Einstein equations in the null quasi-spherical gauge III: numerical algorithms

We describe numerical techniques used in the construction of our 4th order evolution for the full Einstein equations, and assess the accuracy of representative solutions. The code is based on a null gauge with a quasi-spherical radial coordinate, and simulates the interaction of a single black hole with gravitational radiation. Techniques used include spherical harmonic representations, convolution spline interpolation and filtering, and an RK4 "method of lines" evolution. For sample initial data of "intermediate" size (gravitational field with 19% of the black hole mass), the code is accurate to 1 part in 10^5, until null time z=55 when the coordinate condition breaks down.Comment: Latex, 38 pages, 29 figures (360Kb compressed

TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the entangled geometric complexity and biological complexity. We introduce topology, i.e., element specific persistent homology (ESPH), to untangle geometric complexity and biological complexity. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains crucial biological information via a multichannel image representation. It is able to reveal hidden structure-function relationships in biomolecules. We further integrate ESPH and convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the limitations to deep learning arising from small and noisy training sets, we present a multitask topological convolutional neural network (MT-TCNN). We demonstrate that the present TopologyNet architectures outperform other state-of-the-art methods in the predictions of protein-ligand binding affinities, globular protein mutation impacts, and membrane protein mutation impacts.Comment: 20 pages, 8 figures, 5 table