18 Search Results for "Stadler, Peter F."

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
DOI: 10.4230/LIPIcs.ESA.2025.15
Linear Layouts Revisited: Stacks, Queues, and Exact Algorithms

Authors: Thomas Depian, Simon D. Fink, Robert Ganian, and Vaishali Surianarayanan

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

Abstract
In spite of the extensive study of stack and queue layouts, many fundamental questions remain open concerning the complexity-theoretic frontiers for computing stack and queue layouts. A stack (resp. queue) layout places vertices along a line and assigns edges to pages so that no two edges on the same page are crossing (resp. nested). We provide three new algorithms which together substantially expand our understanding of these problems: 1) A fixed-parameter algorithm for computing minimum-page stack and queue layouts w.r.t. the vertex integrity of an n-vertex graph G. This result is motivated by an open question in the literature and generalizes the previous algorithms parameterizing by the vertex cover number of G. The proof relies on a newly developed Ramsey pruning technique. Vertex integrity intuitively measures the vertex deletion distance to a subgraph with only small connected components. 2) An n^𝒪(q 𝓁) algorithm for computing 𝓁-page stack and queue layouts of page width at most q. This is the first algorithm avoiding a double-exponential dependency on the parameters. The page width of a layout measures the maximum number of edges one needs to cross on any page to reach the outer face. 3) A 2^𝒪(n) algorithm for computing 1-page queue layouts. This improves upon the previously fastest n^𝒪(n) algorithm and can be seen as a counterpart to the recent subexponential algorithm for computing 2-page stack layouts [ICALP'24], but relies on an entirely different technique.
Cite as

Thomas Depian, Simon D. Fink, Robert Ganian, and Vaishali Surianarayanan. Linear Layouts Revisited: Stacks, Queues, and Exact Algorithms. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{depian_et_al:LIPIcs.ESA.2025.15,
  author =	{Depian, Thomas and Fink, Simon D. and Ganian, Robert and Surianarayanan, Vaishali},
  title =	{{Linear Layouts Revisited: Stacks, Queues, and Exact Algorithms}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{15:1--15:18},
  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.2025.15},
  URN =		{urn:nbn:de:0030-drops-244835},
  doi =		{10.4230/LIPIcs.ESA.2025.15},
  annote =	{Keywords: stack layouts, queue layouts, parameterized algorithms, vertex integrity, Ramsey theory}
}
Document
DOI: 10.4230/LIPIcs.ITC.2025.8
On the Definition of Malicious Private Information Retrieval

Authors: Bar Alon and Amos Beimel

Published in: LIPIcs, Volume 343, 6th Conference on Information-Theoretic Cryptography (ITC 2025)

Abstract
A multi-server private information retrieval (PIR) protocol allows a client to obtain an entry of its choice from a database, held by one or more servers, while hiding the identity of the entry from small enough coalitions of servers. In this paper, we study PIR protocols in which some of the servers are malicious and may not send messages according to the pre-described protocol. In previous papers, such protocols were defined by requiring that they are correct, private, and robust to malicious servers, i.e., by listing 3 properties that they should satisfy. However, 40 years of experience in studying secure multiparty protocols taught us that defining the security of protocols by a list of required properties is problematic. In this paper, we rectify this situation and define the security of PIR protocols with malicious servers using the real vs. ideal paradigm. We study the relationship between the property-based definition of PIR protocols and the real vs. ideal definition, showing the following results: - We prove that if we require full security from PIR protocols, e.g., the client outputs the correct value of the database entry with high probability even if a minority of the servers are malicious, then the two definitions are equivalent. This implies that constructions of such protocols that were proven secure using the property-based definition are actually secure under the "correct" definition of security. - We show that if we require security-with-abort from PIR protocols (called PIR protocols with error-detection in previous papers), i.e., protocols in which the user either outputs the correct value or an abort symbol, then there are protocols that are secure under the property-based definition; however, they do not satisfy the real vs. ideal definition, that is, they can be attacked allowing selective abort. This shows that the property-based definition of PIR protocols with security-with-abort is problematic. - We consider the compiler of Eriguchi et al. (TCC 22) that starts with a PIR protocol that is secure against semi-honest servers and constructs a PIR protocol with security-with-abort; this compiler implies the best-known PIR protocols with security-with-abort. We show that applying this compiler does not result in PIR protocols that are secure according to the real vs. ideal definition. However, we prove that a simple modification of this compiler results in PIR protocols that are secure according to the real vs. ideal definition.
Cite as

