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libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

Jocelyn Sunseri, David Ryan Koes
Department of Computational and Sytems Biology, University of Pittsburgh
arXiv:1912.04822 [cs.LG], (10 Dec 2019)

@misc{sunseri2019libmolgrid,

   title={libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications},

   author={Jocelyn Sunseri and David Ryan Koes},

   year={2019},

   eprint={1912.04822},

   archivePrefix={arXiv},

   primaryClass={cs.LG}

}

There are many ways to represent a molecule as input to a machine learning model and each is associated with loss and retention of certain kinds of information. In the interest of preserving three-dimensional spatial information, including bond angles and torsions, we have developed libmolgrid, a general-purpose library for representing three-dimensional molecules using multidimensional arrays. This library also provides functionality for composing batches of data suited to machine learning workflows, including data augmentation, class balancing, and example stratification according to a regression variable or data subgroup, and it further supports temporal and spatial recurrences over that data to facilitate work with recurrent neural networks, dynamical data, and size extensive modeling. It was designed for seamless integration with popular deep learning frameworks, including Caffe, PyTorch, and Keras, providing good performance by leveraging graphical processing units (GPUs) for computationally-intensive tasks and efficient memory usage through the use of memory views over preallocated buffers. libmolgrid is a free and open source project that is actively supported, serving the growing need in the molecular modeling community for tools that streamline the process of data ingestion, representation construction, and principled machine learning model development.
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