An enhanced protein secondary structure prediction using deep learning framework on hybrid profile based features

Accurate protein secondary structure prediction (PSSP) is essential to identify structural classes, protein folds, and its tertiary structure. To identify the secondary structure, experimental methods exhibit higher precision with the trade-off of high cost and time. In this study, we propose an effective prediction model which consists of hybrid features of 42-dimensions with the combination of convolutional neural network (CNN) and bidirectional recurrent neural network (BRNN). The proposed model is accessed on four benchmark datasets such as CB6133, CB513, CASP10, and CAP11 using Q3, Q8, and segment overlap (Sov) metrics. The proposed model reported Q3 accuracy of 85.4%, 85.4%, 83.7%, 81.5%, and Q8 accuracy 75.8%, 73.5%, 72.2%, and 70% on CB6133, CB513, CASP10, and CAP11 datasets respectively. The results of the proposed model are improved by a minimum factor of 2.5% and 2.1% in Q3 and Q8 accuracy respectively, as compared to the popular existing models on CB513 dataset. Further, the quality of the Q3 results is validated by structural class prediction and compared with PSI-PRED. The experiment showed that the quality of the Q3 results of the proposed model is higher than that of PSI-PRED.     

基于深度学习的八类蛋白质二级结构预测算法

蛋白质二级结构预测是结构生物学中的一个重要问题。针对八类蛋白质二级结构预测,提出了一种基于递归神经网络和前馈神经网络的深度学习预测算法。该算法通过双向递归神经网络建模氨基酸间的局部和长程相互作用,递归神经网络的隐层输出进一步送入到三层的前馈神经网络以便进行八类蛋白质二级结构预测。实验结果表明,提出的算法在CB513数据集上达到了67.9%的Q₈预测精度,显著地优于SSpro8和SC-GSN。     

The prediction of protein secondary structure with a Cascade Correlation Learning Architecture of neural networks

A Cascade Correlation Learning Architecture (CCLA) of neural networks is tested on the task of predicting the secondary structure of proteins. The results are compared with those obtained with Neural Networks (NN) trained with the back-propagation algorithm (BPNN) and generated with genetic algorithms. CCLA proceeds towards the global minimum of the error function more efficiently than BPNN. However, only a slight improvement in the average efficiency value is noticeable (61.82% as compared with 61.61% obtained with BPNN). The values of the three correlation coefficients for the discriminated secondary structures are also rather similar (C_t8,C ,C and C_coil are 0.36, 0.29 and 0.36 with CCLA, and 0.36, 0.31 and 0.35 with BPNN). This indicates that the efficiency of the prediction does not depend upon the training algorithm, and confirms our previous observation that when single sequences are used as input code to the network system, different NN architectures can perform similarly.     

Multiple-valued feedback and recurrent correlation neural networks

In this paper we consider two kinds of neural networks in which the activation function of each neuron is a multiple valued, piecewised-constant function. The main advantages of the proposed models are that they can store patterns with different grey levels, and that they can store binary patterns with much fewer neurons than the existing models. We prove theoretically the convergence property of the proposed models. Different synthesis methods are developed to guarantee the storage of desired patterns as asymptotic equilibria. Simulation results confirm the effectiveness of the new models.     

带有稳定学习的递归神经网络动态偏最小二乘建模

针对目前非线性动态偏最小二乘(PLS)建模方法在拟合较强非线性化工过程时存在的问题, 提出一种基于稳定学习的递归神经网络动态PLS建模方法. 该算法将递归神经网络与Hammerstein模型相结合, 对外部PLS提取的特征向量进行内部建模, 具有逼近较强非线性化工过程的能力, 改善了模型的适用范围. 此外, 采用带有稳定学习的参数更新算法对模型参数进行在线修正, 改善了模型的预测精度和自适应能力. 将此方法应用于氧化铝生产过程铝酸钠溶液组分浓度建模实验, 仿真结果表明, 本方法是可行有效的.     

A multimodal neural network with single-state predictions for protein secondary structure

Prediction of protein secondary structure is considered to be an important step toward elucidating the three-dimensional structure and function of proteins. We have developed a multimodal neural network (MNN) to predict protein secondary structure. The MNN is composed of several subclassifiers for single-state predictions using neural networks and a decision neural network (DNN). Each subclassifier employs a number of subnetworks to predict the single-state of the secondary structure individually and produces the final results by majority decision. The DNN uses a three-layer neural network to produce the final overall prediction from the outputs of the single-state predictions. The MNN gives an overall accuracy of 71.1% with corresponding Matthews correlation coefficients of C_H = 0.62 and C_E = 0.53. The prediction test is based on a database of 126 nonhomologous protein sequences. This work was presented, in part, at the 8th International Symposium on Artificial Life and Robotics, Oita, Japan, January 24#x2013;26, 2003.     

Some multistability properties of bidirectional associative memory recurrent neural networks with unsaturating piecewise linear transfer functions

Multistability is an important dynamical property in neural networks in order to enable certain applications where monostable networks could be computationally restrictive. This paper studies some multistability properties for a class of bidirectional associative memory recurrent neural networks with unsaturating piecewise linear transfer functions. Based on local inhibition, conditions for globally exponential attractivity are established. These conditions allow coexistence of stable and unstable equilibrium points. By constructing some energy-like functions, complete convergence is studied.     

