Related papers: A Linear Time Algorithm for Seeds Computation
Motivation: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the…
A factorization $f_1, \ldots, f_m$ of a string $w$ of length $n$ is called a repetition factorization of $w$ if $f_i$ is a repetition, i.e., $f_i$ is a form of $x^kx'$, where $x$ is a non-empty string, $x'$ is a (possibly-empty) proper…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
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…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in many diverse applications, including data compression, text indexing, and pattern discovery. We describe new linear time LZ factorization…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
A factor $u$ of a word $w$ is a cover of $w$ if every position in $w$ lies within some occurrence of $u$ in $w$. A word $w$ covered by $u$ thus generalizes the idea of a repetition, that is, a word composed of exact concatenations of $u$.…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
A maximal repetition, or run, in a string, is a maximal periodic substring whose smallest period is at most half the length of the substring. In this paper, we consider runs that correspond to a path on a trie, or in other words, on a…
We consider the selection problem on a completely connected network of $n$ processors with no shared memory. Each processor initially holds a given numeric item of $b$ bits allowed to send a message of $\max ( b, \lg n )$ bits to another…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
Weakly-supervised text classification aims to induce text classifiers from only a few user-provided seed words. The vast majority of previous work assumes high-quality seed words are given. However, the expert-annotated seed words are…
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
Online bipartite matching is a fundamental problem in online algorithms. The goal is to match two sets of vertices to maximize the sum of the edge weights, where for one set of vertices, each vertex and its corresponding edge weights appear…
In numerical linear algebra, considerable effort has been devoted to obtaining faster algorithms for linear systems whose underlying matrices exhibit structural properties. A prominent success story is the method of generalized nested…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered…
Large Language Models (LLMs) demonstrate remarkable emergent abilities across various tasks, yet fall short of complex reasoning and planning tasks. The tree-search-based reasoning methods address this by surpassing the capabilities of…