Related papers: On Optimal Top-K String Retrieval
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
Fast and high quality document clustering is an important task in organizing information, search engine results obtaining from user query, enhancing web crawling and information retrieval. With the large amount of data available and with a…
For databases consisting of many text documents, one of the most fundamental data analysis tasks is counting (i) how often a pattern appears as a substring in the database (substring counting) and (ii) how many documents in the collection…
We consider the problem of compactly representing the Depth First Search (DFS) tree of a given undirected or directed graph having $n$ vertices and $m$ edges while supporting various DFS related queries efficiently in the RAM with…
In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, the goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that the length-$m$ substrings of $T$ starting at positions $i$ and $j$…
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.…
In submodular $k$-secretary problem, the goal is to select $k$ items in a randomly ordered input so as to maximize the expected value of a given monotone submodular function on the set of selected items. In this paper, we introduce a…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
We study the density estimation problem defined as follows: given $k$ distributions $p_1, \ldots, p_k$ over a discrete domain $[n]$, as well as a collection of samples chosen from a ``query'' distribution $q$ over $[n]$, output $p_i$ that…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
In the Dictionary-based String Matching (DSM) problem, a retrieval system has access to a source sequence and stores the position of a certain number of strings in a posting table. When a user inquires the position of a string, the…
Given an array A of $n$ elements, we wish to support queries for the most frequent and least frequent element in a subrange $[l, r]$ of $A$. We also wish to support updates that change a particular element at index $i$ or insert/ delete an…
Assume that an $N$-bit sequence $S$ of $k$ numbers encoded as Elias gamma codes is given as input. We present space-efficient algorithms for sorting, dense ranking and competitive ranking on $S$ in the word RAM model with word size…
Decision Tree (DT) Learning is a fundamental problem in Interpretable Machine Learning, yet it poses a formidable optimisation challenge. Practical algorithms have recently emerged, primarily leveraging Dynamic Programming and Branch &…