10 Search Results for "Berger, Bonnie"

Document
DOI: 10.4230/LIPIcs.SEA.2026.4
Integer Programming Models for the Median of a 0-1 String Set Under Levenshtein Distance

Authors: Claudio Arbib, Andrea D'Ascenzo, Oya E. Karaşan, and Andrea Pizzuti

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
The Median String Problem calls for finding a string that minimizes the average distance from a given set of strings. Under the Levenshtein (or edit) metric, the problem is NP-hard even for binary strings. We devised two novel integer linear programming models for this case and tested them against the only formulation we are aware of in the literature. Our numerical experiments attest to the efficacy of the proposed approach.
Cite as

Claudio Arbib, Andrea D'Ascenzo, Oya E. Karaşan, and Andrea Pizzuti. Integer Programming Models for the Median of a 0-1 String Set Under Levenshtein Distance. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 4:1-4:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{arbib_et_al:LIPIcs.SEA.2026.4,
  author =	{Arbib, Claudio and D'Ascenzo, Andrea and Kara\c{s}an, Oya E. and Pizzuti, Andrea},
  title =	{{Integer Programming Models for the Median of a 0-1 String Set Under Levenshtein Distance}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{4:1--4:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.4},
  URN =		{urn:nbn:de:0030-drops-260081},
  doi =		{10.4230/LIPIcs.SEA.2026.4},
  annote =	{Keywords: Levenshtein Distance, Median String Problem, Integer Programming}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.49
Algorithms for Euclidean Distance Matrix Completion: Exploiting Proximity to Triviality

Authors: Fedor V. Fomin, Petr A. Golovach, M. S. Ramanujan, and Saket Saurabh

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
In the d-Euclidean Distance Matrix Completion (d-EDMC) problem, one aims to determine whether a given partial matrix of pairwise distances can be extended to a full Euclidean distance matrix in d dimensions. This problem is a cornerstone of computational geometry with numerous applications. While classical work on this problem often focuses on exploiting connections to semidefinite programming typically leading to approximation algorithms, we focus on exact algorithms and propose a novel distance-from-triviality parameterization framework to obtain tractability results for d-EDMC. We identify key structural patterns in the input that capture entry density, including chordal substructures and coverability of specified entries by fully specified principal submatrices. We obtain: 1) The first fixed-parameter algorithm (FPT algorithm) for d-EDMC parameterized by d and the maximum number of unspecified entries per row/column. This is achieved through a novel compression algorithm that reduces a given instance to a submatrix on 𝒪(1) rows (for fixed values of the parameters). 2) The first FPT algorithm for d-EDMC parameterized by d and the minimum number of fully specified principal submatrices whose entries cover all specified entries of the given matrix. This result is also achieved through a compression algorithm. 3) A polynomial-time algorithm for d-EDMC when both d and the minimum fill-in of a natural graph representing the specified entries are fixed constants. This result is achieved by combining tools from distance geometry and algorithms from real algebraic geometry. Our work identifies interesting parallels between EDM completion and graph problems, with our algorithms exploiting techniques from both domains.
Cite as

Fedor V. Fomin, Petr A. Golovach, M. S. Ramanujan, and Saket Saurabh. Algorithms for Euclidean Distance Matrix Completion: Exploiting Proximity to Triviality. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 49:1-49:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{fomin_et_al:LIPIcs.SoCG.2026.49,
  author =	{Fomin, Fedor V. and Golovach, Petr A. and Ramanujan, M. S. and Saurabh, Saket},
  title =	{{Algorithms for Euclidean Distance Matrix Completion: Exploiting Proximity to Triviality}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{49:1--49:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.49},
  URN =		{urn:nbn:de:0030-drops-258552},
  doi =		{10.4230/LIPIcs.SoCG.2026.49},
  annote =	{Keywords: Parameterized Complexity, Euclidean Embedding, Polynomial Compression}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.66
Fast Nearest Neighbor Search for 𝓁_p Metrics

Authors: Robert Krauthgamer and Nir Petruschka

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
The Nearest Neighbor Search (NNS) problem asks to design a data structure that preprocesses an n-point dataset X lying in a metric space ℳ, so that given a query point q ∈ ℳ, one can quickly return a point of X minimizing the distance to q. The efficiency of such a data structure is evaluated primarily by the amount of space it uses and the time required to answer a query. We focus on the fast query-time regime, which is crucial for modern large-scale applications, where datasets are massive and queries must be processed online, and is often modeled by query time poly(d log n) when ℳ is a d-dimensional normed space. Our main result is such a randomized data structure for NNS in 𝓁_p^d spaces, p > 2, that achieves p^{O(1) + log log p} approximation with fast query time and poly(dn) space. Our data structure improves, or is incomparable to, the state-of-the-art for the fast query-time regime from [Bartal and Gottlieb, TCS 2019] and [Krauthgamer, Petruschka and Sapir, FOCS 2025].
Cite as

