diff --git a/docs/api/models.rst b/docs/api/models.rst index 7c3ac7c4b..6880b04db 100644 --- a/docs/api/models.rst +++ b/docs/api/models.rst @@ -206,3 +206,4 @@ API Reference models/pyhealth.models.BIOT models/pyhealth.models.unified_multimodal_embedding_docs models/pyhealth.models.califorest + models/pyhealth.models.AlzheimerCNN diff --git a/docs/api/models/pyhealth.models.alzheimer_cnn.rst b/docs/api/models/pyhealth.models.alzheimer_cnn.rst new file mode 100644 index 000000000..148144a75 --- /dev/null +++ b/docs/api/models/pyhealth.models.alzheimer_cnn.rst @@ -0,0 +1,19 @@ +pyhealth.models.AlzheimerCNN +============================ + +2D CNN for Alzheimer's disease classification from MRI slice images. + +.. autoclass:: pyhealth.models.AlzheimerCNN + :members: + :undoc-members: + :show-inheritance: + +.. autoclass:: pyhealth.models.AlzheimerCNNViT + :members: + :undoc-members: + :show-inheritance: + +.. autoclass:: pyhealth.models.AlzheimerCNNNormVariant + :members: + :undoc-members: + :show-inheritance: \ No newline at end of file diff --git a/examples/alzheimer_mri_classification_alzheimer_cnn.ipynb b/examples/alzheimer_mri_classification_alzheimer_cnn.ipynb new file mode 100644 index 000000000..678c12427 --- /dev/null +++ b/examples/alzheimer_mri_classification_alzheimer_cnn.ipynb @@ -0,0 +1,15276 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "md-0", + "metadata": {}, + "source": [ + "# AlzheimerCNN Ablation Study\n", + "\n", + "This notebook is the ablation study for the `AlzheimerCNN` model contribution to PyHealth.\n", + "\n", + "**Reference paper:** Liu et al. *\"On the design of convolutional neural networks for automatic detection of Alzheimer's disease.\"* ML4H @ NeurIPS 2019. https://arxiv.org/abs/1911.03740\n", + "\n", + "## Experimental Setup\n", + "\n", + "We train five model configurations on the `Falah/Alzheimer_MRI` dataset and compare validation accuracy and macro-F1. All models share the same training recipe:\n", + "\n", + "- **Optimizer:** AdamW, lr=1e-4, weight_decay=1e-5\n", + "- **Epochs:** 50\n", + "- **Batch size:** 32\n", + "- **Train/Val/Test split:** 60% / 20% / 20%\n", + "- **Loss:** Cross-entropy (4-class classification)\n", + "\n", + "## Configurations Tested\n", + "\n", + "| # | Model | Variation | Hypothesis |\n", + "|---|-------|-----------|------------|\n", + "| 1 | `AlzheimerCNN` | `init_channels=32` (baseline) | Reference point |\n", + "| 2 | `AlzheimerCNN` | `init_channels=16` | Smaller capacity may underfit |\n", + "| 3 | `AlzheimerCNN` | `init_channels=64` | Larger capacity may overfit on 5k samples |\n", + "| 4 | `AlzheimerCNNNormVariant` | `norm_type=\"group\"` | GroupNorm may match InstanceNorm at small batch sizes |\n", + "| 5 | `AlzheimerCNNNormVariant` | `norm_type=\"layer\"` | LayerNorm may match InstanceNorm at small batch sizes |\n", + "| 6 | `AlzheimerCNNViT` | CNN + Transformer hybrid | Self-attention may model global context better, but on small set may not be great |\n" + ] + }, + { + "cell_type": "markdown", + "id": "md-1", + "metadata": {}, + "source": [ + "## 1. Setup\n" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "code-2", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/Joey/DL4H_Final_Project/PyHealth/pyhealth/trainer.py:12: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n", + " from tqdm.autonotebook import trange\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using device: mps\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import torch\n", + "import pandas as pd\n", + "\n", + "from pyhealth.datasets import split_by_sample, get_dataloader\n", + "from pyhealth.trainer import Trainer\n", + "from pyhealth.models import (\n", + " AlzheimerCNN,\n", + " AlzheimerCNNNormVariant,\n", + " AlzheimerCNNViT,\n", + ")\n", + "\n", + "# ── Auto-detect device ──────────────────────────────────────────────────\n", + "DEVICE = \"cpu\"\n", + "if torch.cuda.is_available():\n", + " DEVICE = \"cuda\"\n", + "elif torch.backends.mps.is_available():\n", + " DEVICE = \"mps\"\n", + "\n", + "print(f\"Using device: {DEVICE}\")\n", + "\n", + "METRICS = [\"accuracy\", \"f1_macro\", \"balanced_accuracy\"]\n", + "EPOCHS = 50\n", + "BATCH_SIZE = 32\n", + "SEED = 42\n", + "\n", + "torch.manual_seed(SEED)\n" + ] + }, + { + "cell_type": "markdown", + "id": "md-3", + "metadata": {}, + "source": [ + "## 2. Load Dataset\n", + "\n", + "Uses the `AlzheimersDataset` PyHealth-compatible wrapper around `Falah/Alzheimer_MRI` (4-class severity classification: NonDemented, VeryMildDemented, MildDemented, ModerateDemented).\n", + "\n", + "The dataset class auto-downloads from HuggingFace and saves a `alzheimers-metadata.csv` for PyHealth's BaseDataset to consume.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "code-4", + "metadata": {}, + "outputs": [], + "source": [ + "from typing import Any, Dict, List\n", + "from pyhealth.tasks.base_task import BaseTask\n", + "\n", + "\n", + "class AlzheimersClassification(BaseTask):\n", + " \"\"\"Task for classifying Alzheimer's disease from brain images.\"\"\"\n", + "\n", + " task_name: str = \"AlzheimersClassification\"\n", + " input_schema: Dict = {\"image\": (\"image\", {\"mode\": \"L\", \"image_size\": 128})}\n", + " output_schema: Dict[str, str] = {\"label\": \"multiclass\"}\n", + "\n", + " def __call__(self, patient: Any) -> List[Dict[str, Any]]:\n", + " events = patient.get_events(event_type=\"alzheimers\")\n", + " assert len(events) == 1, f\"Expected 1 image, got {len(events)}\"\n", + " event = events[0]\n", + " return [{\"image\": event.path, \"label\": event.label}]" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "e84f74f0", + "metadata": {}, + "outputs": [], + "source": [ + "import logging\n", + "import os\n", + "from pathlib import Path\n", + "from typing import Optional\n", + "\n", + "import pandas as pd\n", + "from datasets import load_dataset\n", + "from pyhealth.datasets.base_dataset import BaseDataset\n", + "\n", + "logger = logging.getLogger(__name__)\n", + "\n", + "\n", + "class AlzheimersDataset(BaseDataset):\n", + " \"\"\"PyHealth-compatible Alzheimer's dataset (auto-download + process).\"\"\"\n", + "\n", + " def __init__(\n", + " self,\n", + " root: str,\n", + " dataset_name: Optional[str] = None,\n", + " config_path: Optional[str] = None,\n", + " cache_dir: Optional[str] = None,\n", + " num_workers: int = 1,\n", + " dev: bool = False,\n", + " hf_dataset_name: str = \"Falah/Alzheimer_MRI\",\n", + " ) -> None:\n", + " self.hf_dataset_name = hf_dataset_name\n", + "\n", + " try:\n", + " base_path = Path(__file__).parent\n", + " except NameError:\n", + " base_path = Path.cwd()\n", + "\n", + " if config_path is None:\n", + " config_path = base_path / \"configs\" / \"alzheimers.yaml\"\n", + "\n", + " metadata_path = os.path.join(root, \"alzheimers-metadata.csv\")\n", + "\n", + " if not os.path.exists(metadata_path):\n", + " self.prepare_metadata(root)\n", + "\n", + " super().