Related papers: Which is faster: Bowtie2GP > Bowtie > Bowtie2 > BW…

The prevailing method of analyzing GWAS data is still to test each marker individually, although from a statistical point of view it is quite obvious that in case of complex traits such single marker tests are not ideal. Recently several…

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…

Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…

Large language models (LLMs) commonly employ autoregressive generation during inference, leading to high memory bandwidth demand and consequently extended latency. To mitigate this inefficiency, we present Bi-directional Tuning for lossless…

Neural network training is inherently sequential where the layers finish the forward propagation in succession, followed by the calculation and back-propagation of gradients (based on a loss function) starting from the last layer. The…

Pedigree GWAS (Option 29) in the current version of the Mendel software is an optimized subroutine for performing large scale genome-wide QTL analysis. This analysis (a) works for random sample data, pedigree data, or a mix of both, (b) is…

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…

We propose a genetic algorithm (GA) for hyperparameter optimization of artificial neural networks which includes chromosomal crossover as well as a decoupling of parameters (i.e., weights and biases) from hyperparameters (e.g., learning…

The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…

Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…

Differential evolution(DE) is a conventional algorithm with fast convergence speed. However, DE may be trapped in local optimal solution easily. Many researchers devote themselves to improving DE. In our previously work, whale swarm…

Biopharmaceutical manufacturing is vital to public health but lacks the agility for rapid, on-demand production of biotherapeutics due to the complexity and variability of bioprocesses. To overcome this, we introduce RApid PosTeriOR…

For various optimization methods, gradient descent-based algorithms can achieve outstanding performance and have been widely used in various tasks. Among those commonly used algorithms, ADAM owns many advantages such as fast convergence…

This study introduces a framework that integrates nonlinear feature extraction, classification, and efficient optimization. First, kernel principal component analysis with a radial basis function kernel reduces dimensionality while…

We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…

This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…

The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…

In this paper, we study the problem of speeding up a type of optimization algorithms called Frank-Wolfe, a conditional gradient method. We develop and employ two novel inner product search data structures, improving the prior fastest…

Genetic Programming (GP) is known to suffer from the burden of being computationally expensive by design. While, over the years, many techniques have been developed to mitigate this issue, data vectorization, in particular, is arguably…

Not all generate-and-test search algorithms are created equal. Bayesian Optimization (BO) invests a lot of computation time to generate the candidate solution that best balances the predicted value and the uncertainty given all previous…