Related papers: All-Pairs Suffix-Prefix on Fully Dynamic Set of St…
The Suffix Array is a classic text index enabling on-line pattern matching queries via simple binary search. The main drawback of the Suffix Array is that it takes linear space in the text's length, even if the text itself is extremely…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
Kernel methods are powerful tools in machine learning. They have to be computationally efficient. In this paper, we present a novel Geometric-based approach to compute efficiently the string subsequence kernel (SSK). Our main idea is that…
The subset sum problem (SSP) can be briefly stated as: given a target integer $E$ and a set $A$ containing $n$ positive integer $a_j$, find a subset of $A$ summing to $E$. The \textit{density} $d$ of an SSP instance is defined by the ratio…
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…
Pattern matching queries on strings can be solved in linear time by Knuth-Morris-Pratt (KMP) algorithm. In 1973, Weiner introduced the suffix tree of a string [FOCS 1973] and showed that the seemingly more difficult problem of computing…
Consider the following distance query for an $n$-node graph $G$ undergoing edge insertions and deletions: given two sets of nodes $I$ and $J$, return the distances between every pair of nodes in $I\times J$. This query is rather general and…
We consider construction of the suffix tree and the directed acyclic word graph (DAWG) indexing data structures for a collection $\mathcal{T}$ of texts, where a new symbol may be appended to any text in $\mathcal{T} = \{T_1, \ldots, T_K\}$,…
The constrained synchronization problem (CSP) asks for a synchronizing word of a given input automaton contained in a regular set of constraints. It could be viewed as a special case of synchronization of a discrete event system under…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
In this paper, we present a new randomized $O(1)$-approximation algorithm for the All-Pairs Shortest Paths (APSP) problem in weighted undirected graphs that runs in just $O(\log \log \log n)$ rounds in the Congested-Clique model. Before our…
Using well-known mathematical problems for encryption is a widely used technique because they are computationally hard and provide security against potential attacks on the encryption method. The subset sum problem (SSP) can be defined as…
String attractors [STOC 2018] are combinatorial objects recently introduced to unify all known dictionary compression techniques in a single theory. A set $\Gamma\subseteq [1..n]$ is a $k$-attractor for a string $S\in[1..\sigma]^n$ if and…
The all pairs shortest path problem is a fundamental optimization problem in graph theory. We deal with re-calculating the all-pairs shortest path (APSP) matrix after a minor modification of a weighted dense graph, e.g., adding a node,…
An instance $I$ of the Stable Matching Problem (SMP) is given by a bipartite graph with a preference list of neighbors for every vertex. A swap in $I$ is the exchange of two consecutive vertices in a preference list. A swap can be viewed as…
In the Shortest-Superstring problem, we are given a set of strings S and want to find a string that contains all strings in S as substrings and has minimum length. This is a classical problem in approximation and the best known…
Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…
We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with…
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…
In this paper, we construct a data structure to efficiently compute the longest increasing subsequence of a sequence subject to dynamic updates. Our data structure supports a query for the longest increasing subsequence in $O(r+\log n)$…