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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>PyHealth Datasets — 21 Clinical Datasets</title>
<meta name="description" content="Browse all 21 clinical datasets supported by PyHealth across EHR, biosignals, medical imaging, genomics, and clinical text.">
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</style>
</head>
<body>
<header class="site-header">
<div class="site-wrap header-inner">
<nav class="nav" aria-label="Main navigation">
<a href="index.html" class="back-link">
<svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2.2" stroke-linecap="round" stroke-linejoin="round"><polyline points="15 18 9 12 15 6"/></svg>
PyHealth
</a>
</nav>
<span style="color: var(--muted); font-size: 0.88rem; font-weight: 500;">Datasets</span>
</div>
</header>
<main class="site-wrap" style="padding: 2.2rem 0 3.5rem;">
<!-- ── Hero ── -->
<section class="ph-hero">
<p class="ph-eyebrow">PyHealth Datasets</p>
<h1>21 Clinical Datasets</h1>
<p class="ph-tagline">A unified API for loading healthcare data across electronic health records, physiological signals, medical imaging, genomics, and clinical text — all ready for machine learning.</p>
<div class="ph-cta-row">
<a href="https://colab.research.google.com/drive/1voSx7wEfzXfEf2sIfW6b-8p1KqMyuWxK?usp=sharing" class="ph-btn primary" target="_blank" rel="noopener">
<svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polygon points="5 3 19 12 5 21 5 3"/></svg>
Open Tutorial Notebook
</a>
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets.html" class="ph-btn outline" target="_blank" rel="noopener">
<svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M4 19.5A2.5 2.5 0 0 1 6.5 17H20"/><path d="M6.5 2H20v20H6.5A2.5 2.5 0 0 1 4 19.5v-15A2.5 2.5 0 0 1 6.5 2z"/></svg>
API Reference
</a>
</div>
<div class="growing-notice">
<span class="dot"></span>
Actively growing — new datasets added regularly. <a href="https://docs.google.com/spreadsheets/d/1PNMgDe-llOm1SM5ZyGLkmPysjC4wwaVblPLAHLxejTw/edit#gid=159213380" target="_blank" rel="noopener" style="color:rgba(255,255,255,0.85); text-decoration:underline; text-underline-offset:2px;">View planned additions →</a>
</div>
</section>
<!-- ── Filter + Grid ── -->
<section class="page-section fade-up">
<div style="display:flex; align-items:baseline; justify-content:space-between; flex-wrap:wrap; gap:0.5rem; margin-bottom:1.2rem;">
<h2 class="section-h2" style="margin:0;">Browse Datasets <span class="count-badge" id="visibleCount">23</span></h2>
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets.html" target="_blank" rel="noopener" style="font-size:0.85rem; color:var(--accent); text-decoration:none; font-weight:500;">Full API reference →</a>
</div>
<div class="filter-bar" role="group" aria-label="Filter by modality">
<button class="filter-btn active" onclick="filterDatasets('all', this)">All <span style="opacity:0.65;">(23)</span></button>
<button class="filter-btn" onclick="filterDatasets('ehr', this)">EHR <span style="opacity:0.65;">(9)</span></button>
<button class="filter-btn" onclick="filterDatasets('signal', this)">Biosignal <span style="opacity:0.65;">(8)</span></button>
<button class="filter-btn" onclick="filterDatasets('image', this)">Image <span style="opacity:0.65;">(2)</span></button>
<button class="filter-btn" onclick="filterDatasets('genomics', this)">Genomics <span style="opacity:0.65;">(3)</span></button>
<button class="filter-btn" onclick="filterDatasets('text', this)">Text <span style="opacity:0.65;">(1)</span></button>
</div>
<div class="dataset-grid" id="datasetGrid">
<!-- ───────────── EHR (7) ───────────── -->
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">MIMIC3Dataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">MIMIC-III Critical Care database with 40K+ ICU stays covering diagnoses, procedures, medications, lab results, and free text notes.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">MIMIC3Dataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">MIMIC3Dataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/mimic3/"</span>,
tables<span class="tok-op">=</span>[<span class="tok-str">"DIAGNOSES_ICD"</span>, <span class="tok-str">"PROCEDURES_ICD"</span>],
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.MIMIC3Dataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/mortality_prediction/mortality_mimic3_rnn.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">MIMIC4Dataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">MIMIC-IV with 300K+ patients spanning hospital and ICU encounters, including structured EHR tables and clinical notes.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">MIMIC4Dataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">MIMIC4Dataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/mimic4/"</span>,
tables<span class="tok-op">=</span>[<span class="tok-str">"diagnoses_icd"</span>, <span class="tok-str">"labevents"</span>],
