Accelerating AutoDock Vina with GPUs.

AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern drug discovery is facing a common scenario of large virtual screening of drug hits from huge compound databases. Due to the seriality characteristic of the AutoDock Vina algorithm, there is no successful report on its parallel acceleration with GPUs. Current acceleration of AutoDock Vina typically relies on the stack of computing power as well as the allocation of resource and tasks, such as the VirtualFlow platform. The vast resource expenditure and the high access threshold of users will greatly limit the popularity of AutoDock Vina and the flexibility of its usage in modern drug discovery. In this work, we proposed a new method, Vina-GPU, for accelerating AutoDock Vina with GPUs, which is greatly needed for reducing the investment for large virtual screens and also for wider application in large-scale virtual screening on personal computers, station servers or cloud computing, etc. Our proposed method is based on a modified Monte Carlo using simulating annealing AI algorithm. It greatly raises the number of initial random conformations and reduces the search depth of each thread. Moreover, a classic optimizer named BFGS is adopted to optimize the ligand conformations during the docking progress, before a heterogeneous OpenCL implementation was developed to realize its parallel acceleration leveraging thousands of GPU cores. Large benchmark tests show that Vina-GPU reaches an average of 21-fold and a maximum of 50-fold docking acceleration against the original AutoDock Vina while ensuring their comparable docking accuracy, indicating its potential for pushing the popularization of AutoDock Vina in large virtual screens.

Wearable on-device deep learning system for hand gesture recognition based on FPGA accelerator.

Gesture recognition is critical in the field of Human-Computer Interaction, especially in healthcare, rehabilitation, sign language translation, etc. Conventionally, the gesture recognition data collected by the inertial measurement unit (IMU) sensors is relayed to the cloud or a remote device with higher computing power to train models. However, it is not convenient for remote follow-up treatment of movement rehabilitation training. In this paper, based on a field-programmable gate array (FPGA) accelerator and the Cortex-M0 IP core, we propose a wearable deep learning system that is capable of locally processing data on the end device. With a pre-stage processing module and serial-parallel hybrid method, the device is of low-power and low-latency at the micro control unit (MCU) level, however, it meets or exceeds the performance of single board computers (SBC). For example, its performance is more than twice as much of Cortex-A53 (which is usually used in Raspberry Pi). Moreover, a convolutional neural network (CNN) and a multilayer perceptron neural network (NN) is used in the recognition model to extract features and classify gestures, which helps achieve a high recognition accuracy at 97%. Finally, this paper offers a software-hardware co-design method that is worth referencing for the design of edge devices in other scenarios.