SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs.
LINGOs are a holographic measure of chemical similarity based on text comparison of SMILES strings. We present a new algorithm for calculating LINGO similarities amenable to parallelization on SIMD architectures (such as GPUs and vector units of modern CPUs). We show that it is nearly 3x as fast as existing algorithms on a CPU, and over 80x faster than existing methods when run on a GPU.
Haque
Imran S
IS
Department of Computer Science, Stanford University, Stanford, California, USA.
Pande
Vijay S
VS
Walters
W Patrick
WP
D000465:Algorithms; D019985:Benchmarking; D003196:Computer Graphics; D003201:Computers; D016208:Databases, Factual; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D013997:Time Factors