__init__(\n", + " root=root,\n", + " tables=[\"alzheimers\"],\n", + " dataset_name=dataset_name or \"alzheimers\",\n", + " config_path=config_path,\n", + " cache_dir=cache_dir,\n", + " num_workers=num_workers,\n", + " dev=dev,\n", + " )\n", + "\n", + " def prepare_metadata(self, root: str) -> None:\n", + " os.makedirs(root, exist_ok=True)\n", + " image_dir = os.path.join(root, \"images\")\n", + " os.makedirs(image_dir, exist_ok=True)\n", + " metadata_path = os.path.join(root, \"alzheimers-metadata.csv\")\n", + "\n", + " ds = load_dataset(self.hf_dataset_name, split=\"train\")\n", + " records = []\n", + " for i, item in enumerate(ds):\n", + " img_path = os.path.join(image_dir, f\"{i}.png\")\n", + " if not os.path.isfile(img_path):\n", + " item[\"image\"].save(img_path)\n", + " records.append({\n", + " \"patient_id\": str(i),\n", + " \"path\": img_path,\n", + " \"label\": str(item[\"label\"]),\n", + " })\n", + " pd.DataFrame(records).to_csv(metadata_path, index=False)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "737a3fd3", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Initializing alzheimers dataset from Downloads (dev mode: False)\n", + "No cache_dir provided. Using default cache dir: /Users/Joey/Library/Caches/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564\n", + "Setting task AlzheimersClassification for alzheimers base dataset...\n", + "Task cache paths: task_df=/Users/Joey/Library/Caches/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/task_df.ld, samples=/Users/Joey/Library/Caches/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/samples_cdbbc602-34e2-5a41-8643-4c76b08829f6.ld\n", + "Found cached processed samples at /Users/Joey/Library/Caches/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/samples_cdbbc602-34e2-5a41-8643-4c76b08829f6.ld, skipping processing.\n", + "Train: 3072 | Val: 1024 | Test: 1024\n" + ] + } + ], + "source": [ + "# Instantiate dataset and create train/val/test splits\n", + "dataset = AlzheimersDataset(root=\"Downloads\")\n", + "dataset_samples = dataset.set_task(AlzheimersClassification(), num_workers=1)\n", + "\n", + "train_samples, val_samples, test_samples = split_by_sample(\n", + " dataset_samples, [0.6, 0.2, 0.2]\n", + ")\n", + "\n", + "train_loader = get_dataloader(train_samples, batch_size=BATCH_SIZE, shuffle=True)\n", + "val_loader = get_dataloader(val_samples, batch_size=BATCH_SIZE, shuffle=False)\n", + "test_loader = get_dataloader(test_samples, batch_size=BATCH_SIZE, shuffle=False)\n", + "\n", + "print(f\"Train: {len(train_samples)} | Val: {len(val_samples)} | Test: {len(test_samples)}\")" + ] + }, + { + "cell_type": "markdown", + "id": "md-5", + "metadata": {}, + "source": [ + "## 3. Training Helper\n", + "\n", + "A single function that trains any model with the shared recipe and returns final validation metrics. This keeps every experiment cell short and ensures all configurations are compared fairly.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "code-6", + "metadata": {}, + "outputs": [], + "source": [ + "import time\n", + "\n", + "def train_and_evaluate(model, name: str) -> dict:\n", + " \"\"\"Train a model and return its final validation metrics.\n", + "\n", + " Args:\n", + " model: An instantiated PyHealth model inheriting from BaseModel.\n", + " name: Human-readable label for the configuration.\n", + "\n", + " Returns:\n", + " Dict with keys 'name', 'accuracy', 'f1_macro', 'balanced_accuracy', 'loss', 'params'.\n", + " \"\"\"\n", + " print(f\"\\n{'='*60}\")\n", + " print(f\"Training: {name}\")\n", + " print(f\"{'='*60}\")\n", + "\n", + " trainer = Trainer(model=model, metrics=METRICS, device=DEVICE)\n", + "\n", + " t0 = time.perf_counter()\n", + " trainer.train(\n", + " train_dataloader=train_loader,\n", + " val_dataloader=val_loader,\n", + " epochs=EPOCHS,\n", + " optimizer_class=torch.optim.AdamW,\n", + " optimizer_params={\"lr\": 1e-4, \"weight_decay\": 1e-5},\n", + " )\n", + " train_time = time.perf_counter() - t0\n", + "\n", + " scores = trainer.evaluate(val_loader)\n", + " num_params = sum(p.numel() for p in model.parameters() if p.requires_grad)\n", + "\n", + " return {\n", + " \"name\": name,\n", + " \"accuracy\": scores.get(\"accuracy\", float(\"nan\")),\n", + " \"f1_macro\": scores.get(\"f1_macro\", float(\"nan\")),\n", + " \"balanced_accuracy\": scores.get(\"balanced_accuracy\", float(\"nan\")),\n", + " \"loss\": scores.get(\"loss\", float(\"nan\")),\n", + " \"params\": num_params,\n", + " \"train_time_seconds\": round(train_time, 1),\n", + " }\n", + "\n", + "\n", + "# Collect all results in this list for the final summary\n", + "results = []\n" + ] + }, + { + "cell_type": "markdown", + "id": "md-7", + "metadata": {}, + "source": [ + "## 4. Experiments\n" + ] + }, + { + "cell_type": "markdown", + "id": "md-8", + "metadata": {}, + "source": [ + "### Experiment 1: Baseline (`init_channels=32`)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "code-9", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "============================================================\n", + "Training: CNN (init_channels=32, baseline)\n", + "============================================================\n", + "AlzheimerCNN(\n", + " (block1): Sequential(\n", + " (0): Conv2d(1, 32, kernel_size=(1, 1), stride=(1, 1), padding=(1, 1))\n", + " (1): InstanceNorm2d(32, eps=1e-05, momentum=0.1, affine=False, track_running_stats=False)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (block2): Sequential(\n", + " (0): Conv2d(32, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): InstanceNorm2d(64, eps=1e-05, momentum=0.1, affine=False, track_running_stats=False)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (block3): Sequential(\n", + " (0): Conv2d(64, 128, kernel_size=(5, 5), stride=(1, 1), padding=(1, 1))\n", + " (1): InstanceNorm2d(128, eps=1e-05, momentum=0.1, affine=False, track_running_stats=False)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (block4): Sequential(\n", + " (0): Conv2d(128, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): InstanceNorm2d(256, eps=1e-05, momentum=0.1, affine=False, track_running_stats=False)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): AdaptiveAvgPool2d(output_size=(1, 1))\n", + " )\n", + " (classifier): Sequential(\n", + " (0): Linear(in_features=256, out_features=128, bias=True)\n", + " (1): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (2): Dropout(p=0.5, inplace=False)\n", + " (3): Linear(in_features=128, out_features=4, bias=True)\n", + " )\n", + ")\n", + "Metrics: ['accuracy', 'f1_macro', 'balanced_accuracy']\n", + "Device: mps\n", + "\n", + "Training:\n", + "Batch size: 32\n", + "Optimizer: \n", + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n", + "Weight decay: 0.0\n", + "Max grad norm: None\n", + "Val dataloader: \n", + "Monitor: None\n", + "Monitor criterion: max\n", + "Epochs: 50\n", + "Patience: None\n", + "\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "1d446d598c76486d99547f9ad624fd67", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Epoch 0 / 50: 0%| | 0/96 [00:00\n", + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n", + "Weight decay: 0.0\n", + "Max grad norm: None\n", + "Val dataloader: \n", + "Monitor: None\n", + "Monitor criterion: max\n", + "Epochs: 50\n", + "Patience: None\n", + "\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "48ea111c93874247a3f801975f724642", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Epoch 0 / 50: 0%| | 0/96 [00:00\n", + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n", + "Weight decay: 0.0\n", + "Max grad norm: None\n", + "Val dataloader: \n", + "Monitor: None\n", + "Monitor criterion: max\n", + "Epochs: 50\n", + "Patience: None\n", + "\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "fff16d5c438948ef9ac53d0e411a53ae", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Epoch 0 / 50: 0%| | 0/96 [00:00\n", + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n", + "Weight