Bar Alon and Amos Beimel. On the Definition of Malicious Private Information Retrieval. In 6th Conference on Information-Theoretic Cryptography (ITC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 343, pp. 8:1-8:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{alon_et_al:LIPIcs.ITC.2025.8,
  author =	{Alon, Bar and Beimel, Amos},
  title =	{{On the Definition of Malicious Private Information Retrieval}},
  booktitle =	{6th Conference on Information-Theoretic Cryptography (ITC 2025)},
  pages =	{8:1--8:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-385-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{343},
  editor =	{Gilboa, Niv},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITC.2025.8},
  URN =		{urn:nbn:de:0030-drops-243581},
  doi =		{10.4230/LIPIcs.ITC.2025.8},
  annote =	{Keywords: Private information retrieval, secure multiparty computation}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.29
Linear Layouts of Graphs with Priority Queues

Authors: Emilio Di Giacomo, Walter Didimo, Henry Förster, Torsten Ueckerdt, and Johannes Zink

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

Abstract
A linear layout of a graph consists of a linear ordering of its vertices and a partition of its edges into pages such that the edges assigned to the same page obey some constraint. The two most prominent and widely studied types of linear layouts are stack and queue layouts, in which any two edges assigned to the same page are forbidden to cross and nest, respectively. The names of these two layouts derive from the fact that, when parsing the graph according to the linear vertex ordering, the edges in a single page can be stored using a single stack or queue, respectively. Recently, the concepts of stack and queue layouts have been extended by using a double-ended queue or a restricted-input queue for storing the edges of a page. We extend this line of study to edge-weighted graphs by introducing priority queue layouts, that is, the edges on each page are stored in a priority queue whose keys are the edge weights. First, we show that there are edge-weighted graphs that require a linear number of priority queues. Second, we characterize the graphs that admit a priority queue layout with a single queue, regardless of the edge-weight function, and we provide an efficient recognition algorithm. Third, we show that the number of priority queues required independently of the edge-weight function is bounded by the pathwidth of the graph, but can be arbitrarily large already for graphs of treewidth two. Finally, we prove that determining the minimum number of priority queues is NP-complete if the linear ordering of the vertices is fixed.
Cite as

Emilio Di Giacomo, Walter Didimo, Henry Förster, Torsten Ueckerdt, and Johannes Zink. Linear Layouts of Graphs with Priority Queues. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 29:1-29:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{digiacomo_et_al:LIPIcs.WADS.2025.29,
  author =	{Di Giacomo, Emilio and Didimo, Walter and F\"{o}rster, Henry and Ueckerdt, Torsten and Zink, Johannes},
  title =	{{Linear Layouts of Graphs with Priority Queues}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{29:1--29:17},
  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.2025.29},
  URN =		{urn:nbn:de:0030-drops-242602},
  doi =		{10.4230/LIPIcs.WADS.2025.29},
  annote =	{Keywords: linear layouts, recognition and characterization, priority queue layouts}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.36
On the Complexity of Minimising the Moving Distance for Dispersing Objects

Authors: Nicolás Honorato-Droguett, Kazuhiro Kurita, Tesshu Hanaka, and Hirotaka Ono

