Reverse engineering of compact suffix trees and links: A novel algorithm

Invented in the 1970s, the Suffix Tree (ST) is a data structure that indexes all substrings of a text in linear space. Although more space demanding than other indexes, the ST remains likely an inspiring index because it represents substrings in a hierarchical tree structure. Along time, STs have acquired a central position in text algorithmics with myriad of algorithms and applications to for instance motif discovery, biological sequence comparison, or text compression. It is well known that different words can lead to the same suffix tree structure with different labels. Moreover, the properties of STs prevent all tree structures from being STs. Even the suffix links, which play a key role in efficient construction algorithms and many applications, are not sufficient to discriminate the suffix trees of distinct words. The question of recognising which trees can be STs has been raised and termed Reverse Engineering on STs. For the case where a tree is given with potential suffix links, a seminal work provides a linear time solution only for binary alphabets. Here, we also investigate the Reverse Engineering problem on ST with links and exhibit a novel approach and algorithm. Hopefully, this new suffix tree characterisation makes up a valuable step towards a better understanding of suffix tree combinatorics.     

On the normalized Laplacian of Möbius phenylene chain and its applications

Let denote a molecular graph of linear [n] phenylene with n hexagons and n squares, and let the Möbius phenylene chain be the graph obtained from the by identifying the opposite lateral edges in reversed way. Utilizing the decomposition theorem of the normalized Laplacian characteristic polynomial, we study the normalized Laplacian spectrum of , which consists of the eigenvalues of two symmetric matrices ℒ _R and ℒ _Q of order 3n. By investigating the relationship between the roots and coefficients of the characteristic polynomials of the two matrices above, we obtain an explicit closed-form formula of the multiplicative degree-Kirchhoff index as well as the number of spanning trees of . Furthermore, we determine the limited value for the quotient of the multiplicative degree-Kirchhoff index and the Gutman index of .     

Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides

A new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Addendum to: “Hamilton-laceable bi-powers of locally finite bipartite graphs” [Discrete Math. 345 (2022) 112777]

In this addendum we give a short and easy negative answer to the two questions raised in the original article.     

On weighting two criteria with a parameter in combinatorial optimization problems

Two criteria in a combinatorial problem are often combined in a weighted sum objective using a weighting parameter between 0 and 1. For special problem types, e.g., when one of the criteria is a bottleneck value, efficient algorithms are known that solve for a given value of the weighting parameter.     

Hierarchical Model-Based Clustering for Large Datasets

In recent years, hierarchical model-based clustering has provided promising results in a variety of applications. However, its use with large datasets has been hindered by a time and memory complexity that are at least quadratic in the number of observations. To overcome this difficulty, this article proposes to start the hierarchical agglomeration from an efficient classification of the data in many classes rather than from the usual set of singleton clusters. This initial partition is derived from a subgraph of the minimum spanning tree associated with the data. To this end, we develop graphical tools that assess the presence of clusters in the data and uncover observations difficult to classify. We use this approach to analyze two large, real datasets: a multiband MRI image of the human brain and data on global precipitation climatology. We use the real datasets to discuss ways of integrating the spatial information in the clustering analysis. We focus on two-stage methods, in which a second stage of processing using established methods is applied to the output from the algorithm presented in this article, viewed as a first stage.     

Método de elementos de borde jerárquico basado en el árbol de Barnes-Hut aplicado a flujo reptante exterior

In this work, a hierarchical variant of a boundary element method and its use in Stokes flow around three-dimensional rigid bodies in steady regime is presented. The proposal is based on the descending hierarchical low-order and self-adaptive algorithm of Barnes-Hut, and it is used in conjunction with an indirect boundary integral formulation of second class, whose source term is a function of the undisturbed velocity. The solution field is the double layer surface density, which is modified in order to complete the eigenvalue spectrum of the integral operator. In this way, the rigid modes are eliminated and both a non-zero force and a non-null torque on the body could be calculated. The elements are low order flat triangles, and an iterative solution by generalized minimal residual (GMRES) is used. Numerical examples include cases with analytical solutions, bodies with edges and vertices, or with intricate shapes. The main advantage of the presented technique is the possibility of considering a greater number of degrees of freedom regarding traditional collocation methods, due to the decreased demand of main memory and the reduction in the computation times.     

Ocean internal waves interpreted as oscillation travelling waves in consideration of ocean dissipation

Most studies of the synthetic aperture radar remote sensing of ocean internal waves are based on the solitary wave solutions of the Korteweg-de Vries （KdV） equation, and the dissipative term in the KdV equation is not taken into account. However, the dissipative term is very important, both in the synthetic aperture radar images and in ocean models. In this paper, the traveling-wave structure to characterize the ocean internal wave phenomenon is modeled, the results of numerical experiments are advanced, and a theoretical hypothesis of the traveling wave to retrieve the ocean internal wave parameters in the synthetic aperture radar images is introduced.     

具有非局部时滞的扩散Nicholson苍蝇方程的波前解

研究了具有非局部时滞的扩散Nicholson苍蝇方程,其中时滞由一个定义在所有过去时间和整个一维空间区域上的积分卷积表示.当时滞核是强生成核时,根据线性链式技巧和几何奇异扰动理论,获得了小时滞时波前解的存在性.     

利用(G'/G)-展开法求广义的(2+1)维ZK-MEW方程的新精确解

结合齐次平衡法原理并利用(G'/G)-展开法,研究了广义的(2+1)维ZK-MEW方程的精确解,从而得到了广义的(2+1)维ZK-MEW方程的用双曲函数和三角函数表示的通解,当双曲函数通解中常数取特殊值时,便得到广义的(2+1)维ZK-MEW方程的孤立波解,获得了与现有文献不同的新精确解.