具时滞的Hopfield型神经网络模型的全局渐近稳定性

本文研究了具时滞的Hopfield型神经网络模型平衡点的全局渐近稳定性,获得了一系列充分条件。     

神经网络在蛋白质二级结构预测中的应用

介绍了蛋白质二级结构预测的研究意义,讨论了用在蛋白质二级结构预测方面的神经网络设计问题,并且较详尽地评述了近些年来用神经网络方法在蛋白质二级结构预测中的主要工作进展情况,展望了蛋白质结构预测的前景。     

Analysis of protein transmembrane helical regions by a neural network.

Neural networks were used to generalize common themes found in transmembrane-spanning protein helices. Various-sized databases were used containing nonoverlapping sequences, each 25 amino acids long. Training consisted of sorting these sequences into 1 of 2 groups: transmembrane helical peptides or nontransmembrane peptides. Learning was measured using a test set 10% the size of the training set. As training set size increased from 214 sequences to 1,751 sequences, learning increased in a nonlinear manner from 75% to a high of 98%, then declined to a low of 87%. The final training database consisted of roughly equal numbers of transmembrane (928) and nontransmembrane (1,018) sequences. All transmembrane sequences were entered into the database with respect to their lipid membrane orientation: from inside the membrane to outside. Generalized transmembrane helix and nontransmembrane peptides were constructed from the maximally weighted connecting strengths of fully trained networks. Four generalized transmembrane helices were found to contain 9 consensus residues: a K-R-F triplet was found at the inside lipid interface, 2 isoleucine and 2 other phenylalanine residues were present in the helical body, and 2 tryptophan residues were found near the outside lipid interface. As a test of the training method, bacteriorhodopsin was examined to determine the position of its 7 transmembrane helices.     

Stability of delayed memristive neural networks with time-varying impulses

This paper addresses the stability problem on the memristive neural networks with time-varying impulses. Based on the memristor theory and neural network theory, the model of the memristor-based neural network is established. Different from the most publications on memristive networks with fixed-time impulse effects, we consider the case of time-varying impulses. Both the destabilizing and stabilizing impulses exist in the model simultaneously. Through controlling the time intervals of the stabilizing and destabilizing impulses, we ensure the effect of the impulses is stabilizing. Several sufficient conditions for the globally exponentially stability of memristive neural networks with time-varying impulses are proposed. The simulation results demonstrate the effectiveness of the theoretical results.     

Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants using amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesian-regularized genetic neural networks

Predicting protein stability changes upon point mutation is important for understanding protein structure and designing new proteins. Autocorrelation vector formalism was extended to amino acid sequences and 3D conformations for encoding protein structural information with modeling purpose. Protein autocorrelation vectors were weighted by 48 amino acid/residue properties selected from the AAindex database. Ensembles of Bayesian-regularized genetic neural networks (BRGNNs) trained with amino acid sequence autocorrelation (AASA) vectors and amino acid 3D autocorrelation (AA3DA) vectors yielded predictive models of the change of unfolding Gibbs free energy change (ΔΔG) of chymotrypsin Inhibitor 2 protein mutants. The ensemble predictor described about 58 and 72% of the data variances in test sets for AASA and AA3DA models, respectively. Optimum sequence and 3D-based ensembles exhibit high effects on relevant structural (volume, solvent-accessible surface area), physico-chemical (hydrophilicity/hydrophobicity-related) and thermodynamic (hydration parameters) properties.     

具有时滞的Hopfield人工神经网络动力系统模型的全局渐近稳定性

Hopfield人工神经网络动力系统模型平衡点的全局渐近稳定性在网络记忆以及最优化等领域具有广泛的应用。本文中,作者研究了一类具有时滞的Hopfield人工神经网络动力系统,通过构造Liapunov泛函的方法,获得了其平衡点全局渐近稳定和局部渐近稳定的充分判定条件。所给出的判定条件只依赖于系统本身的拳数参数和传递函数以及系统中出现的部分时滞。同时,当系统的自身反馈项为负时,此自身反馈项对于系统的稳定性起到稳定化的作用。此外,数值模拟表明时滞的变化对于系统的稳定性具有重要的影响。可破坏系统的稳定性。进而产生周期振动或更为复杂的非线性现象。     

一类中立型Hopfield神经网络的全局吸引集

讨论了中立型Hopfield神经网络模型,利用矩阵谱的性质和微分不等式分析等技巧,给出了其不变集和全局吸引集的判别准则．特别地,当系统有平衡点时,我们也得到了平衡点全局稳定的判别条件．     

Exponential input-to-state stability of recurrent neural networks with multiple time-varying delays

In this paper, input-to-state stability problems for a class of recurrent neural networks model with multiple time-varying delays are concerned with. By utilizing the Lyapunov–Krasovskii functional method and linear matrix inequalities techniques, some sufficient conditions ensuring the exponential input-to-state stability of delayed network systems are firstly obtained. Two numerical examples and its simulations are given to illustrate the efficiency of the derived results.     

