Results 1 to 10 of about 13,679 (262)
Separating layered treewidth and row treewidth [PDF]
Discrete Mathematics & Theoretical Computer Science, 2022 Layered treewidth and row treewidth are recently introduced graph parameters that have been key ingredients in the solution of several well-known open problems.
Prosenjit Bose +4 more
doaj +5 more sources
Treewidth-based algorithms for the small parsimony problem on networks. [PDF]
Algorithms Mol Biol, 2022 Background Phylogenetic reconstruction is one of the paramount challenges of contemporary bioinformatics. A subtask of existing tree reconstruction algorithms is modeled by the Small Parsimony problem: given a tree T and an assignment of character-states
Scornavacca C, Weller M.
europepmc +3 more sources
On the treewidths of graphs of bounded degree. [PDF]
PLoS One, 2015 In this paper, we develop a new technique to study the treewidth of graphs with bounded degree. We show that the treewidth of a graph G = (V, E) with maximum vertex degree d is at most [Formula: see text] for sufficiently large d, where C is a constant.
Song Y, Yu M.
europepmc +6 more sources
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. [PDF]
Algorithms Mol Biol, 2022 Hard graph problems are ubiquitous in Bioinformatics, inspiring the design of specialized Fixed-Parameter Tractable algorithms, many of which rely on a combination of tree-decomposition and dynamic programming.
Marchand B, Ponty Y, Bulteau L.
europepmc +2 more sources
Maximum-scoring path sets on pangenome graphs of constant treewidth. [PDF]
Front BioinformWe generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139–150), from sequences to graphs.
Brejová B +3 more
europepmc +2 more sources
The treewidth of 2-section of hypergraphs [PDF]
Discrete Mathematics & Theoretical Computer Science, 2021 Let $H=(V,F)$ be a simple hypergraph without loops. $H$ is called linear if $|f\cap g|\le 1$ for any $f,g\in F$ with $f\not=g$. The $2$-section of $H$, denoted by $[H]_2$, is a graph with $V([H]_2)=V$ and for any $ u,v\in V([H]_2)$, $uv\in E([H]_2)$ if ...
Ke Liu, Mei Lu
doaj +5 more sources
Automated design of dynamic programming schemes for RNA folding with pseudoknots. [PDF]
Algorithms Mol Biol, 2023 Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play.
Marchand B +4 more
europepmc +2 more sources
Degree-3 Treewidth Sparsifiers [PDF]
, 2014 We study treewidth sparsifiers. Informally, given a graph $G$ of treewidth $k$, a treewidth sparsifier $H$ is a minor of $G$, whose treewidth is close to $k$, $|V(H)|$ is small, and the maximum vertex degree in $H$ is bounded.
Chekuri, Chandra, Chuzhoy, Julia
core +4 more sources
Between Treewidth and Clique-width [PDF]
, 2014 Many hard graph problems can be solved efficiently when restricted to graphs of bounded treewidth, and more generally to graphs of bounded clique-width.
B Courcelle +12 more
core +3 more sources
Benchmarking treewidth as a practical component of tensor network simulations. [PDF]
PLoS One, 2018 Tensor networks are powerful factorization techniques which reduce resource requirements for numerically simulating principal quantum many-body systems and algorithms.
Dumitrescu EF +5 more
europepmc +2 more sources