24 Search Results for "Condon, Anne"

Document
DOI: 10.4230/LIPIcs.FUN.2026.19
Sinks and Ladders: ARRIVAL and SSG with Two Vertices per Level

Authors: Bernd Gärtner, Sebastian Haslebacher, and Hung P. Hoang

Published in: LIPIcs, Volume 366, 13th International Conference on Fun with Algorithms (FUN 2026)

Abstract
ARRIVAL is the problem of deciding whether a token, following a deterministic process, eventually reaches a designated destination. While the problem is known to lie in NP ∩ CoNP, whether it can be solved in polynomial time remains a major open question. In this article, we study ladders, a class of graphs that constitutes a family of worst-case instances for many existing algorithms, including the currently best known algorithm by Gärtner, Haslebacher, and Hoang (ICALP 2021). We show that ARRIVAL restricted to ladders can be solved in polynomial time, and we further extend this result to stopping binary simple stochastic games (SSG).
Cite as

Bernd Gärtner, Sebastian Haslebacher, and Hung P. Hoang. Sinks and Ladders: ARRIVAL and SSG with Two Vertices per Level. In 13th International Conference on Fun with Algorithms (FUN 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 366, pp. 19:1-19:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{gartner_et_al:LIPIcs.FUN.2026.19,
  author =	{G\"{a}rtner, Bernd and Haslebacher, Sebastian and Hoang, Hung P.},
  title =	{{Sinks and Ladders: ARRIVAL and SSG with Two Vertices per Level}},
  booktitle =	{13th International Conference on Fun with Algorithms (FUN 2026)},
  pages =	{19:1--19:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-417-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{366},
  editor =	{Iacono, John},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2026.19},
  URN =		{urn:nbn:de:0030-drops-257385},
  doi =		{10.4230/LIPIcs.FUN.2026.19},
  annote =	{Keywords: ARRIVAL, Rotor-Routing, Simple Stochastic Games}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.31
Lower Bounds for Ranking-Based Pivot Rules

Authors: Yann Disser, Georg Loho, Matthew Maat, and Nils Mosis

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

Abstract
The existence of a polynomial pivot rule for the simplex method for linear programming, policy iteration for Markov decision processes, and strategy improvement for parity games each are prominent open problems in their respective fields. While numerous natural candidates for efficient rules have been eliminated, all existing lower bound constructions are tailored to individual or small sets of pivot rules. We introduce a unified framework for formalizing classes of rules according to the information about the input that they rely on. Within this framework, we show lower bounds for ranking-based classes of rules that base their decisions on orderings of the improving pivot steps induced by the underlying data. Our first result is a superpolynomial lower bound for strategy improvement, obtained via a family of sink parity games, which applies to memory-based generalizations of Bland’s rule that only access the input by comparing the ranks of improving edges in some global order. Our second result is a subexponential lower bound for policy iteration, obtained via a family of Markov decision processes, which applies to memoryless rules that only access the input by comparing improving actions according to their ranks in a global order, their reduced costs, and the associated improvements in objective value. Both results carry over to the simplex method for linear programming.
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Yann Disser, Georg Loho, Matthew Maat, and Nils Mosis. Lower Bounds for Ranking-Based Pivot Rules. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 31:1-31:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{disser_et_al:LIPIcs.STACS.2026.31,
  author =	{Disser, Yann and Loho, Georg and Maat, Matthew and Mosis, Nils},
  title =	{{Lower Bounds for Ranking-Based Pivot Rules}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{31:1--31:19},
  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.2026.31},
  URN =		{urn:nbn:de:0030-drops-255207},
  doi =		{10.4230/LIPIcs.STACS.2026.31},
  annote =	{Keywords: lower bounds, Markov decision processes, parity games, pivot rules, policy iteration, simplex method}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.85
Recovering Communities in Structured Random Graphs

