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https://github.com/cbg-ethz/jnotype

Probabilistic modeling of high-dimensional binary data in JAX

https://github.com/cbg-ethz/jnotype

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

bayesian-statistics cancer-genomics clustering ideal-point-estimation jax probabilistic-machine-learning unsupervised-learning
Last synced: 5 months ago · JSON representation

Repository

Probabilistic modeling of high-dimensional binary data in JAX

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 286 KB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 9
  • Releases: 0
Topics
bayesian-statistics cancer-genomics clustering ideal-point-estimation jax probabilistic-machine-learning unsupervised-learning
Created about 3 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. build Ruff Code style: black PyPI Latest Release

Jnotype

JAX-powered Python package for exploratory analysis of binary data. This includes genotype data, binary images, and data sets used in ecology.

Note: this package is in early development stage.

Installation

Note: The package has not reached a stable API yet. Frequent changes may appear.

We recommend setting up a new virtual environment. You can install the released version of the package from PyPI:

bash $ python -m pip install jnotype

or install the development version from GitHub:

bash $ python -m pip install 'jnotype @ git+https://github.com/cbg-ethz/jnotype'

Using GPU

Instructions above install the CPU version of JAX. To use GPU, you may need to follow the official JAX installation tutorial.

Getting started

Directory examples/ contains Quarto notebooks, which demonstrate basic functionalities of the package.

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
  • Watch event: 1
  • Delete event: 7
  • Member event: 1
  • Push event: 33
  • Pull request event: 15
  • Create event: 9
Last Year
  • Watch event: 1
  • Delete event: 7
  • Member event: 1
  • Push event: 33
  • Pull request event: 15
  • Create event: 9

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 38
  • Total Committers: 1
  • Avg Commits per committer: 38.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 11
  • Committers: 1
  • Avg Commits per committer: 11.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Paweł Czyż p****z@a****h 38
Committer Domains (Top 20 + Academic)
ai.ethz.ch: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 9
  • Total pull requests: 27
  • Average time to close issues: 11 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.11
  • Average comments per pull request: 0.0
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 17 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pawel-czyz (7)
Pull Request Authors
  • pawel-czyz (38)
  • allenxzhao (1)
Top Labels
Issue Labels
🚂type: enhancement (3) ⏳priority: low (2) 🔡action: coding (2) 🐘effort: large (1) ⏳priority: high (1) 🐇effort: small (1) 🦮effort: medium (1)
Pull Request Labels
🚂type: enhancement (13) 🔡action: coding (10) ⏳priority: high (9) 🦮effort: medium (7) 🔡action: refactoring (3) 🐇effort: small (3) 🐘effort: large (2)

Dependencies

.github/workflows/test.yml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • psf/black stable composite
  • snok/install-poetry v1 composite
pyproject.toml pypi
  • arviz ^0.15.1
  • jax ^0.4.6
  • jaxlib ^0.4.6
  • jaxtyping ^0.2.14
  • matplotlib ^3.7.1
  • numpy ^1.24.2
  • numpyro ^0.11.0
  • polyagamma ^1.3.5
  • pymc >=5.0
  • python ^3.9
  • tqdm ^4.65.0
  • xarray ^2023.3.0
requirements.txt pypi
  • arviz ==0.15.0
  • attrs ==22.2.0
  • cachetools ==5.3.0
  • cfgv ==3.3.1
  • click ==8.1.3
  • cloudpickle ==2.2.1
  • colorama ==0.4.6
  • cons ==0.4.5
  • contourpy ==1.0.7
  • coverage ==7.2.1
  • cycler ==0.11.0
  • distlib ==0.3.6
  • etuples ==0.3.8
  • exceptiongroup ==1.1.0
  • execnet ==1.9.0
  • fastprogress ==1.0.3
  • filelock ==3.9.0
  • fonttools ==4.38.0
  • h5netcdf ==1.1.0
  • h5py ==3.8.0
  • identify ==2.5.18
  • importlib-resources ==5.12.0
  • iniconfig ==2.0.0
  • interrogate ==1.5.0
  • kiwisolver ==1.4.4
  • logical-unification ==0.4.5
  • matplotlib ==3.7.0
  • minikanren ==1.0.3
  • multipledispatch ==0.6.0
  • nodeenv ==1.7.0
  • numpy ==1.24.2
  • packaging ==23.0
  • pandas ==1.5.3
  • pillow ==9.4.0
  • platformdirs ==3.0.0
  • pluggy ==1.0.0
  • pre-commit ==3.1.0
  • py ==1.11.0
  • pymc ==5.0.2
  • pyparsing ==3.0.9
  • pytensor ==2.9.1
  • pytest ==7.2.1
  • pytest-cov ==4.0.0
  • pytest-xdist ==3.2.0
  • python-dateutil ==2.8.2
  • pytz ==2022.7.1
  • pyyaml ==6.0
  • ruff ==0.0.253
  • scipy ==1.9.3
  • setuptools ==67.4.0
  • six ==1.16.0
  • tabulate ==0.9.0
  • toml ==0.10.2
  • tomli ==2.0.1
  • toolz ==0.12.0
  • typing-extensions ==4.5.0
  • virtualenv ==20.19.0
  • xarray ==2023.2.0
  • xarray-einstats ==0.5.1
  • zipp ==3.15.0