Related papers: Minimizing the Minimizers via Alphabet Reordering

Sorting is a foundational problem in computer science that is typically employed on sequences or total orders. More recently, a more general form of sorting on partially ordered sets (or posets), where some pairs of elements are…

We consider the following problem: Given a set S of at most n elements from a universe of size m, represent it in memory as a bit string so that membership queries of the form "Is x in S?" can be answered by making at most t probes into the…

The box-constrained integer least squares problem (BILS) arises in MIMO wireless communications applications. Typically a sphere decoding algorithm (a tree search algorithm) is used to solve the problem. In order to make the search…

Merging $T$ sorted, non-redundant lists containing $M$ elements into a single sorted, non-redundant result of size $N \ge M/T$ is a classic problem typically solved practically in $O(M \log T)$ time with a priority-queue data structure the…

We consider the problem of finding the minimizer of a convex function $F: \mathbb R^d \rightarrow \mathbb R$ of the form $F(w) := \sum_{i=1}^n f_i(w) + R(w)$ where a low-rank factorization of $\nabla^2 f_i(w)$ is readily available. We…

We propose an algorithm for the Wireless Sensor Network localization problem, which is based on the well-known algorithmic framework of Alternating Minimization. We start with a non-smooth and non-convex minimization, and transform it into…

We study the IS-algorithm, a well-known linear-time algorithm for computing the suffix array of a word. This algorithm relies on transforming the input word $w$ into another word, called the reduced word of $w$, that will be at least twice…

In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…

The idea that many important classes of signals can be well-represented by linear combinations of a small set of atoms selected from a given dictionary has had dramatic impact on the theory and practice of signal processing. For practical…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…

Let $S$ be a string of length $n$. In this paper we introduce the notion of \emph{string attractor}: a subset of the string's positions $[1,n]$ such that every distinct substring of $S$ has an occurrence crossing one of the attractor's…

A permutation $\sigma \in S_n$ is a $k$-superpattern (or $k$-universal) if it contains each $\tau \in S_k$ as a pattern. This notion of "superpatterns" can be generalized to words on smaller alphabets, and several questions about…

We study the maximum multiplicity $\mathcal{M}(k,n)$ of a simple transposition $s_k=(k \: k+1)$ in a reduced word for the longest permutation $w_0=n \: n-1 \: \cdots \: 2 \: 1$, a problem closely related to much previous work on sorting…

The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…

Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…

A superpermutation on $n$ symbols is a string that contains each of the $n!$ permutations of the $n$ symbols as a contiguous substring. The shortest superpermutation on $n$ symbols was conjectured to have length $\sum_{i=1}^n i!$. The…

Given a graph $G$, the sparsest-cut problem asks to find the set of vertices $S$ which has the least expansion defined as $$\phi_G(S) := \frac{w(E(S,\bar{S}))}{\min \set{w(S), w(\bar{S})}}, $$ where $w$ is the total edge weight of a subset.…

Majorization-minimization (MM) is a family of optimization methods that iteratively reduce a loss by minimizing a locally-tight upper bound, called a majorizer. Traditionally, majorizers were derived by hand, and MM was only applicable to a…

This paper considers the problem of maintaining statistic aggregates over the last W elements of a data stream. First, the problem of counting the number of 1's in the last W bits of a binary stream is considered. A lower bound of…