Authors: Michael Kapralov, Luca Trevisan, and Weronika Wrzos-Kaminska

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
The problem of recovering planted community structure in random graphs has received a lot of attention in the literature on the stochastic block model, where the input is a random graph in which edges crossing between different communities appear with smaller probability than edges induced by communities. The communities themselves form a collection of vertex-disjoint sparse cuts in the expected graph, and can be recovered, often exactly, from a sample as long as a separation condition on the intra- and inter-community edge probabilities is satisfied. In this paper, we ask whether the presence of a large number of overlapping sparsest cuts in the expected graph still allows recovery. For example, the d-dimensional hypercube graph admits d distinct (balanced) sparsest cuts, one for every coordinate. Can these cuts be identified given a random sample of the edges of the hypercube where each edge is present independently with some probability p ∈ (0, 1)? We show that this is the case, in a very strong sense: the sparsest balanced cut in a sample of the hypercube at rate p = Clog d/d for a sufficiently large constant C is 1/poly(d)-close to a coordinate cut with high probability. This is asymptotically optimal and allows approximate recovery of all d cuts simultaneously. Furthermore, for an appropriate sample of hypercube-like graphs recovery can be made exact. The proof is essentially a strong hypercube cut sparsification bound that combines a theorem of Friedgut, Kalai and Naor on boolean functions whose Fourier transform concentrates on the first level of the Fourier spectrum with Karger’s cut counting argument.
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Michael Kapralov, Luca Trevisan, and Weronika Wrzos-Kaminska. Recovering Communities in Structured Random Graphs. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 85:1-85:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kapralov_et_al:LIPIcs.ITCS.2026.85,
  author =	{Kapralov, Michael and Trevisan, Luca and Wrzos-Kaminska, Weronika},
  title =	{{Recovering Communities in Structured Random Graphs}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{85:1--85:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.85},
  URN =		{urn:nbn:de:0030-drops-253727},
  doi =		{10.4230/LIPIcs.ITCS.2026.85},
  annote =	{Keywords: Hypercube graphs, Community detection, Fourier analysis of Boolean functions}
}
Document
DOI: 10.4230/LIPIcs.DISC.2025.23
Boosting Payment Channel Network Liquidity with Topology Optimization and Transaction Selection

Authors: Krishnendu Chatterjee, Jan Matyáš Křišťan, Stefan Schmid, Jakub Svoboda, and Michelle Yeo

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

Abstract
Payment channel networks (PCNs) are a promising technology that alleviates blockchain scalability by shifting the transaction load from the blockchain to the PCN. Nevertheless, the network topology has to be carefully designed to maximise the transaction throughput in PCNs. Additionally, users in PCNs also have to make optimal decisions on which transactions to forward and which to reject to prolong the lifetime of their channels. In this work, we consider an input sequence of transactions over p parties. Each transaction consists of a transaction size, source, and target, and can be either accepted or rejected (entailing a cost). The goal is to design a PCN topology among the p cooperating parties, along with the channel capacities, and then output a decision for each transaction in the sequence to minimise the cost of creating and augmenting channels, as well as the cost of rejecting transactions. Our main contribution is an 𝒪(p) approximation algorithm for the problem with p parties. We further show that with some assumptions on the distribution of transactions, we can reduce the approximation ratio to 𝒪(√p). We complement our theoretical analysis with an empirical study of our assumptions and approach in the context of the Lightning Network.
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Krishnendu Chatterjee, Jan Matyáš Křišťan, Stefan Schmid, Jakub Svoboda, and Michelle Yeo. Boosting Payment Channel Network Liquidity with Topology Optimization and Transaction Selection. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 23:1-23:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chatterjee_et_al:LIPIcs.DISC.2025.23,
  author =	{Chatterjee, Krishnendu and K\v{r}i\v{s}\v{t}an, Jan Maty\'{a}\v{s} and Schmid, Stefan and Svoboda, Jakub and Yeo, Michelle},
  title =	{{Boosting Payment Channel Network Liquidity with Topology Optimization and Transaction Selection}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{23:1--23:22},
  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.2025.23},
  URN =		{urn:nbn:de:0030-drops-248402},
  doi =		{10.4230/LIPIcs.DISC.2025.23},
  annote =	{Keywords: Blockchains, Cryptocurrencies, Payment Channel Networks, Throughput, Optimisation, Graph Algorithms, Approximation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.12
Testing Whether a Subgraph Is Convex or Isometric

