Related papers: Meraculous2: fast accurate short-read assembly of …
Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions…
The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving…
Graph analysis is a critical component of applications such as online social networks, protein interactions in biological networks, and Internet traffic analysis. The arrival of massive graphs with hundreds of millions of nodes, e.g. social…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…
Modern computing systems increasingly rely on composing heterogeneous devices to improve performance and efficiency. Programming these systems is often unproductive: algorithm implementations must be coupled to system-specific logic,…
Pseudo-arclength continuation is a well-established method for generating a numerical curve approximating the solution of an underdetermined system of nonlinear equations. It is an inherently sequential predictor-corrector method in which…
Motivation: RNA-seq has made feasible the analysis of a whole set of expressed mRNAs. Mapping-based assembly of RNA-seq reads sometimes is infeasible due to lack of high-quality references. However, de novo assembly is very challenging due…
We compare different methods for sampling from discrete probability distributions and introduce a new algorithm which is especially efficient on massively parallel processors, such as GPUs. The scheme preserves the distribution properties…
The resampling process employed in widely used methods such as Importance Sampling (IS), with its adaptive extension (AIS), are used to solve challenging problems requiring approximate inference; for example, non-linear, non-Gaussian state…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
Based on Restricted Boltzmann Machines (RBMs), an improved pseudo-stochastic sequential cipher generator is proposed. It is effective and efficient because of the two advantages: this generator includes a stochastic neural network that can…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Multiple signal classification algorithm (MUSICAL) provides a super-resolution microscopy method. In the previous research, MUSICAL has enabled data-parallelism well on a desktop computer or a Linux-based server. However, the running time…
Large transformer models can highly improve Answer Sentence Selection (AS2) tasks, but their high computational costs prevent their use in many real-world applications. In this paper, we explore the following research question: How can we…
We have developed a Python package ZMCintegral for multi-dimensional Monte Carlo integration on multiple Graphics Processing Units(GPUs). The package employs a stratified sampling and heuristic tree search algorithm. We have built three…
The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically -- as long as the algorithm does not…
This article introduces an algorithm, MergeShuffle, which is an extremely efficient algorithm to generate random permutations (or to randomly permute an existing array). It is easy to implement, runs in $n\log_2 n + O(1)$ time, is in-place,…