Related papers: MONI can find k-MEMs

We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…

Let $P$ be a simple polygon with $n$ vertices, and let $A$ be a set of $m$ points or line segments inside $P$. We develop data structures that can efficiently count the number of objects from $A$ that are visible to a query point or a query…

In many applications, it is of interest to approximate data, given by mxn matrix A, by a matrix B of at most rank k, which is much smaller than m and n. The best approximation is given by singular value decomposition, which is too time…

In many data analysis pipelines, a basic and time-consuming process is to produce join results and feed them into downstream tasks. Numerous enumeration algorithms have been developed for this purpose. To be a statistically meaningful…

Increasing the input length has been a driver of progress in language modeling with transformers. We identify conditions where shorter inputs are not harmful, and achieve perplexity and efficiency improvements through two new methods that…

We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…

We propose a new finding $k$-minima algorithm and prove that its query complexity is $\mathcal{O}(\sqrt{kN})$, where $N$ is the number of data indices. Though the complexity is equivalent to that of an existing method, the proposed is…

The maximum coverage problem is to select $k$ sets from a collection of sets such that the cardinality of the union of the selected sets is maximized. We consider $(1-1/e-\epsilon)$-approximation algorithms for this NP-hard problem in three…

We show how to solve a number of problems in numerical linear algebra, such as least squares regression, $\ell_p$-regression for any $p \geq 1$, low rank approximation, and kernel regression, in time $T(A) \poly(\log(nd))$, where for a…

Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…

We give a simple and efficient algorithm for adaptively counting inversions in a sequence of $n$ integers. Our algorithm runs in $O(n + n \sqrt{\lg{(Inv/n)}})$ time in the word-RAM model of computation, where $Inv$ is the number of…

We introduce a data structure for counting pattern occurrences in texts compressed with any run-length context-free grammar. Our structure uses space proportional to the grammar size and counts the occurrences of a pattern of length $m$ in…

We study the classic Text-to-Pattern Hamming Distances problem: given a pattern $P$ of length $m$ and a text $T$ of length $n$, both over a polynomial-size alphabet, compute the Hamming distance between $P$ and $T[i\, .\, . \, i+m-1]$ for…

In this paper, we apply a Threshold-Decreasing Algorithm to maximize $k$-submodular functions under a matroid constraint, which reduces the query complexity of the algorithm compared to the greedy algorithm with little loss in approximation…

A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…

The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…

We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results.…

Real world datasets are sparse, dirty and contain hundreds of items. In such situations, discovering interesting rules (results) using traditional frequent itemset mining approach by specifying a user defined input support threshold is not…

A sequence $e_0,e_1,\ldots$ of edit operations in a string $T$ is called ephemeral if operation $e_i$ constructing string $T^i$, for all $i=2k$ with $k\in\mathbb{N}$, is reverted by operation $e_{i+1}$ that reconstructs $T$. Such a sequence…

We give an $\mathcal{O}(n \log n)$-time, $\mathcal{O}(n)$-space algorithm for factoring a string into the minimum number of palindromic substrings. That is, given a string $S [1..n]$, in $\mathcal{O}(n \log n)$ time our algorithm returns…