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{
"cells": [
{
"cell_type": "markdown",
"id": "048c6b14",
"metadata": {
"id": "048c6b14"
},
"source": [
"# TCGA Histology Images Benchmarking Execution Steps\n",
"\n",
"This notebook follows the README instructions to:\n",
"1. Clone the repository\n",
"2. Set up the environment (install dependencies)\n",
"3. Execute the training script (`extract_train.py`)\n",
"\n",
"We will explain and execute these steps.\n"
]
},
{
"cell_type": "markdown",
"id": "e7d3f2ef",
"metadata": {
"id": "e7d3f2ef"
},
"source": [
"## Step 1: Clone the Repository\n",
"\n",
"Use the following command to clone the target repository.\n"
]
},
{
"cell_type": "code",
"source": [
"# check python version (this example is google colab environment)\n",
"!python --version"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "FccnVVy0GAVR",
"outputId": "e90aefeb-6cd3-4875-cc53-e7241c84589a"
},
"id": "FccnVVy0GAVR",
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Python 3.11.11\n"
]
}
]
},
{
"cell_type": "code",
"source": [
"# set your huggingface token\n",
"import os\n",
"token = \"your huggingface token\""
],
"metadata": {
"id": "48KZGOUK74nm"
},
"id": "48KZGOUK74nm",
"execution_count": 2,
"outputs": []
},
{
"cell_type": "code",
"execution_count": 3,
"id": "7fa0d887",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "7fa0d887",
"outputId": "9ab89093-b365-419f-96d1-c2f09929b36c"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Cloning into 'demo'...\n",
"remote: Enumerating objects: 199, done.\u001b[K\n",
"remote: Counting objects: 100% (43/43), done.\u001b[K\n",
"remote: Compressing objects: 100% (43/43), done.\u001b[K\n",
"remote: Total 199 (delta 21), reused 0 (delta 0), pack-reused 156 (from 1)\u001b[K\n",
"Receiving objects: 100% (199/199), 79.26 KiB | 8.81 MiB/s, done.\n",
"Resolving deltas: 100% (33/33), done.\n",
"Filtering content: 100% (113/113), 11.30 GiB | 45.21 MiB/s, done.\n"
]
}
],
"source": [
"# repository url need to be changed\n",
"!git clone https://oauth2:{token}@huggingface.co/datasets/kooo-sh/demo/"
]
},
{
"cell_type": "markdown",
"id": "86ab67ec",
"metadata": {
"id": "86ab67ec"
},
"source": [
"## Step 2: Environment Setup\n",
"\n",
"Navigate to the cloned directory and install the required Python packages.\n"
]
},
{
"cell_type": "code",
"source": [
"# move directory\n",
"%cd repository_directory"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "RZVfsHws-djt",
"outputId": "83b081d6-9249-4b24-e451-c0347e752d03"
},
"id": "RZVfsHws-djt",
"execution_count": 4,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"/content/drive/MyDrive/demo\n"
]
}
]
},
{
"cell_type": "code",
"source": [
"%ls"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "umN5ZMRHHA7z",
"outputId": "199d9667-1044-4c1a-e004-bf4f5b14a56d"
},
"id": "umN5ZMRHHA7z",
"execution_count": 5,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"config.yaml extract_train.py \u001b[0m\u001b[01;34mlicenses\u001b[0m/ requirements.txt train_val_test_split.csv\n",
"\u001b[01;34mdata\u001b[0m/ \u001b[01;34mfeatures\u001b[0m/ README.md setup.ipynb\n"
]
}
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "56b69da0",
"metadata": {
"id": "56b69da0",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "09cdfc42-751e-432c-c978-7ca0ef4379c4"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Collecting braceexpand==0.1.7 (from -r requirements.txt (line 1))\n",
" Downloading braceexpand-0.1.7-py2.py3-none-any.whl.metadata (3.0 kB)\n",
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" Downloading charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)\n",
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" Downloading MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)\n",
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"\u001b[?25h Installing build dependencies ... \u001b[?25l\u001b[?25hdone\n",
" Getting requirements to build wheel ... \u001b[?25l\u001b[?25hdone\n",
" Preparing metadata (pyproject.toml) ... \u001b[?25l\u001b[?25hdone\n",
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" Downloading nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n",
