diff --git a/README.md b/README.md new file mode 100644 index 0000000..e63439e --- /dev/null +++ b/README.md @@ -0,0 +1,15 @@ +# DINOv2 for cell classification + +This project is a fork of the DINOv2 repo published by meta, aiming to use the methodology presented in their papers to train a series of +model on blood white cells images. +Developping a foundation model for blood white cells is interesting for several reasons: + +- The categories of blood white cells are not unanimous, and hematologists / datasets make different classes. +- Some blood white cells present mutations that are visible on images, and those distinguishible features could be embedded by the model + +## Installing + + +## Training + +Most of the code used for the training \ No newline at end of file diff --git a/conda.yaml b/conda.yaml index 35dfc30..3e68132 100644 --- a/conda.yaml +++ b/conda.yaml @@ -1,22 +1,23 @@ -name: dinov2 +name: cell_sim channels: - - defaults - pytorch - nvidia - - xformers - conda-forge + - defaults dependencies: - - python=3.9 - - pytorch::pytorch=2.0.0 - - pytorch::pytorch-cuda=11.7.0 - - pytorch::torchvision=0.15.0 + - python=3.10 + - xformers>=0.0.18 + - torchmetrics + - torchdata - omegaconf - - torchmetrics=0.10.3 + - submitit - fvcore - iopath - - xformers::xformers=0.0.18 - pip - pip: - - git+https://github.com/facebookincubator/submitit - - --extra-index-url https://pypi.nvidia.com - - cuml-cu11 + - --index-url https://download.pytorch.org/whl/cu118 + - torch==2.3.0+cu118 + - torchvision + - --extra-index-url https://pypi.nvidia.com + - cuml-cu11 + diff --git a/conda_test.yaml b/conda_cpu.yaml similarity index 61% rename from conda_test.yaml rename to conda_cpu.yaml index 3e68132..62a7be3 100644 --- a/conda_test.yaml +++ b/conda_cpu.yaml @@ -15,9 +15,7 @@ dependencies: - iopath - pip - pip: - - --index-url https://download.pytorch.org/whl/cu118 - - torch==2.3.0+cu118 + - --index-url https://download.pytorch.org/whl/cpu + - torch==2.3.0+cpu - torchvision - - --extra-index-url https://pypi.nvidia.com - - cuml-cu11 diff --git a/conda_or.yaml b/conda_or.yaml new file mode 100644 index 0000000..35dfc30 --- /dev/null +++ b/conda_or.yaml @@ -0,0 +1,22 @@ +name: dinov2 +channels: + - defaults + - pytorch + - nvidia + - xformers + - conda-forge +dependencies: + - python=3.9 + - pytorch::pytorch=2.0.0 + - pytorch::pytorch-cuda=11.7.0 + - pytorch::torchvision=0.15.0 + - omegaconf + - torchmetrics=0.10.3 + - fvcore + - iopath + - xformers::xformers=0.0.18 + - pip + - pip: + - git+https://github.com/facebookincubator/submitit + - --extra-index-url https://pypi.nvidia.com + - cuml-cu11 diff --git a/conda-extras.yaml b/condas_or-extras.yaml similarity index 100% rename from conda-extras.yaml rename to condas_or-extras.yaml diff --git a/notebooks/Untitled.ipynb b/notebooks/Untitled.ipynb new file mode 100644 index 0000000..363fcab --- /dev/null +++ b/notebooks/Untitled.ipynb @@ -0,0 +1,6 @@ +{ + "cells": [], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/requirements.txt b/requirements.txt index c4599ff..2cf36ae 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,5 +7,3 @@ fvcore iopath xformers>=0.0.18 submitit ---extra-index-url https://pypi.nvidia.com -cuml-cu11