19 Search Results for "Cooper, Colin"

Document
DOI: 10.4230/LIPIcs.SoCG.2026.42
Compressed Data Structures for Heegaard Splitting

Authors: Henrique Ennes and Clément Maria

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

Abstract
Heegaard splittings provide a natural representation of closed 3-manifolds by gluing handlebodies along a common surface. These splittings can be equivalently given by two finite sets of meridians lying on the surface, which define a Heegaard diagram. We present a data structure to effectively represent Heegaard diagrams as normal curves with respect to triangulations of a surface of complexity measured by the space required to express the normal coordinates' vectors in binary. This structure can be significantly more compressed than triangulations of 3-manifolds, giving exponential gains for some families. Even with this succinct definition of complexity, we establish polynomial-time algorithms for comparing and manipulating diagrams, performing stabilizations, detecting trivial stabilizations and reductions, and computing topological invariants of the underlying manifolds, such as their fundamental and homology groups. We also contrast early implementations of our techniques with standard software programs for 3-manifolds, achieving faster algorithms for the average cases and exponential gains in speed for some particular presentations of the inputs.
Cite as

Henrique Ennes and Clément Maria. Compressed Data Structures for Heegaard Splitting. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 42:1-42:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ennes_et_al:LIPIcs.SoCG.2026.42,
  author =	{Ennes, Henrique and Maria, Cl\'{e}ment},
  title =	{{Compressed Data Structures for Heegaard Splitting}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{42:1--42:15},
  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.2026.42},
  URN =		{urn:nbn:de:0030-drops-258484},
  doi =		{10.4230/LIPIcs.SoCG.2026.42},
  annote =	{Keywords: 3-manifold, Heegaard splitting, curves on surfaces, surface theory, data structure, computational topology}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.71
Broadcast in Almost Mixing Time

Authors: Anton Paramonov and Roger Wattenhofer

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

Abstract
We study the problem of broadcasting multiple messages in the CONGEST model. In this problem, a dedicated source node s possesses a set M of messages with every message of size O(log n) where n is the total number of nodes. The objective is to ensure that every node in the network learns all messages in M. The execution of an algorithm progresses in rounds, and we focus on optimizing the round complexity of broadcasting multiple messages. Our primary contribution is a randomized algorithm for networks with expander topology. The algorithm succeeds with high probability and achieves a round complexity that is optimal up to a factor of the network’s mixing time and polylogarithmic terms. It leverages a multi-COBRA primitive, which uses multiple branching random walks running in parallel. A crucial aspect of our method is the use of these branching random walks to construct an optimal (up to a polylogarithmic factor) tree packing of a random graph, which is then used for efficient broadcasting. We also prove the problem to be NP-hard in a centralized setting and provide insights into why lower bounds that can be matched in expanders, namely graph diameter and |M|/minCut, cannot be tight in general graphs.
Cite as

Anton Paramonov and Roger Wattenhofer. Broadcast in Almost Mixing Time. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 71:1-71:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{paramonov_et_al:LIPIcs.STACS.2026.71,
  author =	{Paramonov, Anton and Wattenhofer, Roger},
  title =	{{Broadcast in Almost Mixing Time}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{71:1--71:20},
  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.2026.71},
  URN =		{urn:nbn:de:0030-drops-255603},
  doi =		{10.4230/LIPIcs.STACS.2026.71},
  annote =	{Keywords: Distributed algorithms, Expander Graphs, Random graphs, Broadcast, Branching random walks, Tree packing, CONGEST model}
}
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.OPODIS.2025.30
Byzantine-Tolerant Phase Clock

Authors: Costas Busch, Paweł Garncarek, and Dariusz R. Kowalski

Published in: LIPIcs, Volume 361, 29th International Conference on Principles of Distributed Systems (OPODIS 2025)

Abstract
A phase clock is a basic synchronization mechanism that keeps distributed nodes closely synchronized to execute the same phase of a distributed algorithm. A phase clock is typically implemented with a local logical counter that keeps track of the current phase count. Phase clocks are particularly useful in population protocols for implementing leader election and majority selection. We study phase clocks that tolerate Byzantine faults. We show that there is a phase clock that tolerates up to f < n/3 faulty nodes, where n is the number of nodes, such that the gap of the local counter values is O(n²log n). The gap can be further lowered to O(log n) when f ≤ n/8. We also show that if f > n/3, then the gap grows to infinity as time increases. While analyzing phase clock we introduce novel techniques and bounds for balls into bins processes, which might be of independent interest. Using the phase clock, we obtain a majority selection population protocol that tolerates up to f faults and decides on the majority value in O(log² n) parallel time using poly-log states per node.
Cite as