Authors: Sergio Cabello

Published in: LIPIcs, Volume 349, 19th International Symposium on Algorithms and Data Structures (WADS 2025)

Abstract
We consider the following two algorithmic problems: given a graph G and a subgraph H ⊆ G, decide whether H is an isometric or a geodesically convex subgraph of G. It is relatively easy to see that the problems can be solved by computing the distances between all pairs of vertices. We provide a conditional lower bound showing that, for sparse graphs with n vertices and Θ(n) edges, we cannot expect to solve the problem in O(n^{2-ε}) time for any constant ε > 0. We also show that the problem can be solved in subquadratic time for planar graphs and in near-linear time for graphs of bounded treewidth. Finally, we provide a near-linear time algorithm for the setting where G is a plane graph and H is defined by a few cycles in G.
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Sergio Cabello. Testing Whether a Subgraph Is Convex or Isometric. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cabello:LIPIcs.WADS.2025.12,
  author =	{Cabello, Sergio},
  title =	{{Testing Whether a Subgraph Is Convex or Isometric}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-398-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{349},
  editor =	{Morin, Pat and Oh, Eunjin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WADS.2025.12},
  URN =		{urn:nbn:de:0030-drops-242439},
  doi =		{10.4230/LIPIcs.WADS.2025.12},
  annote =	{Keywords: convex subgraph, isometric subgraph, plane graph}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.86
Probabilistic Finite Automaton Emptiness Is Undecidable for a Fixed Automaton

Authors: Günter Rote

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
We construct a probabilistic finite automaton (PFA) with 7 states and an input alphabet of 5 symbols for which the PFA Emptiness Problem is undecidable. The only input for the decision problem is the starting distribution. For the proof, we use reductions from special instances of the Post Correspondence Problem. We also consider some variations: The input alphabet of the PFA can be restricted to a binary alphabet at the expense of a larger number of states. If we allow a rational output value for each state instead of a yes-no acceptance decision, the number of states can even be reduced to 6.
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Günter Rote. Probabilistic Finite Automaton Emptiness Is Undecidable for a Fixed Automaton. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 86:1-86:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{rote:LIPIcs.MFCS.2025.86,
  author =	{Rote, G\"{u}nter},
  title =	{{Probabilistic Finite Automaton Emptiness Is Undecidable for a Fixed Automaton}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{86:1--86:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.86},
  URN =		{urn:nbn:de:0030-drops-241930},
  doi =		{10.4230/LIPIcs.MFCS.2025.86},
  annote =	{Keywords: Probabilistic finite automaton, Undecidability, Post Correspondence Problem}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.1
Algorithmic Hardness of the Partition Function for Nucleic Acid Strands

