greylock: A Python Package for Measuring The Composition of Complex Datasets

Code

• github.com/arnaoutlab/diversity
  OfficialIn papernone★ 6

Abstract

Machine-learning datasets are typically characterized by measuring their size and class balance. However, there exists a richer and potentially more useful set of measures, termed diversity measures, that incorporate elements' frequencies and between-element similarities. Although these have been available in the R and Julia programming languages for other applications, they have not been as readily available in Python, which is widely used for machine learning, and are not easily applied to machine-learning-sized datasets without special coding considerations. To address these issues, we developed greylock, a Python package that calculates diversity measures and is tailored to large datasets. greylock can calculate any of the frequency-sensitive measures of Hill's D-number framework, and going beyond Hill, their similarity-sensitive counterparts (Greylock is a mountain). greylock also outputs measures that compare datasets (beta diversities). We first briefly review the D-number framework, illustrating how it incorporates elements' frequencies and between-element similarities. We then describe greylock's key features and usage. We end with several examples - immunomics, metagenomics, computational pathology, and medical imaging - illustrating greylock's applicability across a range of dataset types and fields.

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