Related papers: Space-efficient K-MER algorithm for generalized su…
We show that the compressed suffix array and the compressed suffix tree of a string $T$ can be built in $O(n)$ deterministic time using $O(n\log\sigma)$ bits of space, where $n$ is the string length and $\sigma$ is the alphabet size.…
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…
Indexed pattern search in text has been studied for many decades. For small alphabets, the FM-Index provides unmatched performance, in terms of both space required and search speed. For large alphabets -- for example, when the tokens are…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require $\Omega(\log\log n)$ time for queries provided $O(n\mathop{\mathrm{polylog}} n)$ space is available and weights are…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
The k-Tree algorithm [Wagner 02] is a non-trivial algorithm for the average-case k-SUM problem that has found widespread use in cryptanalysis. Its input consists of k lists, each containing n integers from a range of size m. Wagner's…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
Spherical k-Means is frequently used to cluster document collections because it performs reasonably well in many settings and is computationally efficient. However, the time complexity increases linearly with the number of clusters k, which…
A buffer k-d tree is a k-d tree variant for massively-parallel nearest neighbor search. While providing valuable speed-ups on modern many-core devices in case both a large number of reference and query points are given, buffer k-d trees are…
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…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
Continuing the recent trend, in this article we design several space-efficient algorithms for two well-known graph search methods. Both these search methods share the same name {\it breadth-depth search} (henceforth {\sf BDS}), although…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
While a lot of work in theoretical computer science has gone into optimizing the runtime and space usage of data structures, such work very often neglects a very important component of modern computers: the cache. In doing so, very often,…