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"https://localhost:8080/" + }, + "id": "vXTP8SRNijL0", + "outputId": "b0c2305b-0df1-457e-cb8f-0eaaafaf7471" + }, + "execution_count": 1, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m507.1/507.1 kB\u001b[0m \u001b[31m3.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", + "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m84.1/84.1 kB\u001b[0m \u001b[31m8.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", + "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m265.7/265.7 kB\u001b[0m \u001b[31m23.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", + "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m115.3/115.3 kB\u001b[0m \u001b[31m5.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", + "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m134.8/134.8 kB\u001b[0m \u001b[31m15.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", + "\u001b[?25h" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "# Standard library imports\n", + "import warnings\n", + "\n", + "# Third-party imports\n", + "import evaluate\n", + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "import pandas as pd\n", + "import torch\n", + "import torch.nn as nn\n", + "from datasets import load_dataset\n", + "from sklearn.metrics import ConfusionMatrixDisplay, confusion_matrix, f1_score\n", + "from torchvision.transforms import Compose, Normalize, RandomResizedCrop, ToTensor\n", + "from transformers import (\n", + " AutoImageProcessor,\n", + " AutoModelForImageClassification,\n", + " DefaultDataCollator,\n", + " Trainer,\n", + " TrainingArguments,\n", + " logging,\n", + " pipeline,\n", + ")\n", + "\n", + "# Disabling warnings\n", + "warnings.filterwarnings(\"ignore\")\n", + "logging.set_verbosity_error()" + ], + "metadata": { + "id": "3uWw49lFFyvj" + }, + "execution_count": 2, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "# Loading the MRI dataset" + ], + "metadata": { + "id": "D9UoPJYLjQ-M" + } + }, + { + "cell_type": "code", + "source": [ + "# Loading the dataset from Hugging Face Hub\n", + "mri_data = load_dataset(\"Falah/Alzheimer_MRI\", split=\"train\")" + ], + "metadata": { + "id": "e0MQT_O2GFcc", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 177, + "referenced_widgets": [ + "509f92bf7c1b48de89afe07c4d1793e0", + "bbe61f14e8484bad9b4b7ed6c474e2e5", + "954989698eee47139bab6b0987c9acaf", + "5a7b78ee14654aa7826989f542773fc7", + "43f1706083a34414a81e40a51bf9169e", + "d8a2e71bf7034292a09d81fd522c09ad", + "03443b943dcd47fc9171589fe4e283cc", + "ab5d3fcd036749e0ac55f1e91077ed8b", + "c2def0250e1a4b55b7c33ea07a2349cf", + "b5ca60d6c5a84e4a928e16930bfa6811", + "f50478f4353644b3b89a05aa853ce193", + "c4eba7439c3947c7a4d2cb5d0dfb6cbb", + "ce45554c21a54a50a52cba2bc3830df8", + 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"metadata": {} + }, + { + "output_type": "display_data", + "data": { + "text/plain": [ + "Downloading data: 0%| | 0.00/22.6M [00:00, ?B/s]" + ], + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 0, + "model_id": "c4eba7439c3947c7a4d2cb5d0dfb6cbb" + } + }, + "metadata": {} + }, + { + "output_type": "display_data", + "data": { + "text/plain": [ + "Downloading data: 0%| | 0.00/5.65M [00:00, ?B/s]" + ], + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 0, + "model_id": "309c95578629443cada4caca18d7815c" + } + }, + "metadata": {} + }, + { + "output_type": "display_data", + "data": { + "text/plain": [ + "Generating train split: 0%| | 0/5120 [00:00, ? examples/s]" + ], + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 