Authors: Gwendal Ducloz, Ahmed Shalaby, and Damien Woods

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
To understand and engineer biological and artificial nucleic acid systems, algorithms are employed for prediction of secondary structures at thermodynamic equilibrium. Dynamic programming algorithms are used to compute the most favoured, or Minimum Free Energy (MFE), structure, and the Partition Function (PF) - a tool for assigning a probability to any structure. However, in some situations, such as when there are large numbers of strands, or pseudoknotted systems, NP-hardness results show that such algorithms are unlikely, but only for MFE. Curiously, algorithmic hardness results were not shown for PF, leaving two open questions on the complexity of PF for multiple strands and single strands with pseudoknots. The challenge is that while the MFE problem cares only about one, or a few structures, PF is a summation over the entire secondary structure space, giving theorists the vibe that computing PF should not only be as hard as MFE, but should be even harder. We answer both questions. First, we show that computing PF is #P-hard for systems with an unbounded number of strands, answering a question of Condon Hajiaghayi, and Thachuk [DNA27]. Second, for even a single strand, but allowing pseudoknots, we find that PF is #P-hard. Our proof relies on a novel magnification trick that leads to a tightly-woven set of reductions between five key thermodynamic problems: MFE, PF, their decision versions, and #SSEL that counts structures of a given energy. Our reductions show these five problems are fundamentally related for any energy model amenable to magnification. That general classification clarifies the mathematical landscape of nucleic acid energy models and yields several open questions.
Cite as

Gwendal Ducloz, Ahmed Shalaby, and Damien Woods. Algorithmic Hardness of the Partition Function for Nucleic Acid Strands. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ducloz_et_al:LIPIcs.DNA.31.1,
  author =	{Ducloz, Gwendal and Shalaby, Ahmed and Woods, Damien},
  title =	{{Algorithmic Hardness of the Partition Function for Nucleic Acid Strands}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{1:1--1:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.1},
  URN =		{urn:nbn:de:0030-drops-238504},
  doi =		{10.4230/LIPIcs.DNA.31.1},
  annote =	{Keywords: Partition function, minimum free energy, nucleic acid, DNA, RNA, secondary structure, computational complexity, #P-hardness}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.2
A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs

Authors: Hope Amber Johnson and Anne Condon

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
DNA strand displacement, a collective name for certain behaviors of short strands of DNA, has been used to build many interesting molecular devices over the past few decades. Among those devices are general implementation schemes for Chemical Reaction Networks, suggesting a place in an abstraction hierarchy for complex molecular programming. However, the possibilities of DNA strand displacement are far from fully explored. On a theoretical level, most DNA strand displacement systems are built out of a few simple motifs, with the space of possible motifs otherwise unexplored. On a practical level, the desire for general, large-scale DNA strand displacement systems is not fulfilled. Those systems that are scalable are not general, and those that are general don't scale up well. We have recently been exploring the space of possibilities for DNA strand displacement systems where all input complexes are made out of at most two strands of DNA. As a test case, we've had an open question of whether such systems can implement general Chemical Reaction Networks, in a way that has a certain set of other desirable properties - reversible, systematic, O(1) toeholds, bimolecular reactions, and correct according to CRN bisimulation - that the state-of-the-art implementations with more than 2-stranded inputs have. Until now we've had a few results that have all but one of those desirable properties, including one based on a novel mechanism we called coupled reconfiguration, but that depended on the physically questionable assumption that pseudoknots cannot occur. We wondered whether the same type of mechanism could be done in a pseudoknot-robust way. In this work we show that in fact, coupled reconfiguration can be done in a pseudoknot-robust way, and this mechanism can implement general Chemical Reaction Networks with all inputs being single strands of DNA. Going further, the same motifs used in this mechanism can implement stacks and surface-based bimolecular reactions. Those have been previously studied as part of polymer extensions of the Chemical Reaction Network model, and on an abstract model level, the resulting extensions are Turing-complete in ways the base Chemical Reaction Network model is not. Our mechanisms are significantly different from previously tested DNA strand displacement systems, which raises questions about their ability to be implemented experimentally, but we have some reasons to believe the challenges are solvable. So we present the pseudoknot-robust coupled reconfiguration mechanism and its use for general Chemical Reaction Network implementations; we present the extensions of the mechanism to stack and surface reactions; and we discuss the possible obstacles and solutions to experimental implementation, as well as the theoretical implications of this mechanism.
Cite as

