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

Application of EOS-ELM with binary Jaya-based feature selection to real-time transient stability assessment using PMU data

Recent studies show that pattern-recognition-based transient stability assessment (PRTSA) is a promising approach for predicting the transient stability status of power systems. However, many of the current well-known PRTSA methods suffer from excessive training time and complex tuning of parameters, resulting in inefficiency for real-time implementation and lacking the online model updating ability. In this paper, a novel PRTSA approach based on an ensemble of OS-extreme learning machine (EOSELM) with binary Jaya (BinJaya)-based feature selection is proposed with the use of phasor measurement units (PMUs) data. After briefly describing the principles of OS-ELM, an EOS-ELM-based PRTSA model is built to predict the post-fault transient stability status of power systems in real time by integrating OS-ELM and an online boosting algorithm, respectively, as a weak classifier and an ensemble learning algorithm. Furthermore, a BinJaya-based feature selection approach is put forward for selecting an optimal feature subset from the entire feature space constituted by a group of system-level classification features extracted from PMU data. The application results on the IEEE 39-bus system and a real provincial system show that the proposal has superior computation speed and prediction accuracy than other state-of-the-art sequential learning algorithms. In addition, without sacrificing the classification performance, the dimension of the input space has been reduced to about one-third of its initial value.Comment: Accepted by IEEE Acces