Related papers: The Longest Subsequence-Repeated Subsequence Probl…
Given a string $T$ of length $n$, a substring $u = T[i..j]$ of $T$ is called a shortest unique substring (SUS) for an interval $[s,t]$ if (a) $u$ occurs exactly once in $T$, (b) $u$ contains the interval $[s,t]$ (i.e. $i \leq s \leq t \leq…
Let $W^{(n)}$ be the $n$-letter word obtained by repeating a fixed word $W$, and let $R_n$ be a random $n$-letter word over the same alphabet. We show several results about the length of the longest common subsequence (LCS) between…
In this paper, we focus on the class of complete $S$-partite graphs, for $S$ an undirected graph possibly with self-loops, and address the problem of finding largest $2$-regular subgraphs of these graphs, which can be formulated as an…
Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. The longest arc-preserving common subsequence problem has been introduced as a framework for studying the similarity of…
We show that the number of distinct squares in a packed string of length $n$ over an alphabet of size $\sigma$ can be computed in $O(n/\log_\sigma n)$ time in the word-RAM model. This paper is the first to introduce a sublinear-time…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
In this paper we consider the following problems: how many different subsets of Sigma^n can occur as set of all length-n factors of a finite word? If a subset is representable, how long a word do we need to represent it? How many such…
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…
In this paper, we provide new approximation algorithms for dynamic variations of the longest increasing subsequence (\textsf{LIS}) problem, and the complementary distance to monotonicity (\textsf{DTM}) problem. In this setting, operations…
We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem…
The problem of identification of statistically significant patterns in a sequence of data has been applied to many domains such as intrusion detection systems, financial models, web-click records, automated monitoring systems, computational…
Subset Sum is a classical optimization problem taught to undergraduates as an example of an NP-hard problem, which is amenable to dynamic programming, yielding polynomial running time if the input numbers are relatively small. Formally,…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
Word Break is a prototypical factorization problem in string processing: Given a word $w$ of length $N$ and a dictionary $\mathcal{D} = \{d_1, d_2, \ldots, d_{K}\}$ of $K$ strings, determine whether we can partition $w$ into words from…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
Given a multiset $X=\{x_1,..., x_n\}$ of real numbers, the {\it floating-point set summation} problem asks for $S_n=x_1+...+x_n$. Let $E^*_n$ denote the minimum worst-case error over all possible orderings of evaluating $S_n$. We prove that…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
The expected length of longest common subsequences is a problem that has been in the literature for at least twenty five years. Determining the limiting constants \gamma_k appears to be quite difficult, and the current best bounds leave…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…