相关论文: A Combinatorial Framework for the Pons-Batle Ident…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
We construct the ordinary irreducible representations of the group of automorphisms of a finite rooted tree and we get a natural parametrization of them. To achieve this goals, we introduce and study the combinatorics of tree compositions,…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Recurrent neural networks have been very successful at predicting sequences of words in tasks such as language modeling. However, all such models are based on the conventional classification framework, where the model is trained against…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
Trellises are crucial graphical representations of codes. While conventional trellises are well understood, the general theory of (tail-biting) trellises is still under development. Iterative decoding concretely motivates such theory. In…
The class of Boolean combinations of tree languages recognized by deterministic top-down tree automata (also known as deterministic root-to-frontier automata) is studied. The problem of determining for a given regular tree language whether…
It is known that many networks modeling real-life complex systems are small-word (large local clustering and small diameter) and scale-free (power law of the degree distribution), and very often they are also hierarchical. Although most of…
Generating natural language under complex constraints is a principled formulation towards controllable text generation. We present a framework to allow specification of combinatorial constraints for sentence generation. We propose TSMH, an…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
We propose a novel architecture for Graph Neural Networks that is inspired by the idea behind Tree Kernels of measuring similarity between trees by taking into account their common substructures, named fragments. By imposing a series of…
We study combinatorial properties of a rational Dyck path by decomposing it into a tuple of Dyck paths. The combinatorial models such as $b$-Stirling permutations, $(b+1)$-ary trees, parenthesis presentations, and binary trees play central…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…