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PyHealth
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Getting Started

  • Why PyHealth?
  • Getting Started with PyHealth
  • Installation
  • Tutorials
  • Data Access Guide
  • Additional Examples

Documentation

  • PyHealth Architecture Overview
  • Data
    • pyhealth.data.Event
    • pyhealth.data.Patient
  • Datasets
    • pyhealth.datasets.BaseDataset
    • pyhealth.datasets.SampleDataset
    • pyhealth.datasets.MIMIC3Dataset
    • pyhealth.datasets.MIMIC4Dataset
    • pyhealth.datasets.MedicalTranscriptionsDataset
    • pyhealth.datasets.CardiologyDataset
    • pyhealth.datasets.eICUDataset
    • pyhealth.datasets.ISRUCDataset
    • pyhealth.datasets.MIMICExtractDataset
    • pyhealth.datasets.OMOPDataset
    • pyhealth.datasets.DREAMTDataset
    • pyhealth.datasets.SHHSDataset
    • pyhealth.datasets.SleepEDFDataset
    • pyhealth.datasets.EHRShotDataset
    • pyhealth.datasets.Support2Dataset
    • pyhealth.datasets.BMDHSDataset
    • pyhealth.datasets.COVID19CXRDataset
    • pyhealth.datasets.ChestXray14Dataset
    • pyhealth.datasets.PhysioNetDeIDDataset
    • pyhealth.datasets.TUABDataset
    • pyhealth.datasets.TUEVDataset
    • pyhealth.datasets.ClinVarDataset
    • pyhealth.datasets.COSMICDataset
    • pyhealth.datasets.TCGAPRADDataset
    • pyhealth.datasets.splitter
    • pyhealth.datasets.utils
  • Graph
    • pyhealth.graph.KnowledgeGraph
  • Tasks
    • Base Task
    • In-Hospital Mortality (MIMIC-IV)
    • MIMIC-III ICD-9 Coding
    • Cardiology Detection
    • COVID-19 CXR Classification
    • DKA Prediction (MIMIC-IV)
    • Drug Recommendation
    • Length of Stay Prediction
    • Medical Transcriptions Classification
    • Mortality Prediction (Next Visit)
    • Mortality Prediction (StageNet MIMIC-IV)
    • Patient Linkage (MIMIC-III)
    • Readmission Prediction
    • Sleep Staging
    • Sleep Staging (SleepEDF)
    • Temple University EEG Tasks
    • Sleep Staging v2
    • Benchmark EHRShot
    • ChestX-ray14 Binary Classification
    • De-Identification NER
    • ChestX-ray14 Multilabel Classification
    • Variant Classification (ClinVar)
    • Mutation Pathogenicity (COSMIC)
    • Cancer Survival Prediction (TCGA)
    • Cancer Mutation Burden (TCGA)
  • Models
    • pyhealth.models.BaseModel
    • pyhealth.models.LogisticRegression
    • pyhealth.models.MLP
    • pyhealth.models.CNN
    • pyhealth.models.RNN
    • pyhealth.models.GNN
    • pyhealth.models.Transformer
    • pyhealth.models.TransformersModel
    • pyhealth.models.TransformerDeID
    • pyhealth.models.RETAIN
    • pyhealth.models.GAMENet
    • pyhealth.models.GraphCare
    • pyhealth.models.MICRON
    • pyhealth.models.SafeDrug
    • pyhealth.models.MoleRec
    • pyhealth.models.Deepr
    • pyhealth.models.EHRMamba
    • pyhealth.models.JambaEHR
    • pyhealth.models.ContraWR
    • pyhealth.models.SparcNet
    • pyhealth.models.StageNet
    • pyhealth.models.StageAttentionNet
    • pyhealth.models.AdaCare
    • pyhealth.models.ConCare
    • pyhealth.models.Agent
    • pyhealth.models.GRASP
    • pyhealth.models.MedLink
    • pyhealth.models.TCN
    • pyhealth.models.TFMTokenizer
    • pyhealth.models.GAN
    • pyhealth.models.VAE
    • pyhealth.models.sdoh
    • pyhealth.models.BIOT
    • UnifiedMultimodalEmbeddingModel
