From 3dc6d22a0a0adedaba575b148ef1a53c506ab677 Mon Sep 17 00:00:00 2001 From: SexyERIC0723 Date: Fri, 3 Apr 2026 09:02:43 +0100 Subject: [PATCH] fix: remove deprecated code_mapping, dev, refresh_cache from examples The v2.0 MIMIC3Dataset/MIMIC4Dataset (based on BaseDataset) no longer accepts code_mapping, dev, or refresh_cache parameters. These were part of the legacy BaseEHRDataset API. Update README.rst, example scripts, and leaderboard utilities to use the current v2.0 API. Note: task file docstrings and pyhealth/datasets/mimicextract.py still reference code_mapping but are left for separate PRs since mimicextract.py has not yet been migrated to v2.0. Fixes #535 --- README.rst | 2 -- .../drug_recommendation_mimic4_gamenet.py | 3 --- examples/mortality_prediction/mortality_mimic3_grasp.py | 3 --- examples/patient_linkage_mimic3_medlink.py | 3 --- leaderboard/utils.py | 6 ------ 5 files changed, 17 deletions(-) diff --git a/README.rst b/README.rst index cf12b5874..c3f3e6355 100644 --- a/README.rst +++ b/README.rst @@ -189,8 +189,6 @@ Module 1: 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 diff --git a/examples/drug_recommendation/drug_recommendation_mimic4_gamenet.py b/examples/drug_recommendation/drug_recommendation_mimic4_gamenet.py index 6aeb2c8ce..bd5b33cb0 100644 --- a/examples/drug_recommendation/drug_recommendation_mimic4_gamenet.py +++ b/examples/drug_recommendation/drug_recommendation_mimic4_gamenet.py @@ -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") diff --git a/examples/mortality_prediction/mortality_mimic3_grasp.py b/examples/mortality_prediction/mortality_mimic3_grasp.py index 011bd13fe..e335373d6 100644 --- a/examples/mortality_prediction/mortality_mimic3_grasp.py +++ b/examples/mortality_prediction/mortality_mimic3_grasp.py @@ -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() diff --git a/examples/patient_linkage_mimic3_medlink.py b/examples/patient_linkage_mimic3_medlink.py index 2c38ba184..237d23f14 100644 --- a/examples/patient_linkage_mimic3_medlink.py +++ b/examples/patient_linkage_mimic3_medlink.py @@ -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() diff --git a/leaderboard/utils.py b/leaderboard/utils.py index caeb38400..b8cf41eec 100644 --- a/leaderboard/utils.py +++ b/leaderboard/utils.py @@ -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 @@ -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