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.MIMIC4Dataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/mortality_prediction/mortality_mimic4_transformer.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">MIMIC4FHIR</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">MIMIC-IV-on-FHIR (R4): streams the PhysioNet FHIR export into flattened Patient, Encounter, Condition, Observation, MedicationRequest, and Procedure tables.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">MIMIC4FHIR</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">MIMIC4FHIR</span>(root<span class="tok-op">=</span><span class="tok-str">"data/mimic-iv-fhir/"</span>)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.MIMIC4FHIR.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/mimic4fhir_mpf_ehrmamba.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">FHIRDataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">Generic FHIR loader: a single YAML config describes any NDJSON FHIR export, and PyHealth handles the streaming, flattening, and caching.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets.fhir <span class="tok-kw">import</span> <span class="tok-cl">FHIRDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">FHIRDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/export/"</span>,
config_path<span class="tok-op">=</span><span class="tok-str">"my_fhir.yaml"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.FHIRDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">eICUDataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">Multi-center eICU Collaborative Research Database with 200K+ ICU stays from 208 hospitals across the US.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">eICUDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">eICUDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/eicu/"</span>,
tables<span class="tok-op">=</span>[<span class="tok-str">"diagnosis"</span>, <span class="tok-str">"medication"</span>],
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.eICUDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/mortality_prediction/mortality_prediction_eicu_rnn.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">OMOPDataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">OMOP Common Data Model loader — a standardized format for observational health data used widely across academic medical centers.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">OMOPDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">OMOPDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/omop/"</span>,
tables<span class="tok-op">=</span>[<span class="tok-str">"condition_occurrence"</span>],
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.OMOPDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/omop_dataset_demo.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">MIMICExtractDataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">MIMIC-Extract pre-processed cohort with time-series vitals and lab values for 34K ICU patients, ready for timeseries modeling.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">MIMICExtractDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">MIMICExtractDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/mimic-extract/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.MIMICExtractDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">EHRShotDataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">EHRShot few-shot benchmark derived from EHRSFM with 15 clinical prediction tasks for evaluating foundation models on EHR data.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">EHRShotDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">EHRShotDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/ehrshot/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.EHRShotDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/benchmark_ehrshot_xgboost.ipynb" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="ehr">
<div class="dataset-card-header">
<span class="dataset-classname">Support2Dataset</span>
<span class="modality-tag mod-ehr">EHR</span>
</div>
<p class="dataset-desc">SUPPORT2 study dataset for survival prediction with demographics, vitals, labs, comorbidities, and 2-month / 6-month survival labels.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">Support2Dataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">Support2Dataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/support2/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.Support2Dataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/survival_preprocess_support2_demo.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<!-- ───────────── Biosignal (8) ───────────── -->
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">CardiologyDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">Multi-label ECG dataset for cardiac arrhythmia detection with 12-lead signals annotated across multiple cardiac conditions.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">CardiologyDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">CardiologyDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/cardiology/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.CardiologyDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/cardiology_detection_isAR_SparcNet.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">ISRUCDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">ISRUC-Sleep dataset with polysomnography recordings (EEG, EOG, EMG) from healthy subjects and patients with sleep disorders.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">ISRUCDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">ISRUCDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/isruc/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.ISRUCDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/eeg/sleep_staging/sleep_staging_ISRUC_SparcNet.