Hope Amber Johnson and Anne Condon. A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{johnson_et_al:LIPIcs.DNA.31.2,
  author =	{Johnson, Hope Amber and Condon, Anne},
  title =	{{A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{2:1--2:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.2},
  URN =		{urn:nbn:de:0030-drops-238514},
  doi =		{10.4230/LIPIcs.DNA.31.2},
  annote =	{Keywords: Molecular programming, DNA strand displacement, Chemical Reaction Networks}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.3
Reachability in Deletion-Only Chemical Reaction Networks

Authors: Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
For general discrete Chemical Reaction Networks (CRNs), the fundamental problem of reachability - the question of whether a target configuration can be produced from a given initial configuration - was recently shown to be Ackermann-complete. However, many open questions remain about which features of the CRN model drive this complexity. We study a restricted class of CRNs with void rules, reactions that only decrease species counts. We further examine this regime in the motivated model of step CRNs, which allow additional species to be introduced in discrete stages. With and without steps, we characterize the complexity of the reachability problem for CRNs with void rules. We show that, without steps, reachability remains polynomial-time solvable for bimolecular systems but becomes NP-complete for larger reactions. Conversely, with just a single step, reachability becomes NP-complete even for bimolecular systems. Our results provide a nearly complete classification of void-rule reachability problems into tractable and intractable cases, with only a single exception.
Cite as

Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Reachability in Deletion-Only Chemical Reaction Networks. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 3:1-3:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fu_et_al:LIPIcs.DNA.31.3,
  author =	{Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim},
  title =	{{Reachability in Deletion-Only Chemical Reaction Networks}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{3:1--3:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.3},
  URN =		{urn:nbn:de:0030-drops-238521},
  doi =		{10.4230/LIPIcs.DNA.31.3},
  annote =	{Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions}
}
Document
DOI: 10.4230/LIPIcs.CONCUR.2025.9
A Direct Reduction from Stochastic Parity Games to Simple Stochastic Games

Authors: Raphaël Berthon, Joost-Pieter Katoen, and Zihan Zhou

Published in: LIPIcs, Volume 348, 36th International Conference on Concurrency Theory (CONCUR 2025)

Abstract
Significant progress has been recently achieved in developing efficient solutions for simple stochastic games (SSGs), focusing on reachability objectives. While reductions from stochastic parity games (SPGs) to SSGs have been presented in the literature through the use of multiple intermediate game models, a direct and simple reduction has been notably absent. This paper introduces a novel and direct polynomial-time reduction from quantitative SPGs to quantitative SSGs. By leveraging a gadget-based transformation that effectively removes the priority function, we construct an SSG that simulates the behavior of a given SPG. We formally establish the correctness of our direct reduction. Furthermore, we demonstrate that under binary encoding this reduction is polynomial, thereby directly corroborating the known NP ∩ coNP complexity of SPGs and providing new understanding in the relationship between parity and reachability objectives in turn-based stochastic games.
Cite as

Raphaël Berthon, Joost-Pieter Katoen, and Zihan Zhou. A Direct Reduction from Stochastic Parity Games to Simple Stochastic Games. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{berthon_et_al:LIPIcs.CONCUR.2025.9,
  author =	{Berthon, Rapha\"{e}l and Katoen, Joost-Pieter and Zhou, Zihan},
  title =	{{A Direct Reduction from Stochastic Parity Games to Simple Stochastic Games}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{9:1--9:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-389-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{348},
  editor =	{Bouyer, Patricia and van de Pol, Jaco},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2025.9},
  URN =		{urn:nbn:de:0030-drops-239595},
  doi =		{10.4230/LIPIcs.CONCUR.2025.9},
  annote =	{Keywords: stochastic games, parity, reduction}
}
Document
DOI: 10.4230/LIPIcs.CONCUR.2025.21
Quantitative Language Automata

Authors: Thomas A. Henzinger, Pavol Kebis, Nicolas Mazzocchi, and N. Ege Saraç

Published in: LIPIcs, Volume 348, 36th International Conference on Concurrency Theory (CONCUR 2025)

