相关论文: A SIMD algorithm for the detection of epistatic in…

Epistasis can be defined as the statistical interaction of genes during the expression of a phenotype. It is believed that it plays a fundamental role in gene expression, as individual genetic variants have reported a very small increase in…

Epistasis (gene-gene interaction) is crucial to predicting genetic disease. Our work tackles the computational challenges faced by previous works in epistasis detection by modeling it as a one-step Markov Decision Process where the state is…

In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…

Selecting influential nonlinear interactive features from ultrahigh dimensional data has been an important task in various fields. However, statistical accuracy and computational feasibility are the two biggest concerns when more than half…

A large amount of research has been devoted to the detection and investigation of epistatic interactions in genome-wide association studies (GWASs). Most of the literature focuses on low-order interactions between single-nucleotide…

Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…

Applications often require a fast, single-threaded search algorithm over sorted data, typical in table-lookup operations. We explore various search algorithms for a large number of search candidates over a relatively small array of…

With the recent advent of high-throughput genotyping techniques, genetic data for genome-wide association studies (GWAS) have become increasingly available, which entails the development of efficient and effective statistical approaches.…

Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…

Approaches to gene interactions based on sign epistasis have been highly influential in recent time. Sign epistasis is useful for relating local and global properties of fitness landscapes, as well as for analyzing evolutionary trajectories…

Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is…

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (10pJ/word on-die to 10,000pJ/word on the network). To increase memory locality at the hardware level and reduce…

2 Diabetes is a leading worldwide public health concern, and its increasing prevalence has significant health and economic importance in all nations. The condition is a multifactorial disorder with a complex aetiology. The genetic…

GPU-accelerated Inverted File (IVF) index is one of the industry standards for large-scale vector search but relies on static VRAM layouts that hinder real-time mutability. Our benchmark and analysis reveal that existing designs of GPU IVF…

Recombinant Inbred Lines derived from divergent parental lines can display extensive segregation distortion and long-range linkage disequilibrium (LD) between distant loci. These genomic signatures are consistent with epistatic selection…

The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving…

Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…

More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…

An evolutionary search space can be smoothly transformed via a suitable change of basis; however, it can be difficult to determine an appropriate basis. In this paper, a method is proposed to select an optimum basis can be used to simplify…

In many important applications -- such as search engines and relational database systems -- data is stored in the form of arrays of integers. Encoding and, most importantly, decoding of these arrays consumes considerable CPU time.…