Costas Busch, Paweł Garncarek, and Dariusz R. Kowalski. Byzantine-Tolerant Phase Clock. In 29th International Conference on Principles of Distributed Systems (OPODIS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 361, pp. 30:1-30:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{busch_et_al:LIPIcs.OPODIS.2025.30,
  author =	{Busch, Costas and Garncarek, Pawe{\l} and Kowalski, Dariusz R.},
  title =	{{Byzantine-Tolerant Phase Clock}},
  booktitle =	{29th International Conference on Principles of Distributed Systems (OPODIS 2025)},
  pages =	{30:1--30:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-409-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{361},
  editor =	{Arusoaie, Andrei and Onica, Emanuel and Spear, Michael and Tucci-Piergiovanni, Sara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2025.30},
  URN =		{urn:nbn:de:0030-drops-252036},
  doi =		{10.4230/LIPIcs.OPODIS.2025.30},
  annote =	{Keywords: phase clock, Byzantine nodes, population protocols, balls into bins}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.21
Overlay Network Construction: Improved Overall and Node-Wise Message Complexity

Authors: Yi-Jun Chang, Yanyu Chen, and Gopinath Mishra

Published in: LIPIcs, Volume 360, 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)

Abstract
We consider the problem of constructing distributed overlay networks, where nodes in a reconfigurable system can create or sever connections with nodes whose identifiers they know. Initially, each node knows only its own and its neighbors' identifiers, forming a local channel, while the evolving structure is termed the global channel. The goal is to reconfigure any connected graph into a desired topology, such as a bounded-degree expander graph or a well-formed tree (WFT) with a constant maximum degree and logarithmic diameter, minimizing the total number of rounds and message complexity. This problem mirrors real-world peer-to-peer network construction, where creating robust and efficient systems is desired. We study the overlay reconstruction problem in a network of n nodes in two models: GOSSIP-reply and HYBRID. In the GOSSIP-reply model, each node can send a message and receive a corresponding reply message in one round. In the HYBRID model, a node can send O(1) messages to each neighbor in the local channel and a total of O(log n) messages in the global channel. In both models, we propose protocols for WFT construction with O (n log n) message complexities using messages of O(log n) bits. In the GOSSIP-reply model, our protocol takes O(log n) rounds while in the HYBRID model, our protocol takes O(log² n) rounds. Both protocols use O (n log² n) bits of communication. We obtain improved bounds over prior work: GOSSIP-reply: A recent result by Dufoulon et al. (ITCS 2024) achieved O(log⁵ n) round complexity and O (n log⁵ n) message complexity using messages of at least Ω(log² n) bits in GOSSIP-reply. With messages of size O(log n), our protocol achieves an optimal round complexity of O(log n) and an improved message complexity of O(n log n). HYBRID: Götte et al. (Distributed Computing 2023) showed an optimal O(log n)-round algorithm with O(log² n) global messages per round which incurs a message complexity of Ω(m), where m is the number of edges in the initial topology. At the cost of increasing the round complexity to O(log² n) while using only O(log n) messages globally, our protocol achieves a message complexity that is independent of m. Our approach ensures that the total number of messages for node v, with degree deg(v) in the initial topology, is bounded by O(deg(v) + log n), while the algorithm of Götte et al. requires O(deg(v) + (log⁴ n)/(log log n)) messages per node.
Cite as

Yi-Jun Chang, Yanyu Chen, and Gopinath Mishra. Overlay Network Construction: Improved Overall and Node-Wise Message Complexity. In 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 360, pp. 21:1-21:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chang_et_al:LIPIcs.FSTTCS.2025.21,
  author =	{Chang, Yi-Jun and Chen, Yanyu and Mishra, Gopinath},
  title =	{{Overlay Network Construction: Improved Overall and Node-Wise Message Complexity}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{21:1--21:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-406-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{360},
  editor =	{Aiswarya, C. and Mehta, Ruta and Roy, Subhajit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2025.21},
  URN =		{urn:nbn:de:0030-drops-251025},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.21},
  annote =	{Keywords: Distributed algorithms, Overlay networks, Expander graphs}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.17
Cutoff for the Swendsen–Wang Dynamics on the Complete Graph

