mellon

Mellon

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

Installation

To install Mellon using pip you can run:

pip install mellon

or to install using conda you can run:

conda install -c conda-forge mellon

or to install using mamba you can run:

mamba install -c conda-forge mellon

Any of these calls should install Mellon and its dependencies within less than 1 minute. If the dependency jax is not autimatically installed, please refer to https://github.com/google/jax.

Documentation

Please read the documentation or use this basic tutorial notebook.

Basic Usage

import mellon
import numpy as np

X = np.random.rand(100, 10)  # 10-dimensional state representation for 100 cells
Y = np.random.rand(100, 10)  # arbitrary test data

model = mellon.DensityEstimator()
log_density_x = model.fit_predict(X)
log_density_y = model.predict(Y)

Citations

The Mellon manuscript is available on Nature Methods and a preprint on bioRxiv. If you use Mellon for your work, please cite our paper.

@article{ottoQuantifyingCellstateDensities2024,
  title = {Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes Using {{Mellon}}},
  author = {Otto, Dominik J. and Jordan, Cailin and Dury, Brennan and Dien, Christine and Setty, Manu},
  date = {2024-06-18},
  journaltitle = {Nature Methods},
  issn = {1548-7105},
  doi = {10.1038/s41592-024-02302-w},
  url = {https://www.nature.com/articles/s41592-024-02302-w},
}

You can find our reproducibility repository to reproduce benchmarks and plots of the paper here.

Metadata

Release files for mellon 1.7.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mellon 1.7.1
File	Size	Uploaded	Provenance
mellon-1.7.1.tar.gz	140.0 kB	Apr 10, 2026	Without provenance	Details

Built distribution (wheel)

Table of built distributions (wheels) for mellon 1.7.1
File	Interpreter	ABI	Platform	Reset
mellon-1.7.1-py3-none-any.whl 101.9 kB Apr 10, 2026 Without provenance	Python 3	none	any	Details

Total release size: 241.9 kB

Release files / mellon-1.7.1.tar.gz

Download URL	mellon-1.7.1.tar.gz
Size	140.0 kB
Tags	Source
SHA-256 checksum How to use checksums	`12f6f29478f7b98b1b427a4484aca627df4017a47d2c25bda85005aae5434d32`
BLAKE2b-256 checksum How to use checksums	`29560208c1281124f8f700ef5a843a84d963a702b262c299a113e0bb332ff734`
Upload date	Apr 10, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.12.11`

Release files / mellon-1.7.1-py3-none-any.whl

Download URL	mellon-1.7.1-py3-none-any.whl
Size	101.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`c8120cd8a8b71519bdcc0105d8778c9314afeb6aa8934cfd23fde1f1432581bf`
BLAKE2b-256 checksum How to use checksums	`4c0b75c3e700b7741a127be32985dbdd9522e4b9953ed3e77440dca8c2381dab`
Upload date	Apr 10, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.12.11`

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