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">DREAMTDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">DREAMT study dataset with multi-night wrist-worn EEG data for sleep staging in a free-living environment.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">DREAMTDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">DREAMTDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/dreamt/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.DREAMTDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/datasets_overview.ipynb" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">SHHSDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">Sleep Heart Health Study with overnight polysomnography from 5,800+ participants for sleep staging and cardiovascular risk research.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">SHHSDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">SHHSDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/shhs/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.SHHSDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/eeg/sleep_staging/sleep_staging_shhs_contrawr.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">SleepEDFDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">SleepEDF-78/Cassette dataset with full-night EEG recordings from 78 healthy subjects, widely used for sleep staging benchmarks.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">SleepEDFDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">SleepEDFDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/sleepedf/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.SleepEDFDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/eeg/sleep_staging/sleep_staging_sleepEDF_contrawr.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">BMDHSDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">BMDHS heart sound dataset with phonocardiogram recordings for cardiac valve disease classification and auscultation research.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">BMDHSDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">BMDHSDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/bmdhs/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.BMDHSDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">TUABDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">Temple University EEG Abnormal (TUAB) corpus with clinical EEG recordings labeled as normal or abnormal by board-certified neurologists.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">TUABDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">TUABDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/tuab/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.TUABDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/eeg/tuh_eeg/tuab_abnormal_detection.ipynb" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="signal">
<div class="dataset-card-header">
<span class="dataset-classname">TUEVDataset</span>
<span class="modality-tag mod-signal">Biosignal</span>
</div>
<p class="dataset-desc">Temple University EEG Events (TUEV) corpus annotated with six EEG event types including spike-wave complexes and artifacts.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">TUEVDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">TUEVDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/tuev/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.TUEVDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/eeg/tuh_eeg/tuev_eeg_event_classification.ipynb" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<!-- ───────────── Image (2) ───────────── -->
<div class="dataset-card" data-modality="image">
<div class="dataset-card-header">
<span class="dataset-classname">COVID19CXRDataset</span>
<span class="modality-tag mod-image">Image</span>
</div>
<p class="dataset-desc">COVID-19 chest X-ray dataset for binary classification of COVID-19 vs. normal and pneumonia images across multiple sources.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">COVID19CXRDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">COVID19CXRDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/covid19cxr/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.COVID19CXRDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/cxr/covid19cxr_tutorial.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<div class="dataset-card" data-modality="image">
<div class="dataset-card-header">
<span class="dataset-classname">ChestXray14Dataset</span>
<span class="modality-tag mod-image">Image</span>
</div>
<p class="dataset-desc">NIH ChestX-ray14 with 112K frontal chest X-rays from 30K patients, annotated with 14 disease labels for multi-label classification.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">ChestXray14Dataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">ChestXray14Dataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/chestxray14/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.ChestXray14Dataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
<a href="https://github.com/sunlabuiuc/PyHealth/blob/master/examples/cxr/chestxray14_binary_classification.py" class="example-link" target="_blank" rel="noopener">Example →</a>
</div>
</div>
<!-- ───────────── Genomics (3) ───────────── -->
<div class="dataset-card" data-modality="genomics">
<div class="dataset-card-header">
<span class="dataset-classname">ClinVarDataset</span>
<span class="modality-tag mod-genomics">Genomics</span>
</div>
