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

X-ray outbursts of low-mass X-ray binary transients observed in the RXTE era

We have performed a statistical study of the properties of 110 bright X-ray outbursts in 36 low-mass X-ray binary transients (LMXBTs) seen with the All-Sky Monitor (2--12 keV) on board the {\it Rossi X-ray Timing Explorer} ({\it RXTE}) in 1996--2011. We have measured a number of outburst properties, including peak X-ray luminosity, rate of change of luminosity on a daily timescale, $e$-folding rise and decay timescales, outburst duration, and total radiated energy. We found that the average properties such as peak X-ray luminosity, rise and decay timescales, outburst duration, and total radiated energy of black hole LMXBTs, are at least two times larger than those of neutron star LMXBTs, implying that the measurements of these properties may provide preliminary clues as to the nature of the compact object of a newly discovered LMXBT. We also found that the outburst peak X-ray luminosity is correlated with the rate of change of X-ray luminosity in both the rise and the decay phases, which is consistent with our previous studies. Positive correlations between total radiated energy and peak X-ray luminosity, and between total radiated energy and the $e$-folding rise or decay timescale, are also found in the outbursts. These correlations suggest that the mass stored in the disk before an outburst is the primary initial condition that sets up the outburst properties seen later. We also found that the outbursts of two transient stellar-mass ULXs in M31 also roughly follow the correlations, which indicate that the same outburst mechanism works for the brighter outbursts of these two sources in M31 that reached the Eddington luminosity.Comment: Accepted to Ap

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