Related papers: Enumeration of sequences with large alphabets
In this paper, we focus on the design of binary constant weight codes that admit low-complexity encoding and decoding algorithms, and that have a size $M=2^k$. For every integer $\ell \geq 3$, we construct a $(n=2^\ell, M=2^{k_{\ell}},…
Codes in the Grassmannian space have found recently application in network coding. Representation of $k$-dimensional subspaces of $\F_q^n$ has generally an essential role in solving coding problems in the Grassmannian, and in particular in…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…
Current methods which compress multisets at an optimal rate have computational complexity that scales linearly with alphabet size, making them too slow to be practical in many real-world settings. We show how to convert a compression…
We consider encoding problems for range queries on arrays. In these problems the goal is to store a structure capable of recovering the answer to all queries that occupies the information theoretic minimum space possible, to within lower…
Motivation: Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obvious combinatorial…
The problem of ranking can be described as follows. We have a set of combinatorial objects $S$, such as, say, the k-subsets of n things, and we can imagine that they have been arranged in some list, say lexicographically, and we want to…
We describe a RAM algorithm computing all runs (maximal repetitions) of a given string of length $n$ over a general ordered alphabet in $O(n\log^{\frac{2}3} n)$ time and linear space. Our algorithm outperforms all known solutions working in…
We investigate group coding for arbitrary finite groups acting linearly on a vector space. These yield robust codes based on real or complex matrix groups. We give necessary and sufficient conditions for correct subgroup decoding using…
We propose a routing algorithm that takes a sequence of vectors and computes a new sequence with specified length and vector size. Each output vector maximizes "bang per bit," the difference between a net benefit to use and net cost to…
We propose a new succinct representation of labeled trees which represents a tree T using |T|H_k(T) number of bits (plus some smaller order terms), where |T|H_k(T) denotes the k-th order (tree label) entropy, as defined by Ferragina at al.…
We present a new on-line algorithm for computing the Lempel-Ziv factorization of a string that runs in $O(N\log N)$ time and uses only $O(N\log\sigma)$ bits of working space, where $N$ is the length of the string and $\sigma$ is the size of…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
This paper studies coding schemes for the $q$-ary symmetric channel based on binary low-density parity-check (LDPC) codes that work for any alphabet size $q=2^m$, $m\in\mathbb{N}$, thus complementing some recently proposed packet-based…
We present an explicit and efficient algebraic construction of capacity-achieving list decodable codes with both constant alphabet and constant list sizes. More specifically, for any $R \in (0,1)$ and $\epsilon>0$, we give an algebraic…
We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster,…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…
In many important applications -- such as search engines and relational database systems -- data is stored in the form of arrays of integers. Encoding and, most importantly, decoding of these arrays consumes considerable CPU time.…
Randomised algorithms often employ methods that can fail and that are retried with independent randomness until they succeed. Randomised data structures therefore often store indices of successful attempts, called seeds. If $n$ such seeds…
We introduce the notion of logarithmically concave (or log-concave) sequences in Coding Theory. A sequence $a_0, a_1, \dots, a_n$ of real numbers is called log-concave if $a_i^2 \ge a_{i-1}a_{i+1}$ for all $1 \le i \le n-1$. A natural…