相关论文: Matching reads to many genomes with the $r$-index

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…

Schema linking is a critical step in Text-to-SQL task, aiming to accurately predict the table names and column names required for the SQL query based on the given question. However, current fine-tuning approaches for schema linking models…

Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…

Approximate nearest neighbor algorithms are used to speed up nearest neighbor search in a wide array of applications. However, current indexing methods feature several hyperparameters that need to be tuned to reach an acceptable…

The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…

A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying…

In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…

We propose a new approach of NoSQL database index selection. For different workloads, we select different indexes and their different parameters to optimize the database performance. The approach builds a deep reinforcement learning model…

The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for…

Deep neural networks have achieved significant improvements in information retrieval (IR). However, most existing models are computational costly and can not efficiently scale to long documents. This paper proposes a novel End-to-End neural…

Effect size indices are useful parameters that quantify the strength of association and are unaffected by sample size. There are many available effect size parameters and estimators, but it is difficult to compare effect sizes across…

This work introduces a companion reproducible paper with the aim of allowing the exact replication of the methods, experiments, and results discussed in a previous work [5]. In that parent paper, we proposed many and varied techniques for…

The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent…

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…

For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…

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…

robustloggamma is an R package for robust estimation and inference in the generalized loggamma model. We briefly introduce the model, the estimation procedures and the computational algorithms. Then, we illustrate the use of the package…