A SIMD algorithm for the detection of epistatic interactions of any order

Epistasis is a phenomenon in which a phenotype outcome is determined by the interaction of genetic variation at two or more loci and it cannot be attributed to the additive combination of effects corresponding to the individual loci. Although it has been more than 100 years since William Bateson introduced this concept, it still is a topic under active research. Locating epistatic interactions is a computationally expensive challenge that involves analyzing an exponentially growing number of combinations. Authors in this field have resorted to a multitude of hardware architectures in order to speed up the search, but little to no attention has been paid to the vector instructions that current CPUs include in their instruction sets. This work extends an existing third-order exhaustive algorithm to support the search of epistasis interactions of any order and discusses multiple SIMD implementations of the different functions that compose the search using Intel AVX Intrinsics. Results using the GCC and the Intel compiler show that the 512-bit explicit vector implementation proposed here performs the best out of all of the other implementations evaluated. The proposed 512-bit vectorization accelerates the original implementation of the algorithm by an average factor of 7 and 12, for GCC and the Intel Compiler, respectively, in the scenarios tested.


page 11

page 13


AVX-512 extension to OpenQCD 1.6

We publish an extension of openQCD-1.6 with AVX-512 vector instructions ...

SIMD Vectorization for the Lennard-Jones Potential with AVX2 and AVX-512 instructions

This work describes the SIMD vectorization of the force calculation of t...

Intel HEXL: Accelerating Homomorphic Encryption with Intel AVX512-IFMA52

Modern implementations of homomorphic encryption (HE) rely heavily on po...

TTC: A Tensor Transposition Compiler for Multiple Architectures

We consider the problem of transposing tensors of arbitrary dimension an...

On the Influence of the FPGA Compiler Optimization Options on the Success of the Horizontal Attack

This paper reports about the impact of compiler options on the resistanc...

ECP SOLLVE: Validation and Verification Testsuite Status Update and Compiler Insight for OpenMP

The OpenMP language continues to evolve with every new specification rel...

Optimized Vectorization Implementation of CRYSTALS-Dilithium

CRYSTALS-Dilithium is a lattice-based signature scheme to be standardize...

Please sign up or login with your details

Forgot password? Click here to reset