基于神经网络的蛋白质序列分类算法研究

针对蛋白质序列难以分类的问题,提出了基于神经网络的蛋白质序列分类算法,通过采用基于频繁模式扫描的蛋白质序列特征抽取技术,采集得到了蛋白质序列的特征参数。在此基础上,构建了三层的神经网络,用于蛋白质序列的分类,经过大量数据对神经网络的训练,经测试表明,文章所设计的蛋白质序列分类算法,其精度达到了98%,尤其是对于一些新出现的蛋白质序列分类效果更好。     

数值优化改进的BP网络的模式分类对比

研究了共轭梯度算法、拟牛顿算法、LM算法三类常用的数值优化改进算法,基于这三类数值优化算法分别对BP神经网络进行改进,并构建了相应的BP神经网络分类模型,将构建的分类模型应用于二维向量模式的分类,并进行了泛化能力测试,将不同BP网络分类模型的分类结果进行对比. 仿真结果表明,对于中小规模的网络而言,LM数值优化算法改进的BP网络的分类结果最为精确,收敛速度最快,分类性能最优;共轭梯度数值优化算法改进的BP网络的分类结果误差最大,收敛速度最慢,分类性能最差;拟牛顿数值优化算法改进的BP网络的分类结果误差值、收敛速度及分类性能介于上述两种算法之间.     

基于LM神经网络的一种生物医学数据分类方法

生物医学数据智能化处理是当前医学信息工程中一个研究热点,针对梯度下降BP(反向传播)神经网络收敛速度慢,易于陷入局部极小等缺点,采用LM神经网络对梯度下降算法进行改进。分析了LM算法的原理并通过对一组乳腺癌数据进行分类,表明该算法具有很快的收敛速度及较高的识别准确率,为医学数据分类提供了一种新方法。采用的数据来源于UCI机器学习数据集。     

一种基于哈夫曼判定的蛋白质分类方法

已有的仿射传播聚类算法不能很好地反映复杂蛋白质序列本身的聚类结构。为此,提出一种基于哈夫曼判定的蛋白质分类方法。在计算广义置换式匹配相似度的基础上,使用已有的自适应仿射传播算法聚类蛋白质序列。采用哈夫曼编码方法,通过限制平均码长使聚类结果能反映蛋白质序列家族的聚类结构。在蛋白质同源聚类数据库和蛋白质结构分类数据库的6个数据集上进行实验,结果表明,该方法与adAP、谱聚类、SMS和TribeMCL方法相比,不仅能获得更接近于数据集家族的聚类数目及更紧凑的聚类结构,而且F—measure指标平均估值分别高出19．67％、8．7％、9．5％和43．51％。     

基于Fuzzy ARTMAP神经网络的高分辨率图象土地覆盖分类及其评价

主要讨论了基于Fuzzy ARTMAP神经网络的高分辨率遥感图象土地覆盖分类方法及其实践．首先介绍了Fuzzy ARTMAP神经网络的原理，然后用SPOT XS图象试验数据进行土地覆盖分类．分类结果与传统的最大似然监督分类(MLC)、反馈式(Back Propagation，BP)神经网络的分类结果进行了比较．通过抽取500个样点对3种分类结果进行精度评价表明，Fuzzy ARTMAP神经网络相对其他两种方法，分类精度均有不同程度的改善，具有更好的分类结果，总分类精度比MLC和BP算法分别提高17．41％、7．32％．最后，对不同分类方法对于土地覆盖分类结果的影响进行了评价和分析．试验表明，Fuzzy ARTMAP神经网络用于高分辨图象土地覆盖分类研究可以获得相对较好的分类结果．     

基于BP神经网络的预测建模系统的研究与实现

神经网络具有良好的记忆、归纳和学习能力，对难以用数学方法建立精确模型的信息、工艺等能够进行有效地预测建模。该文通过对BP神经网络的分析和研究，针对传统BP算法的不足，采用Levenberg—Marquardt(LM)优化算法的建立一个基于BP神经网络预测建模系统。在介绍了系统的主要功能之后，给出了用MATLAB软件实现该系统主要模块的具体程序。最后采用该系统对一个制造过程中刀具磨损量的进行了预测建模，实验仿真结果表明：系统具有良好的预测效果，刀具实际磨损量与预测磨损量的误差基本上在10％以下。     

DNA序列分类的神经网络方法

该文将人工神经网络方法用于DNA分类，首先应用概率统计的方法对20个已知类别的人工DNA序列进行特征提取，形成DNA序列的特征向量，并将之作为样本输入BP神经网络进行学习。采用MATLAB软件包中的神经网络工具箱中的反向传播算法来训练神经网络。构造了两个三层BP神经网络，将提取的DNA特征向量集作为样本分别输入这两个网络进行学习，通过训练后，将20个未分类的人工序列样本和182个自然序列样本提取特征向量并输入两个网络进行分类，结果表明，分类方法能够以很高的正确率和精度对DNA进行分类，将人工神经网络用于DNA序列分类是完全可行的。     

