Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics

Abstract

AbstractHard 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. The time/space complexities of such approaches hinge critically on low values for the treewidth tw of the input graph. In order to extend their scope of applicability, we introduce the Tree-Diet problem, i.e. the removal of a minimal set of edges such that a given tree-decomposition can be slimmed down to a prescribed treewidth tw′. Our rationale is that the time gained thanks to a smaller treewidth in a parameterized algorithm compensates the extra post-processing needed to take deleted edges into account.Our core result is an FPT dynamic programming algorithm for Tree-Diet, using 2O(tw)n time and space. We complement this result with parameterized complexity lower-bounds for stronger variants (e.g., NP-hardness when tw′ or tw−tw′ is constant). We propose a prototype implementation for our approach which we apply on difficult instances of selected RNA-based problems: RNA design, sequence-structure alignment, and search of pseudoknotted RNAs in genomes, revealing very encouraging results. This work paves the way for a wider adoption of tree-decomposition-based algorithms in Bioinformatics.2012 ACM Subject ClassificationTheory of computation → Dynamic programming; Theory of computation → Parameterized complexity and exact algorithms; Applied computing → BioinformaticsDigital Object Identifier10.4230/LIPIcs.WABI.2021.