Related papers: Deposition and Extension Approach to Find Longest …
The Longest Common Subsequence (LCS) of two strings is a fundamental string similarity measure with a classical dynamic programming solution taking quadratic time. Despite significant efforts, little progress was made in improving the…
In this paper we present and evaluate a search strategy called Decomposition Based Search (DBS) which is based on two steps: subproblem generation and subproblem solution. The generation of subproblems is done through value ranking and…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…
Lifelong sequence generation (LSG), a problem in continual learning, aims to continually train a model on a sequence of generation tasks to learn constantly emerging new generation patterns while avoiding the forgetting of previous…
A new algorithm named EXPected Similarity Estimation (EXPoSE) was recently proposed to solve the problem of large-scale anomaly detection. It is a non-parametric and distribution free kernel method based on the Hilbert space embedding of…
Large language models (LLMs) have demonstrated limitations in handling combinatorial optimization problems involving long-range reasoning, partially due to causal hallucinations and huge search space. As for causal hallucinations, i.e., the…
We study the problem of computing a longest increasing subsequence in a sequence $S$ of $n$ distinct elements in the presence of persistent comparison errors. In this model, every comparison between two elements can return the wrong result…
Data envelopment analysis (DEA) is a linear program (LP)-based method used to determine the efficiency of a decision making unit (DMU), which transforms inputs to outputs, by peer comparison. This paper presents a new computation algorithm…
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
A linear extension of a poset $P$ is a permutation of the elements of the set that respects the partial order. Let $L(P)$ denote the number of linear extensions. It is a #P complete problem to determine $L(P)$ exactly for an arbitrary…
Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…
Frequent pattern mining is widely used to find ``important'' or ``interesting'' patterns in data. While it is not easy to mathematically define such patterns, maximal frequent patterns are promising candidates, as frequency is a natural…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
As one popular modeling approach for end-to-end speech recognition, attention-based encoder-decoder models are known to suffer the length bias and corresponding beam problem. Different approaches have been applied in simple beam search to…
In this paper, we study for the first time the Diverse Longest Common Subsequences (LCSs) problem under Hamming distance. Given a set of a constant number of input strings, the problem asks to decide if there exists some subset $\mathcal X$…
One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…
Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to…