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Documents authored by Boehmer, Kimon

Artifact
Software
DOI: 10.4230/artifacts.22579
Arcee

Authors: Kimon Boehmer, Lukas Lee George, Fanny Hauser, and Jesse Palarus

Abstract
Cite as

Kimon Boehmer, Lukas Lee George, Fanny Hauser, Jesse Palarus. Arcee (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{Arcee,
   title = {{Arcee}}, 
   author = {Boehmer, Kimon and George, Lukas Lee and Hauser, Fanny and Palarus, Jesse},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:4a1810b816bec954e0780d591b0c79276ac8f285;origin=https://github.com/lucidLuckylee/pace_2024;visit=swh:1:snp:c15056f72ef6b62e3ef8f87b844229391c3a10b8;anchor=swh:1:rev:9269201822ced0770c31bfc3fccb48c45abbfb42}{\texttt{swh:1:dir:4a1810b816bec954e0780d591b0c79276ac8f285}} (visited on 2024-12-05)},
   url = {https://github.com/lucidLuckylee/pace_2024},
   doi = {10.4230/artifacts.22579},
}
Document
PACE Solver Description
DOI: 10.4230/LIPIcs.IPEC.2024.33
PACE Solver Description: Arcee

Authors: Kimon Boehmer, Lukas Lee George, Fanny Hauser, and Jesse Palarus

Published in: LIPIcs, Volume 321, 19th International Symposium on Parameterized and Exact Computation (IPEC 2024)

Abstract
The 2024 PACE Challenge focused on the One-Sided Crossing Minimization (OCM) problem, which aims to minimize edge crossings in a bipartite graph with a fixed order in one partition and a free order in the other. We describe our OCM solver submission that utilizes various reduction rules for OCM and, for the heuristic track, employs local search approaches as well as techniques to escape local minima. The exact solver uses an ILP formulation and branch & bound to solve an equivalent Feedback Arc Set instance.
Cite as

Kimon Boehmer, Lukas Lee George, Fanny Hauser, and Jesse Palarus. PACE Solver Description: Arcee. In 19th International Symposium on Parameterized and Exact Computation (IPEC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 321, pp. 33:1-33:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boehmer_et_al:LIPIcs.IPEC.2024.33,
  author =	{Boehmer, Kimon and George, Lukas Lee and Hauser, Fanny and Palarus, Jesse},
  title =	{{PACE Solver Description: Arcee}},
  booktitle =	{19th International Symposium on Parameterized and Exact Computation (IPEC 2024)},
  pages =	{33:1--33:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-353-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{321},
  editor =	{Bonnet, \'{E}douard and Rz\k{a}\.{z}ewski, Pawe{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2024.33},
  URN =		{urn:nbn:de:0030-drops-222595},
  doi =		{10.4230/LIPIcs.IPEC.2024.33},
  annote =	{Keywords: PACE 2024, One-Sided Crossing Minimization, OCM}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.18
RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions

Authors: Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
RNAs composed of Triplet Repeats (TR) have recently attracted much attention in the field of synthetic biology. We study the mimimum free energy (MFE) secondary structures of such RNAs and give improved algorithms to compute the MFE and the partition function. Furthermore, we study the interaction of multiple RNAs and design a new algorithm for computing MFE and partition function for RNA-RNA interactions, improving the previously known factorial running time to exponential. In the case of TR, we show computational hardness but still obtain a parameterized algorithm. Finally, we propose a polynomial-time algorithm for computing interactions from a base set of RNA strands and conduct experiments on the interaction of TR based on this algorithm. For instance, we study the probability that a base pair is formed between two strands with the same triplet pattern, allowing an assessment of a notion of orthogonality between TR.
Cite as

Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty. RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 18:1-18:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boehmer_et_al:LIPIcs.WABI.2024.18,
  author =	{Boehmer, Kimon and Berkemer, Sarah J. and Will, Sebastian and Ponty, Yann},
  title =	{{RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{18:1--18:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.18},
  URN =		{urn:nbn:de:0030-drops-206625},
  doi =		{10.4230/LIPIcs.WABI.2024.18},
  annote =	{Keywords: RNA folding, RNA interactions, triplet repeats, dynamic programming, NP-hardness}
}
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