    • pyhealth.models.califorest
  • Processors
    • pyhealth.processors.Processor
    • pyhealth.processors.FeatureProcessor
    • pyhealth.processors.TemporalFeatureProcessor
    • pyhealth.processors.ModalityType
    • pyhealth.processors.SampleProcessor
    • pyhealth.processors.DatasetProcessor
    • pyhealth.processors.SequenceProcessor
    • pyhealth.processors.NestedSequenceProcessor
    • pyhealth.processors.NestedFloatsProcessor
    • pyhealth.processors.BinaryLabelProcessor
    • pyhealth.processors.MultiClassLabelProcessor
    • pyhealth.processors.MultiLabelProcessor
    • pyhealth.processors.RegressionLabelProcessor
    • pyhealth.processors.ImageProcessor
    • pyhealth.processors.TextProcessor
    • pyhealth.processors.TupleTimeTextProcessor
    • pyhealth.processors.AudioProcessor
    • pyhealth.processors.SignalProcessor
    • pyhealth.processors.TimeseriesProcessor
    • pyhealth.processors.TemporalTimeseriesProcessor
    • pyhealth.processors.TimeImageProcessor
    • pyhealth.processors.TensorProcessor
    • pyhealth.processors.RawProcessor
    • pyhealth.processors.IgnoreProcessor
    • pyhealth.processors.MultiHotProcessor
    • pyhealth.processors.StageNetProcessor
    • pyhealth.processors.StageNetTensorProcessor
    • pyhealth.processors.GraphProcessor
  • Interpretability
    • pyhealth.interpret.methods.gim
    • pyhealth.interpret.methods.basic_gradient
    • pyhealth.interpret.methods.chefer
    • pyhealth.interpret.methods.deeplift
    • pyhealth.interpret.methods.integrated_gradients
    • pyhealth.interpret.methods.shap
    • pyhealth.interpret.methods.lime
    • pyhealth.interpret.utils
  • Trainer
  • Tokenizer
  • Metrics
    • pyhealth.metrics.multiclass
    • pyhealth.metrics.multilabel
    • pyhealth.metrics.binary
    • [core] calibration
    • [core] prediction_set
    • pyhealth.metrics.fairness
    • pyhealth.metrics.interpretability
  • MedCode
  • Calibration and Uncertainty Quantification
    • pyhealth.calib.calibration
      • pyhealth.calib.calibration.TemperatureScaling
      • pyhealth.calib.calibration.HistogramBinning
      • pyhealth.calib.calibration.DirichletCalibration
      • pyhealth.calib.calibration.KCal
    • pyhealth.calib.predictionset
      • pyhealth.calib.predictionset.LABEL
      • pyhealth.calib.predictionset.SCRIB
      • pyhealth.calib.predictionset.FavMac
      • pyhealth.calib.predictionset.CovariateLabel
      • pyhealth.calib.predictionset.ClusterLabel
      • pyhealth.calib.predictionset.NeighborhoodLabel

Additional Information

  • How to Contribute
  • PyHealth Research Initiative
  • Newsletter
    • November 2025 PyHealth Updates
    • Call to PyHealth Research Initiative (Spring 2026)
    • Memory Optimization: PyHealth Now Runs on 16GB RAM
    • PyHealth 2.0 Early Release Announcement
  • PyHealth Webinar 4/9/25
  • Development logs
  • About us
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Advanced Tutorials#

We provided advanced tutorials for supporting various needs.

Advanced Tutorial 1: Fit your dataset into our pipeline [Video]

Advanced Tutorial 2: Define your own healthcare task

Advanced Tutorial 3: Adopt customized model into pyhealth [Video]

Advanced Tutorial 4: Load your own processed data into pyhealth and try out our ML models [Video]

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