Related papers: Detecting $k$-(Sub-)Cadences and Equidistant Subse…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
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…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
We describe a slightly sub-exponential time algorithm for learning parity functions in the presence of random classification noise. This results in a polynomial-time algorithm for the case of parity functions that depend on only the first…
We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of…
Common algorithms for sentence and word-alignment allow the automatic identification of word translations from parallel texts. This study suggests that the identification of word translations should also be possible with non-parallel and…
Pattern recognition constitutes a particularly important task underlying a great deal of scientific and technologica activities. At the same time, pattern recognition involves several challenges, including the choice of features to…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
Simon's congruence $\sim_k$ is defined as follows: two words are $\sim_k$-equivalent if they have the same set of subsequences of length at most $k$. We propose an algorithm which computes, given two words $s$ and $t$, the largest $k$ for…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…
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. Sampled string…
We study optimization problems that are neither approximable in polynomial time (at least with a constant factor) nor fixed parameter tractable, under widely believed complexity assumptions. Specifically, we focus on Maximum Independent…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
A time-delay embedding (TDE), grounded in the framework of Takens's Theorem, provides a mechanism to represent and analyze the inherent dynamics of time-series data. Recently, topological data analysis (TDA) methods have been applied to…
Logical theories have been developed which have allowed temporal reasoning about eventualities (a la Galton) such as states, processes, actions, events, processes and complex eventualities such as sequences and recurrences of other…
Given permutations $\sigma \in S_k$ and $\pi \in S_n$ with $k<n$, the \emph{pattern matching} problem is to decide whether $\pi$ matches $\sigma$ as an order-isomorphic subsequence. We give a linear-time algorithm in case both $\pi$ and…
We present scalable parallel algorithms with sublinear per-processor communication volume and low latency for several fundamental problems related to finding the most relevant elements in a set, for various notions of relevance: We begin…
An increasing number of scientific applications are making use of irregular data access patterns. An important class of such patterns involve subscripted-subscripts, wherein an array value appears in the index expression of another array.…