GPU-based 3D cryo-EM reconstruction with key-value streams

Abstract

The 3D reconstruction of cryo-electron microscopy (cryo-EM) structural determination process is highly compute-intensive. It inherently requires accesses of a large 3D model in different and variable orientations, brings tough challenges to GPU architecture and has no effective solutions currently. To fill this gap, we propose a novel GPU-based parallel design for cryo-EM 3D reconstruction. The major idea is to reorganize the related problem space as streams of key-value pairs, so that we can achieve both the flexibility and efficiency to compute and accumulate the contribution to the final 3D model from all different 2D image inputs. In addition, we design a hybrid communication mechanism to reduce intra-node communications and enable the solving process on a larger scale.