decay: 0.0\n", + "Max grad norm: None\n", + "Val dataloader: \n", + "Monitor: None\n", + "Monitor criterion: max\n", + "Epochs: 50\n", + "Patience: None\n", + "\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "1b216ba4894d45c9a37b9611bd0e204e", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Epoch 0 / 50: 0%| | 0/96 [00:00\n", + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n", + "Weight decay: 0.0\n", + "Max grad norm: None\n", + "Val dataloader: \n", + "Monitor: None\n", + "Monitor criterion: max\n", + "Epochs: 50\n", + "Patience: None\n", + "\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "6f539c4861eb42e5bb2bd0aa818904ec", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Epoch 0 / 50: 0%| | 0/96 [00:00\n", + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n", + "Weight decay: 0.0\n", + "Max grad norm: None\n", + "Val dataloader: \n", + "Monitor: None\n", + "Monitor criterion: max\n", + "Epochs: 50\n", + "Patience: None\n", + "\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "440ce3e2e2fd4d5c9a5307d02406d9a7", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Epoch 0 / 50: 0%| | 0/96 [00:00" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import torch\n", + "import pandas as pd\n", + "\n", + "from pyhealth.datasets import split_by_sample, get_dataloader\n", + "from pyhealth.trainer import Trainer\n", + "\n", + "# \u2500\u2500 Auto-detect device \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n", + "DEVICE = \"cpu\"\n", + "if torch.cuda.is_available():\n", + " DEVICE = \"cuda\"\n", + "elif torch.backends.mps.is_available():\n", + " DEVICE = \"mps\"\n", + "\n", + "print(f\"Using device: {DEVICE}\")\n", + "\n", + "METRICS = [\"accuracy\", \"f1_macro\", \"balanced_accuracy\"]\n", + "EPOCHS = 50\n", + "BATCH_SIZE = 32\n", + "SEED = 42\n", + "\n", + "torch.manual_seed(SEED)\n" + ] + }, + { + "cell_type": "markdown", + "id": "2e5055de", + "metadata": { + "id": "2e5055de" + }, + "source": [ + "Load Models" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "74c61a69", + "metadata": { + "id": "74c61a69" + }, + "outputs": [], + "source": [ + "from typing import Dict, List, Optional\n", + "import torch\n", + "import torch.nn as nn\n", + "import torch.nn.functional as F\n", + "from pyhealth.datasets import SampleDataset\n", + "from pyhealth.models.base_model import BaseModel\n", + "\n", + "# \u2500\u2500 Swap ACTIVE_CONFIG to switch between the four variants \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n", + "CONFIGS = {\n", + " \"v1_baseline\": {\n", + " \"num_layers\": 8,\n", + " \"kernel_sizes\": None, # None = all-3 kernels\n", + " \"norm_type\": \"batch\",\n", + " },\n", + " \"v2_fewer_layers\": {\n", + " \"num_layers\": 4,\n", + " \"kernel_sizes\": None,\n", + " \"norm_type\": \"batch\",\n", + " },\n", + " \"v3_mixed_kernels\": {\n", + " \"num_layers\": 4,\n", + " \"kernel_sizes\": [1, 3, 5, 3],\n", + " \"norm_type\": \"batch\",\n", + " },\n", + " \"v4_instance_norm\": {\n", + " \"num_layers\": 4,\n", + " \"kernel_sizes\": [1, 3, 5, 3],\n", + " \"norm_type\": \"instance\",\n", + " },\n", + "}\n", + "\n", + "ACTIVE_CONFIG = \"v1_baseline\"\n", + "\n", + "\n", + "def _make_norm(norm_type: str, num_channels: int) -> nn.Module:\n", + " if norm_type == \"batch\":\n", + " return nn.BatchNorm2d(num_channels)\n", + " if norm_type == \"instance\":\n", + " return nn.InstanceNorm2d(num_channels)\n", + " raise ValueError(f\"Unknown norm_type: {norm_type!r}\")\n", + "\n", + "\n", + "class GenericCNN(BaseModel):\n", + " def __init__(\n", + " self,\n", + " dataset: SampleDataset,\n", + " init_channels: int = 32,\n", + " classifier_hidden_dim: int = 128,\n", + " dropout: float = 0.5,\n", + " config_name: str = ACTIVE_CONFIG,\n", + " **kwargs,\n", + " ) -> None:\n", + " super(GenericCNN, self).__init__(dataset=dataset)\n", + "\n", + " cfg = CONFIGS[config_name]\n", + " num_layers: int = cfg[\"num_layers\"]\n", + " kernel_sizes: Optional[List[int]] = cfg[\"kernel_sizes\"]\n", + " norm_type: str = cfg[\"norm_type\"]\n", + "\n", + " # Resolve kernel sizes: explicit list or all-3s\n", + " if kernel_sizes is None:\n", + " kernel_sizes = [3] * num_layers\n", + " assert len(kernel_sizes) == num_layers, (\n", + " f\"kernel_sizes length {len(kernel_sizes)} must match num_layers {num_layers}\"\n", + " )\n", + "\n", + " self.init_channels = init_channels\n", + " self.classifier_hidden_dim = classifier_hidden_dim\n", + "\n", + " # Build convolutional blocks dynamically\n", + " # Channel widening: doubles every block, capped at init_channels * 8\n", + " # (fast for 4 layers, gradual for 8 layers \u2014 driven purely by num_layers)\n", + " blocks: List[nn.Module] = []\n", + " in_ch = 1\n", + " for i, k in enumerate(kernel_sizes):\n", + " # For num_layers=4 channels go 1\u2192C\u21922C\u21924C\u21928C (fast widening)\n", + " # For num_layers=8 channels go 1\u2192C\u2192C\u21922C\u21922C\u21924C\u21924C\u21928C\u21928C (gradual)\n", + " out_ch = init_channels * (2 ** (i * 4 // num_layers))\n", + "\n", + " pool = (\n", + " nn.AdaptiveAvgPool2d((1, 1))\n", + " if i == num_layers - 1\n", + " else nn.MaxPool2d(kernel_size=2, stride=2)\n", + " )\n", + " blocks.append(nn.Sequential(\n", + " nn.Conv2d(in_ch, out_ch, kernel_size=k, stride=1, padding=k // 2),\n", + " _make_norm(norm_type, out_ch),\n", + " nn.LeakyReLU(inplace=True),\n", + " pool,\n", + " ))\n", + " in_ch = out_ch\n", + "\n", + " self.blocks = nn.ModuleList(blocks)\n", + " final_channels = in_ch\n", + "\n", + " # Classifier Head\n", + " output_size = self.get_output_size()\n", + " self.classifier = nn.Sequential(\n", + " nn.Linear(final_channels, classifier_hidden_dim),\n", + " nn.LeakyReLU(inplace=True),\n", + " nn.Dropout(p=dropout),\n", + " nn.Linear(classifier_hidden_dim, output_size),\n", + " )\n", + "\n", + " def forward(self, **kwargs) -> Dict[str, torch.Tensor]:\n", + " x = kwargs[self.feature_keys[0]].to(self.device)\n", + " labels = kwargs[self.label_keys[0]].to(self.device)\n", + "\n", + " for block in self.blocks:\n", + " x = block(x)\n", + "\n", + " emb = torch.flatten(x, 1)\n", + " logits = self.classifier(emb)\n", + " loss = self.get_loss_function()(logits, labels)\n", + " y_prob = self.prepare_y_prob(logits)\n", + "\n", + " return {\n", + " \"loss\": loss,\n", + " \"y_prob\": y_prob,\n", + " \"y_true\": labels,\n", + " \"logit\": logits,\n", + " }" + ] + }, + { + "cell_type": "markdown", + "id": "md-3", + "metadata": { + "id": "md-3" + }, + "source": [ + "## 2. Load Dataset\n", + "\n", + "Uses the `AlzheimersDataset` PyHealth-compatible wrapper around `Falah/Alzheimer_MRI` (4-class severity classification: NonDemented, VeryMildDemented, MildDemented, ModerateDemented).\n", + "\n", + "The dataset class auto-downloads from HuggingFace and saves a `alzheimers-metadata.csv` for PyHealth's BaseDataset to consume.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "code-4", + "metadata": { + "id": "code-4" + }, + "outputs": [], + "source": [ + "from typing import Any, Dict, List\n", + "from pyhealth.tasks.base_task import BaseTask\n", + "\n", + "\n", + "class AlzheimersClassification(BaseTask):\n", + " \"\"\"Task for classifying Alzheimer's disease from brain images.