Related papers: On the locality of the Pr\"ufer code
The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $\pi$…
Pre-transformed polar codes (PTPCs) form a class of codes that perform close to the finite-length capacity bounds. The minimum distance and the number of minimum weight codewords are two decisive properties for their performance. In this…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
Consider a linear [n,k,d]_q code C. We say that that i-th coordinate of C has locality r, if the value at this coordinate can be recovered from accessing some other r coordinates of C. Data storage applications require codes with small…
The rank modulation scheme has been proposed for efficient writing and storing data in non-volatile memory storage. Error-correction in the rank modulation scheme is done by considering permutation codes. In this paper we consider codes in…
Recently we considered a class of random matrices obtained by choosing distinct codewords at random from linear codes over finite fields and proved that under some natural algebraic conditions their empirical spectral distribution converges…
We report our experiences for the development of a neighborhood algorithm implemented via tree-codes to optimize the performance of a discrete element method (DEM) for convex polytopes. Our implementation of the two-dimensional tree code…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Given $n \in \mathbb{N}$ and $\mu \in \mathbb{R}$, a $\textit{$\mu$-height-biased tree of size $n$}$ is a random plane tree $\mathbf{\mathbf{T}}_n$ with $n$ vertices with law given by $\mathbb{P}(\mathbf{T}=t) \propto e^{-\mu h(t)}$, where…
Considering two optimally aligned random sequences, we investigate the effect on the alignment score caused by changing a random letter in one of the two sequences. Using this idea in conjunction with large deviations theory, we show that…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
Random network coding recently attracts attention as a technique to disseminate information in a network. This paper considers a non-coherent multi-shot network, where the unknown and time-variant network is used several times. In order to…
We discuss the performance characteristics of using the modification of the tree code suggested by Barnes \citep{1990JCoPh..87..161B} in the context of the TreePM code. The optimisation involves identifying groups of particles and using…
There exists a bijection between one stack sortable permutations --permutations which avoid the pattern 231-- and planar trees. We define an edit distance between permutations which is coherent with the standard edit distance between trees.…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
We present a new combinatorial characterization for local optimality of a codeword in an irregular Tanner code. The main novelty in this characterization is that it is based on a linear combination of subtrees in the computation trees.…
We study the local limit of the fixed-point forest, a tree structure associated to a simple sorting algorithm on permutations. This local limit can be viewed as an infinite random tree that can be constructed from a Poisson point process…
We calculate the almost sure Hausdorff dimension for a general class of random affine planar code tree fractals. The set of probability measures describing the randomness includes natural measures in random $V$-variable and homogeneous…
We introduce twisted permutation codes, which are frequency permutation arrays analogous to repetition permutation codes, namely, codes obtained from the repetition construction applied to a permutation code. In particular, we show that a…
We provide a local probabilistic description of the limiting statistics of large preferential attachment trees in terms of the ordinary degree (number of neighbors) but augmented with information on leafdegree (number of neighbors that are…