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

Abstract
We study Geometric Graph Edit Distance (GGED), a graph-editing model to compute the minimum edit distance of intersection graphs that uses moving objects as an edit operation. We first show an O(n log n)-time algorithm that minimises the total moving distance to disperse unit intervals. This algorithm is applied to render a given unit interval graph (i) edgeless, (ii) acyclic and (iii) k-clique-free. We next show that GGED becomes strongly NP-hard when rendering a weighted interval graph (i) edgeless, (ii) acyclic and (iii) k-clique-free. Lastly, we prove that minimising the maximum moving distance for rendering a unit disk graph edgeless is strongly NP-hard over the L₁ and L₂ distances.
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Nicolás Honorato-Droguett, Kazuhiro Kurita, Tesshu Hanaka, and Hirotaka Ono. On the Complexity of Minimising the Moving Distance for Dispersing Objects. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 36:1-36:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{honoratodroguett_et_al:LIPIcs.WADS.2025.36,
  author =	{Honorato-Droguett, Nicol\'{a}s and Kurita, Kazuhiro and Hanaka, Tesshu and Ono, Hirotaka},
  title =	{{On the Complexity of Minimising the Moving Distance for Dispersing Objects}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{36:1--36:14},
  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.2025.36},
  URN =		{urn:nbn:de:0030-drops-242673},
  doi =		{10.4230/LIPIcs.WADS.2025.36},
  annote =	{Keywords: Intersection graphs, Optimisation, Graph modification}
}
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.WABI.2025.12
Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms

Authors: Marcos E. González Laffitte, Tieu-Long Phan, and Peter F. Stadler

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

Abstract
Chemical reaction databases typically report the molecular structures of reactant and product compounds, as well as their stoichiometry, but lack information, in particular, on the correspondence of reactant and product atoms. These atom-to-atom maps (AAM), however, are crucial for applications including chemical synthesis planning in organic chemistry and the analysis of isotope labeling experiments in modern metabolomics. AAMs therefore need to be reconstructed computationally. This situation is aggravated, furthermore, by the fact that chemically correct AAMs are, fundamentally, determined by quantum-mechanical phenomena and thus cannot be reliably computed by solving graph-theoretical optimization problems defined by the reactant and product structures. A viable solution for this problem is to shift the focus into first identifying a partial AAM containing the reaction center, i.e., covering the atoms incident with all bonds that change during a reaction. This then leads to the problem of extending the partial map to the full reaction. The AAM of a reaction is faithfully represented by the Imaginary Transition State (ITS) graph, providing a convenient graph-theoretic framework to address the questions of when and how a partial AAM can be extended. We show that an unique extension exists whenever, and only if, these partial AAMs cover the reaction center. In this case their extension can be computed by solving a constrained graph-isomorphism search between specific subgraphs of ITS graphs. We close by benchmarking different tools for this task.
Cite as

Marcos E. González Laffitte, Tieu-Long Phan, and Peter F. Stadler. Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 12:1-12:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gonzalezlaffitte_et_al:LIPIcs.WABI.2025.12,
  author =	{Gonz\'{a}lez Laffitte, Marcos E. and Phan, Tieu-Long and Stadler, Peter F.},
  title =	{{Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{12:1--12:26},
  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.2025.12},
  URN =		{urn:nbn:de:0030-drops-239410},
  doi =		{10.4230/LIPIcs.WABI.2025.12},
  annote =	{Keywords: atom-to-atom maps, imaginary transition state (ITS) graphs, condensed graph of the reaction (CGR), chemical reaction mechanisms, molecular graphs, metabolic networks, chemical synthesis planning, constrained graph isomorphism}
}
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}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.16
A Lightweight Method for Generating Multi-Tier JIT Compilation Virtual Machine in a Meta-Tracing Compiler Framework

Authors: Yusuke Izawa, Hidehiko Masuhara, and Carl Friedrich Bolz-Tereick

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Meta-compiler frameworks, such as RPython and Graal/Truffle, generate high-performance virtual machines (VMs) from interpreter definitions. Although they generate VMs with high-quality just-in-time (JIT) compilers, they still lack an important feature that dedicated VMs (i.e., VMs that are developed for specific languages) have, namely multi-tier compilation. Multi-tier compilation uses light-weight compilers at early stages and highly optimizing compilers at later stages in order to balance between compilation overheads and code quality. We propose a novel approach to enabling multi-tier compilation in the VMs generated by a meta-compiler framework. Instead of extending the JIT compiler backend of the framework, our approach drives an existing (heavyweight) compiler backend in the framework to quickly generate unoptimized native code by merely embedding directives and compile-time operations into interpreter definitions. As a validation of the approach, we developed 2SOM, a Simple Object Machine with a two-tier JIT compiler based on RPython. 2SOM first applies the tier-1 threaded code generator that is generated by our proposed technique, then, to the loops that exceed a threshold, applies the tier-2 tracing JIT compiler that is generated by the original RPython framework. Our performance evaluation that runs a program with a realistic workload showed that 2SOM improved, when compared against an RPython-based VM, warm-up performance by 15%, with merely a 5% reduction in peak performance.
Cite as

Yusuke Izawa, Hidehiko Masuhara, and Carl Friedrich Bolz-Tereick. A Lightweight Method for Generating Multi-Tier JIT Compilation Virtual Machine in a Meta-Tracing Compiler Framework. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 16:1-16:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{izawa_et_al:LIPIcs.ECOOP.2025.16,
  author =	{Izawa, Yusuke and Masuhara, Hidehiko and Bolz-Tereick, Carl Friedrich},
  title =	{{A Lightweight Method for Generating Multi-Tier JIT Compilation Virtual Machine in a Meta-Tracing Compiler Framework}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{16:1--16:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.16},
  URN =		{urn:nbn:de:0030-drops-233090},
  doi =		{10.4230/LIPIcs.ECOOP.2025.16},
  annote =	{Keywords: virtual machine, JIT compiler, multi-tier JIT compiler, meta-tracing JIT compiler, RPython}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.19
Profile-Guided Field Externalization in an Ahead-Of-Time Compiler

Authors: Sebastian Kloibhofer, Lukas Makor, Peter Hofer, David Leopoldseder, and Hanspeter Mössenböck

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Field externalization is a technique to reduce the footprint of objects by removing fields that most frequently contain zero or null. While researchers have developed ways to bring this optimization into the Java world, these have been limited to research compilers or virtual machines for embedded systems. In this work, we present a novel field externalization technique that uses information from static analysis and profiling to determine externalizable fields. During compilation, we remove those fields and define companion classes. These are used in case of non-default-value writes to the externalized fields. Our approach also correctly handles synchronization to prevent issues in multithreaded environments. We integrated our approach into the modern Java ahead-of-time compiler GraalVM Native Image. We conducted an evaluation on a diverse set of benchmarks that includes standard and microservice-based benchmarks. For standard benchmarks, our approach reduces the total allocated bytes by 2.76% and the maximum resident set size (max-RSS) by 2.55%. For microservice benchmarks, we achieved a reduction of 6.88% for normalized allocated bytes and 2.45% for max-RSS. We computed these improvements via the geometric mean. The median reductions are are 1.46% (alloc. bytes) and 0.22% (max-RSS) in standard benchmarks, as well as 3.63% (alloc. bytes) and 0.20% (max-RSS) in microservice benchmarks.
Cite as

