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Documents authored by Groot Koerkamp, Ragnar

Artifact
Software
DOI: 10.4230/artifacts.22525
OCMu64

Authors: Ragnar Groot Koerkamp and Mees de Vries

Abstract
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Ragnar Groot Koerkamp, Mees de Vries. OCMu64 (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22525,
   title = {{OCMu64}}, 
   author = {Groot Koerkamp, Ragnar and de Vries, Mees},
   note = {Software (visited on 2024-12-05)},
   url = {https://github.com/mjdv/ocmu64},
   doi = {10.4230/artifacts.22525},
}
Document
PACE Solver Description
DOI: 10.4230/LIPIcs.IPEC.2024.35
PACE Solver Description: OCMu64, a Solver for One-Sided Crossing Minimization

Authors: Ragnar Groot Koerkamp and Mees de Vries

Published in: LIPIcs, Volume 321, 19th International Symposium on Parameterized and Exact Computation (IPEC 2024)

Abstract
Given a bipartite graph (A,B), the one-sided crossing minimization (OCM) problem is to find an ordering of the vertices of B that minimizes the number of edge crossings when drawn in the plane. We introduce the novel strongly fixed, practically fixed, and practically glued reductions that maximally generalize some existing reductions. We apply these in our exact solver OCMu64, that directly uses branch-and-bound on the ordering of the vertices of B and does not depend on ILP or SAT solvers.
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Ragnar Groot Koerkamp and Mees de Vries. PACE Solver Description: OCMu64, a Solver for One-Sided Crossing Minimization. In 19th International Symposium on Parameterized and Exact Computation (IPEC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 321, pp. 35:1-35:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.IPEC.2024.35,
  author =	{Groot Koerkamp, Ragnar and de Vries, Mees},
  title =	{{PACE Solver Description: OCMu64, a Solver for One-Sided Crossing Minimization}},
  booktitle =	{19th International Symposium on Parameterized and Exact Computation (IPEC 2024)},
  pages =	{35:1--35:5},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-353-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{321},
  editor =	{Bonnet, \'{E}douard and Rz\k{a}\.{z}ewski, Pawe{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2024.35},
  URN =		{urn:nbn:de:0030-drops-222616},
  doi =		{10.4230/LIPIcs.IPEC.2024.35},
  annote =	{Keywords: Graph drawing, crossing number, branch and bound}
}
Artifact
Software
DOI: 10.4230/artifacts.22510
RagnarGrootKoerkamp/astar-pairwise-aligner

Authors: Ragnar Groot Koerkamp

Abstract
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Ragnar Groot Koerkamp. RagnarGrootKoerkamp/astar-pairwise-aligner (Software). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22510,
   title = {{RagnarGrootKoerkamp/astar-pairwise-aligner}}, 
   author = {Groot Koerkamp, Ragnar},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:0da264cc1294d18cb07ee0d76934929e5836e239;origin=https://github.com/RagnarGrootKoerkamp/astar-pairwise-aligner;visit=swh:1:snp:3158598ab43adbfc0661bcb6534fa0cf81397964;anchor=swh:1:rev:d5088352cf2a7474c35b23b046cbda3c4d94c988}{\texttt{swh:1:dir:0da264cc1294d18cb07ee0d76934929e5836e239}} (visited on 2024-11-28)},
   url = {https://github.com/RagnarGrootKoerkamp/astar-pairwise-aligner},
   doi = {10.4230/artifacts.22510},
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.11
The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers

Authors: Ragnar Groot Koerkamp and Giulio Ermanno Pibiri

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Motivation. Given a string S, a minimizer scheme is an algorithm defined by a triple (k,w,𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the smallest k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same k-mer, the set of the sampled k-mers is typically much smaller than S. More generally, we consider substring sampling algorithms that respect a window guarantee: at least one k-mer must be sampled from every window of w consecutive k-mers. As a sampled k-mer is uniquely identified by its absolute position in S, we can define the density of a sampling algorithm as the fraction of distinct sampled positions. Good methods have low density which, by respecting the window guarantee, is lower bounded by 1/w. It is however difficult to design a sequence-agnostic algorithm with provably optimal density. In practice, the order 𝒪 is usually implemented using a pseudo-random hash function to obtain the so-called random minimizer. This scheme is simple to implement, very fast to compute even in streaming fashion, and easy to analyze. However, its density is almost a factor of 2 away from the lower bound for large windows. Methods. In this work we introduce mod-sampling, a two-step sampling algorithm to obtain new minimizer schemes. Given a (small) parameter t, the mod-sampling algorithm finds the position p of the smallest t-mer in a window. It then samples the k-mer at position pod w. The lr-minimizer uses t = k-w and the mod-minimizer uses t≡ k (mod w). Results. These new schemes have provably lower density than random minimizers and other schemes when k is large compared to w, while being as fast to compute. Importantly, the mod-minimizer achieves optimal density when k → ∞. Although the mod-minimizer is not the first method to achieve optimal density for large k, its proof of optimality is simpler than previous work. We provide pseudocode for a number of other methods and compare to them. In practice, the mod-minimizer has considerably lower density than the random minimizer and other state-of-the-art methods, like closed syncmers and miniception, when k > w. We plugged the mod-minimizer into SSHash, a k-mer dictionary based on minimizers. For default parameters (w,k) = (11,21), space usage decreases by 15% when indexing the whole human genome (GRCh38), while maintaining its fast query time.
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Ragnar Groot Koerkamp and Giulio Ermanno Pibiri. The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.WABI.2024.11,
  author =	{Groot Koerkamp, Ragnar and Pibiri, Giulio Ermanno},
  title =	{{The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.11},
  URN =		{urn:nbn:de:0030-drops-206552},
  doi =		{10.4230/LIPIcs.WABI.2024.11},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.17
A*PA2: Up to 19× Faster Exact Global Alignment

Authors: Ragnar Groot Koerkamp

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Motivation. Pairwise alignment is at the core of computational biology. Most commonly used exact methods are either based on O(ns) band doubling or O(n+s²) diagonal transition, where n is the sequence length and s the number of errors. However, as the length of sequences has grown, these exact methods are often replaced by approximate methods based on e.g. seed-and-extend and heuristics to bound the computed region. We would like to develop an exact method that matches the performance of these approximate methods. Recently, Astarix introduced the A* shortest path algorithm with the seed heuristic for exact sequence-to-graph alignment. A*PA adapted and improved this for pairwise sequence alignment and achieves near-linear runtime when divergence (error rate) is low, at the cost of being very slow when divergence is high. Methods. We introduce A*PA2, an exact global pairwise aligner with respect to edit distance. The goal of A*PA2 is to unify the near-linear runtime of A*PA on similar sequences with the efficiency of dynamic programming (DP) based methods. Like Edlib, A*PA2 uses Ukkonen’s band doubling in combination with Myers' bitpacking. A*PA2 1) uses large block sizes inspired by Block Aligner, 2) extends this with SIMD (single instruction, multiple data), 3) introduces a new profile for efficient computations, 4) introduces a new optimistic technique for traceback based on diagonal transition, 5) avoids recomputation of states where possible, and 6) applies the heuristics developed in A*PA and improves them using pre-pruning. Results. With the first 4 engineering optimizations, A*PA2-simple has complexity O(ns) and is 6× to 8× faster than Edlib for sequences ≥ 10 kbp. A*PA2-full also includes the heuristic and is often near-linear in practice for sequences with small divergence. The average runtime of A*PA2 is 19× faster than the exact aligners BiWFA and Edlib on >500 kbp long ONT (Oxford Nanopore Technologies) reads of a human genome having 6% divergence on average. On shorter ONT reads of 11% average divergence the speedup is 5.6× (avg. length 11 kbp) and 0.81× (avg. length 800 bp). On all tested datasets, A*PA2 is competitive with or faster than approximate methods.
Cite as

Ragnar Groot Koerkamp. A*PA2: Up to 19× Faster Exact Global Alignment. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{grootkoerkamp:LIPIcs.WABI.2024.17,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{A*PA2: Up to 19× Faster Exact Global Alignment}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{17:1--17:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.17},
  URN =		{urn:nbn:de:0030-drops-206610},
  doi =		{10.4230/LIPIcs.WABI.2024.17},
  annote =	{Keywords: Edit distance, Pairwise alignment, A*, Shortest path, Dynamic programming}
}
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