Related papers: Fast and Compact Prefix Codes
We present several novel encodings for cardinality constraints, which use fewer clauses than previous encodings and, more importantly, introduce new generally applicable techniques for constructing compact encodings. First, we present a CNF…
Given a probability distribution over a set of n words to be transmitted, the Huffman Coding problem is to find a minimal-cost prefix free code for transmitting those words. The basic Huffman coding problem can be solved in O(n log n) time…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
Universal compression of patterns of sequences generated by independently identically distributed (i.i.d.) sources with unknown, possibly large, alphabets is investigated. A pattern is a sequence of indices that contains all consecutive…
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
We describe an algorithm computing an optimal prefix free code from $N$ unsorted positive integer weights in time linear in the number of machine words holding those weights. This algorithm takes advantage of common non-algebraic…
We give a polynomial-time approximation scheme for the generalization of Huffman Coding in which codeword letters have non-uniform costs (as in Morse code, where the dash is twice as long as the dot). The algorithm computes a…
We study how much memory one-pass compression algorithms need to compete with the best multi-pass algorithms. We call a one-pass algorithm an (f (n, \ell))-footprint compressor if, given $n$, $\ell$ and an $n$-ary string $S$, it stores $S$…
In [3] a short proof is given that some strings have maximal plain Kolmogorov complexity but not maximal prefix-free complexity. The proof uses Levin's symmetry of information, Levin's formula relating plain and prefix complexity and Gacs'…
In the decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), the task is to list the $k$-error occurrences of $P$ in…
Given an undirected graph and $0\le\epsilon\le1$, a set of nodes is called $\epsilon$-near clique if all but an $\epsilon$ fraction of the pairs of nodes in the set have a link between them. In this paper we present a fast synchronous…
We consider the problem of constructing prefix-free codes in which a designated symbol, a space, can only appear at the end of codewords. We provide a linear-time algorithm to construct almost-optimal codes with this property, meaning that…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
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…
A $(k,\delta,\epsilon)$-locally decodable code $C: F_{q}^{n} \to F_{q}^{N}$ is an error-correcting code that encodes each message $\vec{x}=(x_{1},x_{2},...,x_{n}) \in F_{q}^{n}$ to $C(\vec{x}) \in F_{q}^{N}$ and has the following property:…
In this paper we give several new constructions of WOM codes. The novelty in our constructions is the use of the so called Wozencraft ensemble of linear codes. Specifically, we obtain the following results. We give an explicit construction…
Non-uniquely decodable codes can be defined as the codes that cannot be uniquely decoded without additional disambiguation information. These are mainly the class of non-prefix-free codes, where a codeword can be a prefix of other(s), and…