基于差分进化的BP神经网络预测混沌时间序列

针对BP神经网络预测模型收敛速度慢和容易陷入局部极小值的缺点,将差分进化算法和神经网络结合起来,提出了一种基于差分进化算法的BP神经网络预测混沌时间序列的方法,利用差分进化算法的全局寻优能力对BP神经网络的权值和阈值进行优化,然后训练BP神经网络预测模型求得最优解,将该预测方法用到3个典型的混沌时间序列进行算法的有效性验证,并与BP算法的预测精度进行了比较,仿真结果表明该方法对混沌时间序列预测具有更好的非线性拟合能力和更高的预测准确性。     

基于BP神经网络的时间序列预测模型研究

本文阐述了GP算法的基本原理，提出了一种基于BP神经网络的时间序列预测模型，对BP模型应用于时间序列预测进行了较详细的研究和探讨，理论分析和实际应用表明，该方法可利用计算机编程实现，BP神经网络可以成功地用于时间序列的预测。     

基于模式相关的改进BP神经网络算法

针对传统的BP神经网络模式分类算法在各个网络输出值较为接近或者模式类之间的网络输出值接近的情况下容易发生误判的问题,提出一种基于模式相关的BP神经网络分类算法,并结合具体电路,运用该方法进行建模、仿真．实验结果表明,采用模式相关的BP神经网络分类算法能够充分利用网络输出层各个节点的所有输出,增强了网络的输出特性,便于正确、方便的进行模式分类,且分类效果良好,具有一定的通用性．     

Counter-Propagation Neural Networks for Molecular Sequence Classification: Supervised LVQ and Dynamic Node Allocation

A modified counter-propagation (CP) algorithm with supervised learning vector quantizer (LVQ) and dynamic node allocation has been developed for rapid classification of molecular sequences. The molecular sequences were encoded into neural input vectors using an n–gram hashing method for word extraction and a singular value decomposition (SVD) method for vector compression. The neural networks used were three-layered, forward-only CP networks that performed nearest neighbor classification. Several factors affecting the CP performance were evaluated, including weight initialization, Kohonen layer dimensioning, winner selection and weight update mechanisms. The performance of the modified CP network was compared with the back-propagation (BP) neural network and the k–nearest neighbor method. The major advantages of the CP network are its training and classification speed and its capability to extract statistical properties of the input data. The combined BP and CP networks can classify nucleic acid or protein sequences with a close to 100% accuracy at a rate of about one order of magnitude faster than other currently available methods.     

Efficient training algorithms for a class of shunting inhibitory convolutional neural networks

This article presents some efficient training algorithms, based on first-order, second-order, and conjugate gradient optimization methods, for a class of convolutional neural networks (CoNNs), known as shunting inhibitory convolution neural networks. Furthermore, a new hybrid method is proposed, which is derived from the principles of Quickprop, Rprop, SuperSAB, and least squares (LS). Experimental results show that the new hybrid method can perform as well as the Levenberg-Marquardt (LM) algorithm, but at a much lower computational cost and less memory storage. For comparison sake, the visual pattern recognition task of face/nonface discrimination is chosen as a classification problem to evaluate the performance of the training algorithms. Sixteen training algorithms are implemented for the three different variants of the proposed CoNN architecture: binary-, Toeplitz- and fully connected architectures. All implemented algorithms can train the three network architectures successfully, but their convergence speed vary markedly. In particular, the combination of LS with the new hybrid method and LS with the LM method achieve the best convergence rates in terms of number of training epochs. In addition, the classification accuracies of all three architectures are assessed using ten-fold cross validation. The results show that the binary- and Toeplitz-connected architectures outperform slightly the fully connected architecture: the lowest error rates across all training algorithms are 1.95% for Toeplitz-connected, 2.10% for the binary-connected, and 2.20% for the fully connected network. In general, the modified Broyden-Fletcher-Goldfarb-Shanno (BFGS) methods, the three variants of LM algorithm, and the new hybrid/LS method perform consistently well, achieving error rates of less than 3% averaged across all three architectures.     

Neural Networks for Full-Scale Protein Sequence Classification: Sequence Encoding with Singular Value Decomposition

A neural network classification method has been developed as an alternative approach to the search/organization problem of protein sequence databases. The neural networks used are three-layered, feed-forward, back-propagation networks. The protein sequences are encoded into neural input vectors by a hashing method that counts occurrences ofn-gram words. A new SVD (singular value decomposition) method, which compresses the long and sparsen-gram input vectors and captures semantics ofn-gram words, has improved the generalization capability of the network. A full-scale protein classification system has been implemented on a Cray supercomputer to classify unknown sequences into 3311 PIR (Protein Identification Resource) superfamilies/families at a speed of less than 0.05 CPU second per sequence. The sensitivity is close to 90% overall, and approaches 100% for large superfamilies. The system could be used to reduce the database search time and is being used to help organize the PIR protein sequence database.     

Efficient calculation of the Gauss-Newton approximation of the Hessian matrix in neural networks

The Levenberg-Marquardt (LM) learning algorithm is a popular algorithm for training neural networks; however, for large neural networks, it becomes prohibitively expensive in terms of running time and memory requirements. The most time-critical step of the algorithm is the calculation of the Gauss-Newton matrix, which is formed by multiplying two large Jacobian matrices together. We propose a method that uses backpropagation to reduce the time of this matrix-matrix multiplication. This reduces the overall asymptotic running time of the LM algorithm by a factor of the order of the number of output nodes in the neural network.     

基于孤立节点分离策略的改进鲁汶算法

鲁汶算法（LM）是基于模块度优化的复杂网络社区发现算法,有关模块度的现有研究中没有计算节点离开原属社区后模块度增益的方法。针对这一不足,基于模块度的定义和节点合并后模块度增益的计算方法,推导出了节点离开原属社区后模块度增益的计算方法,完善了该领域的理论研究。针对鲁汶算法对存储空间需求高的缺点,提出了基于孤立节点分离策略的改进鲁汶算法,该算法在每次迭代中将输入网络的孤立节点提前分离出去,只令其中的连通节点实际参与迭代过程,并在存储社区发现结果时将孤立节点和非孤立节点分开存储。基于真实网络的相关实验结果表明,采用孤立节点分离策略的改进方法,使算法对存储空间的需求减少了40%以上,并进一步缩短了算法的运行时间。因此,改进后的算法在处理真实网络时更具优势。     

Potential function based neural networks and its application to the classification of complex chemical patterns

A new neural network (NN) using potential function (PF), named PFNN, is proposed for classifying the complex chemical patterns. Correspondingly, a new algorithm called the “+δ” algorithm is proposed to train the networks. With a benchmark classification problem the conventional multilayer feedforward (MLF) neural networks is tested and compared with PFNN. Furthermore, the experiments on classifying complex chemical patterns are performed. The results of these experiments demonstrate that PFNN is good in dealing with classification due to its preciseness and quickness.     

基于空时极向LBP的极光序列事件检测

提出了一种用于检测全天空图像(ASI)序列中的弧状极光事件检测方法.针对弧状极光序列的运动趋势,在现有VLBP的基础上提出了基于空时极向LBP(ST-PVLBP)的极光序列事件检测算法,并用ST-PVLBP对极光序列进行表征.该算法结合序列帧间连续性信息和单帧空间位置信息,在保持高分类精度的同时降低了特征维数.在中国北极黄河站的ASI图像数据上的分类实验结果显示,所提出的方法可以有效检测全天空极光图像序列中的地磁南北向运动的弧状极光序列事件.     

Computational Technique for an Efficient Classification of Protein Sequences With Distance‐Based Sequence Encoding Algorithm

Machine learning is being implemented in bioinformatics and computational biology to solve challenging problems emerged in the analysis and modeling of biological data such as DNA, RNA, and protein. The major problems in classifying protein sequences into existing families/superfamilies are the following: the selection of a suitable sequence encoding method, the extraction of an optimized subset of features that possesses significant discriminatory information, and the adaptation of an appropriate learning algorithm that classifies protein sequences with higher classification accuracy. The accurate classification of protein sequence would be helpful in determining the structure and function of novel protein sequences. In this article, we have proposed a distance‐based sequence encoding algorithm that captures the sequence's statistical characteristics along with amino acids sequence order information. A statistical metric‐based feature selection algorithm is then adopted to identify the reduced set of features to represent the original feature space. The performance of the proposed technique is validated using some of the best performing classifiers implemented previously for protein sequence classification. An average classification accuracy of 92% was achieved on the yeast protein sequence data set downloaded from the benchmark UniProtKB database.     

股票价格短期预测的LM遗传神经网络算法

针对传统神经网络在股票价格预测中易陷入局部最优和预测精度偏低的问题,提出了一种改进的神经网络算法进行求解.改进的算法基于LM算法建立了改进的三层BP神经网络对股票价格建立预测模型,避免算法陷入局部最优,并运用遗传算法优化神经网络的权值和阈值,提高神经网络对股票价格的预测精度.采用Matlab对上述算法模型进行仿真测试,通过预测4支股票价格的实验证明改进后的神经网络预测算法对股票价格的短期预测有较好的精度和稳定性.