15 Search Results for "Doerr¹, Daniel"

Document
DOI: 10.4230/LIPIcs.STACS.2026.6
Threshold-Driven Streaming Graph: Expansion and Rumor Spreading

Authors: Flora Angileri, Andrea Clementi, Emanuele Natale, Michele Salvi, and Isabella Ziccardi

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
A randomized distributed algorithm called RAES was introduced in [Becchetti et al., 2020] to extract a bounded-degree expander from a dense n-vertex expander graph G = (V, E). The algorithm relies on a simple threshold-based procedure. A key assumption in [Becchetti et al., 2020] is that the input graph G is static - i.e., both its vertex set V and edge set E remain unchanged throughout the process - while the analysis of raes in dynamic models is left as a major open question. In this work, we investigate the behavior of RAES under a dynamic graph model induced by a streaming node-churn process (also known as the sliding window model), where, at each discrete round, a new node joins the graph and the oldest node departs. This process yields a bounded-degree dynamic graph 𝒢 = {G_t = (V_t, E_t) : t ∈ ℕ} that captures essential characteristics of peer-to-peer networks - specifically, node churn and threshold on the number of connections each node can manage. We prove that every snapshot G_t in the dynamic graph sequence has good expansion properties with high probability. Furthermore, we leverage this property to establish a logarithmic upper bound on the completion time of the well-known PUSH and PULL rumor spreading protocols over the dynamic graph 𝒢.
Cite as

Flora Angileri, Andrea Clementi, Emanuele Natale, Michele Salvi, and Isabella Ziccardi. Threshold-Driven Streaming Graph: Expansion and Rumor Spreading. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{angileri_et_al:LIPIcs.STACS.2026.6,
  author =	{Angileri, Flora and Clementi, Andrea and Natale, Emanuele and Salvi, Michele and Ziccardi, Isabella},
  title =	{{Threshold-Driven Streaming Graph: Expansion and Rumor Spreading}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{6:1--6:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.6},
  URN =		{urn:nbn:de:0030-drops-254957},
  doi =		{10.4230/LIPIcs.STACS.2026.6},
  annote =	{Keywords: Distributed Algorithms, Randomized Algorithms, Dynamic Random Graphs, Graph Expansion, Rumor Spreading}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.59
When Is Local Search Both Effective and Efficient?

Authors: Artem Kaznatcheev and Sofia Vazquez Alferez

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
Combinatorial optimization problems implicitly define fitness landscapes that combine the numeric structure of the "fitness" function to be maximized with the combinatorial structure of which assignments are "adjacent". Local search starts at an assignment in this landscape and successively moves assignments until no further improvement is possible among the adjacent assignments. Classic analyses of local search algorithms have focused more on the question of effectiveness ("did we find a good solution?") and often implicitly assumed that there are no doubts about their efficiency ("did we find it quickly?"). But there are many reasons to doubt the efficiency of local search. Even if we focus on fitness landscapes on the hypercube that are single peaked on every subcube (known as semismooth fitness landscapes, completely unimodal pseudo-Boolean functions, or acyclic unique sink orientations) where effectiveness is obvious, many local search algorithms are known to be inefficient. Since fitness landscapes are unwieldy exponentially large objects, we focus on their polynomial-sized representations by instances of valued constraint satisfaction problems (VCSP). We define a "direction" for valued constraints such that directed VCSPs generate semismooth fitness landscapes. We call directed VCSPs oriented if they do not have any pair of variables with arcs in both directions. Since recognizing if a VCSP-instance is directed or oriented is coNP-complete, we generalized oriented VCSPs as conditionally-smooth fitness landscapes where the structural property of "conditionally-smooth" is recognizable in polynomial time for a VCSP-instance. We prove that many popular local search algorithms like random ascent, simulated annealing, history-based rules, jumping rules, and the Kernighan-Lin heuristic are very efficient on conditionally-smooth landscapes. But conditionally-smooth landscapes are still expressive enough so that other well-regarded local search algorithms like steepest ascent and random facet require a super-polynomial number of steps to find the fitness peak.
Cite as