Sebastian Kloibhofer, Lukas Makor, Peter Hofer, David Leopoldseder, and Hanspeter Mössenböck. Profile-Guided Field Externalization in an Ahead-Of-Time Compiler. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 19:1-19:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kloibhofer_et_al:LIPIcs.ECOOP.2025.19,
  author =	{Kloibhofer, Sebastian and Makor, Lukas and Hofer, Peter and Leopoldseder, David and M\"{o}ssenb\"{o}ck, Hanspeter},
  title =	{{Profile-Guided Field Externalization in an Ahead-Of-Time Compiler}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{19:1--19:32},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.19},
  URN =		{urn:nbn:de:0030-drops-233121},
  doi =		{10.4230/LIPIcs.ECOOP.2025.19},
  annote =	{Keywords: compilation, instrumentation, profiling, fields, externalization, memory footprint reduction, memory footprint optimization}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.3
Pydrofoil: Accelerating Sail-Based Instruction Set Simulators

Authors: Carl Friedrich Bolz-Tereick, Luke Panayi, Ferdia McKeogh, Tom Spink, and Martin Berger

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
We present Pydrofoil, a multi-stage compiler that generates instruction set simulators (ISSs) from processor instruction set architectures (ISAs) expressed in the high-level, verification-oriented ISA specification language Sail. Pydrofoil achieves a > 230× speedup over the C-based ISS generated by Sail on our benchmarks, thanks to the following insights. (i) An ISS is effectively an interpreter loop, and tracing just-in-time (JIT) compilers have proven effective at accelerating those, albeit mostly for dynamically typed languages. (ii) ISS workloads are highly atypical, dominated by intensive bit manipulation operations. Conventional compiler optimisations for general-purpose programming languages have limited impact for speeding up such workloads. We develop suitable domain-specific optimisations. (iii) Neither tracing JIT compilers, nor ahead-of-time (AOT) compilation alone, even with domain-specific optimisations, suffice for the generation of performant ISSs. Pydrofoil therefore implements a hybrid approach, pairing an AOT compiler with a tracing JIT built on the meta-tracing PyPy framework. AOT and JIT use domain-specific optimisations. Our benchmarks demonstrate that combining AOT and JIT compilers provides significantly greater performance gains than using either compiler alone.
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Carl Friedrich Bolz-Tereick, Luke Panayi, Ferdia McKeogh, Tom Spink, and Martin Berger. Pydrofoil: Accelerating Sail-Based Instruction Set Simulators. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 3:1-3:31, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bolztereick_et_al:LIPIcs.ECOOP.2025.3,
  author =	{Bolz-Tereick, Carl Friedrich and Panayi, Luke and McKeogh, Ferdia and Spink, Tom and Berger, Martin},
  title =	{{Pydrofoil: Accelerating Sail-Based Instruction Set Simulators}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{3:1--3:31},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.3},
  URN =		{urn:nbn:de:0030-drops-232962},
  doi =		{10.4230/LIPIcs.ECOOP.2025.3},
  annote =	{Keywords: Instruction set architecture, processor, domain-specific language, just-in-time compilation, meta-tracing}
}
Document
DOI: 10.4230/LIPIcs.STACS.2025.64
Cluster Editing on Cographs and Related Classes

Authors: Manuel Lafond, Alitzel López Sánchez, and Weidong Luo

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
In the Cluster Editing problem, sometimes known as (unweighted) Correlation Clustering, we must insert and delete a minimum number of edges to achieve a graph in which every connected component is a clique. Owing to its applications in computational biology, social network analysis, machine learning, and others, this problem has been widely studied for decades and is still undergoing active research. There exist several parameterized algorithms for general graphs, but little is known about the complexity of the problem on specific classes of graphs. Among the few important results in this direction, if only deletions are allowed, the problem can be solved in polynomial time on cographs, which are the P₄-free graphs. However, the complexity of the broader editing problem on cographs is still open. We show that even on a very restricted subclass of cographs, the problem is NP-hard, W[1]-hard when parameterized by the number p of desired clusters, and that time n^o(p/log p) is forbidden under the ETH. This shows that the editing variant is substantially harder than the deletion-only case, and that hardness holds for the many superclasses of cographs (including graphs of clique-width at most 2, perfect graphs, circle graphs, permutation graphs). On the other hand, we provide an almost tight upper bound of time n^O(p), which is a consequence of a more general n^O(cw⋅p) time algorithm, where cw is the clique-width. Given that forbidding P₄s maintains NP-hardness, we look at {P₄, C₄}-free graphs, also known as trivially perfect graphs, and provide a cubic-time algorithm for this class.
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Manuel Lafond, Alitzel López Sánchez, and Weidong Luo. Cluster Editing on Cographs and Related Classes. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 64:1-64:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lafond_et_al:LIPIcs.STACS.2025.64,
  author =	{Lafond, Manuel and L\'{o}pez S\'{a}nchez, Alitzel and Luo, Weidong},
  title =	{{Cluster Editing on Cographs and Related Classes}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{64:1--64:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine 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.2025.64},
  URN =		{urn:nbn:de:0030-drops-228895},
  doi =		{10.4230/LIPIcs.STACS.2025.64},
  annote =	{Keywords: Cluster editing, cographs, parameterized algorithms, clique-width, trivially perfect graphs}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.13
Autonomy in the Age of Knowledge Graphs: Vision and Challenges

