Labrador model ml171

LABRADOR_TEST_SUMMARY.md

@@ -0,0 +1,90 @@
+# LabradorModel Test
+
+**Test File:** `tests/core/test_labrador.py`
+
+## Overview
+
+Minimal end-to-end smoke test for `LabradorModel` that verifies:
+- Dataset creation with aligned lab codes and values
+- Model initialization with correct hyperparameters
+- Forward pass with expected output structure
+- Backward pass with gradient computation
+- Embedding extraction when requested
+
+## Test Methods
+
+| Test | Purpose |
+|------|---------|
+| `test_model_initialization` | Verifies model initializes with correct hyperparameters (embed_dim, num_heads, num_layers, feature keys, label key) |
+| `test_model_forward` | Checks forward pass returns `loss`, `y_prob`, `y_true`, `logit` with correct shapes and batch sizes |
+| `test_model_backward` | Confirms backward pass computes gradients on parameters |
+| `test_model_with_embedding` | Validates embedding extraction returns correct shape `[batch_size, embed_dim]` |
+
+---
+
+## Key Implementation Details
+
+## Test Data Structure
+
+**Minimal Synthetic Dataset (2 samples, 4 labs each):**
+```python
+samples = [
+    {
+        "patient_id": "patient-0",
+        "visit_id": "visit-0",
+        "lab_codes": ["lab-1", "lab-2", "lab-3", "lab-4"],      # Categorical
+        "lab_values": [1.0, 2.5, 3.0, 4.5],                     # Continuous
+        "label": 0,
+    },
+    {
+        "patient_id": "patient-1",
+        "visit_id": "visit-1",
+        "lab_codes": ["lab-1", "lab-2", "lab-3", "lab-4"],
+        "lab_values": [2.1, 1.8, 2.9, 3.5],
+        "label": 1,
+    },
+]
+```
+
+**Input Schema:**
+```python
+input_schema = {
+    "lab_codes": "sequence",    # → Categorical tokens [batch, 4]
+    "lab_values": "tensor",     # → Float values [batch, 4]
+}
+output_schema = {"label": "binary"}
+```
+
+**Model Configuration:**
+```python
+LabradorModel(
+    dataset=dataset,
+    code_feature_key="lab_codes",
+    value_feature_key="lab_values",
+    embed_dim=32,               # Lightweight for testing
+    num_heads=2,
+    num_layers=1,
+)
+```
+
+---
+
+## Running the Test
+
+**Option 1: Using pixi (recommended)**
+```bash
+cd /home/leemh/PyHealth
+make init   # First time only
+make test
+```
+
+**Option 2: Direct unittest**
+```bash
+cd /home/leemh/PyHealth
+python3 -m unittest tests.core.test_labrador.TestLabradorModel -v
+```
+
+**Option 3: Single test method**
+```bash
+python3 -m unittest tests.core.test_labrador.TestLabradorModel.test_model_forward -v
+```

docs/api/models.rst

@@ -197,6 +197,7 @@ API Reference
     models/pyhealth.models.MedLink
     models/pyhealth.models.TCN
     models/pyhealth.models.TFMTokenizer
+    models/pyhealth.models.labrador
     models/pyhealth.models.GAN
     models/pyhealth.models.VAE
     models/pyhealth.models.SDOH

docs/api/models/pyhealth.models.labrador.rst

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+pyhealth.models.labrador
+===================================
+
+LabradorModel for aligned lab code and lab value inputs.
+
+.. autoclass:: pyhealth.models.LabradorModel
+    :members:
+    :undoc-members:
+    :show-inheritance: