Related papers: Operads and Phylogenetic Trees
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Pairs of graded graphs, together with the Fomin property of graded graph duality, are rich combinatorial structures providing among other a framework for enumeration. The prototypical example is the one of the Young graded graph of integer…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
We investigate the relationship between symmetric functions and the representation theory of operads, relative operads, and props. We extend the classical character map for symmetric sequences to relative bisymmetric sequences and symmetric…
In this expository paper we give an elementary, hands-on computation of the homology of the little disks operad, showing that the homology of a $d-fold loop space is a Poisson algebra. One aim is to familiarize a greater audience with…
Two operads are said to belong to the same Wilf class if they have the same generating series. We discuss possible Wilf classifications of non-symmetric operads with monomial relations. As a corollary, this would give the same…
This monograph provides a coherent development of operads, infinity operads, and monoidal categories, equipped with equivariant structures encoded by an action operad. A group operad is a planar operad with an action operad equivariant…
The homotopy category of $N_\infty$ operads is equivalent to a finite lattice, and as the ambient group varies, there are various image constructions between these lattices. In this paper, we explain how to lift this algebraic structure…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…
We give a detailed proof of T. Willwacher's theorem arXiv:1009.1654 which links the cohomology of the full graph complex fGC to the cohomology of the deformation complex of the operad GER, governing Gerstenhaber algebras. We also present…
In a first part of this paper, we introduce a homology theory for infinity-operads and for dendroidal spaces which extends the usual homology of differential graded operads defined in terms of the bar construction, and we prove some of its…
Dendriform algebras form a category of algebras recently introduced by Loday. A dendriform algebra is a vector space endowed with two nonassociative binary operations satisfying some relations. Any dendriform algebra is an algebra over the…
In this paper, we use the language of operads to study open dynamical systems. More specifically, we study the algebraic nature of assembling complex dynamical systems from an interconnection of simpler ones. The syntactic architecture of…
We introduce a non-symmetric operad $\mathcal{N}$, whose dimension in degree $n$ is given by the Catalan number $c_{n-1}$. It arises naturally in the study of coalgebra structures defined on compatible associative algebras. We prove that…
Inspired by recent work of Batanin and Berger on the homotopy theory of operads, a general monad-theoretic context for speaking about structures within structures is presented, and the problem of constructing the universal ambient structure…
Markov processes on the lattices with arbitrary dimension are omnipresent in statistical mechanics; however their algebraic description is complete only in dimension 1, for which linear algebra provides many tools complementary to the…
We introduce a generalization of the notion of operad that we call a contractad, whose set of operations is indexed by connected graphs and whose composition rules are numbered by contractions of connected subgraphs. We show that many…
First, we give a functorial construction of a group associated to a symmetric operad. Applied to the endomorphism operad it gives the group of formal diffeomorphisms. Second, we associate a symmetric operad to any family of decorated graphs…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
In this paper, we prove a conjecture of Blumberg and Hill regarding the existence of $N_\infty$-operads associated to given sequences $\mathcal{F} = (\mathcal{F}_n)_{n \in \mathbb{N}}$ of families of subgroups of $G\times \Sigma_n$. For…