champollion-omics 0.1.0

Semi-paired single-cell multimodal integration with Champollion

Champollion

Champollion learns an interpretable cross-modality cost from paired bridge cells and uses it to integrate unpaired single-cell profiles across modalities. It is designed for scverse workflows with AnnData and MuData, and exposes utilities for annotation transfer, barycentric projection, and interpretation of the learned interaction matrix.

Install

Install the latest stable release from PyPI (recommended):

pip install champollion-omics

Optional Weights & Biases logging can be installed with:

pip install "champollion-omics[wandb]"

To install the latest development version from GitHub instead:

pip install "git+https://github.com/cantinilab/champollion.git"

Champollion is designed to take advantage of a GPU and runs much faster with one, typically taking only a few minutes on datasets with thousands of cells.

Documentation

Documentation is available at champollion-omics.readthedocs.io.

Two tutorials are available there to demonstrate classic use cases of the package: fitting Champollion on bridge cells, transporting unpaired cells, transferring annotations, building a joint visualization, interpreting the learnt A matrix.

Getting Started

For a concrete application, see the tutorials; the example below is only a compact overview of the API. Champollion is fitted on a paired bridge stored in a MuData object. It can then be applied to modality-specific AnnData objects containing unpaired cells.

from champollion import Champollion

model = Champollion(
    epsilon=1.0,
    gamma=0.001,
    lambda_prior=20.0,
    use_keops=False,
    device="auto",
    random_state=0,
)

model.fit(
    mdata_bridge,
    modality_1="rna",
    modality_2="atac",
    x_1_rep="X_pca",
    x_2_rep="X_lsi",
    y_prior_1_rep="X_prior",
    y_prior_2_rep="X_prior",
)

result = model.transport(
    {"rna": adata_rna, "atac": adata_atac},
    x_reps={"rna": "X_pca", "atac": "X_lsi"},
    y_prior_reps={"rna": "X_prior", "atac": "X_prior"},
)

predicted_atac_labels = result.transfer_obs(
    key="cell_type",
    source="rna",
    kind="categorical",
)

The learned matrix can be inspected directly:

A = model.A_dataframe()
top_links = model.top_interactions("CD18", modality="protein", k=10)

Citation

The preprint is in preparation. Citation information will be added before the official release. if you're looking for the repository to reproduce the results in the article, please see the champollion_reproducibility repository!