Artem Kaznatcheev and Sofia Vazquez Alferez. When Is Local Search Both Effective and Efficient?. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 59:1-59:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kaznatcheev_et_al:LIPIcs.STACS.2026.59,
  author =	{Kaznatcheev, Artem and Vazquez Alferez, Sofia},
  title =	{{When Is Local Search Both Effective and Efficient?}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{59:1--59:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.59},
  URN =		{urn:nbn:de:0030-drops-255480},
  doi =		{10.4230/LIPIcs.STACS.2026.59},
  annote =	{Keywords: valued constraint satisfaction problem, local search, algorithm analysis, constraint graphs, pseudo-Boolean functions, parameterized complexity}
}
Document
DOI: 10.4230/LIPIcs.DISC.2025.26
Towards Constant Time Multi-Call Rumor Spreading on Small-Set Expanders

Authors: Emilio Cruciani, Sebastian Forster, and Tijn de Vos

Published in: LIPIcs, Volume 356, 39th International Symposium on Distributed Computing (DISC 2025)

Abstract
We study a multi-call variant of the classic PUSH&PULL rumor spreading process where nodes can contact k of their neighbors instead of a single one during both PUSH and PULL operations. We show that rumor spreading can be made faster at the cost of an increased amount of communication between the nodes. As a motivating example, consider the process on a complete graph of n nodes: while the standard PUSH&PULL protocol takes Θ(log n) rounds, we prove that our k-PUSH&PULL variant completes in Θ(log_{k} n) rounds, with high probability. We generalize this result in an expansion-sensitive way, as has been done for the classic PUSH&PULL protocol for different notions of expansion, e.g., conductance and vertex expansion. We consider small-set vertex expanders, graphs in which every sufficiently small subset of nodes has a large neighborhood, ensuring strong local connectivity. In particular, when the expansion parameter satisfies ϕ > 1, these graphs have a diameter of o(log n), as opposed to other standard notions of expansion. Since the graph’s diameter is a lower bound on the number of rounds required for rumor spreading, this makes small-set expanders particularly well-suited for fast information dissemination. We prove that k-PUSH&PULL takes O(log_{ϕ} n ⋅ log_{k} n) rounds in these expanders, with high probability. We complement this with a simple lower bound of Ω(log_{ϕ} n+ log_{k} n) rounds.
Cite as

Emilio Cruciani, Sebastian Forster, and Tijn de Vos. Towards Constant Time Multi-Call Rumor Spreading on Small-Set Expanders. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 26:1-26:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cruciani_et_al:LIPIcs.DISC.2025.26,
  author =	{Cruciani, Emilio and Forster, Sebastian and de Vos, Tijn},
  title =	{{Towards Constant Time Multi-Call Rumor Spreading on Small-Set Expanders}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{26:1--26:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-402-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{356},
  editor =	{Kowalski, Dariusz R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2025.26},
  URN =		{urn:nbn:de:0030-drops-248434},
  doi =		{10.4230/LIPIcs.DISC.2025.26},
  annote =	{Keywords: small set expansion, vertex expansion, rumor spreading, multi-call rumor spreading, push\&pull protocol}
}
Document
DOI: 10.4230/LIPIcs.AFT.2025.14
Optimistic Message Dissemination

Authors: Chen-Da Liu-Zhang, Christian Matt, and Søren Eller Thomsen

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)

Abstract
Message dissemination is a fundamental building block in distributed systems and guarantees that any message sent eventually reaches all parties. State of the art provably secure protocols for disseminating messages have a per-party communication complexity that is linear in the inverse of the fraction of parties that are guaranteed to be honest in the worst case. Unfortunately, this per-party communication complexity arises even in cases where the actual fraction of parties that behave honestly is close to 1. In this paper, we propose an optimistic message dissemination protocol that adopts to the actual conditions in which it is deployed, with optimal worst-case per-party communication complexity. Our protocol cuts the complexity of prior provably secure protocols for 49% worst-case corruption almost in half under optimistic conditions and allows practitioners to combine efficient heuristics with secure fallback mechanisms.
Cite as

