Related papers: Coding methods for string reconstruction from erro…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
A composition of a nonnegative integer (n) is a sequence of positive integers whose sum is (n). A composition is palindromic if it is unchanged when its terms are read in reverse order. We provide a generating function for the number of…
We consider the problem of {\em restructuring} compressed texts without explicit decompression. We present algorithms which allow conversions from compressed representations of a string $T$ produced by any grammar-based compression…
This paper presents lossless prefix codes optimized with respect to a pay-off criterion consisting of a convex combination of maximum codeword length and average codeword length. The optimal codeword lengths obtained are based on a new…
In this paper, we consider the problem of constructing optimal average-length binary codes under the constraint that each codeword must contain at most $D$ ones, where $D$ is a given input parameter. We provide an $O(n^2D)$-time complexity…
A variable-length code is a fix-free code if no codeword is a prefix or a suffix of any other codeword. In a fix-free code any finite sequence of codewords can be decoded in both directions, which can improve the robustness to channel noise…
This paper proposes a polar code construction scheme that reduces constituent-code supplemented decoding latency. Constituent codes are the sub-codewords with specific patterns. They are used to accelerate the successive cancellation…
A \itbf{cover} of a string $x = x[1..n]$ is a proper substring $u$ of $x$ such that $x$ can be constructed from possibly overlapping instances of $u$. A recent paper \cite{FIKPPST13} relaxes this definition --- an \itbf{enhanced cover} $u$…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
A locally recoverable code of locality $r$ over $\mathbb{F}_{q}$ is a code where every coordinate of a codeword can be recovered using the values of at most $r$ other coordinates of that codeword. Locally recoverable codes are efficient at…
We study error-correcting codes in the space $\mathcal{S}_{n,q}$ of length-$n$ multisets over a $q$-ary alphabet, motivated by permutation channels in which ordering is completely lost and errors act solely by deletions of symbols, i.e., by…
We give a new approach to the dictionary learning (also known as "sparse coding") problem of recovering an unknown $n\times m$ matrix $A$ (for $m \geq n$) from examples of the form \[ y = Ax + e, \] where $x$ is a random vector in $\mathbb…
A reconstruction problem of words from scattered factors asks for the minimal information, like multisets of scattered factors of a given length or the number of occurrences of scattered factors from a given set, necessary to uniquely…
There is a large literature devoted to the problem of finding an optimal (min-cost) prefix-free code with an unequal letter-cost encoding alphabet of size. While there is no known polynomial time algorithm for solving it optimally there are…
A cross-bifix-free code is a set of words in which no prefix of any length of any word is the suffix of any word in the set. Cross-bifix-free codes arise in the study of distributed sequences for frame synchronization. We provide a new…
An erasure code is said to be a code with sequential recovery with parameters $r$ and $t$, if for any $s \leq t$ erased code symbols, there is an $s$-step recovery process in which at each step we recover exactly one erased code symbol by…
Best and Brouwer [Discrete Math. 17 (1977), 235-245] proved that triply-shortened and doubly-shortened binary Hamming codes (which have length $2^m-4$ and $2^m-3$, respectively) are optimal. Properties of such codes are here studied,…