带时间延迟的Cohen-Grossberg神经网络全局鲁棒稳定性的一个结果（英文）

在本文中,我们讨论了一类带时间延迟的Cohen-Grossberg神经网络,并研究了这个系统平衡点的全局鲁棒稳定性。利用Lyapunov函数,我们得出了全局鲁棒收敛性的几个充分条件。这些条件以线性矩阵不等式（LMI）的形式表达。因此,从计算的角度出发他们是高效的。另外,这些条件不依赖于时间延迟和神经网络的激发函数。     

带脉冲的BAM神经网络的全局指数稳定性

利用M矩阵理论,推广的微分不等式和Lyapunov函数,研究了一类带时滞和脉冲的BAM神经网络平衡点的存在唯一性和全局指数稳定性条件.文中推广了以往文献脉冲函数的形式,无需时滞的可导性要求,从而减弱了以往结论的条件,并且可以估计网络的指数收敛速率.     

Protein classification artificial neural system.

A neural network classification method is developed as an alternative approach to the large database search/organization problem. The system, termed Protein Classification Artificial Neural System (ProCANS), has been implemented on a Cray supercomputer for rapid superfamily classification of unknown proteins based on the information content of the neural interconnections. The system employs an n-gram hashing function that is similar to the k-tuple method for sequence encoding. A collection of modular back-propagation networks is used to store the large amount of sequence patterns. The system has been trained and tested with the first 2,148 of the 8,309 entries of the annotated Protein Identification Resource protein sequence database (release 29). The entries included the electron transfer proteins and the six enzyme groups (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases), with a total of 620 superfamilies. After a total training time of seven Cray central processing unit (CPU) hours, the system has reached a predictive accuracy of 90%. The classification is fast (i.e., 0.1 Cray CPU second per sequence), as it only involves a forward-feeding through the networks. The classification time on a full-scale system embedded with all known superfamilies is estimated to be within 1 CPU second. Although the training time will grow linearly with the number of entries, the classification time is expected to remain low even if there is a 10-100-fold increase of sequence entries. The neural database, which consists of a set of weight matrices of the networks, together with the ProCANS software, can be ported to other computers and made available to the genome community. The rapid and accurate superfamily classification would be valuable to the organization of protein sequence databases and to the gene recognition in large sequencing projects.     

Improvement of protein secondary structure prediction using binary word encoding

We propose a binary word encoding to improve the protein secondary structure prediction. A binary word encoding encodes a local amino acid sequence to a binary word, which consists of 0 or 1. We use an encoding function to map an amino acid to 0 or 1. Using the binary word encoding, we can statistically extract the multiresidue information, which depends on more than one residue. We combine the binary word encoding with the GOR method, its modified version, which shows better accuracy, and the neural network method. The binary word encoding improves the accuracy of GOR by 2.8%. We obtain similar improvement when we combine this with the modified GOR method and the neural network method. When we use multiple sequence alignment data, the binary word encoding similarly improves the accuracy. The accuracy of our best combined method is 68.2%. In this paper, we only show improvement of the GOR and neural network method, we cannot say that the encoding improves the other methods. But the improvement by the encoding suggests that the multiresidue interaction affects the formation of secondary structure. In addition, we find that the optimal encoding function obtained by the simulated annealing method relates to non-polarity. This means that nonpolarity is important to the multiresidue interaction. Proteins 27:36–46 © 1997 Wiley-Liss, Inc.     

具有分布时滞离散Cohen-Grossberg神经网络的周期解

讨论了一类具有分布时滞离散Cohen-Grossberg神经网络模型,利用M-矩阵理论与适合的Lypunov函数,得到该类模型周期解的存在性与全局指数稳定性．     

Self-organized neural maps of human protein sequences.

We have recently described a method based on artificial neural networks to cluster protein sequences into families. The network was trained with Kohonen''s unsupervised learning algorithm using, as inputs, the matrix patterns derived from the dipeptide composition of the proteins. We present here a large-scale application of that method to classify the 1,758 human protein sequences stored in the SwissProt database (release 19.0), whose lengths are greater than 50 amino acids. In the final 2-dimensional topologically ordered map of 15 x 15 neurons, proteins belonging to known families were associated with the same neuron or with neighboring ones. Also, as an attempt to reduce the time-consuming learning procedure, we compared 2 learning protocols: one of 500 epochs (100 SUN CPU-hours [CPU-h]), and another one of 30 epochs (6.7 CPU-h). A further reduction of learning-computing time, by a factor of about 3.3, with similar protein clustering results, was achieved using a matrix of 11 x 11 components to represent the sequences. Although network training is time consuming, the classification of a new protein in the final ordered map is very fast (14.6 CPU-seconds). We also show a comparison between the artificial neural network approach and conventional methods of biosequence analysis.