join(feat_text))
+        else:
+            proc_text='No procedures were performed. '
+    else:
+        proc_text=''
+    
+    #out
+    if feat_out:  
+        out = data['Out']
+        if out:
+            feat=out.keys()
+            feat_text = [(items[items['itemid']==f]['label']).to_string(index=False) for f in feat]
+            template ='The outputs collected were: {}.'
+            out_text = template.format('; '.join(feat_text))
+        else:
+            out_text='No outputs were collected.'
+    else:
+        out_text=''
 
-        elif self.encoding == 'text' :
-            yield from self._generate_examples_text(filepath)
-            
-        else :
-            yield from self._generate_examples_raw(filepath)
+    return cond_text,chart_text,meds_text,proc_text,out_text