Related papers: Acyclic Orientations and Spanning Trees
Many cellular processes require a polarization axis which generally initially emerges as an inhomogeneous distribution of molecular markers in the cell. We present a simple analytical model of a general mechanism of cell polarization taking…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
We define an algebraic setup of homology for hypergraphs, which defaults to simplicial homology in the case of graphs, and study its basic properties. As part of our study we define algebraic spanning trees of hypergraphs, along with…
We introduce a new graph polynomial that encodes interesting properties of graphs, for example, the number of matchings and the number of perfect matchings. Most importantly, for bipartite graphs the polynomial encodes the number of…
To a simplicial complex, we associate a square-free monomial ideal in the polynomial ring generated by its vertex set over a field. We study algebraic properties of this ideal via combinatorial properties of the simplicial complex. By…
We explore resolutions of monomial ideals supported by simplicial trees. We argue that since simplicial trees are acyclic, the criterion of Bayer, Peeva and Sturmfels for checking if a simplicial complex supports a free resolution of a…
Coloured probability tree models are statistical models coding conditional independence between events depicted in a tree graph. They are more general than the very important class of context-specific Bayesian networks. In this paper, we…
We introduce the simple extension complexity of a polytope P as the smallest number of facets of any simple (i.e., non-degenerate in the sense of linear programming) polytope which can be projected onto P. We devise a combinatorial method…
Our purpose is to study the family of simple undirected graphs whose toric ideal is a complete intersection from both an algorithmic and a combinatorial point of view. We obtain a polynomial time algorithm that, given a graph $G$, checks…
We analyze the complexity of learning directed acyclic graphical models from observational data in general settings without specific distributional assumptions. Our approach is information-theoretic and uses a local Markov boundary search…
We study graph classes modeled by families of non-crossing (NC) connected sets. Two classic graph classes in this context are disk graphs and proper interval graphs. We focus on the cases when the sets are paths and the host is a tree…
Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory…
For networks of coupled dynamical systems we characterize admissible functions, that is, functions whose gradient is an admissible vector field. The schematic representation of a gradient network dynamical system is of an undirected cell…
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…
Probabilistic inferences distill knowledge from graphs to aid human make important decisions. Due to the inherent uncertainty in the model and the complexity of the knowledge, it is desirable to help the end-users understand the inference…
An elimination tree for a connected graph $G$ is a rooted tree on the vertices of $G$ obtained by choosing a root $x$ and recursing on the connected components of $G-x$ to produce the subtrees of $x$. Elimination trees appear in many guises…
Complex networks can be used to analyze structures and systems in the embryo. Not only can we characterize growth and the emergence of form, but also differentiation. The process of differentiation from precursor cell populations to…
We extend Andersson-Madigan-Perlman chain graphs by (i) relaxing the semidirected acyclity constraint so that only directed cycles are forbidden, and (ii) allowing up to two edges between any pair of nodes. We introduce global, and ordered…
Large graphs abound in machine learning, data mining, and several related areas. A useful step towards analyzing such graphs is that of obtaining certain summary statistics - e.g., or the expected length of a shortest path between two…
In this paper we study termination of term graph rewriting, where we restrict our attention to acyclic term graphs. Motivated by earlier work by Plump we aim at a definition of the notion of simplification order for acyclic term graphs. For…