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Drake McAdams

dblp:424/3916 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis
k-mer sampling
0.912025
A near-tight lower bound on the density of forward sampling schemes · Bioinform. 2025
Bioinformatics and computational biology
sequence analysis
0.912025
A near-tight lower bound on the density of forward sampling schemes · Bioinform. 2025
Bioinformatics and computational biology › sequence analysis › k-mer sampling
minimizers scheme
0.312025
A near-tight lower bound on the density of forward sampling schemes · Bioinform. 2025

Methods — techniques the papers use, named apart from their topics

combinatorial lower bound proof · 0.9
YearPublicationVenuePosition
2025 A near-tight lower bound on the density of forward sampling schemes
abstract
MOTIVATION: Sampling k-mers is a ubiquitous task in sequence analysis algorithms. Sampling schemes such as the often-used random minimizer scheme are particularly appealing as they guarantee at least one k-mer is selected out of every w consecutive k-mers. Sampling fewer k-mers often leads to an increase in efficiency of downstream methods. Thus, developing schemes that have low density, i.e. have a small proportion of sampled k-mers, is an active area of research. After over a decade of consistent efforts in both decreasing the density of practical schemes and increasing the lower bound on the best possible density, there is still a large gap between the two. RESULTS: We prove a near-tight lower bound on the density of forward sampling schemes, a class of schemes that generalizes minimizer schemes. For small w and k, we observe that our bound is tight when k≡1(mod w). For large w and k, the bound can be approximated by 1w+k⌈w+kw⌉. Importantly, our lower bound implies that existing schemes are much closer to achieving optimal density than previously known. For example, with the current default minimap2 HiFi settings w = 19 and k = 19, we show that the best known scheme for these parameters, the double decycling-set-based minimizer of Pellow et al. is at most 3% denser than optimal, compared to the previous gap of at most 50%. Furthermore, when k≡1(mod w) and the alphabet size σ goes to ∞, we show that mod-minimizers introduced by Groot Koerkamp and Pibiri achieve optimal density matching our lower bound. AVAILABILITY AND IMPLEMENTATION: Minimizer implementations: github.com/RagnarGrootKoerkamp/minimizers ILP and analysis: github.com/treangenlab/sampling-scheme-analysis.
Bryce Kille, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, Todd J. Treangen
Bioinform.3