\"\"\"\n", + "\n", + " task_name: str = \"AlzheimersClassification\"\n", + " input_schema: Dict = {\"image\": (\"image\", {\"mode\": \"L\", \"image_size\": 128})}\n", + " output_schema: Dict[str, str] = {\"label\": \"multiclass\"}\n", + "\n", + " def __call__(self, patient: Any) -> List[Dict[str, Any]]:\n", + " events = patient.get_events(event_type=\"alzheimers\")\n", + " assert len(events) == 1, f\"Expected 1 image, got {len(events)}\"\n", + " event = events[0]\n", + " return [{\"image\": event.path, \"label\": event.label}]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "e84f74f0", + "metadata": { + "id": "e84f74f0" + }, + "outputs": [], + "source": [ + "import logging\n", + "import os\n", + "from pathlib import Path\n", + "from typing import Optional\n", + "\n", + "import pandas as pd\n", + "from datasets import load_dataset\n", + "from pyhealth.datasets.base_dataset import BaseDataset\n", + "\n", + "logger = logging.getLogger(__name__)\n", + "\n", + "\n", + "class AlzheimersDataset(BaseDataset):\n", + " \"\"\"PyHealth-compatible Alzheimer's dataset (auto-download + process).\"\"\"\n", + "\n", + " def __init__(\n", + " self,\n", + " root: str,\n", + " dataset_name: Optional[str] = None,\n", + " config_path: Optional[str] = None,\n", + " cache_dir: Optional[str] = None,\n", + " num_workers: int = 1,\n", + " dev: bool = False,\n", + " hf_dataset_name: str = \"Falah/Alzheimer_MRI\",\n", + " ) -> None:\n", + " self.hf_dataset_name = hf_dataset_name\n", + "\n", + " try:\n", + " base_path = Path(__file__).parent\n", + " except NameError:\n", + " base_path = Path.cwd()\n", + "\n", + " if config_path is None:\n", + " config_path = base_path / \"configs\" / \"alzheimers.yaml\"\n", + "\n", + " metadata_path = os.path.join(root, \"alzheimers-metadata.csv\")\n", + "\n", + " if not os.path.exists(metadata_path):\n", + " self.prepare_metadata(root)\n", + "\n", + " super().__init__(\n", + " root=root,\n", + " tables=[\"alzheimers\"],\n", + " dataset_name=dataset_name or \"alzheimers\",\n", + " config_path=config_path,\n", + " cache_dir=cache_dir,\n", + " num_workers=num_workers,\n", + " dev=dev,\n", + " )\n", + "\n", + " def prepare_metadata(self, root: str) -> None:\n", + " os.makedirs(root, exist_ok=True)\n", + " image_dir = os.path.join(root, \"images\")\n", + " os.makedirs(image_dir, exist_ok=True)\n", + " metadata_path = os.path.join(root, \"alzheimers-metadata.csv\")\n", + "\n", + " ds = load_dataset(self.hf_dataset_name, split=\"train\")\n", + " records = []\n", + " for i, item in enumerate(ds):\n", + " img_path = os.path.join(image_dir, f\"{i}.png\")\n", + " if not os.path.isfile(img_path):\n", + " item[\"image\"].save(img_path)\n", + " records.append({\n", + " \"patient_id\": str(i),\n", + " \"path\": img_path,\n", + " \"label\": str(item[\"label\"]),\n", + " })\n", + " pd.DataFrame(records).to_csv(metadata_path, index=False)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "737a3fd3", + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 853 + }, + "id": "737a3fd3", + "outputId": "ed7aadf1-a41d-4a63-cb8f-57a8a803cae2" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Initializing alzheimers dataset from Downloads (dev mode: False)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Initializing alzheimers dataset from Downloads (dev mode: False)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "No cache_dir provided. Using default cache dir: /root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:No cache_dir provided. Using default cache dir: /root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting task AlzheimersClassification for alzheimers base dataset...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Setting task AlzheimersClassification for alzheimers base dataset...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Task cache paths: task_df=/root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/task_df.ld, samples=/root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/samples_cdbbc602-34e2-5a41-8643-4c76b08829f6.ld\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Task cache paths: task_df=/root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/task_df.ld, samples=/root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/tasks/AlzheimersClassification_7e906453-ea6b-5cc3-8506-3e00427d79ba/samples_cdbbc602-34e2-5a41-8643-4c76b08829f6.ld\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Applying task transformations on data with 1 workers...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Applying task transformations on data with 1 workers...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "No cached event dataframe found. Creating: /root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/global_event_df.parquet\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:No cached event dataframe found. Creating: /root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/global_event_df.parquet\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Scanning table: alzheimers from /content/Downloads/alzheimers-metadata.csv\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Scanning table: alzheimers from /content/Downloads/alzheimers-metadata.csv\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Caching event dataframe to /root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/global_event_df.parquet...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Caching event dataframe to /root/.cache/pyhealth/5e3d2e44-3165-596e-89d3-ed772a0ed564/global_event_df.parquet...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Detected Jupyter notebook environment, setting num_workers to 1\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Detected Jupyter notebook environment, setting num_workers to 1\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Single worker mode, processing sequentially\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Single worker mode, processing sequentially\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Worker 0 started processing 5120 patients. (Polars threads: 2)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.datasets.base_dataset:Worker 0 started processing 5120 patients. (Polars threads: 2)\n", + " 0%| | 0/5120 [00:00 dict:\n", + " \"\"\"Train a model and return its final validation metrics.\n", + "\n", + " Args:\n", + " model: An instantiated PyHealth model inheriting from BaseModel.\n", + " name: Human-readable label for the configuration.\n", + "\n", + " Returns:\n", + " Dict with keys 'name', 'accuracy', 'f1_macro', 'balanced_accuracy', 'loss', 'params'.