Chen-Da Liu-Zhang, Christian Matt, and Søren Eller Thomsen. Optimistic Message Dissemination. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 14:1-14:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{liuzhang_et_al:LIPIcs.AFT.2025.14,
  author =	{Liu-Zhang, Chen-Da and Matt, Christian and Thomsen, S{\o}ren Eller},
  title =	{{Optimistic Message Dissemination}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{14:1--14:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.14},
  URN =		{urn:nbn:de:0030-drops-247332},
  doi =		{10.4230/LIPIcs.AFT.2025.14},
  annote =	{Keywords: flooding, message dissemination, optimistic}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.47
Time Lower Bounds for the Metropolis Process and Simulated Annealing

Authors: Zongchen Chen, Dan Mikulincer, Daniel Reichman, and Alexander S. Wein

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)

Abstract
The Metropolis process (MP) and Simulated Annealing (SA) are stochastic local search heuristics that are often used in solving combinatorial optimization problems. Despite significant interest, there are very few theoretical results regarding the quality of approximation obtained by MP and SA (with polynomially many iterations) for NP-hard optimization problems. We provide rigorous lower bounds for MP and SA with respect to the classical maximum independent set problem when the algorithms are initialized from the empty set. We establish the existence of a family of graphs for which both MP and SA fail to find approximate solutions in polynomial time. More specifically, we show that for any ε ∈ (0,1) there are n-vertex graphs for which the probability SA (when limited to polynomially many iterations) will approximate the optimal solution within ratio Ω(1/n^{1-ε}) is exponentially small. Our lower bounds extend to graphs of constant average degree d, illustrating the failure of MP to achieve an approximation ratio of Ω(log(d)/d) in polynomial time. In some cases, our lower bounds apply even when the temperature is chosen adaptively. Finally, we prove exponential-time lower bounds when the inputs to these algorithms are bipartite graphs, and even trees, which are known to admit polynomial-time algorithms for the independent set problem.
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Zongchen Chen, Dan Mikulincer, Daniel Reichman, and Alexander S. Wein. Time Lower Bounds for the Metropolis Process and Simulated Annealing. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 47:1-47:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.APPROX/RANDOM.2025.47,
  author =	{Chen, Zongchen and Mikulincer, Dan and Reichman, Daniel and Wein, Alexander S.},
  title =	{{Time Lower Bounds for the Metropolis Process and Simulated Annealing}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{47:1--47:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.47},
  URN =		{urn:nbn:de:0030-drops-244138},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.47},
  annote =	{Keywords: Metropolis Process, Simulated Annealing, Independent Set}
}
Artifact
Software
DOI: 10.4230/artifacts.24320
sqz

Authors: Peter Heringer and Daniel Doerr

Abstract
Cite as

Peter Heringer, Daniel Doerr. sqz (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@misc{dagstuhl-artifact-24320,
   title = {{sqz}}, 
   author = {Heringer, Peter and Doerr, Daniel},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:d7c4cb1cc536abc10166918dda34b0b373987c7b}{\texttt{swh:1:dir:d7c4cb1cc536abc10166918dda34b0b373987c7b}} (visited on 2025-08-15)},
   url = {https://github.com/codialab/sqz},
   doi = {10.4230/artifacts.24320},
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.WABI.2025.2
We Are What We Index; a Primer for the Wheeler Graph Era (Invited Talk)

