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Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…

Data Structures and Algorithms · Computer Science 2012-02-01 Ming-Yang Kao , Henry C. M. Leung , He Sun , Yong Zhang

A $k$-bit delay decodable code-tuple is a lossless source code that can achieve a smaller average codeword length than Huffman codes by using a finite number of code tables and allowing at most $k$-bit delay for decoding. It is known that…

Information Theory · Computer Science 2024-09-23 Kengo Hashimoto , Ken-ichi Iwata

In the wake of the explosive growth in smartphones and cyberphysical systems, there has been an accelerating shift in how data is generated away from centralised data towards on-device generated data. In response, machine learning…

Machine Learning · Computer Science 2021-12-09 Ross Drummond , Mathew C. Turner , Stephen R. Duncan

In this paper we provide a method to obtain tight lower bounds on the minimum redundancy achievable by a Huffman code when the probability distribution underlying an alphabet is only partially known. In particular, we address the case where…

Information Theory · Computer Science 2019-09-04 Ian Blanes , Miguel Hernández-Cabronero , Joan Serra-Sagristà , Michael W. Marcellin

Consider the set of source distributions within a fixed maximum relative entropy with respect to a given nominal distribution. Lossless source coding over this relative entropy ball can be approached in more than one way. A problem…

Information Theory · Computer Science 2011-05-03 Michael B. Baer , Farzad Rezaei , Charalambos D. Charalambous

In this article we mainly study linear codes over $\mathbb{F}_{2^n}$ and their binary subfield codes. We construct linear codes over $\mathbb{F}_{2^n}$ whose defining sets are the certain subsets of $\mathbb{F}_{2^n}^m$ obtained from…

Information Theory · Computer Science 2023-03-17 Hongwei Liu , Zihao Yu

We define the AWGNC, BSC, and max-fractional pseudocodeword redundancy of a code as the smallest number of rows in a parity-check matrix such that the corresponding minimum pseudoweight is equal to the minimum Hamming distance. We show that…

Information Theory · Computer Science 2010-01-12 Jens Zumbragel , Mark F. Flanagan , Vitaly Skachek

A property of prefix codes called strong monotonicity is introduced, and it is proven that for a given source, a prefix code is optimal if and only if it is complete and strongly monotone.

Information Theory · Computer Science 2024-04-11 Spencer Congero , Kenneth Zeger

We present a framework for minimizing costs in constant weight codes while maintaining a certain amount of differentiable codewords. Our calculations are based on a combinatorial view of constant weight codes and relay on simple…

Information Theory · Computer Science 2021-05-07 Pau Vilimelis Aceituno

This paper tightens the best known analysis of Hein's 1989 algorithm to infer the topology of a weighted tree based on the lengths of paths between its leaves. It shows that the number of length queries required for a degree-$k$ tree of $n$…

Data Structures and Algorithms · Computer Science 2024-12-05 Jack Gardiner , Lachlan L. H. Andrew , Junhao Gan , Jean Honorio , Seeun William Umboh

We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…

Data Structures and Algorithms · Computer Science 2019-06-04 Noriki Fujisato , Yuto Nakashima , Shunsuke Inenaga , Hideo Bannai , Masayuki Takeda

In this work, we investigate the problem of constructing codes capable of correcting two deletions. In particular, we construct a code that requires redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is the length…

Information Theory · Computer Science 2018-05-02 Ryan Gabrys , Frederic Sala

The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…

Information Theory · Computer Science 2020-10-22 Ryan Gabrys , Srilakshmi Pattabiraman , Olgica Milenkovic

The Bin Packing Problem is one of the most important Combinatorial Optimization problems in optimization and has a lot of real-world applications. Many approximation algorithms have been presented for this problem because of its NP-hard…

Data Structures and Algorithms · Computer Science 2015-09-22 Abdolahad Noori Zehmakan , Mojtaba Eslahi

This paper computationally obtains optimal bounded-weight, binary, error-correcting codes for a variety of distance bounds and dimensions. We compare the sizes of our codes to the sizes of optimal constant-weight, binary, error-correcting…

Information Theory · Computer Science 2007-10-15 Russell Bent , Michael Schear , Lane A. Hemaspaandra , Gabriel Istrate

Constrained codes are used to prevent errors from occurring in various data storage and data transmission systems. They can help in increasing the storage density of magnetic storage devices, in managing the lifetime of electronic storage…

Information Theory · Computer Science 2022-09-07 Ahmed Hareedy , Beyza Dabak , Robert Calderbank

A text written using symbols from a given alphabet can be compressed using the Huffman code, which minimizes the length of the encoded text. It is necessary, however, to employ a text-specific codebook, i.e. the symbol-codeword dictionary,…

Information Theory · Computer Science 2022-08-02 Armen E. Allahverdyan , Andranik Khachatryan

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…

Information Theory · Computer Science 2017-09-22 Tiben Che , Gwan Choi

We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…

Quantum Physics · Physics 2024-11-06 Tzu-Ching Lee , Han-Hsuan Lin

A new method of constructing optimum constant weight codes over F_2 based on a generalized $(u, u+v)$ construction is presented. We present a new method of constructing superimposed code $C_{(s_1,s_2,\cdots,s_I)}^{(h_1, h_2, \cdots, h_I)}$…

Information Theory · Computer Science 2014-06-24 Masao Kasahara , Shigeichi Hirasawa
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