15411856
Prediction of the Number of Helices for the Twilight Zone Proteins
Protein structure prediction is one of the core research areas in bioinformatics. This paper addresses the protein secondary structure prediction problem for the twilight zone proteins, which are characterized by low, about 25% homology to the sets of known sequences. The commonly used sequence alignment based algorithms fail to provide accurate prediction for sequences of such low homology, and thus alternative solutions should be sought. We propose a novel method that aims at the prediction of the number of helical structures based on the twilight zone protein sequences. The method is based on a custom designed and compact feature based sequences representation and applies a decision tree prediction algorithm. The performed experimental study shows superiority of the proposed method over three other prediction algorithms and the results provided by YASPIN algorithm, which is a state-of-the-art alignment based secondary structure prediction method designed using low homology sequences
193129
Sequence based residue depth prediction using evolutionary information and predicted secondary structure
BackgroundResidue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent accessibility, the depth allows studying deep-level structures and functional sites, and formation of the protein folding nucleus. Accurate prediction of residue depth would provide valuable information for fold recognition, prediction of functional sites, and protein design.ResultsA new method, RDPred, for the real-value depth prediction from protein sequence is proposed. RDPred combines information extracted from the sequence, PSI-BLAST scoring matrices, and secondary structure predicted with PSIPRED. Three-fold/ten-fold cross validation based tests performed on three independent, low-identity datasets show that the distance based depth (computed using MSMS) predicted by RDPred is characterized by 0.67/0.67, 0.66/0.67, and 0.64/0.65 correlation with the actual depth, by the mean absolute errors equal 0.56/0.56, 0.61/0.60, and 0.58/0.57, and by the mean relative errors equal 17.0%/16.9%, 18.2%/18.1%, and 17.7%/17.6%, respectively. The mean absolute and the mean relative errors are shown to be statistically significantly better when compared with a method recently proposed by Yuan and Wang [Proteins 2008; 70:509–516]. The results show that three-fold cross validation underestimates the variability of the prediction quality when compared with the results based on the ten-fold cross validation. We also show that the hydrophilic and flexible residues are predicted more accurately than hydrophobic and rigid residues. Similarly, the charged residues that include Lys, Glu, Asp, and Arg are the most accurately predicted. Our analysis reveals that evolutionary information encoded using PSSM is characterized by stronger correlation with the depth for hydrophilic amino acids (AAs) and aliphatic AAs when compared with hydrophobic AAs and aromatic AAs. Finally, we show that the secondary structure of coils and strands is useful in depth prediction, in contrast to helices that have relatively uniform distribution over the protein depth. Application of the predicted residue depth to prediction of buried/exposed residues shows consistent improvements in detection rates of both buried and exposed residues when compared with the competing method. Finally, we contrasted the prediction performance among distance based (MSMS and DPX) and volume based (SADIC) depth definitions. We found that the distance based indices are harder to predict due to the more complex nature of the corresponding depth profiles.ConclusionThe proposed method, RDPred, provides statistically significantly better predictions of residue depth when compared with the competing method. The predicted depth can be used to provide improved prediction of both buried and exposed residues. The prediction of exposed residues has implications in characterization/prediction of interactions with ligands and other proteins, while the prediction of buried residues could be used in the context of folding predictions and simulations.
7236194
An Empirical Study on Improving the Manufacturing Informatization Index System of China
The manufacturing informatization index system (MIIS) is an indispensable tool to measure the informatization level of Chinese manufacturing industry and evaluate the implementation effect of the manufacturing informatization engineering (MIE) conducted by the government of China. Thus far, the constructs of MIIS has not been validated. This study fills this void by employing structural equation modeling (SEM) to test the MIIS model. The samples in this study come from the standard database of Chinese manufacturing informatization established by the data survey of MIE during the "Tenth Five-Year Plan" period, including 12896 enterprises samples from 11 manufacturing industries and 3472 support samples from 29 provinces of China. Based on the results of SEM analysis, some indexes of MIIS are adjusted and an improved MIIS is got at last. This empirical study proves that combining SEM technology and standard data resources would be an ideal method to improve MIIS.