Authors: Antonio Blanca and Zhezheng Song

Published in: LIPIcs, Volume 360, 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)

Abstract
We study the speed of convergence of the Swendsen-Wang (SW) dynamics for the q-state ferromagnetic Potts model on the n-vertex complete graph, known as the mean-field model. The SW dynamics was introduced as an attractive alternative to the local Glauber dynamics, often offering faster convergence rates to stationarity in a variety of settings. A series of works have characterized the asymptotic behavior of the speed of convergence of the mean-field SW dynamics for all q ≥ 2 and all values of the inverse temperature parameter β > 0. In particular, it is known that when β > q the mixing time of the SW dynamics is Θ(log n). We strengthen this result by showing that for all β > q, there exists a constant c(β,q) > 0 such that the mixing time of the SW dynamics is c(β,q) log n + Θ(1). This implies that the mean-field SW dynamics exhibits the cutoff phenomenon in this temperature regime, demonstrating that this Markov chain undergoes a sharp transition from "far from stationarity" to "well-mixed" within a narrow Θ(1) time window. The presence of cutoff is algorithmically significant, as simulating the chain for fewer steps than its mixing time could lead to highly biased samples.
Cite as

Antonio Blanca and Zhezheng Song. Cutoff for the Swendsen–Wang Dynamics on the Complete Graph. In 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 360, pp. 17:1-17:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{blanca_et_al:LIPIcs.FSTTCS.2025.17,
  author =	{Blanca, Antonio and Song, Zhezheng},
  title =	{{Cutoff for the Swendsen–Wang Dynamics on the Complete Graph}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{17:1--17:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-406-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{360},
  editor =	{Aiswarya, C. and Mehta, Ruta and Roy, Subhajit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2025.17},
  URN =		{urn:nbn:de:0030-drops-250987},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.17},
  annote =	{Keywords: Markov chains, mixing times, cutoff phenomenon, Potts model, mean-field}
}
Document
DOI: 10.4230/LIPIcs.DISC.2025.27
On the h-Majority Dynamics with Many Opinions

Authors: Francesco d'Amore, Niccolò D'Archivio, George Giakkoupis, and Emanuele Natale

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

Abstract
We present the first upper bound on the convergence time to consensus of the well-known h-majority dynamics with k opinions, in the synchronous setting, for h and k that are both non-constant values. We suppose that, at the beginning of the process, there is some initial additive bias towards some plurality opinion, that is, there is an opinion that is supported by x nodes while any other opinion is supported by strictly fewer nodes. We prove that, with high probability, if the bias is ω(√x) and the initial plurality opinion is supported by at least x = ω(log n) nodes, then the process converges to plurality consensus in O(log n) rounds whenever h = ω(n log n / x). A main corollary is the following: if k = o(n / log n) and the process starts from an almost-balanced configuration with an initial bias of magnitude ω(√{n/k}) towards the initial plurality opinion, then any function h = ω(k log n) suffices to guarantee convergence to consensus in O(log n) rounds, with high probability. Our upper bound shows that the lower bound of Ω(k / h²) rounds to reach consensus given by Becchetti et al. (2017) cannot be pushed further than Ω̃(k / h). Moreover, the bias we require is asymptotically smaller than the Ω(√{nlog n}) bias that guarantees plurality consensus in the 3-majority dynamics: in our case, the required bias is at most any (arbitrarily small) function in ω(√x) for any value of k ≥ 2.
Cite as

Francesco d'Amore, Niccolò D'Archivio, George Giakkoupis, and Emanuele Natale. On the h-Majority Dynamics with Many Opinions. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 27:1-27:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{damore_et_al:LIPIcs.DISC.2025.27,
  author =	{d'Amore, Francesco and D'Archivio, Niccol\`{o} and Giakkoupis, George and Natale, Emanuele},
  title =	{{On the h-Majority Dynamics with Many Opinions}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{27:1--27:24},
  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.2025.27},
  URN =		{urn:nbn:de:0030-drops-248448},
  doi =		{10.4230/LIPIcs.DISC.2025.27},
  annote =	{Keywords: Distributed Algorithms, Randomized Algorithms, Markov Chains, Consensus Problem, Opinion dynamics, Plurality Consensus}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.55
Safe Sequences via Dominators in DAGs for Path-Covering Problems

