相关论文: Benchmarking database performance for genomic data

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…

Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…

Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…

Graph neural networks (GNNs) have shown great potential in learning on graphs, but they are known to perform sub-optimally on link prediction tasks. Existing GNNs are primarily designed to learn node-wise representations and usually fail to…

High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…

DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…

Relational databases are extensively utilized in a variety of modern information system applications, and they always carry valuable data patterns. There are a huge number of data mining or machine learning tasks conducted on relational…

Although a few approaches are proposed to convert relational databases to graphs, there is a genuine lack of systematic evaluation across a wider spectrum of databases. Recognising the important issue of query mapping, this paper proposes…

Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such…

Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…

The research community continues to seek increasingly more advanced synthetic data generators to reliably evaluate the strengths and limitations of machine learning methods. This work aims to increase the availability of datasets…

Database search is a widely used approach for identifying metabolites from tandem mass spectra (MS/MS). In this strategy, an experimental spectrum is matched against a user-specified database of candidate metabolites, and candidates are…

Local feature matching remains a fundamental challenge in computer vision. Recent Area to Point Matching (A2PM) methods have improved matching accuracy. However, existing research based on this framework relies on inefficient pixel-level…

One important feature of complex systems are problem domains that have many local minima and substructure. Biological systems manage these local minima by switching between different subsystems depending on their environmental or…

This paper presents a memory-optimized metadata-based data structure for implementation of binary chromosome in Genetic Algorithm. In GA different types of genotypes are used depending on the problem domain. Among these, binary genotype is…

Process mining is an area of research that supports discovering information about business processes from their execution event logs. The increasing amount of event logs in organizations challenges current process mining techniques, which…

The excessively increased volume of data in modern data management systems demands an improved system performance, frequently provided by data distribution, system scalability and performance optimization techniques. Optimized horizontal…

Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…

This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…