Abstract
A quantitative word automaton (QWA) defines a function from infinite words to values. For example, every infinite run of a limit-average QWA 𝒜 obtains a mean payoff, and every word w ∈ Σ^ω is assigned the maximal mean payoff obtained by nondeterministic runs of 𝒜 over w. We introduce quantitative language automata (QLAs) that define functions from language generators (i.e., implementations) to values, where a language generator can be nonprobabilistic, defining a set of infinite words, or probabilistic, defining a probability measure over infinite words. A QLA consists of a QWA and an aggregator function. For example, given a QWA 𝒜, the infimum aggregator maps each language L ⊆ Σ^ω to the greatest lower bound assigned by 𝒜 to any word in L. For boolean value sets, QWAs define boolean properties of traces, and QLAs define boolean properties of sets of traces, i.e., hyperproperties. For more general value sets, QLAs serve as a specification language for a generalization of hyperproperties, called quantitative hyperproperties. A nonprobabilistic (resp. probabilistic) quantitative hyperproperty assigns a value to each set (resp. distribution) G of traces, e.g., the minimal (resp. expected) average response time exhibited by the traces in G. We give several examples of quantitative hyperproperties and investigate three paradigmatic problems for QLAs: evaluation, nonemptiness, and universality. In the evaluation problem, given a QLA 𝔸 and an implementation G, we ask for the value that 𝔸 assigns to G. In the nonemptiness (resp. universality) problem, given a QLA 𝔸 and a value k, we ask whether 𝔸 assigns at least k to some (resp. every) language. We provide a comprehensive picture of decidability for these problems for QLAs with common aggregators as well as their restrictions to ω-regular languages and trace distributions generated by finite-state Markov chains.
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Thomas A. Henzinger, Pavol Kebis, Nicolas Mazzocchi, and N. Ege Saraç. Quantitative Language Automata. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 21:1-21:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{henzinger_et_al:LIPIcs.CONCUR.2025.21,
  author =	{Henzinger, Thomas A. and Kebis, Pavol and Mazzocchi, Nicolas and Sara\c{c}, N. Ege},
  title =	{{Quantitative Language Automata}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{21:1--21:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-389-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{348},
  editor =	{Bouyer, Patricia and van de Pol, Jaco},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2025.21},
  URN =		{urn:nbn:de:0030-drops-239718},
  doi =		{10.4230/LIPIcs.CONCUR.2025.21},
  annote =	{Keywords: Quantitative hyperproperties, quantitative automata, automata-based verification}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.13
Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots

Authors: Mateo Gray, Sebastian Will, and Hosna Jabbari

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

Abstract
Motivation. Determining RNA structure is essential for understanding RNA function and interaction networks. Although experimental techniques yield high‑accuracy structures, they are costly and time‑consuming; thus, computational approaches - especially minimum‑free‑energy (MFE) prediction algorithms - are indispensable. Accurately predicting pseudoknots, however, remains challenging because their inclusion usually leads to prohibitive computational complexity. Recent work demonstrated that sparsification can improve the efficiency of complex pseudoknot prediction algorithms such as Knotty. This finding suggests similar gains are possible for already efficient algorithms like HFold, which targets a complementary class of hierarchically constrained pseudoknots. Results. We introduce Spark, an exact, fully sparsified algorithm for predicting pseudoknotted RNA structures. Like its non‑sparsified predecessor HFold, Spark searches for the minimum‑energy structure under the HotKots 2.0 energy model, a pseudoknot extension of the Turner model. Because the sparsification is non‑heuristic, Spark preserves the asymptotic time‑ and space‑complexity guarantees of HFold while greatly reducing the constant factors. We benchmarked the performance of Spark against HFold and, as a pseudoknot‑free baseline, RNAfold. Compared with HFold, Spark substantially lowers both run time and memory usage, while achieving run‑time figures close to those of RNAfold. Across all tested sequence lengths, Spark used the least memory and consistently ran faster than HFold. Conclusion. By extending non‑heuristic sparsification to hierarchical pseudoknot prediction, Spark delivers an exceptionally fast and memory‑efficient tool accurate prediction of pseudoknotted RNA structures, enabling routine analysis of long sequences. The algorithm broadens the practical scope of computational RNA biology and provides a solid foundation for future advances in structure‑based functional annotation. Availability. Spark’s implementation and detailed results are available at https://github.com/TheCOBRALab/Spark.
Cite as

