New citation:
@Article{D0SC02458A,
author ="Li, Zhiheng and Wellawatte, Geemi P. and Chakraborty, Maghesree and Gandhi, Heta A. and Xu, Chenliang and White, Andrew D.",
title ="Graph neural network based coarse-grained mapping prediction",
journal ="Chem. Sci.",
year ="2020",
pages ="-",
publisher ="The Royal Society of Chemistry",
doi ="10.1039/D0SC02458A",
url ="http://dx.doi.org/10.1039/D0SC02458A",
abstract ="The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the art method is mapping operators manually selected by experts. In this work{,} we demonstrate an automated approach by viewing this problem as supervised learning where we seek to reproduce the mapping operators produced by experts. We present a graph neural network based CG mapping predictor called Deep Supervised Graph Partitioning Model (DSGPM) that treats mapping operators as a graph segmentation problem. DSGPM is trained on a novel dataset{,} Human-annotated Mappings (HAM){,} consisting of 1180 molecules with expert annotated mapping operators. HAM can be used to facilitate further research in this area. Our model uses a novel metric learning objective to produce high-quality atomic features that are used in spectral clustering. The results show that the DSGPM outperforms state-of-the-art methods in the field of graph segmentation. Finally{,} we find that predicted CG mapping operators indeed result in good CG MD models when used in simulation."}
zhihengli-UR
commented
4 years ago
New citation: @Article{D0SC02458A, author ="Li, Zhiheng and Wellawatte, Geemi P. and Chakraborty, Maghesree and Gandhi, Heta A. and Xu, Chenliang and White, Andrew D.", title ="Graph neural network based coarse-grained mapping prediction", journal ="Chem. Sci.", year ="2020", pages ="-", publisher ="The Royal Society of Chemistry", doi ="10.1039/D0SC02458A", url ="http://dx.doi.org/10.1039/D0SC02458A",
abstract ="The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the art method is mapping operators manually selected by experts. In this work{,} we demonstrate an automated approach by viewing this problem as supervised learning where we seek to reproduce the mapping operators produced by experts. We present a graph neural network based CG mapping predictor called Deep Supervised Graph Partitioning Model (DSGPM) that treats mapping operators as a graph segmentation problem. DSGPM is trained on a novel dataset{,} Human-annotated Mappings (HAM){,} consisting of 1180 molecules with expert annotated mapping operators. HAM can be used to facilitate further research in this area. Our model uses a novel metric learning objective to produce high-quality atomic features that are used in spectral clustering. The results show that the DSGPM outperforms state-of-the-art methods in the field of graph segmentation. Finally{,} we find that predicted CG mapping operators indeed result in good CG MD models when used in simulation."}