Authors: Ben Langmead

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Since the arrival of second-generation sequencing, we have needed to build indexes over reference sequences - e.g. genomes and transcriptomes - in order to solve read alignment and classification problems efficiently [Langmead et al., 2009; Li and Durbin, 2009; Li et al., 2009]. The rule has been: what we can index determines what we can do. When indexing strings, we can use methods like suffix arrays [Manber and Myers, 1993], the Burrows-Wheeler Transform (BWT) [Burrows and Wheeler, 1994] / FM Index [Ferragina and Manzini, 2000], or k-mer indexes [Marchet et al., 2021]. What if we want to index objects more complex than strings? A pangenome, for example, is a large collection of similar strings, e.g. the hundreds of assemblies that make up the Human Pangenome Reference [Liao et al., 2023] or all the bacteria in the Refseq database [Goldfarb et al., 2025]. We may wish to combine these strings into a multiple sequence alignment (MSA) or a graph first. Can we index those efficiently? In many useful cases the answer is "yes," but in others the answer is "no." The story of how we learned exactly when the answer is "yes" versus "no" unfolded through a sequence of insights. Here we review this story, eventually arriving at the definition of Wheeler graphs as discovered and formalized by Gagie, Manzini and Sirén [Gagie et al., 2017]. We will focus on indexes based on the BWT, since these (a) are lossless full-text indexes, (b) are widely used in practice [Langmead et al., 2009; Li and Durbin, 2009], and (c) form the theoretical throughline for all the indexing strategies on the path to Wheeler graphs. We will trace the BWT-based indexing story from the early days of the FM Index, though its step-by-step gobbling up of trees (XBW-transform [Ferragina et al., 2005]) and de Bruijn Graphs (BOSS representation [Bowe et al., 2012]), and to the eventual formalization of Wheeler graphs [Gagie et al., 2017]. Along the way, we will define and update our notions of what it means to track a consecutive range of elements in the structure, and what it means for an index to be efficient. We will also connect these notions to automata [Sipser, 1996], noting how the indexability of Wheeler graphs (also called Wheeler automata) is connected to the mechanics of how to efficiently represent and simulate a finite automaton [Alanko et al., 2021]. With this context, we can imagine improved indexes for the future of genomics and pangenomics. De Bruijn are extremely practical and are the most widely used among the non-string data structures that are also Wheeler graphs. But we might prefer other options. For example, de Bruijn graphs have the undesirable property that they usually encode not only the true longer-than-k substrings of the original text, but also "false" substrings that span repeats. Related to this, paths through the de Bruijn graph can "glue" substrings together that are horizontally distant in the MSA. Could other Wheeler graphs be practical alternatives to de Bruijn graphs? For instance, the original GCSA study by Sirén, Välimäki and Mäkinen proposed a way to convert a multiple alignment into an automaton that either is a Wheeler graph or can be made into one [Sirén et al., 2014]. This warrants further exploration, possibly with the help of improved tools for solving the NP-complete problem of recognizing whether a graph is a Wheeler graph [Chao et al., 2023]. The notion of BWT tunnels [Baier, 2018] gives another route: we can begin with a concatenated pangenome strings and compress it by identifying and collapsing BWT tunnels. This yields a Wheeler graph that is compressed like the de Bruijn graph, but without departing from the exact contents or coordinate systems of the original genomes. The future might need us to explore all these Wheeler-graph indexes, along with the also highly practical and always-improving world of indexes buiover collections of strings [Gagie et al., 2018].
Cite as

Ben Langmead. We Are What We Index; a Primer for the Wheeler Graph Era (Invited Talk). In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 2:1-2:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{langmead:LIPIcs.WABI.2025.2,
  author =	{Langmead, Ben},
  title =	{{We Are What We Index; a Primer for the Wheeler Graph Era}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{2:1--2:2},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.2},
  URN =		{urn:nbn:de:0030-drops-239288},
  doi =		{10.4230/LIPIcs.WABI.2025.2},
  annote =	{Keywords: Indexing, Burrows-Wheeler Transform}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.14
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.
Cite as

Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.17
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT

Authors: Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
String matching problems in bioinformatics are typically for finding exact substring matches between a query and a reference text. Previous formulations often focus on maximum exact matches (MEMs). However, multiple occurrences of substrings of the query in the text that are long enough but not maximal may not be captured by MEMs. Such long matches can be informative, especially when the text is a collection of similar sequences such as genomes. In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount of LEMs, so we only consider those above some length threshold ℒ. These are referred to as long LEMs. The purpose of long LEMs is to capture substring matches between a query and a text that are not necessarily maximal in the pattern but still long enough to be important. Therefore efficient long LEMs finding algorithms are desired for these datasets. However, these datasets are too large to query on traditional string indexes. Fortunately, these datasets are very repetitive. Recently, compressed string indexes that take advantage of the redundancy in the data but retain efficient querying capability have been proposed as a solution. We therefore give an efficient algorithm for computing all the long LEMs of a query and a text in a BWT runs compressed string index. We describe an O(m+occ) expected time algorithm that relies on an O(r) words space string index for outputting all long LEMs of a pattern with respect to a text given the matching statistics of the pattern with respect to the text. Here m is the length of the query, occ is the number of long LEMs outputted, and r is the number of runs in the BWT of the text. The O(r) space string index we describe relies on an adaptation of the move data structure by Nishimoto and Tabei. We are able to support LCP[i] queries in constant time given SA[i]. In other words, we answer PLCP[i] queries in constant time. These PLCP queries enable the efficient long LEM query. Long LEMs may provide useful similarity information between a pattern and a text that MEMs may ignore. This information is particularly useful in pangenome and biobank scale haplotype panel contexts.
Cite as

Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sanaullah_et_al:LIPIcs.WABI.2025.17,
  author =	{Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaojie},
  title =	{{An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{17:1--17:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.17},
  URN =		{urn:nbn:de:0030-drops-239433},
  doi =		{10.4230/LIPIcs.WABI.2025.17},
  annote =	{Keywords: BWT, LEM, Long LEM, MEM, Run Length Compressed BWT, Move Data Structure, Pangenome}
}
Document
Extended Abstract
DOI: 10.4230/LIPIcs.WABI.2025.23
Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract)

Authors: Vikram S. Shivakumar and Ben Langmead

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Pangenome collections continue to grow and proliferate to hundreds of high-quality genomes, for example, the expanded v2 version of the Human Pangenome Reference Consortium (HPRC) dataset spanning 474 human haplotypes [Liao et al., 2023]. As the size and complexity of these collections grow, it is increasingly important that our methods for studying and indexing pangenomes be scalable and updateable. Maximal Unique Matches (multi-MUMs), exact substring matches present exactly once in all sequences in a pangenome collection, represent conserved anchor sequences that can comprise a common coordinate system. We previously proposed a framework and tool called Mumemto for rapidly identifying multi-MUMs during construction of a compressed pangenome index [Shivakumar and Langmead, 2025]. Using prefix-free parsing (PFP) [Boucher et al., 2019], a compressed-space method for computing full-text indexes, Mumemto outperforms existing methods for identifying multi-MUMs. However, one drawback remains updateability and scalability. Mumemto can become memory-intensive for large pangenomes (> 300 human genomes), and as newly assembled genomes are added to a pangenome collection, Mumemto requires re-running on the entire updated collection. To address this, we developed a partition-merging approach to compute multi-MUMs with Mumemto. We introduce two strategies for merging of multi-MUMs computed across different collections (see Figure 1), enabling parallelization across partitions and simple computation of multi-MUMs for incrementally-updated collections. The first strategy requires a common sequence in each partition (which we call "anchor-based merging"), which serves as a coordinate system to identify multi-MUM overlaps between partitions. By tracking the next longest match for all multi-MUMs and unique matches (UMs) in an auxiliary data structure, intersections between matches can be filtered out if no longer unique in the union collection. The second strategy identifies overlaps directly from the multi-MUM substrings (called "string-based merging"). The overlaps are identified by running Mumemto over the extracted multi-MUM sequences and are similarly filtered out if they are too short to considered unique. Lastly, we propose an extension to anchor-based merging to enable the computation of partial multi-MUMs, present in only a subset of sequences in the union set. The partition-merging framework introduces a tradeoff space in Mumemto between running time and memory, depending on partition size and the number of threads. Running parallel, per-partition Mumemto processes and merging the results reduces the running time but increases the peak memory footprint, while running a single Mumemto thread over each partition serially yields longer running time but a smaller memory footprint. To evaluate this tradeoff, we computed multi-MUMs across 474 haplotypes of chr19 from the HPRC v2 dataset [Liao et al., 2023] and 69 assemblies of A. thaliana [Lian et al., 2024] (Table 1). The string-based method also enables merging multi-MUMs between disjoint collections, for example subclades in a phylogenetic tree. By merging multi-MUMs along the shape of the tree, we can compute matches at internal nodes of the tree along with the root, revealing clade-specific conservation and structural variation. Multi-MUM merging also enables interspecific match computation, which was previously infeasible with Mumemto due to high memory usage for highly-diverse input sequence collections. We use partition-merging to compute multi-MUMs across 29 primate assemblies, and found a correspondence to ultraconserved elements previously found across mammalian genomes [Cummins et al., 2024]. We show that a partitioned Mumemto enables scalability to growing pangenome collections and expands the applicability of Mumemto to larger, more diverse datasets. As a result, Mumemto is the only method capable of computing exact matches across the entire HPRC v2 dataset (474 haplotypes [Liao et al., 2023]), and can easily incorporate future releases of assemblies without recomputation. This increases the scope for exploration of genomic conservation and variation and highlights the potential for Mumemto as a core method for future pangenomics and comparative genomics research. The partitioned Mumemto framework is implemented in v1.3.0 and is available open-source at https://github.com/vikshiv/mumemto.
Cite as

