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15 changes: 14 additions & 1 deletion pyhealth/datasets/cardiology.py
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Expand Up @@ -10,7 +10,20 @@

class CardiologyDataset(BaseSignalDataset):
"""Base ECG dataset for Cardiology


Download: https://physionet.org/content/challenge-2020/1.0.2/
Access: Requires PhysioNet account.

Required files:
- cpsc_2018/ (directory)
- cpsc_2018_extra/ (directory)
- georgia/ (directory)
- ptb/ (directory)
- ptb-xl/ (directory)
- st_petersburg_incart/ (directory)

Compatible formats: .mat, .hea
Note: All dataset directories must be placed in the root directory.
Dataset is available at https://physionet.org/content/challenge-2020/1.0.2/

Args:
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7 changes: 7 additions & 0 deletions pyhealth/datasets/ehrshot.py
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class EHRShotDataset(BaseDataset):
"""
A dataset class for handling EHRShot data.
Download: https://huggingface.co/datasets/StanfordShahLab/ehrshot
Access: Requires HuggingFace account and dataset agreement.

Required files:
- ehrshot.csv

Compatible formats: .csv
Note: All files must be placed in the root directory.
This class is responsible for loading and managing the EHRShot dataset.

Website: https://som-shahlab.github.io/ehrshot-website/
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18 changes: 17 additions & 1 deletion pyhealth/datasets/eicu.py
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Expand Up @@ -8,7 +8,23 @@


class eICUDataset(BaseDataset):
"""
"""
Download: https://eicu-crd.mit.edu/
Access: Requires PhysioNet credentialed access and DUA agreement.

Required files:
- patient.csv
- hospital.csv
- diagnosis.csv
- treatment.csv
- medication.csv
- lab.csv
- physicalExam.csv
- admissionDx.csv

Compatible formats: .csv
Note: All files must be placed in the root directory.

A dataset class for handling eICU data.

The eICU dataset is a large dataset of de-identified health records of ICU
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13 changes: 13 additions & 0 deletions pyhealth/datasets/mimic3.py
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Expand Up @@ -13,7 +13,20 @@
class MIMIC3Dataset(BaseDataset):
"""
A dataset class for handling MIMIC-III data.
Download: https://physionet.org/content/mimiciii/1.4/
Access: Requires PhysioNet credentialed access and DUA agreement.

Required files:
- ADMISSIONS.csv
- PATIENTS.csv
- DIAGNOSES_ICD.csv
- PROCEDURES_ICD.csv
- PRESCRIPTIONS.csv
- LABEVENTS.csv
- ICUSTAYS.csv

Compatible formats: .csv
Note: All files must be placed in the root directory.
This class is responsible for loading and managing the MIMIC-III dataset,
which includes tables such as patients, admissions, and icustays.

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14 changes: 14 additions & 0 deletions pyhealth/datasets/mimic4.py
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Expand Up @@ -31,6 +31,20 @@ def log_memory_usage(tag=""):
class MIMIC4EHRDataset(BaseDataset):
"""
MIMIC-IV EHR dataset.
Download: https://physionet.org/content/mimiciv/2.2/
Access: Requires PhysioNet credentialed access and DUA agreement.

Required files:
- admissions.csv
- patients.csv
- diagnoses_icd.csv
- procedures_icd.csv
- prescriptions.csv
- labevents.csv
- icustays.csv

Compatible formats: .csv
Note: All files must be placed in the root directory.

This class is responsible for loading and managing the MIMIC-IV EHR dataset,
which includes tables such as patients, admissions, and icustays.
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