novae 0.0.2

Graph-based foundation model for spatial transcriptomics data

💫 Graph-based foundation model for spatial transcriptomics data

Documentation

Check Novae's documentation to get started. It contains installation explanations, API details, and tutorials.

Overview

(a) Novae was trained on a large dataset, and is shared on Hugging Face Hub. (b) Illustration of the main tasks and properties of Novae. (c) Illustration of the method behing Novae (self-supervision on graphs, adapted from SwAV).

Installation

PyPI

novae can be installed via PyPI on all OS, for python>=3.9.

pip install novae

Editable mode

To install novae in editable mode (e.g., to contribute), clone the repository and choose among the options below.

pip install -e .                 # pip, minimal dependencies
pip install -e '.[dev]'          # pip, all extras
poetry install                   # poetry, minimal dependencies
poetry install --all-extras      # poetry, all extras

Usage

Here is a minimal usage example. For more details, refer to the documentation.

import novae

model = novae.Novae.from_pretrained("MICS-Lab/novae-1-medium")

model.compute_representations(adata, zero_shot=True)
model.assign_domains(adata)

Cite us

TODO: submit preprint (coming soon)