Related papers: Operads and Phylogenetic Trees
Let $\phi: A\to A$ be a (not necessarily linear, additive or continuous) map of a standard operator algebra. Suppose for any $a,b\in A$ there is an algebra automorphism $\theta_{a,b}$ of $ A$ such that \begin{align*} \phi(a)\phi(b) =…
We define a construction on operads which yields a new description of the minimal model. The construction also allows us to define algebraic structures on the homology of chain complexes with homologously trivial operad algebra structures,…
We define a category $\mathsf{List}$ whose objects are sets and morphisms are mappings which assign to an element in the domain an ordered sequence (list) of elements in the codomain. We introduce and study a category of simplicial objects…
In this paper, we first endow the space of decorated planar rooted forests with a coproduct that equips it with the structure of a bialgebra and further a Moerdijk Hopf algebra. We also present a combinatorial description of this coproduct,…
We define a family of multigraded operads $O_\lambda$ depending on a scalar parameter, such that forgetting the multigraduation gives back the pre-Lie operad when the parameter $\lambda$ is equal to one, and the NAP operad governing…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
We study quotients of the magmatic operad, that is the free nonsymmetric operad over one binary generator. In the linear setting, we show that the set of these quotients admits a lattice structure and we show an analog of the Grassmann…
Barton Zwiebach constructed the `string products' on the Hilbert space of combined conformal field theory of matter and ghosts. It is well-known that the `tree level' specialization of these products forms a strongly homotopy Lie algebra. A…
We present a general framework for balancing expressions (terms) in form of so called tree straight-line programs. The latter can be seen as circuits over the free term algebra extended by contexts (terms with a hole) and the operations…
We establish and explore a relationship between two approaches to moment-cumulant relations in free probability theory: on one side the main approach, due to Speicher, given in terms of M\"obius inversion on the lattice of noncrossing…
We generalize the classical operad pair theory to a new model for $E_\infty$ ring spaces, which we call ring operad theory, and establish a connection with the classical operad pair theory, allowing the classical multiplicative infinite…
This is the fourth installment in a series of papers offering models of hierarchical structure for dynamical systems, using the language of polynomial functors. The operad underlying the symmetric monoidal category $(\mathbf{Poly}, \otimes,…
In this paper, I introduce a new generalization of the concept of an operad, further generalizing the concept of an opetope introduced by Baez and Dolan, who used this for the definition of their version of non-strict $n$-categories.…
A complete study of an operad $\mathrm{NC} \mathcal{M}$ of noncrossing configurations of chords introduced in previous work of the author is performed. This operad is defined on the linear span of all noncrossing $\mathcal{M}$-cliques.…
Ordered, linear, and other substructural type systems allow us to expose deep properties of programs at the syntactic level of types. In this paper, we develop a family of unary logical relations that allow us to prove consequences of…
We introduce a new perspective on a procedure for generating pseudo-Anosov homemorphisms from postcritically finite interval maps. The central idea is the realization of a tree structure on one such family of pseudo-Anosovs: individual…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
The works of Poincare, Birkhoff, Witt and Cartier, Milnor, Moore on the connected cocommutative Hopf algebras translated in the language of operads means that the triple of operads (Com, As, Lie) endowed with the Hopf compatiblity relation…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…