Robert Krauthgamer and Nir Petruschka. Fast Nearest Neighbor Search for 𝓁_p Metrics. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 66:1-66:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{krauthgamer_et_al:LIPIcs.SoCG.2026.66,
  author =	{Krauthgamer, Robert and Petruschka, Nir},
  title =	{{Fast Nearest Neighbor Search for 𝓁\underlinep Metrics}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{66:1--66:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.66},
  URN =		{urn:nbn:de:0030-drops-258737},
  doi =		{10.4230/LIPIcs.SoCG.2026.66},
  annote =	{Keywords: Nearest neighbor search, metric embeddings, 𝓁\underlinep norm}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.70
Improved Parallel Derandomization via Finite Automata with Applications

Authors: Jeff Giliberti and David G. Harris

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
A central approach to algorithmic derandomization is the construction of small-support probability distributions that "fool” randomized algorithms, often enabling efficient parallel (NC) implementations. An abstraction of this idea is fooling polynomial-space statistical tests computed via finite automata [Sivakumar STOC'02]; this encompasses a wide range of properties including k-wise independence and sums of random variables. We present new parallel algorithms to fool finite-state automata, with significantly reduced processor complexity. Briefly, our approach is to iteratively sparsify distributions using a work-efficient lattice rounding routine and maintain accuracy by tracking an aggregate weighted error that is determined by the Lipschitz value of the statistical tests being fooled. We illustrate with improved applications to the Gale-Berlekamp Switching Game and to approximate MAX-CUT via SDP rounding. These involve further several optimizations, such as the truncation of the state space of the automata and FFT-based convolutions to compute transition probabilities efficiently.
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Jeff Giliberti and David G. Harris. Improved Parallel Derandomization via Finite Automata with Applications. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 70:1-70:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{giliberti_et_al:LIPIcs.ESA.2025.70,
  author =	{Giliberti, Jeff and Harris, David G.},
  title =	{{Improved Parallel Derandomization via Finite Automata with Applications}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{70:1--70:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.70},
  URN =		{urn:nbn:de:0030-drops-245381},
  doi =		{10.4230/LIPIcs.ESA.2025.70},
  annote =	{Keywords: Parallel Algorithms, Derandomization, MAX-CUT, Gale-Berlekamp Switching Game}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.30
Algorithmic Contiguity from Low-Degree Conjecture and Applications in Correlated Random Graphs

Authors: Zhangsong Li

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

Abstract
In this paper, assuming a natural strengthening of the low-degree conjecture, we provide evidence of computational hardness for two problems: (1) the (partial) matching recovery problem in the sparse correlated Erdős-Rényi graphs G(n,q;ρ) when the edge-density q = n^{-1+o(1)} and the correlation ρ < √{α} lies below the Otter’s threshold, this resolves a remaining problem in [Jian Ding et al., 2023]; (2) the detection problem between a pair of correlated sparse stochastic block model S(n,λ/n;k,ε;s) and a pair of independent stochastic block models S(n,λs/n;k,ε) when ε² λ s < 1 lies below the Kesten-Stigum (KS) threshold and s < √α lies below the Otter’s threshold, this resolves a remaining problem in [Guanyi Chen et al., 2024]. One of the main ingredient in our proof is to derive certain forms of algorithmic contiguity between two probability measures based on bounds on their low-degree advantage. To be more precise, consider the high-dimensional hypothesis testing problem between two probability measures ℙ and ℚ based on the sample Y. We show that if the low-degree advantage Adv_{≤D}(dℙ/dℚ) = O(1), then (assuming the low-degree conjecture) there is no efficient algorithm A such that ℚ(A(Y) = 0) = 1-o(1) and ℙ(A(Y) = 1) = Ω(1). This framework provides a useful tool for performing reductions between different inference tasks.
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Zhangsong Li. Algorithmic Contiguity from Low-Degree Conjecture and Applications in Correlated Random Graphs. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 30:1-30:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{li:LIPIcs.APPROX/RANDOM.2025.30,
  author =	{Li, Zhangsong},
  title =	{{Algorithmic Contiguity from Low-Degree Conjecture and Applications in Correlated Random Graphs}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{30:1--30:18},
  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.2025.30},
  URN =		{urn:nbn:de:0030-drops-243965},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.30},
  annote =	{Keywords: Algorithmic Contiguity, Low-degree Conjecture, Correlated Random Graphs}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.7
Sequence Similarity Estimation by Random Subsequence Sketching

