Related papers: Optimal Dynamic Sequence Representations
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…
A superpermutation is a sequence that contains every permutation of $n$ distinct symbols as a contiguous substring. For instance, a valid example for three symbols is a sequence that contains all six permutations. This paper introduces a…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
We consider a range of simply stated dynamic data structure problems on strings. An update changes one symbol in the input and a query asks us to compute some function of the pattern of length $m$ and a substring of a longer text. We give…
We present an algorithm for maintaining maximal matching in a graph under addition and deletion of edges. Our data structure is randomized that takes O(log n) expected amortized time for each edge update where n is the number of vertices in…
We develop dynamic data structures for maintaining a hierarchical k-center clustering when the points come from a discrete space $\{1,\ldots,\Delta\}^d$. Our first data structure is for the low dimensional setting, i.e., d is a constant,…
In this paper we investigate the problem of building a static data structure that represents a string s using space close to its compressed size, and allows fast access to individual characters of s. This type of structures was investigated…
For a set $P$ of $n$ points in the plane and a value $r > 0$, the unit-disk range reporting problem is to construct a data structure so that given any query disk of radius $r$, all points of $P$ in the disk can be reported efficiently. We…
A binary trie is a sequential data structure for a dynamic set on the universe $\{0,\dots,u-1\}$ supporting Search with $O(1)$ worst-case step complexity, and Insert, Delete, and Predecessor operations with $O(\log u)$ worst-case step…
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…
We introduce an improved structure of distance sensitivity oracle (DSO). The task is to pre-process a non-negatively weighted graph so that a data structure can quickly answer replacement path length for every triple of source, terminal and…
A Straight-Line Program (SLP) $G$ for a string $T$ is a context-free grammar (CFG) that derives $T$ only, which can be considered as a compressed representation of $T$. In this paper, we show how to encode $G$ in $n \lceil \lg N \rceil + (n…
Sliding-window aggregation is a widely-used approach for extracting insights from the most recent portion of a data stream. The aggregations of interest can usually be expressed as binary operators that are associative but not necessarily…
We design a space-efficient algorithm for performing depth-first search traversal(DFS) of a graph in $O(m+n\log^* n)$ time using $O(n)$ bits of space. While a normal DFS algorithm results in a DFS-tree (in case the graph is connected), our…
We present a new on-line algorithm for computing the Lempel-Ziv factorization of a string that runs in $O(N\log N)$ time and uses only $O(N\log\sigma)$ bits of working space, where $N$ is the length of the string and $\sigma$ is the size of…
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…
Many signal processing problems can be solved by maximizing the fitness of a segmented model over all possible partitions of the data interval. This letter describes a simple but powerful algorithm that searches the exponentially large…
We propose a B tree representation storing $n$ keys, each of $k$ bits, in either (a) $nk + O(nk / \lg n)$ bits or (b) $nk + O(nk \lg \lg n/ \lg n)$ bits of space supporting all B tree operations in either (a) $O(\lg n )$ time or (b) $O(\lg…