Related papers: Combinatorics of Palindromes
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
The $\ell$-deck of a graph $G$ is the multiset of all induced subgraphs of $G$ on $\ell$ vertices. We say that a graph is reconstructible from its $\ell$-deck if no other graph has the same $\ell$-deck. In 1957, Kelly showed that every tree…
We analyze the performance of graph neural network (GNN) architectures from the perspective of random graph theory. Our approach promises to complement existing lenses on GNN analysis, such as combinatorial expressive power and worst-case…
Sampling from combinatorial families can be difficult. However, complicated families can often be embedded within larger, simpler ones, for which easy sampling algorithms are known. We take advantage of such a relationship to describe a…
The palindromic tree (a.k.a. eertree) for a string $S$ of length $n$ is a tree-like data structure that represents the set of all distinct palindromic substrings of $S$, using $O(n)$ space [Rubinchik and Shur, 2018]. It is known that, when…
We prove that any mixed-integer linear extended formulation for the matching polytope of the complete graph on $n$ vertices, with a polynomial number of constraints, requires $\Omega(\sqrt{\sfrac{n}{\log n}})$ many integer variables. By…
The persistence diagram (PD) is an increasingly popular topological descriptor. By encoding the size and prominence of topological features at varying scales, the PD provides important geometric and topological information about a space.…
Two independent edges in ordered graphs can be nested, crossing or separated. These relations define six types of subgraphs, depending on which relations are forbidden. We refine a remark by Erd\H{o}s and Rado that every 2-coloring of the…
In this paper, we investigate the reconstruction of permutations on {1, 2, ..., n} from betweenness constraints involving the minimum and the maximum element located between t and t+1, for all t=1, 2, ..., n-1. We propose two variants of…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
In this work we present a general and versatile algorithmic framework for exhaustively generating a large variety of different combinatorial objects, based on encoding them as permutations. This approach provides a unified view on many…
We study higher-dimensional analogues of graph-theoretic trees within the class of pure n-simplicial complexes. Focusing on the case m = n-1 in Dewdney's (m, n)-tree framework, we introduce refined notions of path and circuit sequences that…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
We introduce a new construction of embeddings of arbitrary recursive data structures into high dimensional vectors. These embeddings provide an interpretable model for the latent state vectors of transformers. We demonstrate that these…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Hierarchical structure and repetition are prevalent in graphs originating from nature or engineering. These patterns can be represented by a class of parametric-structure graphs, which are defined by templates that generate structure by way…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
A $(k+r,k,l)$ binary array code of length $k+r$, dimension $k$, and sub-packetization $l$ is composed of $l\times(k+r)$ matrices over $\mathbb{F}_2$, with every column of the matrix stored on a separate node in the distributed storage…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
This survey article is devoted to general results in combinatorial enumeration. The first part surveys results on growth of hereditary properties of combinatorial structures. These include permutations, ordered and unordered graphs and…