Mateo Gray, Sebastian Will, and Hosna Jabbari. Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gray_et_al:LIPIcs.WABI.2025.13,
  author =	{Gray, Mateo and Will, Sebastian and Jabbari, Hosna},
  title =	{{Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{13:1--13:18},
  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.2025.13},
  URN =		{urn:nbn:de:0030-drops-239383},
  doi =		{10.4230/LIPIcs.WABI.2025.13},
  annote =	{Keywords: RNA, MFE, Secondary Structure Prediction, Pseudoknot, Sparsification, Space Complexity, Time Complexity}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.17
Space-Bounded Quantum Interactive Proof Systems

Authors: François Le Gall, Yupan Liu, Harumichi Nishimura, and Qisheng Wang

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
We introduce two models of space-bounded quantum interactive proof systems, QIPL and QIP_{U}L. The QIP_{U}L model, a space-bounded variant of quantum interactive proofs (QIP) introduced by Watrous (CC 2003) and Kitaev and Watrous (STOC 2000), restricts verifier actions to unitary circuits. In contrast, QIPL allows logarithmically many pinching intermediate measurements per verifier action, making it the weakest model that encompasses the classical model of Condon and Ladner (JCSS 1995). We characterize the computational power of QIPL and QIP_{U}L. When the message number m is polynomially bounded, QIP_{U}L ⊊ QIPL unless P = NP: - QIPL^HC, a subclass of QIPL defined by a high-concentration condition on yes instances, exactly characterizes NP. - QIP_{U}L is contained in P and contains SAC¹ ∪ BQL, where SAC¹ denotes problems solvable by classical logarithmic-depth, semi-unbounded fan-in circuits. However, this distinction vanishes when m is constant. Our results further indicate that (pinching) intermediate measurements uniquely impact space-bounded quantum interactive proofs, unlike in space-bounded quantum computation, where BQL = BQ_{U}L. We also introduce space-bounded unitary quantum statistical zero-knowledge (QSZK_{U}L), a specific form of QIP_{U}L proof systems with statistical zero-knowledge against any verifier. This class is a space-bounded variant of quantum statistical zero-knowledge (QSZK) defined by Watrous (SICOMP 2009). We prove that QSZK_{U}L = BQL, implying that the statistical zero-knowledge property negates the computational advantage typically gained from the interaction.
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François Le Gall, Yupan Liu, Harumichi Nishimura, and Qisheng Wang. Space-Bounded Quantum Interactive Proof Systems. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 17:1-17:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{legall_et_al:LIPIcs.CCC.2025.17,
  author =	{Le Gall, Fran\c{c}ois and Liu, Yupan and Nishimura, Harumichi and Wang, Qisheng},
  title =	{{Space-Bounded Quantum Interactive Proof Systems}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{17:1--17:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.17},
  URN =		{urn:nbn:de:0030-drops-237115},
  doi =		{10.4230/LIPIcs.CCC.2025.17},
  annote =	{Keywords: Intermediate measurements, Quantum interactive proofs, Space-bounded quantum computation}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.95
ARRIVAL: Recursive Framework & 𝓁₁-Contraction