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" Downloading nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n",
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" Downloading nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n",
"Requirement already satisfied: opencv-python==4.10.0.84 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 24)) (4.10.0.84)\n",
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"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m4.9/4.9 MB\u001b[0m \u001b[31m103.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25h Installing build dependencies ... \u001b[?25l\u001b[?25hdone\n",
" Getting requirements to build wheel ... \u001b[?25l\u001b[?25hdone\n",
" Preparing metadata (pyproject.toml) ... \u001b[?25l\u001b[?25hdone\n",
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" Downloading pillow-10.4.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (9.2 kB)\n",
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"Requirement already satisfied: pytz==2024.2 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 32)) (2024.2)\n",
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"\u001b[?25hRequirement already satisfied: requests==2.32.3 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 35)) (2.32.3)\n",
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" Downloading safetensors-0.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB)\n",
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"\u001b[?25h Installing build dependencies ... \u001b[?25l\u001b[?25hdone\n",
" Getting requirements to build wheel ... \u001b[?25l\u001b[?25hdone\n",
" \u001b[1;31merror\u001b[0m: \u001b[1msubprocess-exited-with-error\u001b[0m\n",
" \n",
" \u001b[31m×\u001b[0m \u001b[32mPreparing metadata \u001b[0m\u001b[1;32m(\u001b[0m\u001b[32mpyproject.toml\u001b[0m\u001b[1;32m)\u001b[0m did not run successfully.\n",
" \u001b[31m│\u001b[0m exit code: \u001b[1;36m1\u001b[0m\n",
" \u001b[31m╰─>\u001b[0m See above for output.\n",
" \n",
" \u001b[1;35mnote\u001b[0m: This error originates from a subprocess, and is likely not a problem with pip.\n",
" Preparing metadata (pyproject.toml) ... \u001b[?25l\u001b[?25herror\n",
"\u001b[1;31merror\u001b[0m: \u001b[1mmetadata-generation-failed\u001b[0m\n",
"\n",
"\u001b[31m×\u001b[0m Encountered error while generating package metadata.\n",
"\u001b[31m╰─>\u001b[0m See above for output.\n",
"\n",
"\u001b[1;35mnote\u001b[0m: This is an issue with the package mentioned above, not pip.\n",
"\u001b[1;36mhint\u001b[0m: See above for details.\n"
]
}
],
"source": [
"# install packages\n",
"!pip install -r requirements.txt"
]
},
{
"cell_type": "code",
"source": [
"# if scikit-leran is not installed, run this command\n",
"# !pip install scikit-learn\n",
"# !pip install scipy six==1.16.0"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 434
},
"id": "kvflBfrrSyU4",
"outputId": "5b10426c-c3e3-4eff-cbcd-0fa1f6f96d46"
},
"id": "kvflBfrrSyU4",
"execution_count": 7,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Requirement already satisfied: scikit-learn in /usr/local/lib/python3.11/dist-packages (1.6.1)\n",
"Requirement already satisfied: numpy>=1.19.5 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (1.26.4)\n",
"Requirement already satisfied: scipy>=1.6.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (1.13.1)\n",
"Requirement already satisfied: joblib>=1.2.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (1.4.2)\n",
"Requirement already satisfied: threadpoolctl>=3.1.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (3.5.0)\n",
"Requirement already satisfied: scipy in /usr/local/lib/python3.11/dist-packages (1.13.1)\n",
"Collecting six==1.16.0\n",
" Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)\n",
"Requirement already satisfied: numpy<2.3,>=1.22.4 in /usr/local/lib/python3.11/dist-packages (from scipy) (1.26.4)\n",
"Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)\n",
"Installing collected packages: six\n",
" Attempting uninstall: six\n",
" Found existing installation: six 1.17.0\n",
" Uninstalling six-1.17.0:\n",
" Successfully uninstalled six-1.17.0\n",