Authors: Jean-Paul Calbimonte, Andrei Ciortea, Timotheus Kampik, Simon Mayer, Terry R. Payne, Valentina Tamma, and Antoine Zimmermann

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
In this position paper, we propose that Knowledge Graphs (KGs) are one of the prime approaches to support the programming of autonomous software systems at the knowledge level. From this viewpoint, we survey how KGs can support different dimensions of autonomy in such systems: For example, the autonomy of systems with respect to their environment, or with respect to organisations; and we discuss related practical and research challenges. We emphasise that KGs need to be able to support systems of autonomous software agents that are themselves highly heterogeneous, which limits how these systems may use KGs. Furthermore, these heterogeneous software agents may populate highly dynamic environments, which implies that they require adaptive KGs. The scale of the envisioned systems - possibly stretching to the size of the Internet - highlights the maintainability of the underlying KGs that need to contain large-scale knowledge, which requires that KGs are maintained jointly by humans and machines. Furthermore, autonomous agents require procedural knowledge, and KGs should hence be explored more towards the provisioning of such knowledge to augment autonomous behaviour. Finally, we highlight the importance of modelling choices, including with respect to the selected abstraction level when modelling and with respect to the provisioning of more expressive constraint languages.
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Jean-Paul Calbimonte, Andrei Ciortea, Timotheus Kampik, Simon Mayer, Terry R. Payne, Valentina Tamma, and Antoine Zimmermann. Autonomy in the Age of Knowledge Graphs: Vision and Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 13:1-13:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{calbimonte_et_al:TGDK.1.1.13,
  author =	{Calbimonte, Jean-Paul and Ciortea, Andrei and Kampik, Timotheus and Mayer, Simon and Payne, Terry R. and Tamma, Valentina and Zimmermann, Antoine},
  title =	{{Autonomy in the Age of Knowledge Graphs: Vision and Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{13:1--13:22},
  ISSN =	{2942-7517},
  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.1.1.13},
  URN =		{urn:nbn:de:0030-drops-194872},
  doi =		{10.4230/TGDK.1.1.13},
  annote =	{Keywords: Knowledge graphs, Autonomous Systems}
}
Document
DOI: 10.4230/DagRep.12.9.150
Machine Learning for Science: Bridging Data-Driven and Mechanistic Modelling (Dagstuhl Seminar 22382)

Authors: Philipp Berens, Kyle Cranmer, Neil D. Lawrence, Ulrike von Luxburg, and Jessica Montgomery

Published in: Dagstuhl Reports, Volume 12, Issue 9 (2023)

