Related papers: Pangenome-guided sequence assembly via binary opti…

Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…

Achieving faster execution with shorter compilation time can foster further diversity and innovation in neural networks. However, the current paradigm of executing neural networks either relies on hand-optimized libraries, traditional…

In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…

A wide range of optimization problems arising in machine learning can be solved by gradient descent algorithms, and a central question in this area is how to efficiently compress a large-scale dataset so as to reduce the computational…

Dynamic graphs are extensively employed for detecting anomalous behavior in nodes within the Internet of Things (IoT). Graph generative models are often used to address the issue of imbalanced node categories in dynamic graphs.…

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…

Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…

A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…

Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory…

Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genomes. Sequence-to-graph alignment is an essential step for the…

In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying…

A key challenge in program synthesis is the astronomical size of the search space the synthesizer has to explore. In response to this challenge, recent work proposed to guide synthesis using learned probabilistic models. Obtaining such a…

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…

Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…

As much as Graph Convolutional Networks (GCNs) have shown tremendous success in recommender systems and collaborative filtering (CF), the mechanism of how they, especially the core components (\textit{i.e.,} neighborhood aggregation)…

This paper proposes an algorithmic framework for various reconfiguration problems using zero-suppressed binary decision diagrams (ZDDs), a data structure for families of sets. In general, a reconfiguration problem checks if there is a…

In this paper, we propose a successive pseudo-convex approximation algorithm to efficiently compute stationary points for a large class of possibly nonconvex optimization problems. The stationary points are obtained by solving a sequence of…