LinkedNN: a neural model of linkage disequilibrium decay for recent effective population size inference
Populations and Evolution
2026-02-16 v1 Quantitative Methods
Abstract
Summary: A bioinformatics tool is presented for estimating recent effective population size by using a neural network to automatically compute linkage disequilibrium-related features as a function of genomic distance between polymorphisms. The new method outperforms existing deep learning and summary statistic-based approaches using relatively few sequenced individuals and variant sites, making it particularly valuable for molecular ecology applications with sparse, unphased data. Availability and implementation: The program is available as an easily installable Python package with documentation here: https://pypi.org/project/linkedNN/. The open source code is available from: https://github.com/the-smith-lab/LinkedNN.
Keywords
Cite
@article{arxiv.2602.13121,
title = {LinkedNN: a neural model of linkage disequilibrium decay for recent effective population size inference},
author = {Chris C R Smith},
journal= {arXiv preprint arXiv:2602.13121},
year = {2026}
}