Authors: Francisco Sena, Romeo Rizzi, and Alexandru I. Tomescu

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

Abstract
A path-covering problem on a directed acyclic graph (DAG) requires finding a set of source-to-sink paths that cover all the nodes, all the arcs, or subsets thereof, and additionally they are optimal with respect to some function. In this paper we study safe sequences of nodes or arcs, namely sequences that appear in some path of every path cover of a DAG. We show that safe sequences admit a simple characterization via cutnodes. Moreover, we establish a connection between maximal safe sequences and leaf-to-root paths in the source- and sink-dominator trees of the DAG, which may be of independent interest in the extensive literature on dominators. With dominator trees, safe sequences admit an O(n)-size representation and a linear-time output-sensitive enumeration algorithm running in time O(m + o), where n and m are the number of nodes and arcs, respectively, and o is the total length of the maximal safe sequences. We then apply maximal safe sequences to simplify Integer Linear Programs (ILPs) for two path-covering problems, LeastSquares and MinPathError, which are at the core of RNA transcript assembly problems from bioinformatics. On various datasets, maximal safe sequences can be computed in under 0.1 seconds per graph, on average, and ILP solvers whose search space is reduced in this manner exhibit significant speed-ups. For example on graphs with a large width, average speed-ups are in the range 50-250× for MinPathError and in the range 80-350× for LeastSquares. Optimizing ILPs using safe sequences can thus become a fast building block of practical RNA transcript assembly tools, and more generally, of path-covering problems.
Cite as

Francisco Sena, Romeo Rizzi, and Alexandru I. Tomescu. Safe Sequences via Dominators in DAGs for Path-Covering Problems. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 55:1-55:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sena_et_al:LIPIcs.ESA.2025.55,
  author =	{Sena, Francisco and Rizzi, Romeo and Tomescu, Alexandru I.},
  title =	{{Safe Sequences via Dominators in DAGs for Path-Covering Problems}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{55:1--55:17},
  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.2025.55},
  URN =		{urn:nbn:de:0030-drops-245230},
  doi =		{10.4230/LIPIcs.ESA.2025.55},
  annote =	{Keywords: directed acyclic graph, path cover, dominator tree, integer linear programming, least squares, minimum path error}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.5
Min-CSPs on Complete Instances II: Polylogarithmic Approximation for Min-NAE-3-SAT

Authors: Aditya Anand, Euiwoong Lee, Davide Mazzali, and Amatya Sharma

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

Abstract
This paper studies complete k-Constraint Satisfaction Problems (CSPs), where an n-variable instance has exactly one nontrivial constraint for each subset of k variables, i.e., it has binom(n,k) constraints. A recent work started a systematic study of complete k-CSPs [Anand, Lee, Sharma, SODA'25], and showed a quasi-polynomial time algorithm that decides if there is an assignment satisfying all the constraints of any complete Boolean-alphabet k-CSP, algorithmically separating complete instances from dense instances. The tractability of this decision problem is necessary for any nontrivial (multiplicative) approximation for the minimization version, whose goal is to minimize the number of violated constraints. The same paper raised the question of whether it is possible to obtain nontrivial approximation algorithms for complete Min-k-CSPs with k ≥ 3. In this work, we make progress in this direction and show a quasi-polynomial time polylog(n)-approximation to Min-NAE-3-SAT on complete instances, which asks to minimize the number of 3-clauses where all the three literals equal the same bit. To the best of our knowledge, this is the first known example of a CSP whose decision version is NP-Hard in general (and dense) instances while admitting a polylog(n)-approximation in complete instances. Our algorithm presents a new iterative framework for rounding a solution from the Sherali-Adams hierarchy, where each iteration interleaves the two well-known rounding tools: the conditioning procedure, in order to "almost fix" many variables, and the thresholding procedure, in order to "completely fix" them. Finally, we improve the running time of the decision algorithms of Anand, Lee, and Sharma and show a simple algorithm that decides any complete Boolean-alphabet k-CSP in polynomial time.
Cite as

