Related papers: Morphisms of Coloured Petri Nets
Inspired by the $S^n$ colored version of Khovanov and Khovanov-Rozansky homology, we define a colored version of knot Floer homology by studying the colimit of a directed system of link Floer homology with infinite full twists.…
Quandle coloring quivers are directed graph-valued invariants of oriented knots and links, defined using a choice of finite quandle $X$ and set $S\subset\mathrm{Hom}(X,X)$ of endomorphisms. From a quandle coloring quiver, a polynomial knot…
We investigate the common underlying discrete structures for various smooth and discrete nets. The main idea is to impose the characteristic properties of the nets not only on elementary quadrilaterals but also on larger parameter…
We define the notion of a trace kernel on a manifold M. Roughly speaking, it is a sheaf on M x M for which the formalism of Hochschild homology applies. We associate a microlocal Euler class to such a kernel, a cohomology class with values…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
We introduce a new combinatorial object called a web world that consists of a set of web diagrams. The diagrams of a web world are generalizations of graphs, and each is built on the same underlying graph. Instead of ordinary vertices the…
We classify all additive invariants of open Petri nets: these are $\mathbb{N}$-valued invariants which are additive with respect to sequential and parallel composition of open Petri nets. In particular, we prove two classification theorems:…
In graph learning, maps between graphs and their subgraphs frequently arise. For instance, when coarsening or rewiring operations are present along the pipeline, one needs to keep track of the corresponding nodes between the original and…
Petri nets proved useful to describe various real-world systems, but many of their properties are very hard to check. To alleviate this difficulty, subclasses are often considered. The class of weighted marked graphs with relaxed place…
There exists an injective, information-preserving function that maps a semantic network (i.e a directed labeled network) to a directed network (i.e. a directed unlabeled network). The edge label in the semantic network is represented as a…
We construct cobordism maps on link Floer homology associated to decorated link cobordisms. The maps are defined on a curved chain homotopy type invariant. We describe the construction, and prove invariance. We also make a comparison with…
Dominator coloring of a graph is a proper (vertex) coloring with the property that every vertex is either alone in its color class or adjacent to all vertices of at least one color class. A dominated coloring of a graph is a proper coloring…
We investigate an algebraic problem related to the determination of the fundamental group of a class of spaces of configurations on surfaces. The configuration spaces are spaces of points grouped into colors. Whether two points are allowed…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
In recent work by Johnson et al. (2022), a framework was described for the study of graph problems over classes specified by omitting each of a finite set of graphs as subgraphs. If a problem falls into the framework then its computational…
In this paper, we explore complex network properties of word collocation networks (Ferret, 2002) from four different genres. Each document of a particular genre was converted into a network of words with word collocations as edges. We…
Gene regulatory network (GRN) plays a central role in system biology and genomics. It provides a promising way to model and study complex biological processes. Several computational methods have been developed for the construction and…
This paper investigates the coloring problem on Fibonacci-Cayley tree, which is a Cayley graph whose vertex set is the Fibonacci sequence. More precisely, we elucidate the complexity of shifts of finite type defined on Fibonacci-Cayley tree…
Path graphs are intersection graphs of paths in a tree.~In this paper we give a "6\ good characterization" of path graphs, namely, we prove that path graph membership is in $NP\cap CoNP$ without resorting to existing polynomial time…