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fix: remove deprecated code_mapping, dev, refresh_cache from examples and README #935

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Merged
jhnwu3 merged 1 commit into from
Apr 8, 2026
Merged

fix: remove deprecated code_mapping, dev, refresh_cache from examples and README #935

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2 changes: 0 additions & 2 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -189,8 +189,6 @@ Module 1: <pyhealth.datasets>
root="https://storage.googleapis.com/pyhealth/Synthetic_MIMIC-III/",
# raw CSV table name
tables=["DIAGNOSES_ICD", "PROCEDURES_ICD", "PRESCRIPTIONS"],
# map all NDC codes to CCS codes in these tables
code_mapping={"NDC": "CCSCM"},
)

.. image:: figure/structured-dataset.png
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3 changes: 0 additions & 3 deletions examples/drug_recommendation/drug_recommendation_mimic4_gamenet.py
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Expand Up @@ -25,9 +25,6 @@ def prepare_drug_task_data():
mimicvi = MIMIC4Dataset(
root="/srv/local/data/physionet.org/files/mimiciv/2.0/hosp",
tables=["diagnoses_icd", "procedures_icd", "prescriptions"],
code_mapping={"NDC": ("ATC", {"target_kwargs": {"level": 3}})},
dev=_DEV,
refresh_cache=False,
)

print("stat")
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3 changes: 0 additions & 3 deletions examples/mortality_prediction/mortality_mimic3_grasp.py
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Expand Up @@ -9,9 +9,6 @@
base_dataset = MIMIC3Dataset(
root="/srv/local/data/physionet.org/files/mimiciii/1.4",
tables=["DIAGNOSES_ICD", "PROCEDURES_ICD", "PRESCRIPTIONS"],
code_mapping={"ICD9CM": "CCSCM", "ICD9PROC": "CCSPROC", "NDC": "ATC"},
dev=False,
refresh_cache=False,
)
base_dataset.stat()

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3 changes: 0 additions & 3 deletions examples/patient_linkage_mimic3_medlink.py
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Expand Up @@ -29,9 +29,6 @@
base_dataset = MIMIC3Dataset(
root="/srv/local/data/physionet.org/files/mimiciii/1.4",
tables=["DIAGNOSES_ICD"],
code_mapping={"ICD9CM": ("CCSCM", {})},
dev=False,
refresh_cache=False,
)
base_dataset.stat()

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6 changes: 0 additions & 6 deletions leaderboard/utils.py
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Expand Up @@ -64,9 +64,6 @@ def get_dataset(dataset_name):
mimic3dataset = MIMIC3Dataset(
root="/srv/local/data/physionet.org/files/mimiciii/1.4",
tables=["DIAGNOSES_ICD", "PROCEDURES_ICD", "PRESCRIPTIONS"],
dev=False,
code_mapping={"NDC": "ATC"},
refresh_cache=False,
)
dataset = mimic3dataset

Expand All @@ -83,9 +80,6 @@ def get_dataset(dataset_name):
mimic4dataset = MIMIC4Dataset(
root="/srv/local/data/physionet.org/files/mimiciv/2.0/hosp",
tables=["diagnoses_icd", "procedures_icd", "prescriptions"],
dev=False,
code_mapping={"NDC": "ATC"},
refresh_cache=False,
)
dataset = mimic4dataset

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