\n", + " \"\"\"\n", + " print(f\"\\n{'='*60}\")\n", + " print(f\"Training: {name}\")\n", + " print(f\"{'='*60}\")\n", + "\n", + " trainer = Trainer(model=model, metrics=METRICS, device=DEVICE)\n", + "\n", + " t0 = time.perf_counter()\n", + " trainer.train(\n", + " train_dataloader=train_loader,\n", + " val_dataloader=val_loader,\n", + " epochs=EPOCHS,\n", + " optimizer_class=torch.optim.AdamW,\n", + " optimizer_params={\"lr\": 1e-4, \"weight_decay\": 1e-5},\n", + " )\n", + " train_time = time.perf_counter() - t0\n", + "\n", + " scores = trainer.evaluate(val_loader)\n", + " num_params = sum(p.numel() for p in model.parameters() if p.requires_grad)\n", + "\n", + " return {\n", + " \"name\": name,\n", + " \"accuracy\": scores.get(\"accuracy\", float(\"nan\")),\n", + " \"f1_macro\": scores.get(\"f1_macro\", float(\"nan\")),\n", + " \"balanced_accuracy\": scores.get(\"balanced_accuracy\", float(\"nan\")),\n", + " \"loss\": scores.get(\"loss\", float(\"nan\")),\n", + " \"params\": num_params,\n", + " \"train_time_seconds\": round(train_time, 1),\n", + " }\n", + "\n", + "\n", + "# Collect all results in this list for the final summary\n", + "results = []\n" + ] + }, + { + "cell_type": "markdown", + "id": "md-7", + "metadata": { + "id": "md-7" + }, + "source": [ + "## 4. Experiments\n" + ] + }, + { + "cell_type": "markdown", + "id": "md-8", + "metadata": { + "id": "md-8" + }, + "source": [ + "### Experiment 1: Baseline (`init_channels=32`)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "code-9", + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000, + "referenced_widgets": [ + "4b8b6c76f6aa40f5ab5d519fcd6266f5", + "0df3ae76c7dc4063840f32ae437bd97f", + "f38d79fe282d48bbbe345ed239710a98", + "608c45c8370f42a0bf479fa2c774170a", + "ba3707faa71943e5b253f2675c784ea4", + "0ffd8f8ac01b42019917e053ef31b650", + "2b7e1d95ab304e568246e0bbb8d92380", + "ad5f9013007a499e9212c120db9e38a7", + "218c0dfae89b4e29860688baafd6f3ab", + "2bea2b0409f645e499b5e27bd16fe0b0", + "ba74df70369849878f6e93e4e7049782", + "4961a072b68544cc82a2b3412f2ad01f", + "1868ccc202014a94a72f881e088c685e", + "a2406344cd2a4822a0b0db47bea8b2cf", + "bf920a409b194b6c8de271863bbe61a0", + "f7d5de5e7c884323bbd5b94813cb2ff7", + 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3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(16, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (1): Sequential(\n", + " (0): Conv2d(16, 16, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(16, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (2): Sequential(\n", + " (0): Conv2d(16, 32, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(32, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (3): Sequential(\n", + " (0): Conv2d(32, 32, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(32, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (4): Sequential(\n", + " (0): Conv2d(32, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (5): Sequential(\n", + " (0): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (6): Sequential(\n", + " (0): Conv2d(64, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (7): Sequential(\n", + " (0): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): AdaptiveAvgPool2d(output_size=(1, 1))\n", + " )\n", + " )\n", + " (classifier): Sequential(\n", + " (0): Linear(in_features=128, out_features=128, bias=True)\n", + " (1): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (2): Dropout(p=0.5, inplace=False)\n", + " (3): Linear(in_features=128, out_features=4, bias=True)\n", + " )\n", + ")\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:GenericCNN(\n", + " (blocks): ModuleList(\n", + " (0): Sequential(\n", + " (0): Conv2d(1, 16, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(16, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (1): Sequential(\n", + " (0): Conv2d(16, 16, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(16, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (2): Sequential(\n", + " (0): Conv2d(16, 32, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(32, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (3): Sequential(\n", + " (0): Conv2d(32, 32, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(32, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (4): Sequential(\n", + " (0): Conv2d(32, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (5): Sequential(\n", + " (0): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (6): Sequential(\n", + " (0): Conv2d(64, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)\n", + " )\n", + " (7): Sequential(\n", + " (0): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))\n", + " (1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n", + " (2): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (3): AdaptiveAvgPool2d(output_size=(1, 1))\n", + " )\n", + " )\n", + " (classifier): Sequential(\n", + " (0): Linear(in_features=128, out_features=128, bias=True)\n", + " (1): LeakyReLU(negative_slope=0.01, inplace=True)\n", + " (2): Dropout(p=0.5, inplace=False)\n", + " (3): Linear(in_features=128, out_features=4, bias=True)\n", + " )\n", + ")\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Metrics: ['accuracy', 'f1_macro', 'balanced_accuracy']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:Metrics: ['accuracy', 'f1_macro', 'balanced_accuracy']\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Device: cuda\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:Device: cuda\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Training:\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:Training:\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Batch size: 32\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:Batch size: 32\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Optimizer: \n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:Optimizer: \n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:pyhealth.trainer:Optimizer params: {'lr': 0.0001, 'weight_decay': 1e-05}\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Weight decay: 0.0\n" + ] + }, + { + "name": "stderr", + "output_type": 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AlzheimerCNNNormVariant, + PatchEmbedding, +) \ No newline at end of file diff --git a/pyhealth/models/alzheimer_cnn.py b/pyhealth/models/alzheimer_cnn.py new file mode 100644 index 000000000..7668b0052 --- /dev/null +++ b/pyhealth/models/alzheimer_cnn.py @@ -0,0 +1,442 @@ +from typing import Dict, List, Optional + +import torch +import torch.nn as nn +import torch.nn.functional as F + +from pyhealth.datasets import SampleDataset +from pyhealth.models.base_model import BaseModel + + +class AlzheimerCNN(BaseModel): + """AlzheimerCNN model + + This model uses a CNN architecture to classify MRI brain scans for Alzheimers Disease + + The model expects one input: + - 2D MRI Brainscan: shape (batch, width, height) + + Args: + dataset: the dataset to train the model + init_channels: inital # of channels. Default is 32 + classifier_hidden_dim: # of hidden dimension. Default is 128 + dropout: the dropout rate. Default is 0.5 + """ + + def __init__( + self, + dataset: SampleDataset, + init_channels: int = 32, + classifier_hidden_dim: int = 128, + dropout: float = 0.5, + **kwargs, + ) -> None: + super(AlzheimerCNN, self).__init__(dataset=dataset) + + self.init_channels = init_channels + self.classifier_hidden_dim = classifier_hidden_dim + + # CNN Blocks + # 2D convolution, 2D Instance Normalization, LeakyReLU activation function, 2D Max Pooling + self.block1 = nn.Sequential( + nn.Conv2d(1, init_channels, kernel_size=1, stride=1, padding=1), + nn.InstanceNorm2d(init_channels), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), + ) + self.block2 = nn.Sequential( + nn.Conv2d( + init_channels, init_channels * 2, kernel_size=3, stride=1, padding=1 + ), + nn.InstanceNorm2d(init_channels * 2), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), + ) + self.block3 = nn.Sequential( + nn.Conv2d( + init_channels * 2, init_channels * 4, kernel_size=5, stride=1, padding=1 + ), + nn.InstanceNorm2d(init_channels * 4), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), + ) + + # Uses Average Pooling rather than MaxPool + self.block4 = nn.Sequential( + nn.Conv2d( + init_channels * 4, init_channels * 8, kernel_size=3, stride=1, padding=1 + ), + nn.InstanceNorm2d(init_channels * 8), + nn.LeakyReLU(inplace=True), + nn.AdaptiveAvgPool2d((1, 1)), + ) + + # ── Classifier: FC(8C → hidden_dim) → LeakyReLU → Dropout → FC(hidden_dim → output) ─ + output_size = self.get_output_size() + # Classifier Layer using: + # Linear layer w/ our input hidden_dim + # LeakyReLU activation function + # Dropout using input arg + # Final linear layer determing output (size 4) + self.classifier = nn.Sequential( + nn.Linear(init_channels * 8, classifier_hidden_dim), + nn.LeakyReLU(inplace=True), + nn.Dropout(p=dropout), + nn.Linear(classifier_hidden_dim, output_size), + ) + + def forward(self, **kwargs) -> Dict[str, torch.Tensor]: + # Extract inputs + x = kwargs[self.feature_keys[0]].to(self.device) + labels = kwargs[self.label_keys[0]].to(self.device) + + # CNN Architecture + x = self.block1(x) + x = self.block2(x) + x = self.block3(x) + x = self.block4(x) + + # Flatten: (B, 8C, 1, 1) → (B, 8C) + # Input: (Batch Size, 8 * init_channels, 1, 1) + # Output: (Batch Size, 8 * init_channels) + emb = torch.flatten(x, 1) + + # Classifier Layer + logits = self.classifier(emb) + + # Loss + metrics via BaseModel helpers + loss = self.get_loss_function()(logits, labels) + y_prob = self.prepare_y_prob(logits) + + # Return everything required by BaseModel + return { + "loss": loss, + "y_prob": y_prob, + "y_true": labels, + "logit": logits, + } + + +# Ablation Number One where we use group normalization +class AlzheimerCNNNormVariant(BaseModel): + + def __init__( + self, + dataset, + norm_type: str = "instance", + num_groups: int = 8, + init_channels: int = 32, + classifier_hidden_dim: int = 128, + dropout: float = 0.5, + **kwargs, + ) -> None: + super(AlzheimerCNNNormVariant, self).__init__(dataset=dataset) + + if norm_type not in ("instance", "group", "layer"): + raise ValueError( + f"norm_type must be 'instance', 'group', or 'layer', got '{norm_type}'" + ) + + self.norm_type = norm_type + self.num_groups = num_groups + self.init_channels = init_channels + + def _get_norm(channels: int) -> nn.Module: + """Build the appropriate normalization layer for a given channel count. + + Args: + channels: Number of feature map channels to normalise. + + Returns: + An nn.Module normalisation layer. + """ + if norm_type == "instance": + return nn.InstanceNorm2d(channels) + elif norm_type == "group": + # Ensure num_groups evenly divides channels + groups = min(num_groups, channels) + while channels % groups != 0: + groups //= 2 + return nn.GroupNorm(groups, channels) + else: + # layer norm: GroupNorm(1, C) is equivalent to + # LayerNorm over the channel dimension + return nn.GroupNorm(1, channels) + + self.block1 = nn.Sequential( + nn.Conv2d(1, init_channels, kernel_size=1, stride=1, padding=1), + _get_norm(init_channels), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), + ) + self.block2 = nn.Sequential( + nn.Conv2d( + init_channels, init_channels * 2, kernel_size=3, stride=1, padding=1 + ), + _get_norm(init_channels * 2), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), + ) + self.block3 = nn.Sequential( + nn.Conv2d(init_channels * 2, init_channels * 4, kernel_size=5, stride=1, padding=1), + _get_norm(init_channels * 4), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), + ) + self.block4 = nn.Sequential( + nn.Conv2d( + init_channels * 4, init_channels * 8, kernel_size=3, stride=1, padding=1 + ), + _get_norm(init_channels * 8), + nn.LeakyReLU(inplace=True), + nn.AdaptiveAvgPool2d((1, 1)), + ) + output_size = self.get_output_size() + self.classifier = nn.Sequential( + nn.Linear(init_channels * 8, classifier_hidden_dim), + nn.LeakyReLU(inplace=True), + nn.Dropout(p=dropout), + nn.Linear(classifier_hidden_dim, output_size), + ) + + def forward(self, **kwargs) -> Dict[str, torch.Tensor]: + # Input and Device Management + x = kwargs[self.feature_keys[0]].to(self.device) + labels = kwargs[self.label_keys[0]].to(self.device) + + # Convolutions + x = self.block1(x) + x = self.block2(x) + x = self.block3(x) + x = self.block4(x) + + # Flatten + emb = torch.flatten(x, 1) + + logits = self.classifier(emb) + + # Metrics + loss = self.get_loss_function()(logits, labels) + y_prob = self.prepare_y_prob(logits) + + return { + "loss": loss, + "y_prob": y_prob, + "y_true": labels, + "logit": logits, + } + + +# Ablation 2, where we use a vision transformer to try and capture global traits as well +class PatchEmbedding(nn.Module): + """Converts a CNN feature map into a sequence of patch tokens. + + Splits a (B, C, H, W) feature map into non-overlapping patches of size + patch_size x patch_size, projects each flattened patch to embed_dim via + a linear layer, prepends a learnable (CLS) token, and adds learnable + positional embeddings. + + Args: + in_channels: Number of channels in the input feature map. + patch_size: Height and width of each square patch. + embed_dim: Dimensionality of the projected patch tokens. + feature_map_size: Spatial height (and width) of the input feature map. + Assumed to be square. + """ + + def __init__( + self, + in_channels: int, + patch_size: int, + embed_dim: int, + feature_map_size: int, + ) -> None: + super().__init__() + self.patch_size = patch_size + num_patches = (feature_map_size // patch_size) ** 2 + + # Each patch is flattened to (C * patch_size * patch_size) dims + patch_dim = in_channels * patch_size * patch_size + self.projection = nn.Linear(patch_dim, embed_dim) + + # Learnable (CLS) token: one per batch item + self.cls_token = nn.Parameter(torch.zeros(1, 1, embed_dim)) + + # Learnable positional embeddings: one per patch + one for (CLS) + self.pos_embedding = nn.Parameter(torch.zeros(1, num_patches + 1, embed_dim)) + + def forward(self, x: torch.Tensor) -> torch.Tensor: + """Tokenize a CNN feature map into a patch sequence with CLS token. + + Args: + x: Feature map of shape (B, C, H, W). + + Returns: + Token sequence of shape (B, num_patches + 1, embed_dim). + """ + B, C, H, W = x.shape + p = self.patch_size + + # (B, C, H, W) → (B, C, H//p, W//p, p, p) + x = x.unfold(2, p, p).unfold(3, p, p) + # (B, C, num_patches, p*p) + x = x.contiguous().view(B, C, -1, p * p) + # (B, num_patches, C, p*p) + x = x.permute(0, 2, 1, 3) + # (B, num_patches, C*p*p) + x = x.contiguous().view(B, -1, C * p * p) + + # Project each patch to embed_dim + x = self.projection(x) # (B, num_patches, embed_dim) + + # Prepend (CLS) token and add positional embeddings + cls_tokens = self.cls_token.expand(B, -1, -1) + x = torch.cat([cls_tokens, x], dim=1) # (B, num_patches + 1, embed_dim) + x = x + self.pos_embedding + + return x + + +class AlzheimerCNNViT(BaseModel): + """CNN + Vision Transformer hybrid for Alzheimer's disease classification. + + Combines a two-block CNN backbone for local feature extraction with a + Transformer encoder for global context modelling over patch tokens. The + CNN reduces the 128x128 input to a 32x32 feature map, which is then split + into 4x4 patches and fed to the Transformer. Classification is performed + on the output [CLS] token. + + Architecture:: + + Input (B, 1, 128, 128) + block1: Conv2d, InstanceNorm2d, LeakyReLU, MaxPool: Size (B, C, 64, 64) + block2: Conv2d, InstanceNorm2d, LeakyReLU, MaxPool: Size (B, 2C, 32, 32) + PatchEmbedding (patch_size=4) -> (B, 65, embed_dim) + TransformerEncoder (num_transformer_layers) + (CLS) token, Linear, LeakyReLU, Dropout, Linear, logits + + Args: + dataset: The dataset to train the model. Must expose input_schema, + output_schema, and output_processors to satisfy BaseModel. + init_channels: Base number of CNN filters. Blocks use C and 2C + channels. Default is 32. + embed_dim: Dimensionality of Transformer patch token embeddings. + Default is 128. + num_heads: Number of attention heads in the Transformer encoder. + Must evenly divide embed_dim. Default is 4. + num_transformer_layers: Number of Transformer encoder layers. + Default is 4. + classifier_hidden_dim: Number of units in the hidden FC layer of + the classifier head. Default is 128. + dropout: Dropout probability applied in the Transformer and before + the output linear layer. Default is 0.1. + """ + + def __init__( + self, + dataset, + init_channels: int = 32, + embed_dim: int = 128, + num_heads: int = 4, + num_transformer_layers: int = 4, + classifier_hidden_dim: int = 128, + dropout: float = 0.1, + **kwargs, + ) -> None: + super(AlzheimerCNNViT, self).