Aditya Anand, Euiwoong Lee, Davide Mazzali, and Amatya Sharma. Min-CSPs on Complete Instances II: Polylogarithmic Approximation for Min-NAE-3-SAT. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{anand_et_al:LIPIcs.APPROX/RANDOM.2025.5,
  author =	{Anand, Aditya and Lee, Euiwoong and Mazzali, Davide and Sharma, Amatya},
  title =	{{Min-CSPs on Complete Instances II: Polylogarithmic Approximation for Min-NAE-3-SAT}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{5:1--5:23},
  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.2025.5},
  URN =		{urn:nbn:de:0030-drops-243712},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.5},
  annote =	{Keywords: Constraint Satisfiability Problems, Approximation Algorithms, Sherali Adams}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

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

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  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.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2024.36
Distributed Branching Random Walks and Their Applications

Authors: Vijeth Aradhya, Seth Gilbert, and Thorsten Götte

Published in: LIPIcs, Volume 324, 28th International Conference on Principles of Distributed Systems (OPODIS 2024)

Abstract
In recent years, the explosion of big data and analytics has necessitated distributed storage and processing with several compute nodes (e.g., multiple datacenters). These nodes collaboratively perform parallel computation, where the data is typically partitioned across these nodes to ensure scalability, redundancy and load-balancing. But the nodes may not always be co-located; in many cases, they are part of a larger communication network. Since those nodes only need to communicate among themselves, a key challenge is to design efficient routes catered to that subnetwork. In this work, we initiate the study of distributed sampling and routing problems for subnetworks in any well-connected network. Given any network G = (V, E) with mixing time τ_mix, consider the canonical problem of permutation routing [Ghaffari, Kuhn and Su, PODC 2017] that aims to minimize both congestion and dilation of the routes, where the demands (i.e., set of source-terminal pairs) are such that each node sends or receives number of messages proportional to its degree. We show that the permutation routing problem, when demands are restricted to any subset S ⊆ V (i.e., subnetwork), can be solved in exp(O(√(log|S|))) ⋅ Õ(τ_mix) rounds (where Õ(⋅) hides polylogarithmic factors of |V|). This means that the running time depends subpolynomially on the subnetwork size (i.e., not on the entire network size). The ability to solve permutation routing efficiently immediately implies that a large class of parallel algorithms can be simulated efficiently on the subnetwork. As a prerequisite to constructing efficient routes, we design and analyze distributed branching random walks that distribute tokens started by the nodes in the subnetwork. At a high-level, these algorithms operate by always moving each token according to a (lazy) simple random walk, but also branching a token into multiple tokens at some specified intervals; ultimately, if a node starts a branching walk, with its id in a token, then by the end of execution, several tokens with its id would be randomly distributed among the nodes. As these random walks can be started by many nodes, a crucial challenge is to ensure low-congestion, which is a primary focus of this paper.
Cite as

Vijeth Aradhya, Seth Gilbert, and Thorsten Götte. Distributed Branching Random Walks and Their Applications. In 28th International Conference on Principles of Distributed Systems (OPODIS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 324, pp. 36:1-36:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{aradhya_et_al:LIPIcs.OPODIS.2024.36,
  author =	{Aradhya, Vijeth and Gilbert, Seth and G\"{o}tte, Thorsten},
  title =	{{Distributed Branching Random Walks and Their Applications}},
  booktitle =	{28th International Conference on Principles of Distributed Systems (OPODIS 2024)},
  pages =	{36:1--36:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-360-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{324},
  editor =	{Bonomi, Silvia and Galletta, Letterio and Rivi\`{e}re, Etienne and Schiavoni, Valerio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2024.36},
  URN =		{urn:nbn:de:0030-drops-225723},
  doi =		{10.4230/LIPIcs.OPODIS.2024.36},
  annote =	{Keywords: Distributed Graph Algorithms, Random Walks, Permutation Routing}
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
Cite as

James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2023.10
Discrete Incremental Voting

Authors: Colin Cooper, Tomasz Radzik, and Takeharu Shiraga

Published in: LIPIcs, Volume 286, 27th International Conference on Principles of Distributed Systems (OPODIS 2023)

