Add multimodal RNN support

docs/api/models/pyhealth.models.RNN.rst

@@ -10,6 +10,11 @@ The separate callable RNNLayer and the complete RNN model.
     :show-inheritance:
 
 .. autoclass:: pyhealth.models.RNN
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: pyhealth.models.MultimodalRNN
     :members:
     :undoc-members:
     :show-inheritance:

examples/mortality_prediction/mortality_mimic4_multimodal_rnn.py

@@ -0,0 +1,176 @@
+"""
+Mortality Prediction on MIMIC-IV with MultimodalRNN
+
+This example demonstrates how to use the MultimodalRNN model with mixed
+input modalities for in-hospital mortality prediction on MIMIC-IV.
+
+The MultimodalRNN model can handle:
+- Sequential features (diagnoses, procedures, lab timeseries) → RNN processing
+- Non-sequential features (demographics, static measurements) → Direct embedding
+
+This example shows:
+1. Loading MIMIC-IV data with mixed feature types
+2. Applying a mortality prediction task
+3. Training a MultimodalRNN model with both sequential and non-sequential inputs
+4. Evaluating the model performance
+"""
+
+from pyhealth.datasets import MIMIC4Dataset
+from pyhealth.datasets import split_by_patient, get_dataloader
+from pyhealth.models import MultimodalRNN
+from pyhealth.tasks import InHospitalMortalityMIMIC4
+from pyhealth.trainer import Trainer
+
+
+if __name__ == "__main__":
+    # STEP 1: Load MIMIC-IV base dataset
+    print("=" * 60)
+    print("STEP 1: Loading MIMIC-IV Dataset")
+    print("=" * 60)
+
+    base_dataset = MIMIC4Dataset(
+        ehr_root="/srv/local/data/physionet.org/files/mimiciv/2.2/",
+        ehr_tables=["diagnoses_icd", "procedures_icd", "labevents"],
+        dev=True,  # Use development mode for faster testing
+        num_workers=4,
+    )
+    base_dataset.stats()
+
+    # STEP 2: Apply mortality prediction task with multimodal features
+    print("\n" + "=" * 60)
+    print("STEP 2: Setting Mortality Prediction Task")
+    print("=" * 60)
+
+    # Use the InHospitalMortalityMIMIC4 task
+    # This task will create sequential features from diagnoses, procedures, and labs
+    task = InHospitalMortalityMIMIC4()
+    sample_dataset = base_dataset.set_task(
+        task,
+        num_workers=4,
+    )
+
+    print(f"\nTotal samples: {len(sample_dataset)}")
+    print(f"Input schema: {sample_dataset.input_schema}")
+    print(f"Output schema: {sample_dataset.output_schema}")
+
+    # Inspect a sample
+    if len(sample_dataset) > 0:
+        sample = sample_dataset[0]
+        print("\nSample structure:")
+        print(f"  Patient ID: {sample['patient_id']}")
+        for key in sample_dataset.input_schema.keys():
+            if key in sample:
+                if isinstance(sample[key], (list, tuple)):
+                    print(f"  {key}: length {len(sample[key])}")
+                else:
+                    print(f"  {key}: {type(sample[key])}")
+        print(f"  Mortality: {sample.get('mortality', 'N/A')}")
+
+    # STEP 3: Split dataset
+    print("\n" + "=" * 60)
+    print("STEP 3: Splitting Dataset")
+    print("=" * 60)
+
+    train_dataset, val_dataset, test_dataset = split_by_patient(
+        sample_dataset, [0.8, 0.1, 0.1]
+    )
+
+    print(f"Train samples: {len(train_dataset)}")
+    print(f"Val samples: {len(val_dataset)}")
+    print(f"Test samples: {len(test_dataset)}")
+
+    # Create dataloaders
+    train_loader = get_dataloader(train_dataset, batch_size=64, shuffle=True)
+    val_loader = get_dataloader(val_dataset, batch_size=64, shuffle=False)
