Related papers: Valid plane trees: Combinatorial models for RNA se…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
For an arbitrary word $w$ on an alphabet, we can define the alternating symbol graph, $G(w)$, as the graph in which the edge $(a, b)$ is in $E$ iff the letters $a$ and $b$ alternate in the word $w$. A graph $G = (V, E)$ is said to be…
We study the secondary structure of RNA determined by Watson-Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant,…
In this paper, in the context of the ``Dessins d'enfants'' theory, we give a combinatorial criterion for a plane tree to cover a tree from the classes of "chains" or "stars''. Besides, we discuss some applications of this result which are…
A compacted binary tree is a directed acyclic graph encoding a binary tree in which common subtrees are factored and shared, such that they are represented only once. We show that the number of compacted binary trees of size $n$ grows…
The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Neural networks with tree-based sentence encoders have shown better results on many downstream tasks. Most of existing tree-based encoders adopt syntactic parsing trees as the explicit structure prior. To study the effectiveness of…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
We describe an attentive encoder that combines tree-structured recursive neural networks and sequential recurrent neural networks for modelling sentence pairs. Since existing attentive models exert attention on the sequential structure, we…
Net-trees are a general purpose data structure for metric data that have been used to solve a wide range of algorithmic problems. We give a simple randomized algorithm to construct net-trees on doubling metrics using $O(n\log n)$ time in…
Monadic second order logic can be used to express many classical notions of sets of vertices of a graph as for instance: dominating sets, induced matchings, perfect codes, independent sets or irredundant sets. Bounds on the number of sets…
We exhibit a recurrence on the number of discrete line segments joining two integer points in the plane using an encoding of such segments as balanced words of given length and height over the two-letter alphabet $\{0,1\}$. We give…
A radix sort tree arises when storing distinct infinite binary words in the leaves of a binary tree such that for any two words their common prefixes coincide with the common prefixes of the corresponding two leaves. If one deletes the…
The mushroom body of the fruit fly brain is one of the best studied systems in neuroscience. At its core it consists of a population of Kenyon cells, which receive inputs from multiple sensory modalities. These cells are inhibited by the…
A tree automatic structure is a structure whose domain can be encoded by a regular tree language such that each relation is recognisable by a finite automaton processing tuples of trees synchronously. Words can be regarded as specific…
In this paper, we survey some properties, encoding, and bijections involving combinatorial maps, double occurrence words, and chord diagrams. We particularly study quasi-trees from a purely combinatorial point of view and derive a…
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy…
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
The Raney numbers $R_{p,r}(n)$ are a two-parameter generalization of the Catalan numbers that were introduced by Raney in his investigation of functional composition patterns \cite{Raney}. We give a new combinatorial interpretation for all…