Abstract
We consider a type of pull voting suitable for discrete numeric opinions which can be compared on a linear scale, for example, 1 ("disagree strongly"), 2 ("disagree"), …, 5 ("agree strongly"). On observing the opinion of a random neighbour, a vertex changes its opinion incrementally towards the value of the neighbour’s opinion, if different. For opinions drawn from a set {1,2,…,k}, the opinion of the vertex would change by +1 if the opinion of the neighbour is larger, or by -1, if it is smaller. It is not clear how to predict the outcome of this process, but we observe that the total weight of the system, that is, the sum of the individual opinions of all vertices, is a martingale. This allows us analyse the outcome of the process on some classes of dense expanders such as complete graphs K_n and random graphs G_{n,p} for suitably large p. If the average of the original opinions satisfies i ≤ c ≤ i+1 for some integer i, then the asymptotic probability that opinion i wins is i+1-c, and the probability that opinion i+1 wins is c-i. With high probability, the winning opinion cannot be other than i or i+1. To contrast this, we show that for a path and opinions 0,1,2 arranged initially in non-decreasing order along the path, the outcome is very different. Any of the opinions can win with constant probability, provided that each of the two extreme opinions 0 and 2 is initially supported by a constant fraction of vertices.
Cite as

Colin Cooper, Tomasz Radzik, and Takeharu Shiraga. Discrete Incremental Voting. In 27th International Conference on Principles of Distributed Systems (OPODIS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 286, pp. 10:1-10:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cooper_et_al:LIPIcs.OPODIS.2023.10,
  author =	{Cooper, Colin and Radzik, Tomasz and Shiraga, Takeharu},
  title =	{{Discrete Incremental Voting}},
  booktitle =	{27th International Conference on Principles of Distributed Systems (OPODIS 2023)},
  pages =	{10:1--10:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-308-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{286},
  editor =	{Bessani, Alysson and D\'{e}fago, Xavier and Nakamura, Junya and Wada, Koichi and Yamauchi, Yukiko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2023.10},
  URN =		{urn:nbn:de:0030-drops-195005},
  doi =		{10.4230/LIPIcs.OPODIS.2023.10},
  annote =	{Keywords: Random distributed processes, Pull voting}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
DOI: 10.4230/LIPIcs.DISC.2019.32
Phase Transitions of Best-of-Two and Best-of-Three on Stochastic Block Models

Authors: Nobutaka Shimizu and Takeharu Shiraga

Published in: LIPIcs, Volume 146, 33rd International Symposium on Distributed Computing (DISC 2019)

Abstract
This paper is concerned with voting processes on graphs where each vertex holds one of two different opinions. In particular, we study the Best-of-two and the Best-of-three. Here at each synchronous and discrete time step, each vertex updates its opinion to match the majority among the opinions of two random neighbors and itself (the Best-of-two) or the opinions of three random neighbors (the Best-of-three). Previous studies have explored these processes on complete graphs and expander graphs, but we understand significantly less about their properties on graphs with more complicated structures. In this paper, we study the Best-of-two and the Best-of-three on the stochastic block model G(2n,p,q), which is a random graph consisting of two distinct Erdős-Rényi graphs G(n,p) joined by random edges with density q <= p. We obtain two main results. First, if p=omega(log n/n) and r=q/p is a constant, we show that there is a phase transition in r with threshold r^* (specifically, r^*=sqrt{5}-2 for the Best-of-two, and r^*=1/7 for the Best-of-three). If r>r^*, the process reaches consensus within O(log log n+log n/log (np)) steps for any initial opinion configuration with a bias of Omega(n). By contrast, if r<r^*, then there exists an initial opinion configuration with a bias of Omega(n) from which the process requires at least 2^{Omega(n)} steps to reach consensus. Second, if p is a constant and r>r^*, we show that, for any initial opinion configuration, the process reaches consensus within O(log n) steps. To the best of our knowledge, this is the first result concerning multiple-choice voting for arbitrary initial opinion configurations on non-complete graphs.
Cite as

Nobutaka Shimizu and Takeharu Shiraga. Phase Transitions of Best-of-Two and Best-of-Three on Stochastic Block Models. In 33rd International Symposium on Distributed Computing (DISC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 146, pp. 32:1-32:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{shimizu_et_al:LIPIcs.DISC.2019.32,
  author =	{Shimizu, Nobutaka and Shiraga, Takeharu},
  title =	{{Phase Transitions of Best-of-Two and Best-of-Three on Stochastic Block Models}},
  booktitle =	{33rd International Symposium on Distributed Computing (DISC 2019)},
  pages =	{32:1--32:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-126-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{146},
  editor =	{Suomela, Jukka},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2019.32},
  URN =		{urn:nbn:de:0030-drops-113397},
  doi =		{10.4230/LIPIcs.DISC.2019.32},
  annote =	{Keywords: Distributed Voting, Consensus Problem, Random Graph}
}
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