LinkedNN: a neural model of linkage disequilibrium decay for recent effective population size inference
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arXiv
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| Format: | Preprint |
| Veröffentlicht: |
2026
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| _version_ | 1866918336983465984 |
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| author | Smith, Chris C R |
| author_facet | Smith, Chris C R |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2602_13121 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | LinkedNN: a neural model of linkage disequilibrium decay for recent effective population size inference Smith, Chris C R Populations and Evolution Quantitative Methods 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. |
| title | LinkedNN: a neural model of linkage disequilibrium decay for recent effective population size inference |
| topic | Populations and Evolution Quantitative Methods |
| url | https://arxiv.org/abs/2602.13121 |