0, + "model_id": "896f547c21ac4658bc120f2e61658c39" + } + }, + "metadata": {} + }, + { + "output_type": "display_data", + "data": { + "text/plain": [ + "Generating test split: 0%| | 0/1280 [00:00, ? examples/s]" + ], + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 0, + "model_id": "745b1cd43acf4ad481575ee749897802" + } + }, + "metadata": {} + } + ] + }, + { + "cell_type": "code", + "source": [ + "# Splitting the data into training and validation sets\n", + "mri_data_split = mri_data.train_test_split(\n", + " test_size=0.2,\n", + " stratify_by_column=\"label\",\n", + " seed=12345,\n", + ")\n", + "mri_data_split" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "Dyd7pfAcGLIb", + "outputId": "b7a247f2-0357-43da-a54b-4560387887ef" + }, + "execution_count": 4, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "DatasetDict({\n", + " train: Dataset({\n", + " features: ['image', 'label'],\n", + " num_rows: 4096\n", + " })\n", + " test: Dataset({\n", + " features: ['image', 'label'],\n", + " num_rows: 1024\n", + " })\n", + "})" + ] + }, + "metadata": {}, + "execution_count": 4 + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "# Data analysis" + ], + "metadata": { + "id": "1FPS6VONnKHT" + } + }, + { + "cell_type": "code", + "source": [ + "labels = mri_data_split[\"train\"].features[\"label\"].names\n", + "labels" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "yugFU2J7nKYs", + "outputId": "06f945f1-df5e-450b-cdea-75c4558f879d" + }, + "execution_count": 5, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "['Mild_Demented', 'Moderate_Demented', 'Non_Demented', 'Very_Mild_Demented']" + ] + }, + "metadata": {}, + "execution_count": 5 + } + ] + }, + { + "cell_type": "code", + "source": [ + "# Computing the numbers of examples for each class (train/validation)\n", + "class_counts_train = np.bincount(mri_data_split[\"train\"][\"label\"])\n", + "class_counts_valid = np.bincount(mri_data_split[\"test\"][\"label\"])\n", + "\n", + "# Creating a summary DataFrame\n", + "dataset_info = {\n", + " \"train\": class_counts_train,\n", + " \"test\": class_counts_valid\n", + "}\n", + "class_counts_info = pd.DataFrame(data=dataset_info, index=labels)\n", + "class_counts_info" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 174 + }, + "id": "bEouAIqVnKz3", + "outputId": "e8b79143-de3a-4949-fb86-b01a9b8393a3" + }, + "execution_count": 6, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + " train test\n", + "Mild_Demented 579 145\n", + "Moderate_Demented 39 10\n", + "Non_Demented 2053 513\n", + "Very_Mild_Demented 1425 356" + ], + "text/html": [ + "\n", + "
\n", + " | train | \n", + "test | \n", + "
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Mild_Demented | \n", + "579 | \n", + "145 | \n", + "
Moderate_Demented | \n", + "39 | \n", + "10 | \n", + "
Non_Demented | \n", + "2053 | \n", + "513 | \n", + "
Very_Mild_Demented | \n", + "1425 | \n", + "356 | \n", + "
Epoch | \n", + "Training Loss | \n", + "Validation Loss | \n", + "F1 | \n", + "
---|---|---|---|
1 | \n", + "1.121800 | \n", + "0.941877 | \n", + "0.574249 | \n", + "
2 | \n", + "0.940000 | \n", + "0.905402 | \n", + "0.602930 | \n", + "
3 | \n", + "0.912300 | \n", + "0.901887 | \n", + "0.526183 | \n", + "
4 | \n", + "0.862500 | \n", + "0.846535 | \n", + "0.602914 | \n", + "
5 | \n", + "0.810400 | \n", + "0.781023 | \n", + "0.631924 | \n", + "
6 | \n", + "0.724400 | \n", + "0.727819 | \n", + "0.703721 | \n", + "
7 | \n", + "0.697000 | \n", + "0.629985 | \n", + "0.748010 | \n", + "
8 | \n", + "0.586500 | \n", + "0.565929 | \n", + "0.766220 | \n", + "
9 | \n", + "0.519900 | \n", + "0.544534 | \n", + "0.772069 | \n", + "
10 | \n", + "0.473400 | \n", + "0.674992 | \n", + "0.718480 | \n", + "
