Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

DOPE: Distributed Optimization for Pairwise Energies

We formulate an Alternating Direction Method of Mul-tipliers (ADMM) that systematically distributes the computations of any technique for optimizing pairwise functions, including non-submodular potentials. Such discrete functions are very useful in segmentation and a breadth of other vision problems. Our method decomposes the problem into a large set of small sub-problems, each involving a sub-region of the image domain, which can be solved in parallel. We achieve consistency between the sub-problems through a novel constraint that can be used for a large class of pair-wise functions. We give an iterative numerical solution that alternates between solving the sub-problems and updating consistency variables, until convergence. We report comprehensive experiments, which demonstrate the benefit of our general distributed solution in the case of the popular serial algorithm of Boykov and Kolmogorov (BK algorithm) and, also, in the context of non-submodular functions.Comment: Accepted at CVPR 201

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500 Hz to 1 kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2 ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates