相关论文: A Combinatorial Framework for the Pons-Batle Ident…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
We build on recent work of Yeats, Courtiel, and others involving connected chord diagrams. We first derive from a Hopf-algebraic foundation a class of tree-like functional equations and prove that they are solved by weighted generating…
We introduce and study some affine Hecke algebras of type ADE, generalising the affine Hecke algebras of GL. We construct irreducible calibrated representations and describe the calibrated spectrum. This is done in terms of new families of…
Combinatorial spiders are a model for the invariant space of the tensor product of representations. The basic objects, webs, are certain directed planar graphs with boundary; algebraic operations on representations correspond to…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
Catalan numbers and their interpretations in terms of Dyck paths are widely used in different topics of applied mathematics and computer science. Here, we consider a general approach for constrained Dyck paths. In particular, we study Dyck…
The family of graphs that can be constructed from isolated vertices by disjoint union and graph join operations are called cographs. These graphs can be represented in a tree-like representation termed parse tree or cotree. In this paper,…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
The paper discusses the limitations of deep learning models in identifying and utilizing features that remain invariant under a bijective transformation on the data entries, which we refer to as combinatorial patterns. We argue that the…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
We give exact relations for certain types of the hierarchic fractal structures. In the blatant distinction from regular networks of the "small world" (SW) topology [1], regular fractal networks manifests the logarithmic dependence of the…
We consider locally checkable labeling LCL problems in the LOCAL model of distributed computing. Since 2016, there has been a substantial body of work examining the possible complexities of LCL problems. For example, it has been established…
The family of graphs of reduced words of a certain subcollection of permutations in the union $\cup_{n\geq 4}\frak{S}_{n}$ of symmetic groups is investigated. The subcollection is characterised by the hook cycle type $(n-2,1,1)$ with…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…