Related papers: Universal Gr\"obner Bases of Toric Ideals of Combi…
Combinatorial neural codes are $0/1$ vectors that are used to model the co-firing patterns of a set of place cells in the brain. One wide-open problem in this area is to determine when a given code can be algorithmically drawn in the plane…
Neural codes are binary codes in $\{0,1\}^n$; here we focus on the ones which represent the firing patterns of a type of neurons called place cells. There is much interest in determining which neural codes can be realized by a collection of…
Each linear code can be described by a code ideal given as the sum of a toric ideal and a non-prime ideal. In this way, several concepts from the theory of toric ideals can be translated into the setting of code ideals. It will be shown…
A combinatorial neural code is a subset of the power set $2^{[n]}$ on $[n]=\{1,\dots, n\}$, in which each $1\leq i\leq n$ represents a neuron and each element (codeword) represents the co-firing event of some neurons. Consider a space…
Convex neural codes are combinatorial structures describing the intersection pattern of a collection of convex sets. Inductively pierced codes are a particularly nice subclass of neural codes introduced in the information visualization…
Two correspondences have been provided that associate any linear code over a finite field with a binomial ideal. In this paper, algorithms for computing their Graver bases and universal Gr\"obner bases are given. To this end, a connection…
A combinatorial neural code $\mathscr C\subseteq 2^{[n]}$ is convex if it arises as the intersection pattern of convex open subsets of $\mathbb R^d$. We relate the emerging theory of convex neural codes to the established theory of oriented…
A neural code $\mathcal{C}$ is a collection of binary vectors of a given length n that record the co-firing patterns of a set of neurons. Our focus is on neural codes arising from place cells, neurons that respond to geographic stimulus. In…
Relying on the combinatorial classification of toric ideals using their bouquet structure, we focus on toric ideals of hypergraphs and study how they relate to general toric ideals. We show that hypergraphs exhibit a surprisingly general…
The "neural code" is the way the brain characterizes, stores, and processes information. Unraveling the neural code is a key goal of mathematical neuroscience. Topology, coding theory, and, recently, commutative algebra are some the…
Associated to any vector configuration A is a toric ideal encoded by vectors in the kernel of A. Each toric ideal has two special generating sets: the universal Gr\"obner basis and the Graver basis. While the former is generally a proper…
A combinatorial code $\mathcal{C}$ is a collection of subsets of $[n]$, or equivalently a set of points in $\{0,1\}^n$. A morphism of codes is a map from one combinatorial code to another such that the coordinates of points in the image can…
The brain processes information about the environment via neural codes. The neural ideal was introduced recently as an algebraic object that can be used to better understand the combinatorial structure of neural codes. Every neural ideal…
Associated to any hypergraph is a toric ideal encoding the algebraic relations among its edges. We study these ideals and the combinatorics of their minimal generators, and derive general degree bounds for both uniform and non-uniform…
The universal Gr\"obner basis of an ideal is a Gr\"obner basis with respect to all term orders simultaneously. The aim of this paper is to present an algorithmic approach to compute the universal Gr\"obner basis for the toric ideal…
Neural codes allow the brain to represent, process, and store information about the world. Combinatorial codes, comprised of binary patterns of neural activity, encode information via the collective behavior of populations of neurons. A…
Recently, it was shown that a binary linear code can be associated to a binomial ideal given as the sum of a toric ideal and a non-prime ideal. Since then two different generalizations have been provided which coincide for the binary case.…
Based on the theoretical neuroscience, G. Cotardo and A. Ravagnavi in \cite{CR} introduced a kind of asymmetric binary codes called combinatorial neural codes (CN codes for short), with a "matched metric" $\delta_{r}$ called asymmetric…
The universal Gr\"{o}bner basis of $I$, is a Gr\"{o}bner basis for $I$ with respect to all term orders simultaneously. Let $I_G$ be the toric ideal of a graph $G$. We characterize in graph theoretical terms the elements of the universal…
Convex neural codes are subsets of the Boolean lattice that record the intersection patterns of convex sets in Euclidean space. Much work in recent years has focused on finding combinatorial criteria on codes that can be used to classify…