12408273
Multilevel algorithm for a Poisson noise removal model with total-variation regularization
Many commonly used models for the fundamental image processing task of noise removal can deal with Gaussian white noise. However, such Gaussian models are not effective in restoring images with Poisson noise, which is ubiquitous in certain applications. Recently, Le–Chartrand–Asaki derived a new data-fitting term in the variational model for Poisson noise. This paper proposes a multilevel algorithm for efficiently solving this variational model. As expected of a multilevel method, it delivers the same numerical solution many orders of magnitude faster than the standard single-level method of coordinate descent time-marching. Supporting numerical experiments on 2D gray scale images are presented.
1757195
Combining linear discriminant functions with neural networks for supervised learning
A novel supervised learning method is proposed by combining linear discriminant functions with neural networks. The proposed method results in a tree-structured hybrid architecture. Due to constructive learning, the binary tree hierarchical architecture is automatically generated by a controlled growing process for a specific supervised learning task. Unlike the classic decision tree, the linear discriminant functions are merely employed in the intermediate level of the tree for heuristically partitioning a large and complicated task into several smaller and simpler subtasks in the proposed method. These subtasks are dealt with by component neural networks at the leaves of the tree accordingly. For constructive learning, growing and credit-assignment algorithms are developed to serve for the hybrid architecture. The proposed architecture provides an efficient way to apply existing neural networks (e.g. multi-layered perceptron) for solving a large scale problem. We have already applied the proposed method to a universal approximation problem and several benchmark classification problems in order to evaluate its performance. Simulation results have shown that the proposed method yields better results and faster training in comparison with the multilayered perceptron.
7778586
Simulink Modeling and Comparison of Zhang Neural Networks and Gradient Neural Networks for Time-Varying Lyapunov Equation Solving
In view of the great potential in parallel processing and ready implementation via hardware, neural networks are now often employed to solve online matrix algebraic problems. Recently, a special kind of recurrent neural network has been proposed by Zhang et al, which could be generalized to solving online Lyapunov equation with time-varying coefficient matrices. In comparison with gradient-based neural networks (GNN), the resultant Zhang neural networks (ZNN) perform much better on solving these time-varying problems. This paper investigates the MATLAB Simulink modeling, simulative verification and comparison of ZNN and GNN models for time-varying Lyapunov equation solving. Computer-simulation results verify that superior convergence and efficacy could be achieved by such ZNN models when solving the time-varying Lyapunov matrix equation, as compared to the GNN models.
6083596
Improved learning algorithms for mixture of experts in multiclass classification
Mixture of experts (ME) is a modular neural network architecture for supervised learning. A double-loop Expectation-Maximization (EM) algorithm has been introduced to the ME architecture for adjusting the parameters and the iteratively reweighted least squares (IRLS) algorithm is used to perform maximization in the inner loop [Jordan, M.I., Jacobs, R.A. (1994). Hierarchical mixture of experts and the EM algorithm, Neural Computation, 6(2), 181-214]. However, it is reported in literature that the IRLS algorithm is of instability and the ME architecture trained by the EM algorithm, where IRLS algorithm is used in the inner loop, often produces the poor performance in multiclass classification. In this paper, the reason of this instability is explored. We find out that due to an implicitly imposed incorrect assumption on parameter independence in multiclass classification, an incomplete Hessian matrix is used in that IRLS algorithm. Based on this finding, we apply the Newton-Raphson method to the inner loop of the EM algorithm in the case of multiclass classification, where the exact Hessian matrix is adopted. To tackle the expensive computation of the Hessian matrix and its inverse, we propose an approximation to the Newton-Raphson algorithm based on a so-called generalized Bernoulli density. The Newton-Raphson algorithm and its approximation have been applied to synthetic data, benchmark, and real-world multiclass classification tasks. For comparison, the IRLS algorithm and a quasi-Newton algorithm called BFGS have also been applied to the same tasks. Simulation results have shown that the use of the proposed learning algorithms avoids the instability problem and makes the ME architecture produce good performance in multiclass classification. In particular, our approximation algorithm leads to fast learning. In addition, the limitation of our approximation algorithm is also empirically investigated in this paper.