Authors: Ke Chen, Vinamratha Pattar, and Mingfu Shao

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

Abstract
Sequence similarity estimation is essential for many bioinformatics tasks, including functional annotation, phylogenetic analysis, and overlap graph construction. Alignment-free methods aim to solve large-scale sequence similarity estimation by mapping sequences to more easily comparable features that can approximate edit distances efficiently. Substrings or k-mers, as the dominant choice of features, face an unavoidable compromise between sensitivity and specificity when selecting the proper k-value. Recently, subsequence-based features have shown improved performance, but they are computationally demanding, and determining the ideal subsequence length remains an intricate art. In this work, we introduce SubseqSketch, a novel alignment-free scheme that maps a sequence to an integer vector, where the entries correspond to dynamic, rather than fixed, lengths of random subsequences. The cosine similarity between these vectors exhibits a strong correlation with the edit similarity between the original sequences. Through experiments on benchmark datasets, we demonstrate that SubseqSketch is both efficient and effective across various alignment-free tasks, including nearest neighbor search and phylogenetic clustering. A C++ implementation of SubseqSketch is openly available at https://github.com/Shao-Group/SubseqSketch.
Cite as

Ke Chen, Vinamratha Pattar, and Mingfu Shao. Sequence Similarity Estimation by Random Subsequence Sketching. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.WABI.2025.7,
  author =	{Chen, Ke and Pattar, Vinamratha and Shao, Mingfu},
  title =	{{Sequence Similarity Estimation by Random Subsequence Sketching}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{7:1--7:17},
  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.2025.7},
  URN =		{urn:nbn:de:0030-drops-239332},
  doi =		{10.4230/LIPIcs.WABI.2025.7},
  annote =	{Keywords: Alignment-free sequence comparison, Phylogenetic clustering, Nearest neighbor search, Edit distance embedding}
}
Document
Research
DOI: 10.4230/OASIcs.Grossi.10
Faster Run-Length Compressed Suffix Arrays

Authors: Nathaniel K. Brown, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, and Marinella Sciortino

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract
We first review how we can store a run-length compressed suffix array (RLCSA) for a text T of length n over an alphabet of size σ whose Burrows-Wheeler Transform (BWT) consists of r runs in O (r log (n / r) + r log σ + σ) bits such that later, given character a and the suffix-array (SA) interval for P, we can find the SA interval for a P in O (log r_a + log log n) time, where r_a is the number of runs of copies of a in the BWT. We then show how to modify the RLCSA such that we find the SA interval for a P in only O (log r_a) time, without increasing its asymptotic space bound. Our key idea is applying a result by Nishimoto and Tabei (ICALP 2021) and then replacing rank queries on sparse bitvectors by a constant number of select queries. We also review two-level indexing and discuss how our faster RLCSA may be useful in improving it. Finally, we briefly discuss how two-level indexing may speed up a recent heuristic for finding maximal exact matches of a pattern with respect to an indexed text.
Cite as

Nathaniel K. Brown, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, and Marinella Sciortino. Faster Run-Length Compressed Suffix Arrays. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 10:1-10:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{brown_et_al:OASIcs.Grossi.10,
  author =	{Brown, Nathaniel K. and Gagie, Travis and Manzini, Giovanni and Navarro, Gonzalo and Sciortino, Marinella},
  title =	{{Faster Run-Length Compressed Suffix Arrays}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{10:1--10:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.10},
  URN =		{urn:nbn:de:0030-drops-238095},
  doi =		{10.4230/OASIcs.Grossi.10},
  annote =	{Keywords: Run-length compressed suffix arrays, interpolative coding, two-level indexing}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.20
SimdMinimizers: Computing Random Minimizers, fast

Authors: Ragnar Groot Koerkamp and Igor Martayan

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

Abstract
Motivation. Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers. As DNA sequencers are getting more accurate, some applications can afford to use a larger w and hence sparser and smaller sketches. And as sketches get smaller, their analysis becomes faster, so the time spent sketching the full-sized input becomes more of a bottleneck. Methods. Our library simd-minimizers implements a random minimizer algorithm using SIMD instructions. It supports both AVX2 and NEON architectures. Its main novelty is two-fold. First, it splits the input into 8 chunks that are streamed over in parallel through all steps of the algorithm. This is enabled by using the completely deterministic two-stacks sliding window minimum algorithm, which seems not to have been used before for finding minimizers. Results. Our library is up to 6.8× faster than a scalar implementation of the rescan method when w = 5 is small, and 3.4× faster for larger w = 19. Computing canonical minimizers is less than 50% slower than computing forward minimizers, and over 15× faster than the existing implementation in the minimizer-iter crate. Our library finds all (canonical) minimizers of a 3.2 Gbp human genome in 5.2 (resp. 6.7) seconds.
Cite as