基于神经网络集成的蛋白质二级结构预测模型

为了提高蛋白质二级结构预测精度,本文尝试采用一种基于串联BP网络集成的二级结构预测模型。首先根据二级结构是由其一级序列决定以及神经网络输出之间具有相关性,采用串联BP作为集成的子网络分类器,在训练过程中采用“剪枝法”和“早停”来防止过拟合。其次为增加网络的差异度,利用bagging方法对样本重采样并加入随机噪声。把单独训练的具有一定差异度的5个子网络利用相对多数“投票规则”进行整合。以Rs126中的90个蛋白质共15 377个氨基酸进行10倍率交叉验证,仿真结果表明此网络集成可以较好地对二级结构进行分类。     

Locally recurrent neural networks for wind speed prediction using spatial correlation

This paper deals with the wind speed prediction in wind farms, using spatial information from remote measurement stations. Owing to the temporal complexity of the problem, we employ local recurrent neural networks with internal dynamics, as advanced forecast models. To improve the prediction performance, the training task is accomplished using on-line learning algorithms based on the recursive prediction error (RPE) approach. A global RPE (GRPE) learning scheme is first developed where all adjustable weights are simultaneously updated. In the following, through weight grouping we devise a simplified method, the decoupled RPE (DRPE), with reduced computational demands. The partial derivatives required by the learning algorithms are derived using the adjoint model approach, adapted to the architecture of the networks being used. The efficiency of the proposed approach is tested on a real-world wind farm problem, where multi-step ahead wind speed estimates from 15 min to 3 h are sought. Extensive simulation results demonstrate that our models exhibit superior performance compared to other network types suggested in the literature. Furthermore, it is shown that the suggested learning algorithms outperform three gradient descent algorithms, in training of the recurrent forecast models.     

Sensor data reconstruction using bidirectional recurrent neural network with application to bridge monitoring

Sensors are now commonly employed for monitoring and controlling of engineering systems. Despite significant advances in sensor technologies and their reliability, sensor fault is inevitable. Sensor data reconstruction methods have been studied to recover the missing or faulty sensor data, as well as to enable sensor fault detection and identification. Most existing sensor data reconstruction methods use only the spatial correlations among the sensor data, but they rarely consider the temporal correlations among the data. Use of temporal correlations among the sensor data can potentially improve the accuracy for reconstructing the data. This paper presents a data-driven bidirectional recurrent neural network (BRNN) for sensor data reconstruction, taking into consideration the spatiotemporal correlations among the sensor data. The methodology is demonstrated using the sensor data collected from the Telegraph Road Bridge located along the I-275 Corridor in Michigan. The results show that the BRNN-based method performs better than other current data-driven methods for accurately reconstructing the sensor data.     

Exponential Lagrange stability for impulses in discrete-time delayed recurrent neural networks

This paper focuses on the problem of exponential stability in the sense of Lagrange for impulses in discrete-time delayed recurrent neural networks. By establishing a delayed impulsive discrete inequality and a novel difference inequality, combining with inequality techniques, some novel sufficient conditions are obtained to ensure exponential Lagrange stability for impulses in discrete-time delayed recurrent neural networks. Meanwhile, exponentially convergent scope of neural network is given. Finally, several numerical simulations are given to demonstrate the effectiveness of our results.     

改进型动态隧道神经网络在蛋白质预测的应用

神经网络具有容易陷入局部极小的缺点,动态隧道神经网络通过“钻隧道”方式,让目标函数跳出局部最小,找到更小的可行域,从而避免神经网络陷入局部极小。传统的动态隧道技术隧道方向单一并且随意,因此具有不稳定性。为了有效提高动态隧道的搜索效率,提出了一种改进型动态隧道神经网络算法。该算法增加搜索的隧道数,引入夹角弹性系数控制隧道方向,考察隧道之间的相互影响。在对alpha、beta和coil型蛋白质的二级结构预测的实验中,改进型动态隧道神经网络算法预测的效果优于神经网络算法和传统的动态隧道神经网络算法。     

Indirect adaptive control of nonlinear dynamic systems using self recurrent wavelet neural networks via adaptive learning rates

This paper proposes an indirect adaptive control method using self recurrent wavelet neural networks (SRWNNs) for dynamic systems. The architecture of the SRWNN is a modified model of the wavelet neural network (WNN). However, unlike the WNN, since a mother wavelet layer of the SRWNN is composed of self-feedback neurons, the SRWNN can store the past information of wavelets. In the proposed control architecture, two SRWNNs are used as both an identifier and a controller. The SRWNN identifier approximates dynamic systems and provides the SRWNN controller with information about the system sensitivity. The gradient-descent method using adaptive learning rates (ALRs) is applied to train all weights of the SRWNN. The ALRs are derived from discrete Lyapunov stability theorem, which are applied to guarantee the convergence of the proposed control system. Finally, we perform some simulations to verify the effectiveness of the proposed control scheme.     

Adjoint EKF learning in recurrent neural networks for nonlinear active noise control

In this paper, active noise control using recurrent neural networks is addressed. A new learning algorithm for recurrent neural networks based on Adjoint Extended Kalman Filter is developed for active noise control. The overall control structure for active noise control is constructed using two recurrent neural networks: the first neural network is used to model secondary path of active noise control while the second one is employed to generate control signal. Real-time experiment of the proposed algorithm using digital signal processor is carried-out to show the effectiveness of the method.     

Fuzzy logic in the gravitational search algorithm enhanced using fuzzy logic with dynamic alpha parameter value adaptation for the optimization of modular neural networks in echocardiogram recognition

In this paper the main goal is to find the optimal architecture of modular neural networks, which means finding out the optimal number of modules, layers and nodes of the neural network. The fuzzy gravitational search algorithm with dynamic parameter adaptation is used for optimizing the modular neural network in a particular pattern recognition application. The proposed method is applied to medical images in echocardiogram recognition. One of the most common methods for detection and analysis of diseases in the human body, by physicians and specialists, is the use of medical images. Simulation results of the proposed approach in echocardiogram recognition show the advantages of using the fuzzy gravitational search in the optimization of modular neural networks. In this case the proposed approach provides a very good 99.49% echocardiogram recognition rate.