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

Note on neutron star equation of state in the light of GW170817

From the very first multimessenger event of GW170817, clean robust constraints can be obtained for the tidal deformabilities of the two stars involved in the merger, which provides us unique opportunity to study the equation of states (EOSs) of dense stellar matter. In this contribution, we employ a model from the quark level, describing consistently a nucleon and many-body nucleonic system from a quark potential. We check that our sets of EOSs are consistent with available experimental and observational constraints at both sub-nuclear saturation densities and higher densities. The agreements with ab-initio calculations are also good. Especially, we tune the density dependence of the symmetry energy (characterized by its slope at nuclear saturation $L$) and study its influence on the tidal deformability. The so-called $QMF18$ EOS is named after the case of $L=40~\rm MeV$, and it gives $M_{\rm TOV} =2.08~M_\odot$ and $R= 11.77~\rm km$, $\Lambda=331$ for a $1.4\,M_\odot$ star. The tidal signals are demonstrated to be insensitive to the uncertain crust-core matching, despite the good correlation between the symmetry energy slope and the radius of the star.Comment: 8 pages, 6 figures, Submitted to the AIP Proceedings of the Xiamen-CUSTIPEN Workshop on the EOS of Dense Neutron-Rich Matter in the Era of Gravitational Wave Astronomy, Jan. 3-7, Xiamen, Chin

Graph state basis for Pauli Channels

We introduce graph state basis diagonalization to calculate the coherent information of a quantum code passing through a Pauli channel. The scheme is 5000 times faster than the best known one for some concatenated repetition codes, providing us a practical constructive way of approaching the quantum capacity of a Pauli channel. The calculation of the coherent information of non-additive quantum code can also be greatly simplified in graph state basis.Comment: 5 page

The analysis of the charmonium-like states X∗(3860)X^{*}(3860),X(3872)X(3872), X(3915)X(3915), X(3930)X(3930) and X(3940)X(3940) according to its strong decay behaviors

Inspired by the newly observed state $X^{*}(3860)$, we analyze the strong decay behaviors of some charmonium-like states $X^{*}(3860)$,$X(3872)$, $X(3915)$, $X(3930)$ and $X(3940)$ by the $^{3}P_{0}$ model. We carry out our work based on the hypothesis that these states are all being the charmonium systems. Our analysis indicates that $0^{++}$ charmonium state can be a good candidate for $X^{*}(3860)$ and $1^{++}$ state is the possible assignment for $X(3872)$. Considering as the $3^{1}S_{0}$ state, the decay behavior of $X(3940)$ is inconsistent with the experimental data. So, we can not assign $X(3940)$ as the $3^{1}S_{0}$ charmonium state by present work. Besides, our analysis imply that it is reasonable to assign $X(3915)$ and $X(3930)$ to be the same state, $2^{++}$. However, combining our analysis with that of Zhou~\cite{ZhouZY}, we speculate that $X(3915)$/$X(3930)$ might not be a pure $c\overline{c}$ systems

Analysis of the strong coupling form factors of ΣbNB\Sigma_bNB and ΣcND\Sigma_c ND in QCD sum rules

In this article, we study the strong interaction of the vertexes $\Sigma_bNB$ and $\Sigma_c ND$ using the three-point QCD sum rules under two different dirac structures. Considering the contributions of the vacuum condensates up to dimension $5$ in the operation product expansion, the form factors of these vertexes are calculated. Then, we fit the form factors into analytical functions and extrapolate them into time-like regions, which giving the coupling constant. Our analysis indicates that the coupling constant for these two vertexes are $G_{\Sigma_bNB}=0.43\pm0.01GeV^{-1}$ and $G_{\Sigma_cND}=3.76\pm0.05GeV^{-1}$.Comment: 6 figure