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

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. 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 2^O(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.

Tangles, Trees and Flowers

<p>A tangle of order k in a connectivity function λ may be thought of as a "k-connected component" of λ. For a connectivity function λ and a tangle in λ of order k that satisfies a certain robustness condition, we describe a tree decomposition of λ that displays, up to a certain natural equivalence, all of the k-separations of λ that are non-trivial with respect to the tangle. In particular, for a tangle in a matroid or graph of order k that satisfies a certain robustness condition, we describe a tree decomposition of the matroid or graph that displays, up to a certain natural equivalence, all of the k- separations of the matroid or graph that are non-trivial with respect to the tangle.</p>

Tangles, Trees and Flowers

<p>A tangle of order k in a connectivity function λ may be thought of as a "k-connected component" of λ. For a connectivity function λ and a tangle in λ of order k that satisfies a certain robustness condition, we describe a tree decomposition of λ that displays, up to a certain natural equivalence, all of the k-separations of λ that are non-trivial with respect to the tangle. In particular, for a tangle in a matroid or graph of order k that satisfies a certain robustness condition, we describe a tree decomposition of the matroid or graph that displays, up to a certain natural equivalence, all of the k- separations of the matroid or graph that are non-trivial with respect to the tangle.</p>

Choosing the Root of the Tree Decomposition When Solving WCSPs: Preliminary Results

In this paper we analyze the effect of selecting the root in a tree decomposition when using decomposition-based backtracking algorithms. We focus on optimization tasks for Graphical Models using the BTD algorithm. We show that the choice of the root typically has a dramatic effect in the solving performance. Then we investigate different simple measures to predict near optimal roots. Our study shows that correlations are often low, so the automatic selection of a near optimal root will require more sophisticated techniques.

Constructing tree decompositions of graphs with bounded gonality

In this paper, we give a constructive proof of the fact that the treewidth of a graph is at most its divisorial gonality. The proof gives a polynomial time algorithm to construct a tree decomposition of width at most k, when an effective divisor of degree k that reaches all vertices is given. We also give a similar result for two related notions: stable divisorial gonality and stable gonality.

A Proof of Parikh’s Theorem via Dickson’s Lemma

In this paper, we give a proof of Parikh’s semilinear theorem via Dickson’s lemma. It is notable that our proof provides a clear separation between properties derived from Dickson’s lemma and tree decomposition for context-free grammars.