Related papers: Operads and Phylogenetic Trees

We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any $n$-node static tree can be represented in $2n + o(n)$ bits and a number of operations on the tree can be supported in…

We study homotopy-coherent commutative multiplicative structures on equivariant spaces and spectra. We define N-infinity operads, equivariant generalizations of E-infinity operads. Algebras in equivariant spectra over an N-infinity operad…

Let M be a bicomplete, closed symmetric monoidal category. Let P be an operad in M, i.e., a monoid in the category of symmetric sequences of objects in M, with its composition monoidal structure. Let R be a P-co-ring, i.e., a comonoid in…

This paper discusses the question of how to recognize whether an operad is E_n (ie. equivalent to the little n-cubes operad). A construction is given which produces many new examples of E_n operads. This construction is developed in the…

We introduce bud generating systems, which are used for combinatorial generation. They specify sets of various kinds of combinatorial objects, called languages. They can emulate context-free grammars, regular tree grammars, and synchronous…

We present a new class of metrics for unrooted phylogenetic $X$-trees derived from the Gromov-Hausdorff distance for (compact) metric spaces. These metrics can be efficiently computed by linear or quadratic programming. They are robust…

We consider the endomorphism operad of a functor, which is roughly the object of natural transformations from (monoidal) powers of that functor to itself. There are many examples from geometry, topology, and algebra where this object has…

We define a notion of homotopy Segal cooperad in the category of $ E_\infty $-algebras. This model of Segal cooperad that we define in the paper, which we call homotopy Segal $ E_\infty $-Hopf cooperad, covers examples given by the cochain…

Combinatorial Hopf algebras of trees exemplify the connections between operads and bialgebras. Painted trees were introduced recently as examples of how graded Hopf operads can bequeath Hopf structures upon compositions of coalgebras. We…

We study (plane) tree-valued Markov chains $(T_n,n \geq 1)$ with uniform backward dynamics and show that they can be obtained by sampling from a real tree. As non--plane trees, every such Markov chain is represented by a weighted real tree.…

This thesis is divided into two parts. The first one is composed of recollections on operad theory, model categories, simplicial homotopy theory, rational homotopy theory, Maurer-Cartan spaces, and deformation theory. The second part deals…

A theory is developed which uses "networks" (directed acyclic graphs with some extra structure) as a formalism for expressions in multilinear algebra. It is shown that this formalism is valid for arbitrary PROPs (short for 'PROducts and…

We study a coloured operad involving rooted trees and directed cycles of rooted trees that generalizes the operad of rooted trees of Chapoton and Livernet. We describe all the relations between the generators of a certain suboperad of that…

In a previous work, we gave a coalgebraic framework of directed graphs equipped with weights (or probability vectors) in terms of (Markov) L-coalgebras. They are K-vector spaces equipped with two co-operations, \Delta_M, \tilde{\Delta}_M…

We study differential graded operads and $p$-adic stable homotopy theory. We first construct a new class of differential graded operads, which we call the stable operads. These operads are, in a particular sense, stabilizations of…

In this paper, we prove that the self-dual morphological hierarchical structure computed on a n-D gray-level wellcomposed image u by the algorithm of G{\'e}raud et al. [1] is exactly the mathematical structure defined to be the tree of…

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 show that every action operad gives rise to a notion of monoidal category via the categorical version of the Borel construction, embedding action operads into the category of 2-monads on $\mathbf{Cat}$. We characterize those 2-monads in…

The theory of operads (May, cyclic, modular, PROPs, etc) is extended to include higher dimensional phenomena, i.e. operations between operations, mimicking the algebraic structure on varieties of arbitrary dimensions, having marked…

A new hierarchy of combinatorial operads is introduced, involving families of regular polygons with configurations of arcs, called decorated cliques. This hierarchy contains, among others, operads on noncrossing configurations, Motzkin…