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Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
Given a set of vectors (the data) in a Hilbert space H, we prove the existence of an optimal collection of subspaces minimizing the sum of the square of the distances between each vector and its closest subspace in the collection. This…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
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…
Counting integer solutions of linear constraints has found interesting applications in various fields. It is equivalent to the problem of counting lattice points inside a polytope. However, state-of-the-art algorithms for this problem…
Merging $T$ sorted, non-redundant lists containing $M$ elements into a single sorted, non-redundant result of size $N \ge M/T$ is a classic problem typically solved practically in $O(M \log T)$ time with a priority-queue data structure the…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any…
A mode of a multiset $S$ is an element $a \in S$ of maximum multiplicity; that is, $a$ occurs at least as frequently as any other element in $S$. Given a list $A[1:n]$ of $n$ items, we consider the problem of constructing a data structure…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
We describe the first self-indexes able to count and locate pattern occurrences in optimal time within a space bounded by the size of the most popular dictionary compressors. To achieve this result we combine several recent findings,…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
We present an $O(n\sqrt{\log n})$ time and linear space algorithm for sorting real numbers. This breaks the long time illusion that real numbers have to be sorted by comparison sorting and take $\Omega (n\log n)$ time to be sorted.
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
A palindrome is a string that reads the same forward and backward. A palindromic substring $P$ of a string $S$ is called a shortest unique palindromic substring ($\mathit{SUPS}$) for an interval $[x, y]$ in $S$, if $P$ occurs exactly once…
In this paper, we consider the problem of efficiently representing a set $S$ of $n$ items out of a universe $U=\{0,...,u-1\}$ while supporting a number of operations on it. Let $G=g_1...g_n$ be the gap stream associated with $S$, $gap$ its…
Most of the attention in statistical compression is given to the space used by the compressed sequence, a problem completely solved with optimal prefix codes. However, in many applications, the storage space used to represent the prefix…
Given $n$ intervals on a line $\ell$, we consider the problem of moving these intervals on $\ell$ such that no two intervals overlap and the maximum moving distance of the intervals is minimized. The difficulty for solving the problem lies…
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…