相关论文: Finite Width Model Sequence Comparison

Recognizing subtle historical patterns is central to modeling and forecasting problems in time series analysis. Here we introduce and develop a new approach to quantify deviations in the underlying hidden generators of observed data…

Binary code similarity approaches compare two or more pieces of binary code to identify their similarities and differences. The ability to compare binary code enables many real-world applications on scenarios where source code may not be…

We consider the problem of updating the information about multiple longest common sub-sequences. This kind of sub-sequences is used to highlight information that is shared across several information sequences, therefore it is extensively…

Identifying a temporal pattern of events is a fundamental task of on-line (real-time) verification. We present efficient schemes for on-line monitoring of events for identifying desired/undesired patterns of events. The schemes use…

In optimization or machine learning problems we are given a set of items, usually points in some metric space, and the goal is to minimize or maximize an objective function over some space of candidate solutions. For example, in clustering…

In Natural Language Processing (NLP), it is important to detect the relationship between two sequences or to generate a sequence of tokens given another observed sequence. We call the type of problems on modelling sequence pairs as sequence…

Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…

In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…

Regression models are essential for a wide range of real-world applications. However, in practice, target values are not always precisely known; instead, they may be represented as intervals of acceptable values. This challenge has led to…

Recent advances in self-supervised learning and neural network scaling have enabled the creation of large models, known as foundation models, which can be easily adapted to a wide range of downstream tasks. The current paradigm for…

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…

This paper introduces a new similarity measure, the covering similarity, that we formally define for evaluating the similarity between a symbolic sequence and a set of symbolic sequences. A pair-wise similarity can also be directly derived…

Process equivalences are formal methods that relate programs and system which, informally, behave in the same way. Since there is no unique notion of what it means for two dynamic systems to display the same behaviour there are a multitude…

Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…

A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…

In post genomic era with the advent of new technologies a huge amount of complex molecular data are generated with high throughput. The management of this biological data is definitely a challenging task due to complexity and heterogeneity…

This study focuses on an alignment-free sequence comparison method: the number of words of length k shared between two sequences, also known as the D_2 statistic. The advantages of the use of this statistic over alignment-based methods are…

Hypernetwork is a useful way to depict multiple connections between nodes, making it an ideal tool for representing complex relationships in network science. In recent years, there has been a marked increase in studies on hypernetworks,…

The goal of constraint-based sequence mining is to find sequences of symbols that are included in a large number of input sequences and that satisfy some constraints specified by the user. Many constraints have been proposed in the…

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…