4 Search Results for "Clote, Peter"

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.CALCO.2025.9
Safety and Strong Completeness via Reducibility for Many-Valued Coalgebraic Dynamic Logics

Authors: Helle Hvid Hansen and Wolfgang Poiger

Published in: LIPIcs, Volume 342, 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)

Abstract
We present a coalgebraic framework for studying generalisations of dynamic modal logics such as PDL and game logic in which both the propositions and the semantic structures can take values in an algebra 𝐀 of truth-degrees. More precisely, we work with coalgebraic modal logic via 𝐀-valued predicate liftings where 𝐀 is an FLew-algebra, and interpret actions (abstracting programs and games) as 𝖥-coalgebras where the functor 𝖥 represents some type of 𝐀-weighted system. We also allow combinations of crisp propositions with 𝐀-weighted systems and vice versa. We introduce coalgebra operations and tests, with a focus on operations which are reducible in the sense that modalities for composed actions can be reduced to compositions of modalities for the constituent actions. We prove that reducible operations are safe for bisimulation and behavioural equivalence, and prove a general strong completeness result, from which we obtain new strong completeness results for 𝟐-valued iteration-free PDL with 𝐀-valued accessibility relations when 𝐀 is a finite chain, and for many-valued iteration-free game logic with many-valued strategies based on finite Lukasiewicz logic.
Cite as

Helle Hvid Hansen and Wolfgang Poiger. Safety and Strong Completeness via Reducibility for Many-Valued Coalgebraic Dynamic Logics. In 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 342, pp. 9:1-9:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hansen_et_al:LIPIcs.CALCO.2025.9,
  author =	{Hansen, Helle Hvid and Poiger, Wolfgang},
  title =	{{Safety and Strong Completeness via Reducibility for Many-Valued Coalgebraic Dynamic Logics}},
  booktitle =	{11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)},
  pages =	{9:1--9:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-383-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{342},
  editor =	{C\^{i}rstea, Corina and Knapp, Alexander},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2025.9},
  URN =		{urn:nbn:de:0030-drops-235681},
  doi =		{10.4230/LIPIcs.CALCO.2025.9},
  annote =	{Keywords: dynamic logic, many-valued coalgebraic logic, safety, strong completeness}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.22
New Bounds for the Ideal Proof System in Positive Characteristic

Authors: Amik Raj Behera, Nutan Limaye, Varun Ramanathan, and Srikanth Srinivasan

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

Abstract
In this work, we prove upper and lower bounds over fields of positive characteristics for several fragments of the Ideal Proof System (IPS), an algebraic proof system introduced by Grochow and Pitassi (J. ACM 2018). Our results extend the works of Forbes, Shpilka, Tzameret, and Wigderson (Theory of Computing 2021) and also of Govindasamy, Hakoniemi, and Tzameret (FOCS 2022). These works primarily focused on proof systems over fields of characteristic 0, and we are able to extend these results to positive characteristic. The question of proving general IPS lower bounds over positive characteristic is motivated by the important question of proving AC⁰[p]-Frege lower bounds. This connection was observed by Grochow and Pitassi (J. ACM 2018). Additional motivation comes from recent developments in algebraic complexity theory due to Forbes (CCC 2024) who showed how to extend previous lower bounds over characteristic 0 to positive characteristic. In our work, we adapt the functional lower bound method of Forbes et al. (Theory of Computing 2021) to prove exponential-size lower bounds for various subsystems of IPS. In order to establish these size lower bounds, we first prove a tight degree lower bound for a variant of Subset Sum over positive characteristic. This forms the core of all our lower bounds. Additionally, we derive upper bounds for the instances presented above. We show that they have efficient constant-depth IPS refutations. This demonstrates that constant-depth IPS refutations are stronger than the proof systems considered above even in positive characteristic. We also show that constant-depth IPS can efficiently refute a general class of instances, namely all symmetric instances, thereby further uncovering the strength of these algebraic proofs in positive characteristic.
Cite as

Amik Raj Behera, Nutan Limaye, Varun Ramanathan, and Srikanth Srinivasan. New Bounds for the Ideal Proof System in Positive Characteristic. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 22:1-22:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{behera_et_al:LIPIcs.ICALP.2025.22,
  author =	{Behera, Amik Raj and Limaye, Nutan and Ramanathan, Varun and Srinivasan, Srikanth},
  title =	{{New Bounds for the Ideal Proof System in Positive Characteristic}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{22:1--22:20},
  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.2025.22},
  URN =		{urn:nbn:de:0030-drops-233992},
  doi =		{10.4230/LIPIcs.ICALP.2025.22},
  annote =	{Keywords: Ideal Proof Systems, Algebraic Complexity, Positive Characteristic}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.6
An IP Algorithm for RNA Folding Trajectories

Authors: Amir H. Bayegan and Peter Clote

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Vienna RNA Package software Kinfold implements the Gillespie algorithm for RNA secondary structure folding kinetics, for the move sets MS1 [resp. MS2], consisting of base pair additions and removals [resp. base pair addition, removals and shifts]. In this paper, for arbitrary secondary structures s, t of a given RNA sequence, we present the first optimal algorithm to compute the shortest MS2 folding trajectory s = s0, s1, . . . , sm = t, where each intermediate structure si+1 is obtained from its predecessor by the addition, removal or shift of a single base pair. The shortest MS1 trajectory between s and t is trivially equal to the number of base pairs belonging to s but not t, plus the number of base pairs belonging to t but not s. Our optimal algorithm applies integer programming (IP) to solve (essentially) the minimum feedback vertex set (FVS) problem for the "conflict digraph" associated with input secondary structures s, t, and then applies topological sort, in order to generate an optimal MS2 folding pathway from s to t that maximizes the use of shift moves. Since the optimal algorithm may require excessive run time, we also sketch a fast, near-optimal algorithm (details to appear elsewhere). Software for our algorithm will be publicly available at http://bioinformatics.bc.edu/clotelab/MS2distance/.
Cite as

Amir H. Bayegan and Peter Clote. An IP Algorithm for RNA Folding Trajectories. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{bayegan_et_al:LIPIcs.WABI.2017.6,
  author =	{Bayegan, Amir H. and Clote, Peter},
  title =	{{An IP Algorithm for RNA Folding Trajectories}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{6:1--6:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.6},
  URN =		{urn:nbn:de:0030-drops-76437},
  doi =		{10.4230/LIPIcs.WABI.2017.6},
  annote =	{Keywords: Integer programming, RNA secondary structure, folding trajectory, feedback vertex problem, conflict digraph}
}
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