相关论文: An Algorithm for Alignment-free Sequence Compariso…

We propose Fuzzy Jaccard Index (FUJI) -- a scale-invariant score for assessment of the similarity between two ranked/ordered lists. FUJI improves upon the Jaccard index by incorporating a membership function which takes into account the…

The Fuzzy Gene Filter (FGF) is an optimised Fuzzy Inference System designed to rank genes in order of differential expression, based on expression data generated in a microarray experiment. This paper examines the effectiveness of the FGF…

This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…

Score matching is an alternative to maximum likelihood (ML) for estimating a probability distribution parametrized up to a constant of proportionality. By fitting the ''score'' of the distribution, it sidesteps the need to compute this…

In recent years, thanks to advances in automatic music transcription (AMT), several large-scale datasets of automatically transcribed piano solo music have been released. While these datasets undoubtedly offer extensive material for…

Proposed in Hyv\"arinen (2005), score matching is a parameter estimation procedure that does not require computation of distributional normalizing constants. In this work we utilize the geometric median of means to develop a robust score…

We consider the problem of aligning a pair of databases with jointly Gaussian features. We consider two algorithms, complete database alignment via MAP estimation among all possible database alignments, and partial alignment via a…

We describe a seriation algorithm for ranking a set of items given pairwise comparisons between these items. Intuitively, the algorithm assigns similar rankings to items that compare similarly with all others. It does so by constructing a…

Automated answer matching, which leverages LLMs to evaluate free-text responses by comparing them to a reference answer, shows substantial promise as a scalable and aligned alternative to human evaluation. However, its reliability requires…

We propose a new method for shape recognition and retrieval based on dynamic programming. Our approach uses the dynamic programming algorithm to compute the optimal score and to find the optimal alignment between two strings. First, each…

This paper employs the linear nested sequent framework to design a new cut-free calculus LNIF for intuitionistic fuzzy logic--the first-order G\"odel logic characterized by linear relational frames with constant domains. Linear nested…

Recent works have revealed the great potential of speculative decoding in accelerating the autoregressive generation process of large language models. The success of these methods relies on the alignment between draft candidates and the…

Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the…

In this paper, harmony search algorithm is applied to curriculum-based course timetabling. The implementation, specifically the process of improvisation consists of memory consideration, random consideration and pitch adjustment. In memory…

We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…

The increasing rise in artificial intelligence has made the use of imprecise language in computer programs like ChatGPT more prominent. Fuzzy logic addresses this form of imprecise language by introducing the concept of fuzzy sets, where…

Best-of-n sampling improves the accuracy of large language models (LLMs) and large reasoning models (LRMs) by generating multiple candidate solutions and selecting the one with the highest reward. The key challenge for reasoning tasks is…

In relational verification, judicious alignment of computational steps facilitates proof of relations between programs using simple relational assertions. Relational Hoare logics (RHL) provide compositional rules that embody various…

Alignment-based conformance checking is the state-of-the-art approach for comparing observed process executions with normative process models. The standard exact solution relies on an A*-based heuristic search, which can exhibit exponential…

We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…