Related papers: Small Longest Tandem Scattered Subsequences
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
We say a string has a cadence if a certain character is repeated at regular intervals, possibly with intervening occurrences of that character. We call the cadence anchored if the first interval must be the same length as the others. We…
An absent factor of a string $w$ is a string $u$ which does not occur as a contiguous substring (a.k.a. factor) inside $w$. We extend this well-studied notion and define absent subsequences: a string $u$ is an absent subsequence of a string…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Motivated by problems of learning to rank long item sequences, we introduce a variant of the cascading bandit model that considers flexible length sequences with varying rewards and losses. We formulate two generative models for this…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
Finding anomalous subsequence in a long time series is a very important but difficult problem. Existing state-of-the-art methods have been focusing on searching for the subsequence that is the most dissimilar to the rest of the…
The problem of finding dense components of a graph is a widely explored area in data analysis, with diverse applications in fields and branches of study including community mining, spam detection, computer security and bioinformatics. This…
We propose novel algorithms for sequence prediction based on ideas from stringology. These algorithms are time and space efficient and satisfy mistake bounds related to particular stringological complexity measures of the sequence. In this…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In the Palindrome Problem one tries to find all palindromes (palindromic substrings) in a given string. A palindrome is defined as a string which reads forwards the same as backwards, e.g., the string "racecar". A related problem is the…
Given a random text over a finite alphabet, we study the frequencies at which fixed-length words occur as subsequences. As the data size grows, the joint distribution of word counts exhibits a rich asymptotic structure. We investigate all…
Semantic Similarity between two sentences can be defined as a way to determine how related or unrelated two sentences are. The task of Semantic Similarity in terms of distributed representations can be thought to be generating sentence…
Given two sequences $A[1..n]$ and $B[1..m]$ over a totally ordered alphabet, the \emph{Longest Common Bitonic Subsequence} (LCBS) problem asks for a longest common subsequence that is strictly increasing up to a single peak element and…
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
We exhibit an online algorithm finding all distinct palindromes inside a given string in time $\Theta(n\log|\Sigma|)$ over an ordered alphabet and in time $\Theta(n|\Sigma|)$ over an unordered alphabet. Using a reduction from a…
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…