No abstract uploaded!

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 geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep 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 deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/

No abstract uploaded!

No abstract uploaded!

Yuan’s theorem of the alternative is an important theoretical tool in optimization, which provides a checkable certificate for the infeasibility of a strict inequality system involving two homogeneous quadratic functions. In this paper, we provide a tractable extension of Yuan’s theorem of the alternative to the symmetric tensor setting. As an application, we establish that the optimal value of a class of nonconvex polynomial optimization problems with suitable sign structure (or more explicitly, with essentially nonpositive coefficients) can be computed by a related convex conic programming problem, and the optimal solution of these nonconvex polynomial optimization problems can be recovered from the corresponding solution of the convex conic programming problem. Moreover, we obtain that this class of nonconvex polynomial optimization problems enjoy exact sum-of-squares relaxation, and so, can be solved via a single semidefinite programming problem.