Summary: The biological functions of proteins are determined by the chemical and geometric properties of their surfaces. Recently, with the booming progress of deep learning, a series of learning-based surface descriptors have been proposed and achieved inspirational performance in many tasks such as protein design, protein–protein interaction prediction, etc. However, they are still limited by the problem of label scarcity, since the labels are typically obtained through wet experiments. Inspired by the great success of self-supervised learning in natural language processing and computer vision, we introduce ProteinMAE, a self-supervised framework specifically designed for protein surface representation to mitigate label scarcity. Specifically, we propose an efficient network and utilize a large number of accessible unlabeled protein data to pretrain it by self-supervised learning. Then we use the pretrained weights as initialization and fine-tune the network on downstream tasks. To demonstrate the effectiveness of our method, we conduct experiments on three different downstream tasks including binding site identification in protein surface, ligand-binding protein pocket classification, and protein–protein interaction prediction. The extensive experiments show that our method not only successfully improves the network’s performance on all downstream tasks, but also achieves competitive performance with state-of-the-art methods. Moreover, our proposed network also exhibits significant advantages in terms of computational cost, which only requires less than a tenth of memory cost of previous methods. Availability and implementation: https://github.com/phdymz/ProteinMAE.

Deep point cloud neural networks have achieved promising performance in remote sensing applications, and the prevalence of Transformer in natural language processing and computer vision is in stark contrast to underexplored point-based methods. In this paper, we propose an effective transformer-based network for point cloud learning. To better learn global and local information, we propose a group-in-group relation-based transformer architecture to learn the relationships between point groups to model global information and between points within each group to model local semantic information. To further enhance the local feature representation, we propose a Radius Feature Abstraction (RFA) module to extract radius-based density features characterizing the sparsity of local point clouds. Extensive evaluation on public benchmark datasets demonstrate the effectiveness and competitive performance of our proposed method on point cloud classification and part segmentation.

In recent years, Neural Radiance Fields (NeRF) have been used as a map of 3D scene to estimate the 6-DoF pose of new observed images - given an image, estimate the relative rotation and translation of a camera using a trained NeRF. However, existing NeRF-based pose estimation methods have a small convergence region and need to be optimized iteratively over a given initial pose, which makes them slow and sensitive to the initial pose. In this paper, we propose PI-NeRF that directly outputs the pose of a given image without pose initialization and iterative optimization. This is achieved by integrating NeRF with invertible neural network (INN). Our method employs INNs to establish a bijective mapping between the rays and pixel features, which allows us to directly estimate the ray corresponding to each image pixel using the feature map extracted by an image encoder. Based on these rays, we can directly estimate the pose of the image using the PnP algorithm. Experiments conducted on both synthetic and real-world datasets demonstrate that our method is two orders of magnitude faster than existing NeRF-based methods, while the accuracy is competitive without initial pose. The accuracy of our method also outperforms NeRF-free absolute pose regression methods by a large margin.

Kernels are scheduled on Graphics Processing Units (GPUs) in the granularity of GPU warp, which is a bunch of threads that must be scheduled together. When executing kernels with conditional branches, the threads within a warp may execute different branches sequentially, resulting in a considerable utilization loss and unpredictable execution time. This problem is known as the control flow divergence. In this work, we propose a novel method to predict threads' execution path before the launch of the kernel by deploying a branch prediction network on the GPU's tensor cores, which can efficiently parallel run with the kernels on CUDA cores, so that the divergence problem can be eased in a large extent with the lowest overhead. Combined with a well-designed thread data reorganization algorithm, this solution can better mitigate GPUs' control flow divergence problem.