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Fix broken GAMENet example; flag legacy LOC scripts as 1.1.6-only #1206

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Fix broken GAMENet example; flag legacy LOC scripts as 1.1.6-only #1206

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1 change: 1 addition & 0 deletions examples/benchmark_perf/loc/minimal_legacy_drug_rec.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# Requires pyhealth==1.1.6 (legacy 1.x task_fn/Visit API) -- not runnable against pyhealth 2.0
from pyhealth.data import Patient,Visit; from pyhealth.datasets import MIMIC4Dataset

def drug_recommendation_mimic4_fn(patient):
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1 change: 1 addition & 0 deletions examples/benchmark_perf/loc/minimal_legacy_los.py
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@@ -1,3 +1,4 @@
# Requires pyhealth==1.1.6 (legacy 1.x task_fn/Visit API) -- not runnable against pyhealth 2.0
from pyhealth.datasets import MIMIC4Dataset

def categorize_los(d): return 0 if d<1 else (d if d<=7 else (8 if d<=14 else 9))
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1 change: 1 addition & 0 deletions examples/benchmark_perf/loc/minimal_legacy_mortality.py
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# Requires pyhealth==1.1.6 (legacy 1.x task_fn/Visit API) -- not runnable against pyhealth 2.0
from collections import defaultdict; from pyhealth.data import Patient; from pyhealth.datasets import MIMIC4Dataset
from typing import Dict,List

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27 changes: 8 additions & 19 deletions examples/drug_recommendation/drug_recommendation_mimic4_gamenet.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,8 @@
# import pyhealth
import pyhealth

# import mimic4 dataset and drug recommendaton task
# import mimic4 dataset and drug recommendation task
from pyhealth.datasets import MIMIC4Dataset
from pyhealth.tasks import drug_recommendation_mimic4_fn
from pyhealth.tasks import DrugRecommendationMIMIC4

# import dataloader related functions
from pyhealth.datasets.splitter import split_by_patient
from pyhealth.datasets import split_by_patient, get_dataloader

# import gamenet model
Expand All @@ -23,16 +19,14 @@

def prepare_drug_task_data():
mimicvi = MIMIC4Dataset(
root="/srv/local/data/physionet.org/files/mimiciv/2.0/hosp",
tables=["diagnoses_icd", "procedures_icd", "prescriptions"],
ehr_root="/srv/local/data/physionet.org/files/mimiciv/2.0/hosp",
ehr_tables=["diagnoses_icd", "procedures_icd", "prescriptions"],
dev=_DEV,
)

print("stat")
mimicvi.stat()
print("info")
mimicvi.info()
mimicvi.stats()

mimic4_sample = mimicvi.set_task(drug_recommendation_mimic4_fn)
mimic4_sample = mimicvi.set_task(DrugRecommendationMIMIC4())
print(mimic4_sample[0])

return mimic4_sample
Expand All @@ -50,14 +44,10 @@ def get_dataloaders(mimic4_sample):


def train_gamenet(mimic4_sample, train_loader, val_loader):
# gamenet = GAMENet(mimicvi)
gamenet = GAMENet(mimic4_sample)
gamenet = GAMENet(dataset=mimic4_sample)

# print(gamenet.generate_ddi_adj())
trainer = Trainer(
model=gamenet,
# metrics = ["jaccard_weighted", "pr_auc_micro", "pr_auc_macro"],
# metrics = ["jaccard", "pr_auc_micro", "pr_auc_macro"],
metrics=[
"jaccard_samples",
"accuracy",
Expand All @@ -67,7 +57,6 @@ def train_gamenet(mimic4_sample, train_loader, val_loader):
"pr_auc_samples",
"f1_samples",
],
device="cuda",
exp_name="drug_recommendation",
)

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