Authors: Sebastian Haslebacher

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

Abstract
ARRIVAL is the problem of deciding which out of two possible destinations will be reached first by a token that moves deterministically along the edges of a directed graph, according to so-called switching rules. It is known to lie in NP ∩ CoNP, but not known to lie in 𝖯. The state-of-the-art algorithm due to Gärtner et al. (ICALP `21) runs in time 2^{𝒪(√n log n)} on an n-vertex graph. We prove that ARRIVAL can be solved in time 2^{𝒪(k log² n)} on n-vertex graphs of treewidth k. Our algorithm is derived by adapting a simple recursive algorithm for a generalization of ARRIVAL called G-ARRIVAL. This simple recursive algorithm acts as a framework from which we can also rederive the subexponential upper bound of Gärtner et al. Our second result is a reduction from G-ARRIVAL to the problem of finding an approximate fixed point of an 𝓁₁-contracting function f : [0, 1]ⁿ → [0, 1]ⁿ. Finding such fixed points is a well-studied problem in the case of the 𝓁₂-metric and the 𝓁_∞-metric, but little is known about the 𝓁₁-case. Both of our results highlight parallels between ARRIVAL and the Simple Stochastic Games (SSG) problem. Concretely, Chatterjee et al. (SODA `23) gave an algorithm for SSG parameterized by treewidth that achieves a similar bound as we do for ARRIVAL, and SSG is known to reduce to 𝓁_∞-contraction.
Cite as

Sebastian Haslebacher. ARRIVAL: Recursive Framework & 𝓁₁-Contraction. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 95:1-95:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{haslebacher:LIPIcs.ICALP.2025.95,
  author =	{Haslebacher, Sebastian},
  title =	{{ARRIVAL: Recursive Framework \& 𝓁₁-Contraction}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{95:1--95:17},
  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.2025.95},
  URN =		{urn:nbn:de:0030-drops-234723},
  doi =		{10.4230/LIPIcs.ICALP.2025.95},
  annote =	{Keywords: ARRIVAL, G-ARRIVAL, Deterministic Random Walk, Rotor-Routing, 𝓁₁-Contraction, Banach Fixed Point}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.130
An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands

Authors: Ahmed Shalaby and Damien Woods

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

Abstract
The information-encoding molecules RNA and DNA bind via base pairing to form an exponentially large set of secondary structures. Practitioners need algorithms to predict the most favoured structures, called minimum free energy (MFE) structures, or to compute a partition function that allows assigning a probability to any structure. MFE prediction is NP-hard in the presence pseudoknots - base pairings that violate a restricted planarity condition. However, for single-stranded unpseudoknotted structures, there are polynomial time dynamic programming algorithms. For multiple strands, the problem is significantly more complicated: Codon, Hajiaghayi and Thachuk [DNA27, 2021] proved it NP-hard for N bases and 𝒪(N) strands. Dirks, Bois, Schaeffer, Winfree and Pierce [SIAM Review, 2007] gave a polynomial time partition function algorithm for multiple (𝒪(1)) strands, now widely-used, however their technique did not generalise to MFE which they left open. We give an 𝒪(N⁴) time algorithm for unpseudoknotted multiple (𝒪(1)) strand MFE prediction, answering the open problem from Dirks et al. The challenge lies in considering the rotational symmetry of secondary structures, a global feature not immediately amenable to local subproblem decomposition used in dynamic programming. Our proof has two main technical contributions: First, a characterisation of symmetric secondary structures implying only quadratically many need to be considered when computing the rotational symmetry penalty. Second, that bound is leveraged by a backtracking algorithm to efficiently find the MFE in an exponential space of contenders.
Cite as

Ahmed Shalaby and Damien Woods. An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 130:1-130:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shalaby_et_al:LIPIcs.ICALP.2025.130,
  author =	{Shalaby, Ahmed and Woods, Damien},
  title =	{{An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{130:1--130:20},
  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.2025.130},
  URN =		{urn:nbn:de:0030-drops-235071},
  doi =		{10.4230/LIPIcs.ICALP.2025.130},
  annote =	{Keywords: Minimum free energy, MFE, partition function, nucleic acid, DNA, RNA, secondary structure, computational complexity, algorithm analysis and design, dynamic programming}
}
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