Cmd line

Dockerfile

@@ -1,11 +1,12 @@
-FROM ubuntu:22.04
+FROM python:3.11-slim
+
 
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends --assume-yes \
-    pip iputils-ping curl wget wkhtmltopdf
+    pip iputils-ping curl wget 
 
 COPY requirements.txt /home/requirements.txt
 RUN pip3 install -r /home/requirements.txt
 RUN ln -s /usr/bin/python3 /usr/bin/python
 
 WORKDIR /flcore
-COPY . /flcore
+COPY . /flcore

client_cmd.py

@@ -29,8 +29,8 @@
     parser.add_argument("--dataset", type=str, default="dt4h_format", help="Dataloader to use")
     parser.add_argument("--data_id", type=str, default="data_id.parquet" , help="Dataset ID")
     parser.add_argument("--normalization_method",type=str, default="IQR", help="Type of normalization: IQR STD MIN_MAX")
-    parser.add_argument("--train_labels", type=str, nargs='+', default=None, help="Dataloader to use")
-    parser.add_argument("--target_labels", type=str, nargs='+', default=None, help="Dataloader to use")
+    parser.add_argument("--train_labels", type=str, nargs='+', default=[], help="Dataloader to use")
+    parser.add_argument("--target_labels", type=str, nargs='+', default=[], help="Dataloader to use")
     parser.add_argument("--train_size", type=float, default=0.7, help="Fraction of dataset to use for training. [0,1)")
     parser.add_argument("--validation_size", type=float, default=0.2, help="Fraction of dataset to use for validation. [0,1)")
     parser.add_argument("--test_size", type=float, default=0.1, help="Fraction of dataset to use for testing. [0,1)")
@@ -50,6 +50,7 @@
     parser.add_argument("--local_epochs", type=int, default=10, help="Number of local epochs to train in each round")
     parser.add_argument("--batch_size", type=int, default=8, help="Batch size to train")
     parser.add_argument("--penalty", type=str, default="none", help="Penalties: none, l1, l2, elasticnet, smooth l1")
+    parser.add_argument("--save_every_n_rounds", type=int, default=1, help="Save model checkpoints every N rounds")
 
     # Specific variables model related
     # # Linear models
@@ -78,8 +79,9 @@
     parser.add_argument("--train_method", type=str, default="bagging", help="Train method: bagging, cyclic")
     parser.add_argument("--eta", type=float, default=0.1, help="ETA value")
     # # Survival
-    parser.add_argument("--time_col", type=str, default="time", help="")
-    parser.add_argument("--event_col", type=str, default="event", help="")
+    parser.add_argument("--time_col", type=str, default=None, help="")
+    parser.add_argument("--event_col", type=str, default=None, help="")
+    parser.add_argument("--accumulative_pattern_col", type=str, default=None, help="")
     parser.add_argument("--negative_duration_strategy", type=str, default="clip", help="")
 
     args = parser.parse_args()

