Related papers: Faster STR-IC-LCS computation via RLE
Park et al. [TCS 2020] observed that the similarity between two (numerical) strings can be captured by the Cartesian trees: The Cartesian tree of a string is a binary tree recursively constructed by picking up the smallest value of the…
The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
A $\lambda$-cover of a string $S$ is a set of strings $\{C_i\}_1^\lambda$ such that every index in $S$ is contained in an occurrence of at least one string $C_i$. The existence of a $1$-cover defines a well-known class of quasi-periodic…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
We consider the constrained Linear Inverse Problem (LIP), where a certain atomic norm (like the $\ell_1 $ norm) is minimized subject to a quadratic constraint. Typically, such cost functions are non-differentiable, which makes them not…
Locally decodable codes (LDCs) are error-correcting codes $C : \Sigma^k \to \Sigma^n$ that admit a local decoding algorithm that recovers each individual bit of the message by querying only a few bits from a noisy codeword. An important…
This paper studies parallel algorithms for the longest increasing subsequence (LIS) problem. Let $n$ be the input size and $k$ be the LIS length of the input. Sequentially, LIS is a simple problem that can be solved using dynamic…
The Minimum Consistent Subset (MCS) problem arises naturally in the context of supervised clustering and instance selection. In supervised clustering, one aims to infer a meaningful partitioning of data using a small labeled subset.…
Integer programs with m constraints are solvable in pseudo-polynomial time in $\Delta$, the largest coefficient in a constraint, when m is a fixed constant. We give a new algorithm with a running time of $O(\sqrt{m}\Delta)^{2m} + O(nm)$,…
The $L_0$-regularized least squares problem (a.k.a. best subsets) is central to sparse statistical learning and has attracted significant attention across the wider statistics, machine learning, and optimization communities. Recent work has…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Given an arbitrary bitstream, we consider the problem of finding the longest substring whose ratio of ones to zeroes equals a given value. The central result of this paper is an algorithm that solves this problem in linear time. The method…
Large language models (LLMs) iteratively generate text token by token, with memory usage increasing with the length of generated token sequences. Since the request generation length is generally unpredictable, it is difficult to estimate…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
This paper studies the problem of, given the structure of a linear-time invariant system and a set of possible inputs, finding the smallest subset of input vectors that ensures system's structural controllability. We refer to this problem…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
Solving an integer least squares (ILS) problem usually consists of two stages: reduction and search. This thesis is concerned with the reduction process for the ordinary ILS problem and the ellipsoid-constrained ILS problem. For the…