<p class="dataset-desc">NCBI ClinVar database of genomic variants and their clinical significance, used for variant pathogenicity classification.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">ClinVarDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">ClinVarDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/clinvar/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.ClinVarDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
<div class="dataset-card" data-modality="genomics">
<div class="dataset-card-header">
<span class="dataset-classname">COSMICDataset</span>
<span class="modality-tag mod-genomics">Genomics</span>
</div>
<p class="dataset-desc">Catalogue of Somatic Mutations in Cancer (COSMIC) for predicting the functional impact of somatic mutations in cancer.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">COSMICDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">COSMICDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/cosmic/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.COSMICDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
<div class="dataset-card" data-modality="genomics">
<div class="dataset-card-header">
<span class="dataset-classname">TCGAPRADDataset</span>
<span class="modality-tag mod-genomics">Genomics</span>
</div>
<p class="dataset-desc">TCGA Prostate Adenocarcinoma (PRAD) multi-omics dataset for cancer survival prediction using RNA-seq, CNV, and mutation profiles.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">TCGAPRADDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">TCGAPRADDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/tcga/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.TCGAPRADDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
<!-- ───────────── Text (1) ───────────── -->
<div class="dataset-card" data-modality="text">
<div class="dataset-card-header">
<span class="dataset-classname">MedicalTranscriptionsDataset</span>
<span class="modality-tag mod-text">Text</span>
</div>
<p class="dataset-desc">Kaggle medical transcriptions dataset with 5K+ clinical notes across 40 specialties for specialty classification and NLP tasks.</p>
<pre class="dataset-code"><span class="tok-kw">from</span> pyhealth.datasets <span class="tok-kw">import</span> <span class="tok-cl">MedicalTranscriptionsDataset</span>
dataset <span class="tok-op">=</span> <span class="tok-cl">MedicalTranscriptionsDataset</span>(
root<span class="tok-op">=</span><span class="tok-str">"data/medical_transcriptions/"</span>,
)</pre>
<div class="dataset-card-footer">
<a href="https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.MedicalTranscriptionsDataset.html" class="docs-link" target="_blank" rel="noopener">Docs →</a>
</div>
</div>
</div><!-- /dataset-grid -->
</section>
<!-- ── Custom Dataset Note ── -->
<section class="page-section fade-up">
<div style="background:var(--paper); border:1px solid var(--line); border-radius:14px; padding:1.6rem 1.8rem; display:flex; gap:1.2rem; align-items:flex-start;">
<div style="flex-shrink:0; width:40px; height:40px; border-radius:10px; background:rgba(201,95,38,0.1); display:flex; align-items:center; justify-content:center;">
<svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="var(--accent)" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><circle cx="12" cy="12" r="10"/><line x1="12" y1="8" x2="12" y2="12"/><line x1="12" y1="16" x2="12.01" y2="16"/></svg>
</div>
<div>
<h3 style="margin:0 0 0.4rem; font-size:1rem;">Need a custom dataset?</h3>
<p style="margin:0 0 0.8rem; font-size:0.88rem; color:var(--muted); line-height:1.55;">PyHealth makes it easy to add your own data source by inheriting <code style="font-family:monospace; font-size:0.85rem; background:rgba(0,0,0,0.05); padding:0.1rem 0.35rem; border-radius:4px;">BaseDataset</code>. Your custom dataset immediately gets access to all PyHealth tasks, models, and the trainer — no extra wiring needed.</p>
<div style="display:flex; gap:0.6rem; flex-wrap:wrap;">
<a href="https://pyhealth.readthedocs.io/en/latest/tutorials/custom_dataset.html" target="_blank" rel="noopener" style="font-size:0.83rem; font-weight:500; color:var(--accent); text-decoration:none; padding:0.3rem 0.75rem; border:1.5px solid rgba(201,95,38,0.3); border-radius:7px; transition:background 0.15s;" onmouseover="this.style.background='rgba(201,95,38,0.07)'" onmouseout="this.style.background=''">Custom Dataset Tutorial →</a>
<a href="https://github.com/sunlabuiuc/PyHealth" target="_blank" rel="noopener" style="font-size:0.83rem; font-weight:500; color:var(--muted); text-decoration:none; padding:0.3rem 0.75rem; border:1.5px solid var(--line); border-radius:7px; transition:background 0.15s;" onmouseover="this.style.background='rgba(0,0,0,0.03)'" onmouseout="this.style.background=''">View Source on GitHub →</a>
</div>
</div>
</div>
</section>
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<script>
document.getElementById('year').textContent = new Date().getFullYear();
function filterDatasets(modality, btn) {
// Update active button
document.querySelectorAll('.filter-btn').forEach(b => b.classList.remove('active'));
btn.classList.add('active');
// Show/hide cards
const cards = document.querySelectorAll('#datasetGrid .dataset-card');
let visible = 0;
cards.forEach(card => {
const show = modality === 'all' || card.dataset.modality === modality;
card.style.display = show ? '' : 'none';
if (show) visible++;
});
document.getElementById('visibleCount').textContent = visible;
}
</script>
</body>
</html>