ArticleAlgorithms for molecular biology : AMB2025
Estimating similarity and distance using FracMinHash.
Article in Algorithms for molecular biology : AMB, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- The gift of novelty: repeat-robust k-mer-based estimators of mutation rates.Bioinformatics (Oxford, England) · 2026Article
- DipSkmer: Reference-free population genomics with diploid genome skims.bioRxiv : the preprint server for biology · 2026Article
- The gift of novelty: repeat-robustbioRxiv : the preprint server for biology · 2026Article
- MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements.bioRxiv : the preprint server for biology · 2025Article
- Estimation of substitution and indel rates viaAlgorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Estimation of substitution and indel rates viabioRxiv : the preprint server for biology · 2025Article
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Abstract
motivationThe increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing THEORETICAL CONTRIBUTIONS: In this paper, we present a theoretical framework for estimating similarity/distance metrics by using FracMinHash sketches, when the metric is expressible in a certain form. We establish conditions under which such an estimation is sound and recommend a minimum scale factor s for accurate results. Experimental evidence supports our theoretical findings. PRACTICAL CONTRIBUTIONS: We also present frac-kmc, a fast and efficient FracMinHash sketch generator program. frac-kmc is the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. frac-kmc is also the first parallel tool for this task, allowing for speeding up sketch generation using multiple CPU cores - an option lacking in existing serialized tools. We show that by computing FracMinHash sketches using frac-kmc, we can estimate pairwise similarity speedily and accurately on real data. frac-kmc is freely available here: https://github.com/KoslickiLab/frac-kmc/.
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