Vikram S. Shivakumar and Ben Langmead. Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract). In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 23:1-23:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shivakumar_et_al:LIPIcs.WABI.2025.23,
  author =	{Shivakumar, Vikram S. and Langmead, Ben},
  title =	{{Partitioned Multi-MUM Finding for Scalable Pangenomics}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{23:1--23:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.23},
  URN =		{urn:nbn:de:0030-drops-239490},
  doi =		{10.4230/LIPIcs.WABI.2025.23},
  annote =	{Keywords: Pangenomics, Comparative genomics, Compressed indexing}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.13
Pangenome Graph Indexing via the Multidollar-BWT

Authors: Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, and Paola Bonizzoni

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Indexing pangenome graphs is a major algorithmic challenge in computational pangenomics, a recent and active research field that seeks to use graphs as representations of multiple genomes. Since these graphs are constructed from whole genome sequences of a species population, they can become very large, making indexing one of the most challenging problems. In this paper, we propose gindex, a novel indexing approach to solve the Graph Pattern Matching Problem based on the multidollar-BWT. Specifically, gindex aims to find all occurrences of a pattern in a sequence-labeled graph by overcoming two main limitations of GCSA2, one of the most widely used graph indexes: handling queries of arbitrary length and scaling to large graphs without pruning any complex regions. Moreover, we show how a smart preprocessing step can optimize the use of multidollar-BWT to skip small redundant sub-patterns and enhance gindex’s querying capabilities. We demonstrate the effectiveness of our approach by comparing it to GCSA2 in terms of index construction and query time, using different preprocessing modes on three pangenome graphs: one built from Drosophila genomes and two produced by the Human Pangenome Reference Consortium. The results show that gindex can scale on human pangenome graphs - which GCSA2 cannot index using large amounts of RAM - with acceptable memory and time requirements. Moreover, gindex achieves fast query times, although not as fast as GCSA2, which may produce false positives.
Cite as

Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, and Paola Bonizzoni. Pangenome Graph Indexing via the Multidollar-BWT. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cozzi_et_al:LIPIcs.SEA.2025.13,
  author =	{Cozzi, Davide and Riccardi, Brian and Denti, Luca and Ciccolella, Simone and Sadakane, Kunihiko and Bonizzoni, Paola},
  title =	{{Pangenome Graph Indexing via the Multidollar-BWT}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.13},
  URN =		{urn:nbn:de:0030-drops-232515},
  doi =		{10.4230/LIPIcs.SEA.2025.13},
  annote =	{Keywords: Multidollar-BWT, Graph Index, Graph Pattern Matching, Pangenome Graph}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.22
Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem

Authors: Leonard Bohnenkämper

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
One of the most fundamental problems in genome rearrangement is the (genomic) distance problem. It is typically formulated as finding the minimum number of rearrangements under a model that are needed to transform one genome into the other. A powerful multi-chromosomal model is the Double Cut and Join (DCJ) model. While the DCJ model is not able to deal with some situations that occur in practice, like duplicated or lost regions, it was extended over time to handle these cases. First, it was extended to the DCJ-indel model, solving the issue of lost markers. Later ILP-solutions for so called natural genomes, in which each genomic region may occur an arbitrary number of times, were developed, enabling in theory to solve the distance problem for any pair of genomes. However, some theoretical and practical issues remained unsolved. On the theoretical side of things, there exist two disparate views of the DCJ-indel model, motivated in the same way, but with different conceptualizations that could not be reconciled so far. On the practical side, while the solutions for natural genomes typically perform well on telomere to telomere resolved genomes, they have been shown in recent years to quickly loose performance on genomes with a large number of contigs or linear chromosomes. This has been linked to a particular technique increasing the solution space superexponentially named capping. Recently, we introduced a new conceptualization of the DCJ-indel model within the context of another rearrangement problem. In this manuscript, we will apply this new conceptualization to the distance problem. In doing this, we uncover the relation between the disparate conceptualizations of the DCJ-indel model. We are also able to derive an ILP solution to the distance problem that does not rely on capping and therefore significantly improves upon the performance of previous solutions for genomes with high numbers of contigs while still solving the problem exactly. To the best of our knowledge, our approach is the first allowing for an exact computation of the DCJ-indel distance for natural genomes with large numbers of linear chromosomes. We demonstrate the performance advantage as well as limitations in comparison to an existing solution on simulated genomes as well as showing its practical usefulness in an analysis of 11 Drosophila genomes.
Cite as

