Authors
Jamhuri, M., Irawan, A.
Abstract
Alignment-free lineage assignment from k-mer frequency profiles is widely used for SARS-CoV-2 surveillance, and the methods that do it are ranked against each other by margins of one or two percentage points. Those rankings rest on an unchecked protocol. Public repositories hold many near-duplicate genomes, and stratified random splitting puts members of such a group on both sides of the split, so a classifier is credited for sequences it has already seen. This study measures the effect and offers a remedy. We propose quantised profile hashing, which finds near duplicates directly in k-mer feature space by rounding each frequency vector and hashing it. No sequence is compared with any other, so one pass over the feature matrix suffices and no similarity threshold has to be chosen. Rounding is also what makes the groups well defined, and they are then kept whole across the training, validation and test sets. On 255,611 genomes from seven Pango lineages, random splitting leaves 5.09% of test sequences with a near duplicate in training, as large as the margins separating published methods. Ten update rules were then trained twice, identically except for the partition. The contaminated benchmark separates one rule from the leader at 0.05; the clean one separates none. The two orderings are uncorrelated, Kendall tau = +0.022, with rules moving 3.2 positions on average and the leader of one benchmark ranking eighth on the other. A ranking obtained under contamination therefore says nothing about the ranking without it, and the quantity worth reporting beside a score is the leakage rate of the split.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 16 Aug 2026.
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