Abstract
This report documents the programme and the outcomes of Dagstuhl Seminar 22382 "Machine Learning for Science: Bridging Data-Driven and Mechanistic Modelling". Today’s scientific challenges are characterised by complexity. Interconnected natural, technological, and human systems are influenced by forces acting across time- and spatial-scales, resulting in complex interactions and emergent behaviours. Understanding these phenomena - and leveraging scientific advances to deliver innovative solutions to improve society’s health, wealth, and well-being - requires new ways of analysing complex systems. The transformative potential of AI stems from its widespread applicability across disciplines, and will only be achieved through integration across research domains. AI for science is a rendezvous point. It brings together expertise from AI and application domains; combines modelling knowledge with engineering know-how; and relies on collaboration across disciplines and between humans and machines. Alongside technical advances, the next wave of progress in the field will come from building a community of machine learning researchers, domain experts, citizen scientists, and engineers working together to design and deploy effective AI tools. This report summarises the discussions from the seminar and provides a roadmap to suggest how different communities can collaborate to deliver a new wave of progress in AI and its application for scientific discovery.
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Philipp Berens, Kyle Cranmer, Neil D. Lawrence, Ulrike von Luxburg, and Jessica Montgomery. Machine Learning for Science: Bridging Data-Driven and Mechanistic Modelling (Dagstuhl Seminar 22382). In Dagstuhl Reports, Volume 12, Issue 9, pp. 150-199, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{berens_et_al:DagRep.12.9.150,
  author =	{Berens, Philipp and Cranmer, Kyle and Lawrence, Neil D. and von Luxburg, Ulrike and Montgomery, Jessica},
  title =	{{Machine Learning for Science: Bridging Data-Driven and Mechanistic Modelling (Dagstuhl Seminar 22382)}},
  pages =	{150--199},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2023},
  volume =	{12},
  number =	{9},
  editor =	{Berens, Philipp and Cranmer, Kyle and Lawrence, Neil D. and von Luxburg, Ulrike and Montgomery, Jessica},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.12.9.150},
  URN =		{urn:nbn:de:0030-drops-178125},
  doi =		{10.4230/DagRep.12.9.150},
  annote =	{Keywords: machine learning, artificial intelligence, life sciences, physical sciences, environmental sciences, simulation, causality, modelling}
}
Document
DOI: 10.4230/LIPIcs.WABI.2020.10
Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

Authors: Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, and Peter F. Stadler

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract
Ongoing developments in genome sequencing have caused a fundamental paradigm shift in the field in recent years. With ever lower sequencing costs, projects are no longer limited by available raw data, but rather by computational demands. The high complexity of eukaryotic genomes in concordance with increasing data sizes creates unique demands on methods to assemble full genomes. We describe a new approach to assemble genomes from a combination of low-coverage short and long reads. LazyB starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs, which are then reduced to a long-read overlap graph G. Instead of the more conventional approach of removing tips, bubbles, and other local features, LazyB stepwisely extracts subgraphs whose global properties approach a disjoint union of paths. First, a consistently oriented subgraph is extracted, which in a second step is reduced to a directed acyclic graph. In the next step, properties of proper interval graphs are used to extract contigs as maximum weight paths. These are translated into genomic sequences only in the final step. A prototype implementation of LazyB, entirely written in python, not only yields significantly more accurate assemblies of the yeast and fruit fly genomes compared to state-of-the-art pipelines but also requires much less computational effort. Our findings demonstrate a new low-cost method that enables the assembly of even large genomes with low computational effort.
Cite as

Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, and Peter F. Stadler. Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 10:1-10:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{gatter_et_al:LIPIcs.WABI.2020.10,
  author =	{Gatter, Thomas and von L\"{o}hneysen, Sarah and Drozdova, Polina and Hartmann, Tom and Stadler, Peter F.},
  title =	{{Economic Genome Assembly from Low Coverage Illumina and Nanopore Data}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{10:1--10:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.10},
  URN =		{urn:nbn:de:0030-drops-127991},
  doi =		{10.4230/LIPIcs.WABI.2020.10},
  annote =	{Keywords: Nanopore sequencing, Illumina sequencing, genome assembly, spanning tree, unitigs, anchors}
}
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