Ragnar Groot Koerkamp and Igor Martayan. SimdMinimizers: Computing Random Minimizers, fast. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.SEA.2025.20,
  author =	{Groot Koerkamp, Ragnar and Martayan, Igor},
  title =	{{SimdMinimizers: Computing Random Minimizers, fast}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{20:1--20:19},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-232581},
  doi =		{10.4230/LIPIcs.SEA.2025.20},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.35
Near-Optimal Directed Low-Diameter Decompositions

Authors: Karl Bringmann, Nick Fischer, Bernhard Haeupler, and Rustam Latypov

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
Low Diameter Decompositions (LDDs) are invaluable tools in the design of combinatorial graph algorithms. While historically they have been applied mainly to undirected graphs, in the recent breakthrough for the negative-length Single Source Shortest Path problem, Bernstein, Nanongkai, and Wulff-Nilsen [FOCS '22] extended the use of LDDs to directed graphs for the first time. Specifically, their LDD deletes each edge with probability at most O(1/D ⋅ log²n), while ensuring that each strongly connected component in the remaining graph has a (weak) diameter of at most D. In this work, we make further advancements in the study of directed LDDs. We reveal a natural and intuitive (in hindsight) connection to Expander Decompositions, and leveraging this connection along with additional techniques, we establish the existence of an LDD with an edge-cutting probability of O(1/D ⋅ log n log log n). This improves the previous bound by nearly a logarithmic factor and closely approaches the lower bound of Ω(1/D ⋅ log n). With significantly more technical effort, we also develop two efficient algorithms for computing our LDDs: a deterministic algorithm that runs in time Õ(m poly(D)) and a randomized algorithm that runs in near-linear time Õ(m). We believe that our work provides a solid conceptual and technical foundation for future research relying on directed LDDs, which will undoubtedly follow soon.
Cite as

Karl Bringmann, Nick Fischer, Bernhard Haeupler, and Rustam Latypov. Near-Optimal Directed Low-Diameter Decompositions. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 35:1-35:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bringmann_et_al:LIPIcs.ICALP.2025.35,
  author =	{Bringmann, Karl and Fischer, Nick and Haeupler, Bernhard and Latypov, Rustam},
  title =	{{Near-Optimal Directed Low-Diameter Decompositions}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{35:1--35:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.35},
  URN =		{urn:nbn:de:0030-drops-234125},
  doi =		{10.4230/LIPIcs.ICALP.2025.35},
  annote =	{Keywords: Low Diameter Decompositions, Expander Decompositions, Directed Graphs}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.1
A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models

Authors: Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
Elemental balance, the property of having the same number of each type of atom on both sides of the equation, is a fundamental feature of chemical reactions. In metabolic network models, this property is typically verified on a reaction-by-reaction basis. In this paper we show how violations of elemental balance can be efficiently detected in an entire network, without the need for specifying the chemical formula of each of the metabolites, which enhances a modeler's ability to automatically verify that their model satisfies elemental balance. Our method makes use of duality theory, linear programming, and mixed integer linear programming, and runs efficiently on genome-scale metabolic networks (GSMNs). We detect elemental balance violations in 40 out of 84 metabolic network models in the BiGG database. We also identify a short list of reactions that are candidates for being elementally imbalanced. Out of these candidates, nearly half turn out to be truly imbalanced reactions, and the rest can be seen as witnesses of elemental balance violations elsewhere in the network. The majority of these violations involve a proton imbalance, a known challenge of metabolic network reconstruction. Our approach is efficient, easy to use and powerful. It can be helpful to metabolic network modelers during model verification. Our methods are fully integrated into the MONGOOSE software suite and are available at https://github.com/WGS-TB/MongooseGUI3.
Cite as

Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch. A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 1:1-1:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{zabeti_et_al:LIPIcs.WABI.2018.1,
  author =	{Zabeti, Hooman and Stephen, Tamon and Berger, Bonnie and Chindelevitch, Leonid},
  title =	{{A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{1:1--1:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.1},
  URN =		{urn:nbn:de:0030-drops-93034},
  doi =		{10.4230/LIPIcs.WABI.2018.1},
  annote =	{Keywords: Metabolic network analysis, elemental imbalance, linear programming, model verification}
}
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