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It is well-known in the field of programming languages that dealing with variable names and binders may lead to conflicts such as undesired captures when implementing interpreters or compilers. This situation has been overcome by resorting…
In this paper we provide a unified combinatorial approach to establish a connection between Stirling permutations, cycle structures of permutations and perfect matchings. The main tool of our investigations is MY-sequences. In particular,…
This work studies the complexity of refuting the existence of a perfect matching in spectral expanders with an odd number of vertices, in the Polynomial Calculus (PC) and Sum of Squares (SoS) proof system. Austrin and Risse [SODA, 2021]…
Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…
Universal cycles are generalizations of de Bruijn cycles and Gray codes that were introduced originally by Chung, Diaconis, and Graham in 1992. They have been developed by many authors since, for various combinatorial objects such as…
We construct feedback functions of Nonlinear Feedback Shift Registers from those of Linear Feedback Shift Registers using the cross-join pairs method and the Zech logarithms in finite fields. We present a hypothetical algorithm to generate…
Universal cycles, such as De Bruijn cycles, are cyclic sequences of symbols that represent every combinatorial object from some family exactly once as a consecutive subsequence. Graph universal cycles are a graph analogue of universal…
We present a general approach to rounding semidefinite programming relaxations obtained by the Sum-of-Squares method (Lasserre hierarchy). Our approach is based on using the connection between these relaxations and the Sum-of-Squares proof…
Let $M_n$ denote the algebra of complex $n\times n $ matrices and write $M$ for the direct sum of the $M_n$. So a typical element of $M$ has the form \[x = x_1\oplus x_2 \... \oplus x_n \oplus \...,\] where $x_n \in M_n$ and $\|x\| =…
An additive system for the nonnegative integers is a family (A_i)_{i\in I} of sets of nonnegative integers with 0 \in A_i for all i \in I such that every nonnegative integer can be written uniquely in the form \sum_{i\in I} a_i with a_i \in…
Ewens-Pitman's partition structure arises as a system of sampling consistent probability distributions on set partitions induced by the Pitman-Yor process. It is widely used in statistical applications, particularly in species sampling…
In computational genomics, many analyses rely on efficient storage and traversal of $k$-mers, motivating compact representations such as spectrum-preserving string sets (SPSS), which store strings whose $k$-mer spectrum matches that of the…
We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
De Bruijn tori, or perfect maps, are two-dimensional periodic arrays of letters from a finite alphabet, where each possible pattern of shape (m,n) appears exactly once in a single period. While the existence of certain de Bruijn tori, such…
We propose a novel construction for the well-known prefer-max De Bruijn sequence, based on the cycle joining technique. We further show that the construction implies known results from the literature in a straightforward manner. First, it…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
By using computers to do experimental manipulations on Fourier series, we construct additional series with interesting properties. We construct several series whose sums remain unchanged when the $n^{th}$ term is multiplied by $\sin(n)/n$.…
This paper describes algorithms to deal with nested symbolic sums over combinations of harmonic series, binomial coefficients and denominators. In addition it treats Mellin transforms and the inverse Mellin transformation for functions that…
We present an algebraic construction of trace-based De Bruijn tori over finite fields, focusing on the nonzero variant that omits the all-zero pattern. The construction arranges nonzero field elements on a toroidal grid using two…