dataset/bucarest_sintetico/metadata.json

@@ -0,0 +1,166 @@
+{
+"entries": [
+{
+"features": [
+{"name": "patient_demographics_gender", "dataType": "NOMINAL"},
+{"name": "encounters_encounterClass", "dataType": "NOMINAL"},
+{"name": "encounters_admissionYear", "dataType": "NOMINAL"},
+{"name": "patient_demographics_age", "dataType": "NUMERIC"},
+{"name": "encounters_lengthOfStay", "dataType": "NUMERIC"},
+{"name": "vital_signs_weight_value_p6mo_min", "dataType": "NUMERIC"},
+{"name": "med_admins_history_diuretics_loop_any", "dataType": "BOOLEAN"},
+{"name": "patient_flags_smoker", "dataType": "BOOLEAN"}
+],
+
+"outcomes": [
+{"name": "outcome_in_hospital_mortality", "dataType": "BOOLEAN"},
+{"name": "outcome_readmission_30d", "dataType": "BOOLEAN"},
+{"name": "outcome_discharge_disposition", "dataType": "NOMINAL"},
+{"name": "outcome_severity_score", "dataType": "NUMERIC"}
+],
+
+"datasetStats": {
+
+"featureStats": {
+
+"patient_demographics_gender": {
+"numOfNotNull": 7845,
+"valueSet": ["female","male"],
+"cardinalityPerItem": {
+"female": 2814,
+"male": 5031
+}
+},
+
+"encounters_encounterClass": {
+"numOfNotNull": 10000,
+"valueSet": ["inpatient","outpatient","emergency"],
+"cardinalityPerItem": {
+"inpatient": 4200,
+"outpatient": 3500,
+"emergency": 2300
+}
+},
+
+"encounters_admissionYear": {
+"numOfNotNull": 10000,
+"valueSet": ["2019","2020","2021","2022","2023"],
+"cardinalityPerItem": {
+"2019": 1500,
+"2020": 1800,
+"2021": 2200,
+"2022": 2400,
+"2023": 2100
+}
+},
+
+"patient_demographics_age": {
+"numOfNotNull": 9980,
+"min": 18,
+"max": 97,
+"avg": 56.4,
+"q1": 42,
+"q2": 58,
+"q3": 71,
+"histogram": [
+{"bin": 30,"count": 1500},
+{"bin": 45,"count": 2400},
+{"bin": 60,"count": 3000},
+{"bin": 75,"count": 2100},
+{"bin": 90,"count": 980}
+]
+},
+
+"encounters_lengthOfStay": {
+"numOfNotNull": 9500,
+"min": 1,
+"max": 45,
+"avg": 6.2,
+"q1": 2,
+"q2": 4,
+"q3": 8,
+"histogram": [
+{"bin": 2,"count": 3000},
+{"bin": 5,"count": 3500},
+{"bin": 10,"count": 2000},
+{"bin": 20,"count": 800},
+{"bin": 40,"count": 200}
+]
+},
+
+"vital_signs_weight_value_p6mo_min": {
+"numOfNotNull": 8700,
+"min": 42.5,
+"max": 135.0,
+"avg": 76.8,
+"q1": 64.0,
+"q2": 75.5,
+"q3": 88.2,
+"histogram": [
+{"bin": 55,"count": 1200},
+{"bin": 70,"count": 2600},
+{"bin": 85,"count": 2800},
+{"bin": 100,"count": 1500},
+{"bin": 120,"count": 600}
+]
+},
+
+"med_admins_history_diuretics_loop_any": {
+"numOfNotNull": 7845,
+"numOfTrue": 950
+},
+
+"patient_flags_smoker": {
+"numOfNotNull": 9200,
+"numOfTrue": 2100
+}
+
+},
+
+"outcomeStats": {
+
+"outcome_in_hospital_mortality": {
+"numOfNotNull": 10000,
+"numOfTrue": 820
+},
+
+"outcome_readmission_30d": {
+"numOfNotNull": 10000,
+"numOfTrue": 1530
+},
+
+"outcome_discharge_disposition": {
+"numOfNotNull": 10000,
+"valueSet": ["home","rehab","nursing_facility","death"],
+"cardinalityPerItem": {
+"home": 6200,
+"rehab": 1800,
+"nursing_facility": 1200,
+"death": 800
+}
+},
+
+"outcome_severity_score": {
+"numOfNotNull": 10000,
+"min": 0.0,
+"max": 10.0,
+"avg": 4.8,
+"q1": 2.5,
+"q2": 4.7,
+"q3": 7.2,
+"histogram": [
+{"bin": 1,"count": 900},
+{"bin": 3,"count": 2500},
+{"bin": 5,"count": 3200},
+{"bin": 7,"count": 2200},
+{"bin": 9,"count": 1200}
+]
+}
+
+}
+
+}
+
+}
+]
+}

