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Primary Publication
Imran S. Haque, Vijay S. Pande, and W. Patrick Walters. SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. Journal of Chemical Information and Modeling 2010, 50(4), pp 560-564. (2010)  View
Abstract

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.

Related Publications
Haque IH, Pande VS, and Walters WP. SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. Journal of Chemical Information and Modeling, 2010. Published online ahead of print, DOI:10.1021/ci100011z (2010)  View
Abstract

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 3× as fast as existing algorithms on a CPU, and over 80× faster than existing methods when run on a GPU.

Imran S. Haque, Vijay S. Pande, and W. Patrick Walters. SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. Journal of Chemical Information and Modeling 2010, 50(4), pp 560-564. (2010)  View
Abstract

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.

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