11 | \n", + "0.439900 | \n", + "0.489264 | \n", + "0.827378 | \n", + "
12 | \n", + "0.381700 | \n", + "0.557753 | \n", + "0.784368 | \n", + "
13 | \n", + "0.331800 | \n", + "0.469930 | \n", + "0.822824 | \n", + "
14 | \n", + "0.309600 | \n", + "0.445963 | \n", + "0.839947 | \n", + "
15 | \n", + "0.278700 | \n", + "0.410541 | \n", + "0.839936 | \n", + "
16 | \n", + "0.251700 | \n", + "0.348793 | \n", + "0.857752 | \n", + "
17 | \n", + "0.234600 | \n", + "0.387677 | \n", + "0.877273 | \n", + "
18 | \n", + "0.228600 | \n", + "0.341952 | \n", + "0.857452 | \n", + "
19 | \n", + "0.191400 | \n", + "0.412256 | \n", + "0.868153 | \n", + "
20 | \n", + "0.184400 | \n", + "0.289442 | \n", + "0.891273 | \n", + "
21 | \n", + "0.173000 | \n", + "0.319741 | \n", + "0.888702 | \n", + "
22 | \n", + "0.168700 | \n", + "0.262622 | \n", + "0.907471 | \n", + "
23 | \n", + "0.160100 | \n", + "0.295084 | \n", + "0.906839 | \n", + "
24 | \n", + "0.146600 | \n", + "0.266578 | \n", + "0.904947 | \n", + "
25 | \n", + "0.146800 | \n", + "0.213564 | \n", + "0.910279 | \n", + "
26 | \n", + "0.122600 | \n", + "0.238661 | \n", + "0.912666 | \n", + "
27 | \n", + "0.118600 | \n", + "0.213083 | \n", + "0.927114 | \n", + "
28 | \n", + "0.095100 | \n", + "0.252022 | \n", + "0.912958 | \n", + "
29 | \n", + "0.104900 | \n", + "0.209648 | \n", + "0.925930 | \n", + "
30 | \n", + "0.093600 | \n", + "0.187472 | \n", + "0.930865 | \n", + "
"
+ ]
+ },
+ "metadata": {}
+ },
+ {
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": [
+ "TrainOutput(global_step=1920, training_loss=0.3936845714847247, metrics={'train_runtime': 2362.4807, 'train_samples_per_second': 52.013, 'train_steps_per_second': 0.813, 'total_flos': 9.52238637305561e+18, 'train_loss': 0.3936845714847247, 'epoch': 30.0})"
+ ]
+ },
+ "metadata": {},
+ "execution_count": 25
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "trainer.push_to_hub()"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/",
+ "height": 52
+ },
+ "id": "vbfO9xPPdOm1",
+ "outputId": "b9a26771-d432-472e-cc13-8fd8836efebd"
+ },
+ "execution_count": 26,
+ "outputs": [
+ {
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": [
+ "CommitInfo(commit_url='https://huggingface.co/spolivin/alz-mri-vit/commit/b2b0ecb84e796d5b50af69bcf0e3ebddfce7672b', commit_message='End of training', commit_description='', oid='b2b0ecb84e796d5b50af69bcf0e3ebddfce7672b', pr_url=None, pr_revision=None, pr_num=None)"
+ ],
+ "application/vnd.google.colaboratory.intrinsic+json": {
+ "type": "string"
+ }
+ },
+ "metadata": {},
+ "execution_count": 26
+ }
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "# Inference"
+ ],
+ "metadata": {
+ "id": "1d903JNhuOZW"
+ }
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "mri_data_test = load_dataset(\"Falah/Alzheimer_MRI\", split=\"test\")"
+ ],
+ "metadata": {
+ "id": "C5QWE6aaJQxQ"
+ },
+ "execution_count": 27,
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "id = -9\n",
+ "image = mri_data_test[\"image\"][id]\n",
+ "print(id2label[str(mri_data_test[\"label\"][id])])"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "id": "BTK1oVf3TbNx",
+ "outputId": "ba039f1a-49d4-45d5-951b-3c1fa3c666b6"
+ },
+ "execution_count": 28,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Mild_Demented\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "image"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/",
+ "height": 145
+ },
+ "id": "8uZk7V9pT1tk",
+ "outputId": "ef256bc3-c809-4e17-dc2e-e776d989d56b"
+ },
+ "execution_count": 29,
+ "outputs": [
+ {
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": [
+ "