Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks

Protein secondary structure prediction is an important problem in bioinformatics. Inspired by the recent successes of deep neural networks, in this paper, we propose an end-to-end deep network that predicts protein secondary structures from integrated local and global contextual features. Our deep architecture leverages convolutional neural networks with different kernel sizes to extract multiscale local contextual features. In addition, considering long-range dependencies existing in amino acid sequences, we set up a bidirectional neural network consisting of gated recurrent unit to capture global contextual features. Furthermore, multi-task learning is utilized to predict secondary structure labels and amino-acid solvent accessibility simultaneously. Our proposed deep network demonstrates its effectiveness by achieving state-of-the-art performance, i.e., 69.7% Q8 accuracy on the public benchmark CB513, 76.9% Q8 accuracy on CASP10 and 73.1% Q8 accuracy on CASP11. Our model and results are publicly available.Comment: 8 pages, 3 figures, Accepted by International Joint Conferences on Artificial Intelligence (IJCAI

Computational Discovery of A New Rhombohedral Diamond Phase

We identify by first-principles calculations a new diamond phase in R¯3c (D63d) symmetry, which has a 16-atom rhombohedral primitive cell, thus termed R16 carbon. This rhombohedral diamond comprises a characteristic all-sp3 six-membered-ring bonding network, and it is energetically more stable than previously identified diamondlike six-membered-ring bonded BC8 and BC12 carbon phases. A phonon mode analysis verifies the dynamic structural stability of R16 carbon, and electronic band calculations reveal that it is an insulator with a direct band gap of 4.45 eV. Simulated x-ray diffraction patterns provide an excellent match to recently reported distinct diffraction peaks found in milled fullerene soot, suggesting a viable experimental synthesis route. These findings pave the way for further exploration of this new diamond phase and its outstanding properties