Leonard Bohnenkämper. Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bohnenkamper:LIPIcs.WABI.2023.22,
  author =	{Bohnenk\"{a}mper, Leonard},
  title =	{{Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{22:1--22:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.22},
  URN =		{urn:nbn:de:0030-drops-186484},
  doi =		{10.4230/LIPIcs.WABI.2023.22},
  annote =	{Keywords: Comparative Genomics, Genome Rearrangement, Double-Cut-And-Join, Indels, Integer Linear Programming, Capping}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.6
Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

Authors: Konstantinn Bonnet, Tobias Marschall, and Daniel Doerr¹

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different copies of the same sequence, then called non-allelic homologous recombination (NAHR). This process can result in genomic rearrangements - including deletion, duplication, and inversion - and is underlying many genomic disorders. Despite its importance for genome evolution and disease, there is a lack of computational models to study genomic loci prone to NAHR. In this work, we propose such a computational model, providing a unified framework for both (allelic) homologous recombination and NAHR. Our model represents a set of genomes as a graph, where human haplotypes correspond to walks through this graph. We formulate two founder set problems under our recombination model, provide flow-based algorithms for their solution, and demonstrate scalability to problem instances arising in practice.
Cite as

Konstantinn Bonnet, Tobias Marschall, and Daniel Doerr¹. Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bonnet_et_al:LIPIcs.WABI.2022.6,
  author =	{Bonnet, Konstantinn and Marschall, Tobias and Doerr¹, Daniel},
  title =	{{Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{6:1--6:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.6},
  URN =		{urn:nbn:de:0030-drops-170403},
  doi =		{10.4230/LIPIcs.WABI.2022.6},
  annote =	{Keywords: founder set reconstruction, variation graph, pangenomics, NAHR, homologous recombination}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.13
A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance

Authors: Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, and Jens Stoye

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. A genome is circular when it contains only circular chromosomes. Different distances of canonical circular genomes can be derived from a structure called breakpoint graph, which represents the relation between the two given genomes as a collection of cycles of even length. Then, the breakpoint distance is equal to n-c_2, where n is the number of genes and c_2 is the number of cycles of length 2. Similarly, when the considered rearrangements are those modeled by the double-cut-and-join (DCJ) operation, the rearrangement distance is n-c, where c is the total number of cycles. The distance problem is a basic unit for several other combinatorial problems related to genome evolution and ancestral reconstruction, such as median or double distance. Interestingly, both median and double distance problems can be solved in polynomial time for the breakpoint distance, while they are NP-hard for the rearrangement distance. One way of exploring the complexity space between these two extremes is to consider a σ_k distance, defined to be n-(c_2+c_4+…+c_k), and increasingly investigate the complexities of median and double distance for the σ₄ distance, then the σ₆ distance, and so on. While for the median much effort was done in our and in other research groups but no progress was obtained even for the σ₄ distance, for solving the double distance under σ₄ and σ₆ distances we could devise linear time algorithms, which we present here.
Cite as

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, and Jens Stoye. A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{braga_et_al:LIPIcs.WABI.2022.13,
  author =	{Braga, Mar{\'\i}lia D. V. and Brockmann, Leonie R. and Klerx, Katharina and Stoye, Jens},
  title =	{{A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{13:1--13:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.13},
  URN =		{urn:nbn:de:0030-drops-170472},
  doi =		{10.4230/LIPIcs.WABI.2022.13},
  annote =	{Keywords: Comparative genomics, genome rearrangement, breakpoint distance, double-cut-and-join (DCJ) distance, double distance}
}
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