Related papers: Systolic Array Technique for Determining Common Ap…

In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…

We present an approach for efficiently taking snapshots of the state of a collection of CAS objects. Taking a snapshot allows later operations to read the value that each CAS object had at the time the snapshot was taken. Taking a snapshot…

String-averaging is an algorithmic structure used when handling a family of operators in situations where the algorithm at hand requires to employ the operators in a specific order. Sequential orderings are well-known and a simultaneous…

The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…

Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess $n$ strings of length $d$, to quickly answer queries $q$ of…

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 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized…

We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…

Longest common subsequence ($\mathsf{LCS}$) is a classic and central problem in combinatorial optimization. While $\mathsf{LCS}$ admits a quadratic time solution, recent evidence suggests that solving the problem may be impossible in truly…

We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…

Covers being one of the most popular form of regularities in strings, have drawn much attention over time. In this paper, we focus on the problem of linear time inference of strings from cover arrays using the least sized alphabet possible.…

In this note, we first introduce a new problem called the longest common subsequence and substring problem. Let $X$ and $Y$ be two strings over an alphabet $\Sigma$. The longest common subsequence and substring problem for $X$ and $Y$ is to…

A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique which we call accelerated sampling. It runs in optimal O(n/p) local computation and communication, and requires a near…

Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…

Despite significant progress, state-of-the-art abstractive summarization methods are still prone to hallucinate content inconsistent with the source document. In this paper, we propose Constrained Abstractive Summarization (CAS), a general…

Given a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…

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"…

Let $T=t_0 ... t_{n-1}$ be a text and $P = p_0 ... p_{m-1}$ a pattern taken from some finite alphabet set $\Sigma$, and let $\dist$ be a metric on $\Sigma$. We consider the problem of calculating the sum of distances between the symbols of…

The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…

Single-shot time resolved Coherent Anti-Stokes Raman Scattering (CARS) is presented as a viable method for fast measurements of molecular spectra. The method is based on the short spatial extension of femtosecond pulses and maps time delays…