__init__(dataset=dataset) + + self.init_channels = init_channels + self.embed_dim = embed_dim + + # CNN Layer: local feature extraction + # Two pooling stages reduce 128×128 -> 32×32 + self.block1 = nn.Sequential( + nn.Conv2d(1, init_channels, kernel_size=1, stride=1, padding=1), + nn.InstanceNorm2d(init_channels), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), # 128 → 64 + ) + self.block2 = nn.Sequential( + nn.Conv2d( + init_channels, init_channels * 2, kernel_size=3, stride=1, padding=1 + ), + nn.InstanceNorm2d(init_channels * 2), + nn.LeakyReLU(inplace=True), + nn.MaxPool2d(kernel_size=2, stride=2), # 64 → 32 + ) + + # Patch embedding: 32×32 feature map -> 64 patch tokens + CLS + # patch_size=4 gives (32/4)^2 = 64 patches + self.patch_embed = PatchEmbedding( + in_channels=init_channels * 2, + patch_size=4, + embed_dim=embed_dim, + feature_map_size=32, + ) + + # Transformer encoder: global context over patch sequence + encoder_layer = nn.TransformerEncoderLayer( + d_model=embed_dim, + nhead=num_heads, + dim_feedforward=embed_dim * 4, + dropout=dropout, + batch_first=True, + ) + self.transformer = nn.TransformerEncoder( + encoder_layer, + num_layers=num_transformer_layers, + ) + + # Classifier head: operates on the (CLS) token output + output_size = self.get_output_size() + self.classifier = nn.Sequential( + nn.Linear(embed_dim, classifier_hidden_dim), + nn.LeakyReLU(inplace=True), + nn.Dropout(p=0.5), + nn.Linear(classifier_hidden_dim, output_size), + ) + + def forward(self, **kwargs) -> Dict[str, torch.Tensor]: + """Forward propagation. + + Args: + **kwargs: Keys match the dataset's input_schema and output_schema. + Expects an image tensor of shape (B, 1, H, W) and an integer + label per sample. + + Returns: + A dict with keys: + - loss: scalar cross-entropy loss tensor. + - y_prob: predicted probabilities, shape (B, num_classes). + - y_true: ground-truth label tensor. + - logit: raw logits, shape (B, num_classes). + """ + # Extract inputs + x = kwargs[self.feature_keys[0]].to(self.device) + labels = kwargs[self.label_keys[0]].to(self.device) + + # CNN local feature extraction + x = self.block1(x) # (B, C, 64, 64) + x = self.block2(x) # (B, 2C, 32, 32) + + # Patch tokenization + x = self.patch_embed(x) # (B, 65, embed_dim) + + # Transformer global context modelling + x = self.transformer(x) # (B, 65, embed_dim) + + # Extract (CLS) token (index 0) for classification + cls_output = x[:, 0, :] # (B, embed_dim) + + # Classifier Layer + logits = self.classifier(cls_output) # (B, num_classes) + + loss = self.get_loss_function()(logits, labels) + y_prob = self.prepare_y_prob(logits) + + return { + "loss": loss, + "y_prob": y_prob, + "y_true": labels, + "logit": logits, + } diff --git a/pyproject.toml b/pyproject.toml index 98f88d47b..ea44e3342 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,6 +45,9 @@ dependencies = [ "more-itertools~=10.8.0", "einops>=0.8.0", "linear-attention-transformer>=0.19.1", + "datasets (>=4.8.4,<5.0.0)", + "ipywidgets (>=8.1.8,<9.0.0)", + "jupyter (>=1.1.1,<2.0.0)", ] license = "BSD-3-Clause" license-files = ["LICENSE.md"] @@ -176,3 +179,14 @@ export = "pixi workspace export conda-environment" args = [{ "arg" = "args", "default" = "" }] env = { CLASS = "zensols.relpo.cli", PYTHONPATH = "src" } cmd = "\npython -c \"from $CLASS import main;print('_'*80);main('{{args}}'.split())\"" + + +[[tool.poetry.source]] +name = "pytorch" +url = "https://download.pytorch.org/whl/cu121" +priority = "primary" + +[dependency-groups] +dev = [ + "ipykernel (>=7.2.0,<8.0.0)" +] diff --git a/tests/core/test_alzheimer_cnn.py b/tests/core/test_alzheimer_cnn.py new file mode 100644 index 000000000..378b3fbeb --- /dev/null +++ b/tests/core/test_alzheimer_cnn.py @@ -0,0 +1,319 @@ +"""Unit tests for AlzheimerCNN, AlzheimerCNNViT, and AlzheimerCNNNormVariant. + + +Coverage per model: + - Instantiation with default and custom hyperparameters + - Forward pass produces the expected output dictionary + - Output shapes match (batch_size, num_classes) + - Loss is a scalar tensor with valid gradient + - Backward pass populates gradients on all trainable parameters + - Probability outputs sum to 1.0 across the class dimension (softmax) +""" + +import shutil +import tempfile +import unittest +from pathlib import Path + +import torch +from torch.utils.data import Dataset + +from pyhealth.models import ( + AlzheimerCNN, + AlzheimerCNNNormVariant, + AlzheimerCNNViT, +) + + +# ───────────────────────────────────────────────────────────────────────────── +# Synthetic dataset stand-in +# ───────────────────────────────────────────────────────────────────────────── + +class _SyntheticOutputProcessor: + """Minimal stand-in for PyHealth's output processor.""" + + def __init__(self, num_classes: int) -> None: + self.num_classes = num_classes + + def size(self) -> int: + return self.num_classes + + +class _SyntheticAlzheimerDataset(Dataset): + """Synthetic dataset with the schema attributes BaseModel requires. + + Generates random (1, H, W) image tensors and integer labels in [0, num_classes). + Used only for unit testing — no real medical data involved. + """ + + input_schema = {"image": "image"} + output_schema = {"label": "multiclass"} + + def __init__( + self, + num_samples: int = 4, + image_size: int = 128, + num_classes: int = 4, + ) -> None: + self.num_samples = num_samples + self.image_size = image_size + self.num_classes = num_classes + self.output_processors = { + "label": _SyntheticOutputProcessor(num_classes) + } + # Pre-generate to ensure reproducibility within a test + torch.manual_seed(0) + self._images = torch.randn(num_samples, 1, image_size, image_size) + self._labels = torch.randint(0, num_classes, (num_samples,)) + + def __len__(self) -> int: + return self.num_samples + + def __getitem__(self, idx: int) -> dict: + return { + "image": self._images[idx], + "label": int(self._labels[idx].item()), + } + + +def _make_batch( + batch_size: int = 2, + image_size: int = 128, + num_classes: int = 4, +) -> dict: + """Create a synthetic batch dict of the form expected by the models' forward pass.""" + torch.manual_seed(42) + return { + "image": torch.randn(batch_size, 1, image_size, image_size), + "label": torch.randint(0, num_classes, (batch_size,)), + } + + +# ───────────────────────────────────────────────────────────────────────────── +# Test cases +# ───────────────────────────────────────────────────────────────────────────── + +class TestAlzheimerCNN(unittest.TestCase): + """Tests for the base AlzheimerCNN model.""" + + @classmethod + def setUpClass(cls) -> None: + cls.tmp_dir = Path(tempfile.mkdtemp(prefix="alzheimer_cnn_test_")) + cls.dataset = _SyntheticAlzheimerDataset(num_samples=4, num_classes=4) + cls.batch_size = 2 + cls.num_classes = 4 + + @classmethod + def tearDownClass(cls) -> None: + if cls.tmp_dir.exists(): + shutil.rmtree(cls.tmp_dir) + + def test_instantiation_with_defaults(self) -> None: + """Model instantiates with default hyperparameters.""" + model = AlzheimerCNN(dataset=self.dataset) + self.assertIsInstance(model, AlzheimerCNN) + self.assertEqual(model.init_channels, 32) + + def test_instantiation_with_custom_hyperparameters(self) -> None: + """Model accepts custom init_channels, classifier_hidden_dim, and dropout.""" + model = AlzheimerCNN( + dataset=self.dataset, + init_channels=16, + classifier_hidden_dim=64, + dropout=0.3, + ) + self.assertEqual(model.init_channels, 16) + self.assertEqual(model.classifier_hidden_dim, 64) + + def test_forward_returns_expected_keys(self) -> None: + """Forward pass returns dict with loss, y_prob, y_true, and logit.""" + model = AlzheimerCNN(dataset=self.dataset) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertIn("loss", output) + self.assertIn("y_prob", output) + self.assertIn("y_true", output) + self.assertIn("logit", output) + + def test_forward_output_shapes(self) -> None: + """Logits and probabilities have shape (batch_size, num_classes).""" + model = AlzheimerCNN(dataset=self.dataset) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertEqual(output["logit"].shape, (self.batch_size, self.num_classes)) + self.assertEqual(output["y_prob"].shape, (self.batch_size, self.num_classes)) + + def test_softmax_probabilities_sum_to_one(self) -> None: + """Predicted probabilities sum to 1.0 across the class dimension.""" + model = AlzheimerCNN(dataset=self.dataset) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + prob_sums = output["y_prob"].sum(dim=1) + self.assertTrue(torch.allclose(prob_sums, torch.ones(self.batch_size), atol=1e-5)) + + def test_loss_is_scalar(self) -> None: + """Loss is a scalar tensor.""" + model = AlzheimerCNN(dataset=self.dataset) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertEqual(output["loss"].ndim, 0) + + def test_gradient_flow(self) -> None: + """Backward pass populates gradients on all trainable parameters.""" + model = AlzheimerCNN(dataset=self.dataset) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + output["loss"].backward() + for name, param in model.named_parameters(): + if name == "_dummy_param": + continue + if param.requires_grad: + self.assertIsNotNone(param.grad, f"No gradient on {name}") + self.assertFalse( + torch.isnan(param.grad).any(), + f"NaN in gradient on {name}", + ) + + +class TestAlzheimerCNNViT(unittest.TestCase): + """Tests for the CNN + Vision Transformer hybrid model.""" + + @classmethod + def setUpClass(cls) -> None: + cls.tmp_dir = Path(tempfile.mkdtemp(prefix="alzheimer_cnn_vit_test_")) + cls.dataset = _SyntheticAlzheimerDataset(num_samples=4, num_classes=4) + cls.batch_size = 2 + cls.num_classes = 4 + + @classmethod + def tearDownClass(cls) -> None: + if cls.tmp_dir.exists(): + shutil.rmtree(cls.tmp_dir) + + def test_instantiation_with_defaults(self) -> None: + """Model instantiates with default hyperparameters.""" + model = AlzheimerCNNViT(dataset=self.dataset) + self.assertIsInstance(model, AlzheimerCNNViT) + self.assertEqual(model.embed_dim, 128) + + def test_instantiation_with_custom_hyperparameters(self) -> None: + """Model accepts custom embed_dim, num_heads, and num_transformer_layers.""" + model = AlzheimerCNNViT( + dataset=self.dataset, + embed_dim=64, + num_heads=2, + num_transformer_layers=2, + ) + self.assertEqual(model.embed_dim, 64) + + def test_forward_output_shapes(self) -> None: + """Logits and probabilities have shape (batch_size, num_classes).""" + model = AlzheimerCNNViT( + dataset=self.dataset, + embed_dim=64, + num_heads=2, + num_transformer_layers=2, + ) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertEqual(output["logit"].shape, (self.batch_size, self.num_classes)) + self.assertEqual(output["y_prob"].shape, (self.batch_size, self.num_classes)) + + def test_softmax_probabilities_sum_to_one(self) -> None: + """Predicted probabilities sum to 1.0 across the class dimension.""" + model = AlzheimerCNNViT( + dataset=self.dataset, + embed_dim=64, + num_heads=2, + num_transformer_layers=2, + ) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + prob_sums = output["y_prob"].sum(dim=1) + self.assertTrue(torch.allclose(prob_sums, torch.ones(self.batch_size), atol=1e-5)) + + def test_gradient_flow(self) -> None: + """Backward pass populates gradients on all trainable parameters.""" + model = AlzheimerCNNViT( + dataset=self.dataset, + embed_dim=64, + num_heads=2, + num_transformer_layers=2, + ) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + output["loss"].backward() + for name, param in model.named_parameters(): + if name == "_dummy_param": + continue + if param.requires_grad: + self.assertIsNotNone(param.grad, f"No gradient on {name}") + + +class TestAlzheimerCNNNormVariant(unittest.TestCase): + """Tests for the swappable-normalization variant.""" + + @classmethod + def setUpClass(cls) -> None: + cls.tmp_dir = Path(tempfile.mkdtemp(prefix="alzheimer_cnn_norm_test_")) + cls.dataset = _SyntheticAlzheimerDataset(num_samples=4, num_classes=4) + cls.batch_size = 2 + cls.num_classes = 4 + + @classmethod + def tearDownClass(cls) -> None: + if cls.tmp_dir.exists(): + shutil.rmtree(cls.tmp_dir) + + def test_instance_norm_variant(self) -> None: + """norm_type='instance' instantiates and runs forward pass.""" + model = AlzheimerCNNNormVariant(dataset=self.dataset, norm_type="instance") + self.assertEqual(model.norm_type, "instance") + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertEqual(output["logit"].shape, (self.batch_size, self.num_classes)) + + def test_group_norm_variant(self) -> None: + """norm_type='group' instantiates and runs forward pass.""" + model = AlzheimerCNNNormVariant( + dataset=self.dataset, norm_type="group", num_groups=8 + ) + self.assertEqual(model.norm_type, "group") + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertEqual(output["logit"].shape, (self.batch_size, self.num_classes)) + + def test_layer_norm_variant(self) -> None: + """norm_type='layer' instantiates and runs forward pass.""" + model = AlzheimerCNNNormVariant(dataset=self.dataset, norm_type="layer") + self.assertEqual(model.norm_type, "layer") + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + self.assertEqual(output["logit"].shape, (self.batch_size, self.num_classes)) + + def test_invalid_norm_type_raises(self) -> None: + """Invalid norm_type raises ValueError.""" + with self.assertRaises(ValueError): + AlzheimerCNNNormVariant(dataset=self.dataset, norm_type="batch") + + def test_gradient_flow_all_norm_types(self) -> None: + """Gradient flows correctly for all valid norm types.""" + for norm_type in ("instance", "group", "layer"): + with self.subTest(norm_type=norm_type): + model = AlzheimerCNNNormVariant( + dataset=self.dataset, norm_type=norm_type + ) + batch = _make_batch(self.batch_size, num_classes=self.num_classes) + output = model(**batch) + output["loss"].backward() + for name, param in model.named_parameters(): + if name == "_dummy_param": + continue + if param.requires_grad: + self.assertIsNotNone( + param.grad, f"No gradient on {name} ({norm_type})" + ) + + +if __name__ == "__main__": + unittest.main() \ No newline at end of file