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The present and future of evolutionary algorithms depends on the proper use of modern parallel and distributed computing infrastructures. Although still sequential approaches dominate the landscape, available multi-core, many-core and…
Optimal 3-way comparison search trees (3WCST's) can be computed using standard dynamic programming in time O(n^3), and this can be further improved to O(n^2) by taking advantage of the Monge property. In contrast, the fastest algorithm in…
We propose a fast beam orientation selection method, based on deep neural networks (DNN), capable of developing a plan comparable to those by the state-of-the-art column generation method. The novelty of Our model lies in its supervised…
A general approach to optimizing fast processes using a gender genetic algorithm is described. Its difference from the more traditional genetic algorithm it contains division the artificial population into two sexes. Male subpopulations…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and…
Literature reviews are essential for any researcher trying to keep up to date with the burgeoning software engineering literature. FAST$^2$ is a novel tool for reducing the effort required for conducting literature reviews by assisting the…
Non-dominated Sorting Genetic Algorithm (NSGA) has established itself as a benchmark algorithm for Multiobjective Optimization. The determination of pareto-optimal solutions is the key to its success. However the basic algorithm suffers…
Gravitational-wave detection strategies are based on a signal analysis technique known as matched filtering. Despite the success of matched filtering, due to its computational cost, there has been recent interest in developing deep…
The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…
Transformer neural networks (TNN) have been widely utilized on a diverse range of applications, including natural language processing (NLP), machine translation, and computer vision (CV). Their widespread adoption has been primarily driven…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
Bayesian networks (BNs) are attractive, because they are graphical and interpretable machine learning models. However, exact inference on BNs is time-consuming, especially for complex problems. To improve the efficiency, we propose a fast…
Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques employed for increasing…
Identification of cognates across related languages is one of the primary problems in historical linguistics. Automated cognate identification is helpful for several downstream tasks including identifying sound correspondences,…
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there is a lack of comparison between these recent approaches and…
The Gillespie algorithm is commonly used to simulate and analyze complex chemical reaction networks. Here, we leverage recent breakthroughs in deep learning to develop a fully differentiable variant of the Gillespie algorithm. The…
Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations.…