"Successfully installed six-1.16.0\n"
]
},
{
"output_type": "display_data",
"data": {
"application/vnd.colab-display-data+json": {
"pip_warning": {
"packages": [
"six"
]
},
"id": "9f6ede4ac0cd447db545799914707e3b"
}
},
"metadata": {}
}
]
},
{
"cell_type": "markdown",
"id": "d725eb4d",
"metadata": {
"id": "d725eb4d"
},
"source": [
"### Troubleshooting SPAMS Library Installation\n",
"\n",
"If you encounter issues installing the SPAMS library from `requirements.txt`, try executing the following alternative command.\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "d3d70745",
"metadata": {
"id": "d3d70745",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "2c674c7b-d821-43be-aad1-8172985e9439"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Collecting spams-bin\n",
" Downloading spams_bin-2.6.10-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (754 bytes)\n",
"Requirement already satisfied: numpy>=1.21.3 in /usr/local/lib/python3.11/dist-packages (from spams-bin) (1.26.4)\n",
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"\u001b[?25hDownloading braceexpand-0.1.7-py2.py3-none-any.whl (5.9 kB)\n",
"Building wheels for collected packages: staintools\n",
" Building wheel for staintools (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for staintools: filename=staintools-2.1.2-py3-none-any.whl size=14051 sha256=6034d47a7b5770d1df676df5a81768c52bd79b644f8b330025603148bc15249e\n",
" Stored in directory: /root/.cache/pip/wheels/0c/c4/69/fc8068103fe40879db0187cd442d181b1e741e849f33814600\n",
"Successfully built staintools\n",
"Installing collected packages: braceexpand, webdataset, urllib3, triton, tqdm, tomli, sympy, nvidia-nvtx-cu12, nvidia-nccl-cu12, nvidia-cusparse-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, nvidia-cusolver-cu12, nvidia-cudnn-cu12, torch, staintools, torchvision, tokenizers, transformers, timm\n",
" Attempting uninstall: urllib3\n",
" Found existing installation: urllib3 2.3.0\n",
" Uninstalling urllib3-2.3.0:\n",
" Successfully uninstalled urllib3-2.3.0\n",
" Attempting uninstall: triton\n",
" Found existing installation: triton 3.1.0\n",
" Uninstalling triton-3.1.0:\n",
" Successfully uninstalled triton-3.1.0\n",
" Attempting uninstall: tqdm\n",
" Found existing installation: tqdm 4.67.1\n",
" Uninstalling tqdm-4.67.1:\n",
" Successfully uninstalled tqdm-4.67.1\n",
" Attempting uninstall: sympy\n",
" Found existing installation: sympy 1.13.1\n",
" Uninstalling sympy-1.13.1:\n",
" Successfully uninstalled sympy-1.13.1\n",
" Attempting uninstall: nvidia-nvtx-cu12\n",
" Found existing installation: nvidia-nvtx-cu12 12.4.127\n",
" Uninstalling nvidia-nvtx-cu12-12.4.127:\n",
" Successfully uninstalled nvidia-nvtx-cu12-12.4.127\n",
" Attempting uninstall: nvidia-nccl-cu12\n",
" Found existing installation: nvidia-nccl-cu12 2.21.5\n",
" Uninstalling nvidia-nccl-cu12-2.21.5:\n",
" Successfully uninstalled nvidia-nccl-cu12-2.21.5\n",
" Attempting uninstall: nvidia-cusparse-cu12\n",
" Found existing installation: nvidia-cusparse-cu12 12.5.1.3\n",
" Uninstalling nvidia-cusparse-cu12-12.5.1.3:\n",
" Successfully uninstalled nvidia-cusparse-cu12-12.5.1.3\n",
" Attempting uninstall: nvidia-curand-cu12\n",
" Found existing installation: nvidia-curand-cu12 10.3.6.82\n",
" Uninstalling nvidia-curand-cu12-10.3.6.82:\n",
" Successfully uninstalled nvidia-curand-cu12-10.3.6.82\n",
" Attempting uninstall: nvidia-cufft-cu12\n",
" Found existing installation: nvidia-cufft-cu12 11.2.3.61\n",
" Uninstalling nvidia-cufft-cu12-11.2.3.61:\n",
" Successfully uninstalled nvidia-cufft-cu12-11.2.3.61\n",
" Attempting uninstall: nvidia-cuda-runtime-cu12\n",
" Found existing installation: nvidia-cuda-runtime-cu12 12.5.82\n",
" Uninstalling nvidia-cuda-runtime-cu12-12.5.82:\n",
" Successfully uninstalled nvidia-cuda-runtime-cu12-12.5.82\n",
" Attempting uninstall: nvidia-cuda-nvrtc-cu12\n",
" Found existing installation: nvidia-cuda-nvrtc-cu12 12.5.82\n",
" Uninstalling nvidia-cuda-nvrtc-cu12-12.5.82:\n",
" Successfully uninstalled nvidia-cuda-nvrtc-cu12-12.5.82\n",
" Attempting uninstall: nvidia-cuda-cupti-cu12\n",
" Found existing installation: nvidia-cuda-cupti-cu12 12.5.82\n",
