相关论文: Efficient Sequential and Parallel Algorithms for P…

In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…

The aim of sequential pattern mining (SPM) is to discover potentially useful information from a given se-quence. Although various SPM methods have been investigated, most of these focus on mining all of the patterns. However, users…

We present a study of several generic tree search techniques applied to the Sequential Ordering Problem. This study enables us to propose a simple and competitive tree search algorithm. It consists of an iterative Beam Search algorithm that…

In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…

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 $P=\{P_1,\cdots,P_d\}$…

Prompt engineering has proven to be a crucial step in leveraging pretrained large language models (LLMs) in solving various real-world tasks. Numerous solutions have been proposed that seek to automate prompt engineering by using the model…

Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat…

We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…

Large Language Models (LLMs) exhibit remarkable proficiency in addressing a diverse array of tasks within the Natural Language Processing (NLP) domain, with various prompt design strategies significantly augmenting their capabilities.…

Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…

The problem of finding dense components of a graph is a widely explored area in data analysis, with diverse applications in fields and branches of study including community mining, spam detection, computer security and bioinformatics. This…

Mixed-integer linear programs (MILPs) are extensively used to model practical problems such as planning and scheduling. A prominent method for solving MILPs is large neighborhood search (LNS), which iteratively seeks improved solutions…

This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for…

Low-precision networks, with weights and activations quantized to low bit-width, are widely used to accelerate inference on edge devices. However, current solutions are uniform, using identical bit-width for all filters. This fails to…

Motifs are the most repetitive/frequent patterns of a time-series. The discovery of motifs is crucial for practitioners in order to understand and interpret the phenomena occurring in sequential data. Currently, motifs are searched among…

Language models are now capable of solving tasks that require dealing with long sequences consisting of hundreds of thousands of tokens. However, they often fail on tasks that require repetitive use of simple rules, even on sequences that…

Background: The computation of the statistical properties of motif occurrences has an obviously relevant practical application: for example, patterns that are significantly over- or under-represented in the genome are interesting candidates…

Foundation models and their checkpoints have significantly advanced deep learning, boosting performance across various applications. However, fine-tuned models often struggle outside their specific domains and exhibit considerable…

Given two sequences $A[1..n]$ and $B[1..m]$ over a totally ordered alphabet, the \emph{Longest Common Bitonic Subsequence} (LCBS) problem asks for a longest common subsequence that is strictly increasing up to a single peak element and…