+    test_loader = get_dataloader(test_dataset, batch_size=64, shuffle=False)
+
+    # STEP 4: Initialize MultimodalRNN model
+    print("\n" + "=" * 60)
+    print("STEP 4: Initializing MultimodalRNN Model")
+    print("=" * 60)
+
+    model = MultimodalRNN(
+        dataset=sample_dataset,
+        embedding_dim=128,
+        hidden_dim=128,
+        rnn_type="GRU",
+        num_layers=2,
+        dropout=0.3,
+        bidirectional=False,
+    )
+
+    num_params = sum(p.numel() for p in model.parameters())
+    print(f"Model initialized with {num_params:,} parameters")
+
+    # Print feature classification
+    print(f"\nSequential features (RNN processing): {model.sequential_features}")
+    print(f"Non-sequential features (direct embedding): {model.non_sequential_features}")
+
+    # Calculate expected embedding dimensions
+    seq_dim = len(model.sequential_features) * model.hidden_dim
+    non_seq_dim = len(model.non_sequential_features) * model.embedding_dim
+    total_dim = seq_dim + non_seq_dim
+    print(f"\nPatient representation dimension:")
+    print(f"  Sequential contribution: {seq_dim}")
+    print(f"  Non-sequential contribution: {non_seq_dim}")
+    print(f"  Total: {total_dim}")
+
+    # STEP 5: Train the model
+    print("\n" + "=" * 60)
+    print("STEP 5: Training Model")
+    print("=" * 60)
+
+    trainer = Trainer(
+        model=model,
+        device="cuda:0",  # Change to "cpu" if no GPU available
+        metrics=["pr_auc", "roc_auc", "accuracy", "f1"],
+    )
+
+    trainer.train(
+        train_dataloader=train_loader,
+        val_dataloader=val_loader,
+        epochs=10,
+        monitor="roc_auc",
+        optimizer_params={"lr": 1e-3},
+    )
+
+    # STEP 6: Evaluate on test set
+    print("\n" + "=" * 60)
+    print("STEP 6: Evaluating on Test Set")
+    print("=" * 60)
+
+    results = trainer.evaluate(test_loader)
+    print("\nTest Results:")
+    for metric, value in results.items():
+        print(f"  {metric}: {value:.4f}")
+
+    # STEP 7: Demonstrate model predictions
+    print("\n" + "=" * 60)
+    print("STEP 7: Sample Predictions")
+    print("=" * 60)
+
+    import torch
+
+    sample_batch = next(iter(test_loader))
+    with torch.no_grad():
+        output = model(**sample_batch)
+
+    print(f"\nBatch size: {output['y_prob'].shape[0]}")
+    print(f"First 10 predicted probabilities:")
+    for i, (prob, true_label) in enumerate(
+        zip(output['y_prob'][:10], output['y_true'][:10])
+    ):
+        print(f"  Sample {i+1}: prob={prob.item():.4f}, true={int(true_label.item())}")
+
+    # Summary
+    print("\n" + "=" * 60)
+    print("SUMMARY: MultimodalRNN Training Complete")
+    print("=" * 60)
+    print(f"Model: MultimodalRNN")
+    print(f"Dataset: MIMIC-IV")
+    print(f"Task: In-Hospital Mortality Prediction")
+    print(f"Sequential features: {len(model.sequential_features)}")
+    print(f"Non-sequential features: {len(model.non_sequential_features)}")
+    print(f"Best validation ROC-AUC: {max(results.get('roc_auc', 0), 0):.4f}")
+    print("=" * 60)
+

pyhealth/models/__init__.py

@@ -17,7 +17,7 @@
 from .mlp import MLP
 from .molerec import MoleRec, MoleRecLayer
 from .retain import RETAIN, RETAINLayer
-from .rnn import RNN, RNNLayer
+from .rnn import MultimodalRNN, RNN, RNNLayer
 from .safedrug import SafeDrug, SafeDrugLayer
 from .sparcnet import DenseBlock, DenseLayer, SparcNet, TransitionLayer
 from .stagenet import StageNet, StageNetLayer