" Uninstalling nvidia-cuda-cupti-cu12-12.5.82:\n",
" Successfully uninstalled nvidia-cuda-cupti-cu12-12.5.82\n",
" Attempting uninstall: nvidia-cublas-cu12\n",
" Found existing installation: nvidia-cublas-cu12 12.5.3.2\n",
" Uninstalling nvidia-cublas-cu12-12.5.3.2:\n",
" Successfully uninstalled nvidia-cublas-cu12-12.5.3.2\n",
" Attempting uninstall: nvidia-cusolver-cu12\n",
" Found existing installation: nvidia-cusolver-cu12 11.6.3.83\n",
" Uninstalling nvidia-cusolver-cu12-11.6.3.83:\n",
" Successfully uninstalled nvidia-cusolver-cu12-11.6.3.83\n",
" Attempting uninstall: nvidia-cudnn-cu12\n",
" Found existing installation: nvidia-cudnn-cu12 9.3.0.75\n",
" Uninstalling nvidia-cudnn-cu12-9.3.0.75:\n",
" Successfully uninstalled nvidia-cudnn-cu12-9.3.0.75\n",
" Attempting uninstall: torch\n",
" Found existing installation: torch 2.5.1+cu124\n",
" Uninstalling torch-2.5.1+cu124:\n",
" Successfully uninstalled torch-2.5.1+cu124\n",
" Attempting uninstall: torchvision\n",
" Found existing installation: torchvision 0.20.1+cu124\n",
" Uninstalling torchvision-0.20.1+cu124:\n",
" Successfully uninstalled torchvision-0.20.1+cu124\n",
" Attempting uninstall: tokenizers\n",
" Found existing installation: tokenizers 0.21.0\n",
" Uninstalling tokenizers-0.21.0:\n",
" Successfully uninstalled tokenizers-0.21.0\n",
" Attempting uninstall: transformers\n",
" Found existing installation: transformers 4.47.1\n",
" Uninstalling transformers-4.47.1:\n",
" Successfully uninstalled transformers-4.47.1\n",
" Attempting uninstall: timm\n",
" Found existing installation: timm 1.0.14\n",
" Uninstalling timm-1.0.14:\n",
" Successfully uninstalled timm-1.0.14\n",
"\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
"torchaudio 2.5.1+cu124 requires torch==2.5.1, but you have torch 2.4.1 which is incompatible.\u001b[0m\u001b[31m\n",
"\u001b[0mSuccessfully installed braceexpand-0.1.7 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-9.1.0.70 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.20.5 nvidia-nvtx-cu12-12.1.105 staintools-2.1.2 sympy-1.13.3 timm-1.0.9 tokenizers-0.19.1 tomli-2.0.2 torch-2.4.1 torchvision-0.19.1 tqdm-4.66.5 transformers-4.44.2 triton-3.0.0 urllib3-2.2.3 webdataset-0.2.100\n"
]
}
],
"source": [
"!pip install spams-bin\n",
"!pip install PyOpenGL PyOpenGL_accelerate\n",
"!pip install staintools==2.1.2 sympy==1.13.3 threadpoolctl==3.5.0 timm==1.0.9 tokenizers==0.19.1 tomli==2.0.2 torch torchvision tqdm==4.66.5 transformers==4.44.2 triton==3.0.0 typing_extensions==4.12.2 urllib3==2.2.3 wcwidth==0.2.13 webdataset==0.2.100"
]
},
{
"cell_type": "markdown",
"id": "d86a7b1c",
"metadata": {
"id": "d86a7b1c"
},
"source": [
"## Step 3: Execute the Training Script\n",
"\n",
"Run `extract_train.py` to start the following processes:\n",
"\n",
"- Feature extraction using the specified foundation model\n",
"- Saving features in H5 format\n",
"- Linear probing evaluation (outputting Accuracy and Balanced Accuracy)\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "5f3a7c3e",
"metadata": {
"id": "5f3a7c3e",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "b7639582-b37b-4e71-e459-8b56266c7ef4"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"{'model_name': 'h_optimus', 'split_type': 'internal', 'device': 'cuda', 'feature_exist': True, 'max_iter': 1000, 'cost': 0.0001, 'model_path': 'hf-hub:bioptimus/H-optimus-0'}\n",
"Directory already exists: ./features\n",
"Accuracy = 0.830, Balanced Accuracy = 0.739\n"
]
}
],
"source": [
"!python extract_train.py"
]
},
{
"cell_type": "markdown",
"id": "5873d257",
"metadata": {
"id": "5873d257"
},
"source": [
"This completes the repository cloning, environment setup, and training script execution.\n",
"\n",
"If you encounter any errors during any step, follow the error messages and take necessary actions such as adjusting package versions or installing system libraries.\n"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"name": "python3"
},
"language_info": {
"name": "python",
"version": "3.x"
},
"colab": {
"provenance": [],
"gpuType": "T4"
},
"accelerator": "GPU"
},
"nbformat": 4,
"nbformat_minor": 5
} |