Related papers: Transposition diameter on circular binary strings
The discrepancy of a binary string refers to the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. We provide an investigation of the discrepancy of…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Binary embedding is a nonlinear dimension reduction methodology where high dimensional data are embedded into the Hamming cube while preserving the structure of the original space. Specifically, for an arbitrary $N$ distinct points in…
We reexamine democratic open string field theories, namely, theories in which string fields are not constrained to a single picture number and picture changing is obtained as a gauge transformation. We describe several possibilities for…
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 $\pi$…
A flip-swap language is a set S of binary strings of length n such that $S \cup 0^n$ is closed under two operations (when applicable): (1) Flip the leftmost 1; and (2) Swap the leftmost 1 with the bit to its right. Flip-swap languages model…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
Let x, y be strings of equal length. The Hamming distance h(x,y) between x and y is the number of positions in which x and y differ. If x is a cyclic shift of y, we say x and y are conjugates. We consider f(x,y), the Hamming distance…
Cyclic codes are an interesting class of linear codes due to their efficient encoding and decoding algorithms as well as their theoretical importance. BCH codes form a subclass of cyclic codes and are very important in both theory and…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
We characterize the minimum-length sequences of independent lazy simple transpositions whose composition is a uniformly random permutation. For every reduced word of the reverse permutation there is exactly one valid way to assign…
In diffusion based molecular communication, the intersymbol interference (ISI) is an important reason for system performance degradation, which is caused by the random movement, out-of-order arrival and indistinguishability of the…
In string-bit models, string is described as a polymer of point-like constituents. We attempt to use string-bit ideas to investigate how the size of string is affected by string interactions in a non-perturbative context. Lacking adequate…
A residue design is an artistic geometric construction in which we have $n$ equally-spaced points on a circle numbered 0 through $n-1$ and we join with a line segment each point $k$ to $ak$ modulo $n$ for some fixed $a\ge 2.$ The envelopes…
Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…
The calculation of Euclidean distance between points is generalized to one-dimensional objects such as strings or polymers. Necessary and sufficient conditions for the minimal transformation between two polymer configurations are derived.…
This paper is concerned with practical implementations of approximate string dictionaries that allow edit errors. In this problem, we have as input a dictionary $D$ of $d$ strings of total length $n$ over an alphabet of size $\sigma$. Given…
Using techniques and results from Kudekar et al. we strengthen the bounds on the weight distribution of linear codes achieving capacity on the BEC, which were shown by the first author. In particular, we show that for any doubly transitive…