HelixFold: An Efficient Implementation of AlphaFold2 using PaddlePaddle

Accurate protein structure prediction can significantly accelerate the development of life science. The accuracy of AlphaFold2, a frontier end-to-end structure prediction system, is already close to that of the experimental determination techniques. Due to the complex model architecture and large memory consumption, it requires lots of computational resources and time to implement the training and inference of AlphaFold2 from scratch. The cost of running the original AlphaFold2 is expensive for most individuals and institutions. Therefore, reducing this cost could accelerate the development of life science. We implement AlphaFold2 using PaddlePaddle, namely HelixFold, to improve training and inference speed and reduce memory consumption. The performance is improved by operator fusion, tensor fusion, and hybrid parallelism computation, while the memory is optimized through Recompute, BFloat16, and memory read/write in-place. Compared with the original AlphaFold2 (implemented with Jax) and OpenFold (implemented with PyTorch), HelixFold needs only 7.5 days to complete the full end-to-end training and only 5.3 days when using hybrid parallelism, while both AlphaFold2 and OpenFold take about 11 days. HelixFold saves 1x training time. We verified that HelixFold's accuracy could be on par with AlphaFold2 on the CASP14 and CAMEO datasets. HelixFold's code is available on GitHub for free download: https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold, and we also provide stable web services on https://paddlehelix.baidu.com/app/drug/protein/forecast.

DOOBNet: Deep Object Occlusion Boundary Detection from an Image

Object occlusion boundary detection is a fundamental and crucial research problem in computer vision. This is challenging to solve as encountering the extreme boundary/non-boundary class imbalance during training an object occlusion boundary detector. In this paper, we propose to address this class imbalance by up-weighting the loss contribution of false negative and false positive examples with our novel Attention Loss function. We also propose a unified end-to-end multi-task deep object occlusion boundary detection network (DOOBNet) by sharing convolutional features to simultaneously predict object boundary and occlusion orientation. DOOBNet adopts an encoder-decoder structure with skip connection in order to automatically learn multi-scale and multi-level features. We significantly surpass the state-of-the-art on the PIOD dataset (ODS F-score of .702) and the BSDS ownership dataset (ODS F-score of .555), as well as improving the detecting speed to as 0.037s per image on the PIOD dataset.