Related papers: Bijective enumeration of general stacks
In this paper, we review the problem of matrix completion and expose its intimate relations with algebraic geometry, combinatorics and graph theory. We present the first necessary and sufficient combinatorial conditions for matrices of…
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…
Biological sequence comparison is a key step in inferring the relatedness of various organisms and the functional similarity of their components. Thanks to the Next Generation Sequencing efforts, an abundance of sequence data is now…
Walks on Young's lattice of integer partitions encode many objects of algebraic and combinatorial interest. Chen et al. established connections between such walks and arc diagrams. We show that walks that start at $\varnothing$, end at a…
Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range…
This paper concentrates on the set $\mathcal{V}_n$ of weighted Dyck paths of length $2n$ with special restrictions on the level of valleys. We first give its explicit formula of the counting generating function in terms of certain weight…
Our goal is to quickly find top $k$ lists of nodes with the largest degrees in large complex networks. If the adjacency list of the network is known (not often the case in complex networks), a deterministic algorithm to find a node with the…
Inspired by a new mathematical model for bobbin lace, this paper considers finite lattice paths formed from the set of step vectors $\mathfrak{A}=$$\{\rightarrow,$ $\nearrow,$ $\searrow,$ $\uparrow,$ $\downarrow\}$ with the restriction that…
Various lattice path models are reviewed. The enumeration is done using generating functions. A few bijective considerations are woven in as well. The kernel method is often used. Computer algebra was an essential tool. Some results are…
We present three bijections, the first between little Schr\"{o}der paths and a class of growth-constrained integer sequences, the second between lattice paths consisting of steps with nonnegative slope and another class of…
The intersection graph of a collection of trapezoids with corner points lying on two parallel lines is called a trapezoid graph. Using binary indexed tree data structure, we improve algorithms for calculating the size and the number of…
We consider maps on orientable surfaces. A map is called \emph{unicellular} if it has a single face. A \emph{covered map} is a map (of genus $g$) with a marked unicellular spanning submap (which can have any genus in $\{0,1,...,g\}$). Our…
We present an algorithm for enumerating exactly the number of Hamiltonian chains on regular lattices in low dimensions. By definition, these are sets of k disjoint paths whose union visits each lattice vertex exactly once. The well-known…
We study modeling and identification of processes with a spectral density matrix of low rank. Equivalently, we consider processes having an innovation of reduced dimension for which Prediction Error Methods (PEM) algorithms are not directly…
Density matrices of graphs are combinatorial laplacians normalized to have trace one (Braunstein \emph{et al.} \emph{Phys. Rev. A,} \textbf{73}:1, 012320 (2006)). If the vertices of a graph are arranged as an array, then its density matrix…
A hypergraph is simple if it has no loops and no repeated edges, and a hypergraph is linear if it is simple and each pair of edges intersects in at most one vertex. For $n\geq 3$, let $r= r(n)\geq 3$ be an integer and let $\boldsymbol{k} =…
For a labeled tree on the vertex set $\set{1,2,\ldots,n}$, the local direction of each edge $(i\,j)$ is from $i$ to $j$ if $i<j$. For a rooted tree, there is also a natural global direction of edges towards the root. The number of edges…
Finding interactions between variables in large and high-dimensional datasets is often a serious computational challenge. Most approaches build up interaction sets incrementally, adding variables in a greedy fashion. The drawback is that…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
This is a book on higher-categorical diagrams, including pasting diagrams. It aims to provide a thorough and modern reference on the subject, collecting, revisiting and expanding results scattered across the literature, informed by recent…