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kaov

https://github.com/lmjl-alea/kaov

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Repository

Basic Info
  • Host: GitHub
  • Owner: LMJL-Alea
  • License: cc0-1.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 1.48 MB
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  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed 11 months ago
Metadata Files
Readme License Authors Codemeta

README.md

kAOV: Kernel Analysis of Variance

A Python library for general kernel hypothesis testing, accompanying [1].

Installation

Install from GitHub: console $ pip install kaov@git+https://github.com/LMJL-Alea/kAOV@main

How to use

Load a dataset: ```python

import pandas as pd url = "https://raw.githubusercontent.com/LMJL-Alea/kAOV/refs/heads/main/Data/reversionkAOV.csv" data = pd.readcsv(url, indexcol=0) Write a formula using OneHot encoding: python formula = ' + '.join(data.columns[:-2]) + ' ~ C(Medium, OneHot) + C(Batch, OneHot)' print(formula) AACS + ACSL6 + ACSS1 + ALAS1 + AMDHD2 + ARHGEF2 + BATF + BCL11A + betaglobin + BPI + CD151 + CD44 + CREG1 + CRIP2 + CTCF + CTSA + CYP51A1 + DCP1A + DCTD + DHCR24 + DHCR7 + DPP7 + EGFR + EMB + FAM208B + FHL3 + FNIP1F1R1 + GLRX5 + GPT2 + GSN + HMGCS1 + HRAS1 + HSD17B7 + HSP90AA1 + HYAL1 + LCP1 + LDHA + MAPK12 + MFSD2B + MID2 + MKNK2 + MTFR1 + MVD + MYO1G + NCOA4 + NSDHL + PDLIM7 + PIK3CG + PLAG1 + PLS1 + PLS3 + PPP1R15B + PTPRC + RBM38 + REXO2 + RFFL + RPL22L1 + RSFR + RUNX2 + sca2 + SCD + SERPINI1 + SLC25A37 + SLC6A9 + SLC9A3R2 + SMPD1 + SNX22 + SNX27 + SQLE + SQSTM1 + STARD4 + STX12 + SULF2 + SULT1E1 + TADA2L + TBC1D7 + TNFRSF21 + TPP1 + TTYH2 + UCK1 + VDAC3 + WDR91 + XPNPEP1 ~ C(Medium, OneHot) + C(Batch, OneHot) Create a model and run a test: python from kaov import AOV kfit = AOV.fromformula(formula, data=data) kfit.test().summary()

Kernel Analysis of Variance

Medium | Trunc. T=1 T=2 T=3 T=4 T=5 

    |    TKHL 204.6946 423.7650 528.7334 552.0367 1263.0267
    | P-value   0.0000   0.0000   0.0000   0.0000    0.0000

Batch |  Trunc.   T=1     T=2      T=3      T=4      T=5   

      |    TKHL 85.9009 209.6519 315.4264 401.4933 465.7612
      | P-value  0.0000   0.0000   0.0000   0.0000   0.0000

=============================================================== ```

For more details see the tutorial.

References

[1] Anthony Ozier-Lafontaine, Polina Arsenteva, Franck Picard, Bertrand Michel. Extending Kernel Testing To General Designs. 2024. Preprint, arXiv:2405.13799

Owner

  • Name: ALEA - Statistics Team of the Department of Mathematics Jean Leray
  • Login: LMJL-Alea
  • Kind: organization
  • Location: France

CodeMeta (codemeta.json) 

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  "relatedLink": "https://arxiv.org/abs/2405.13799",
  "version": "0.2.9",
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Dependencies

pyproject.toml pypi
  • anthony_project_tools @ git+https://github.com/lereldarion/anthony_project_tools.git
  • matplotlib *
  • numpy *
  • pandas *
  • patsy *
  • scipy *
  • statsmodels >= 0.14.0
  • torch >= 2.2.0