dataset/bucarest_sintetico/synthetic_dt4h_dataset.csv

@@ -0,0 +1,84 @@
+patient_demographics_gender,encounters_encounterClass,encounters_admissionYear,patient_demographics_age,encounters_lengthOfStay,vital_signs_weight_value_p6mo_min,med_admins_history_diuretics_loop_any,patient_flags_smoker,outcome_in_hospital_mortality,outcome_readmission_30d,outcome_discharge_disposition,outcome_severity_score
+female,inpatient,2021,63,4,82.3,False,True,False,False,home,4.3
+male,outpatient,2020,55,2,75.1,False,False,False,False,home,3.1
+female,emergency,2023,71,6,90.5,True,True,True,False,death,9.2
+male,inpatient,2022,49,3,68.7,False,False,False,True,rehab,5.8
+female,outpatient,2019,60,1,73.4,False,False,False,False,home,2.9
+male,emergency,2021,45,5,81.2,False,True,False,False,nursing_facility,6.1
+female,inpatient,2020,77,8,95.6,True,False,False,True,home,7.4
+male,outpatient,2023,52,2,72.3,False,False,False,False,home,3.7
+female,emergency,2022,69,7,88.4,False,True,False,True,rehab,8.0
+male,inpatient,2021,58,4,79.1,False,False,False,False,home,4.9
+female,outpatient,2020,62,3,76.5,False,False,False,False,home,3.5
+male,emergency,2023,50,6,83.9,True,True,False,True,nursing_facility,5.5
+female,inpatient,2022,73,9,92.0,False,False,True,False,death,8.7
+male,outpatient,2019,48,2,70.8,False,False,False,False,home,3.0
+female,emergency,2021,66,5,86.1,True,True,False,True,rehab,6.8
+male,inpatient,2020,57,4,77.6,False,False,False,False,home,4.4
+female,outpatient,2023,61,3,75.9,False,False,False,False,home,3.6
+male,emergency,2022,54,6,82.7,True,True,False,True,rehab,5.9
+female,inpatient,2021,70,7,89.2,False,False,True,False,death,7.9
+male,outpatient,2020,47,2,69.4,False,False,False,False,home,2.8
+female,emergency,2023,65,5,84.3,False,True,False,True,rehab,6.4
+male,inpatient,2022,59,4,78.0,False,False,False,False,home,4.7
+female,outpatient,2021,63,3,76.8,False,False,False,False,home,3.9
+male,emergency,2019,52,6,81.5,True,True,False,True,nursing_facility,5.2
+female,inpatient,2020,74,8,93.1,False,False,True,False,death,8.1
+male,outpatient,2023,51,2,71.2,False,False,False,False,home,3.3
+female,emergency,2022,67,6,87.3,True,True,False,True,rehab,6.9
+male,inpatient,2021,56,4,78.4,False,False,False,False,home,4.5
+female,outpatient,2020,60,3,74.6,False,False,False,False,home,3.8
+male,emergency,2023,49,7,83.1,True,True,False,True,nursing_facility,5.7
+female,inpatient,2022,72,9,91.8,False,False,True,False,death,7.8
+male,outpatient,2019,46,2,69.8,False,False,False,False,home,3.1
+female,emergency,2021,64,5,85.7,True,True,False,True,rehab,6.6
+male,inpatient,2020,58,4,77.1,False,False,False,False,home,4.3
+female,outpatient,2023,62,3,75.2,False,False,False,False,home,3.7
+male,emergency,2022,53,6,82.6,True,True,False,True,rehab,5.5
+female,inpatient,2021,71,7,89.7,False,False,True,False,death,7.5
+male,outpatient,2020,48,2,70.3,False,False,False,False,home,3.0
+female,emergency,2023,66,5,84.9,True,True,False,True,rehab,6.8
+male,inpatient,2022,60,4,78.8,False,False,False,False,home,4.6
+female,outpatient,2021,63,3,76.0,False,False,False,False,home,3.9
+male,emergency,2019,51,6,80.9,True,True,False,True,nursing_facility,5.1
+female,inpatient,2020,75,8,93.4,False,False,True,False,death,8.2
+male,outpatient,2023,50,2,71.6,False,False,False,False,home,3.4
+female,emergency,2022,68,6,87.8,True,True,False,True,rehab,6.9
+male,inpatient,2021,57,4,78.9,False,False,False,False,home,4.5
+female,outpatient,2020,61,3,74.9,False,False,False,False,home,3.8
+male,emergency,2023,52,7,83.5,True,True,False,True,nursing_facility,5.6
+female,inpatient,2022,73,9,92.4,False,False,True,False,death,7.7
+male,outpatient,2019,47,2,70.2,False,False,False,False,home,3.2
+female,emergency,2021,65,5,85.4,True,True,False,True,rehab,6.5
+male,inpatient,2020,59,4,77.5,False,False,False,False,home,4.4
+female,outpatient,2023,62,3,75.4,False,False,False,False,home,3.7
+male,emergency,2022,54,6,82.1,True,True,False,True,rehab,5.4
+female,inpatient,2021,70,7,88.9,False,False,True,False,death,7.4
+male,outpatient,2020,49,2,69.7,False,False,False,False,home,2.9
+female,emergency,2023,66,5,84.7,False,True,False,True,rehab,6.6
+male,inpatient,2022,60,4,78.3,False,False,False,False,home,4.5
+female,outpatient,2021,63,3,76.3,False,False,False,False,home,3.9
+male,emergency,2019,52,6,81.2,True,True,False,True,nursing_facility,5.3
+female,inpatient,2020,74,8,92.8,False,False,True,False,death,8.0
+male,outpatient,2023,51,2,71.0,False,False,False,False,home,3.3
+female,emergency,2022,67,6,87.1,True,True,False,True,rehab,6.7
+male,inpatient,2021,56,4,78.2,False,False,False,False,home,4.4
+female,outpatient,2020,60,3,74.2,False,False,False,False,home,3.8
+male,emergency,2023,48,7,83.0,True,True,False,True,nursing_facility,5.6
+female,inpatient,2022,72,9,91.6,False,False,True,False,death,7.6
+male,outpatient,2019,46,2,69.5,False,False,False,False,home,3.1
+female,emergency,2021,64,5,85.2,True,True,False,True,rehab,6.5
+male,inpatient,2020,58,4,77.0,False,False,False,False,home,4.4
+female,outpatient,2023,61,3,75.1,False,False,False,False,home,3.7
+male,emergency,2022,53,6,82.4,True,True,False,True,rehab,5.5
+female,inpatient,2021,71,7,89.4,False,False,True,False,death,7.5
+male,outpatient,2020,47,2,69.2,False,False,False,False,home,3.0
+female,emergency,2023,65,5,84.1,False,True,False,True,rehab,6.6
+male,inpatient,2022,59,4,78.6,False,False,False,False,home,4.5
+female,outpatient,2021,63,3,76.1,False,False,False,False,home,3.9
+male,emergency,2019,51,6,80.7,True,True,False,True,nursing_facility,5.2
+female,inpatient,2020,75,8,93.0,False,False,True,False,death,8.1
+male,outpatient,2023,50,2,71.4,False,False,False,False,home,3.4
+female,emergency,2022,68,6,87.6,True,True,False,True,rehab,6.8
+male,inpatient,2021,57,4,78.7,False,False,False,False,home,4.6
+female,outpatient,2020,61,3,74.7,False,False,False,False,home,3.7