基于蛋白质二级结构内容的域结构类预测

运用加入竞争层的BP网络,研究了基于蛋白质二级结构内容的域结构类预测问题.在BP网络中嵌入一竞争,层显著提高了网络预测性能.仅使用了一个小的训练集和简单的网络结构,获得了很高的预测精度自支持精度97.62%,jack-knife测试精度97.62%,及平均外推精度90.74%.在建立更完备的域结构类特征向量和更有代表性的训练集的基础上,所述方法将为蛋白质域结构分类领域提供新的分类基准.     

两种预测模型在地下水动态中的比较与应用

预测陕西洛惠渠灌区地下水动态变化情况,在综合分析了各种地下水动态研究方法的基础上,提出了基于支持向量机和改进的BP神经网络模型的灌区地下水动态预测方法,并在MATLAB中编制了相应的计算机程序,建立了相应的地下水动态预测模型。以灌区多年实例数据为学习样本和测试样本,比较了两种模型的地下水动态预测优劣性。研究表明,支持向量机模型和BP网络模型在样本训练学习过程中都具较高的模拟精度,而在样本学习阶段,支持向量机的预测精度明显优于BP网络,可以很好的描述地下水动态复杂的耦合关系。支持向量机方法切实可行,更加适合大型灌区地下水动态预测,是对传统地下水动态研究方法的补充与完善。     

基于BP神经网络的SARS传播预测

政府的控制措施作为影响SARS传播的因素,利用BP网络,对SARS的传播规律进行预测.以北京市的SARS数据来进行验证,结果显示,该方法准确率非常高.     

利用BP神经网络方法预测西湖叶绿素a的浓度

在西湖共设了 8个采样点 ,通过主成分分析选取了最能代表西湖水质状况的 7号点 (湖心 )作为研究对象。根据 2 0 0 0年 1月至 2 0 0 1年 4月西湖常规监测的水生生态数据 ,并用插值的方法使其生成足够多的样本数 ,利用 BP人工神经网络 ,探索其用于西湖水生生态状况 (叶绿素 a的浓度 )的短期变化趋势预测的可行性 ,从中找出最能反映西湖水生生态状况变化趋势的水质因子用来建立网络。并用 3号点的数据来检验网络的泛化性能 ,发现网络输出值与实际值吻合度较高。结果表明 ,水温和叶绿素a对未来一周的叶绿素 a含量影响最大 ,以这两者作为输入变量建立的网络简单、快捷 ,比其他线性数值模拟预测有较大的优势。说明人工神经网络对叶绿素 a的预测是一种有效工具 ,可为西湖富营养化治理提供科学依据。     

应用BP神经网络对荒漠啮齿动物种群数量的预测研究

群落的格局与动态是群落生态学研究的核心内容,种群数量预测是研究群落动态的主要途径之一。本研究尝试采用2006~2014年阿拉善荒漠区啮齿动物数量数据建立BP神经网络模型,对啮齿动物群落全部组成物种的总个体数量进行模拟与预测。BP神经网络通过模拟学习,建立模型,能够实现对啮齿动物群落数量动态规律进行模拟与预测。本研究以阿拉善荒漠为试验区,以啮齿动物个体数量为研究对象,采用标志重捕法,监测2006~2014年每年4~10月的数量,建立BP神经网络预测模型,利用2006~2013年的数据建立训练网络,以2014年的数据进行验证与测试,比较单层隐含层、双层隐含层和三层隐含层BP神经网络模型。结果表明:单隐含层模型的隐含层节点数为6时,最大误差百分比为16.13%,决定系数0.998 0(P=0.006 0)。双隐含层模型的两层隐含层节点数均为6时,最大误差百分比为8.58%,决定系数0.999 5(P=0.002 3)。三层隐含层模型的三层隐含层节点数分别为1、10和7时,最大误差百分比为5.87%,决定系数0.999 2(P0.000 1)。不同隐含层网络模型的预测效果均取得了满意效果,通过比较最大误差百分比、平均误差百分比、决定系数及拟合优度,三层隐含层优于单隐含层及双隐含层的BP神经网络模型。本文认为三层隐含层的BP神经网络模型更适合于阿拉善荒漠区啮齿动物群落全部组成物种的总个体数量的预测研究。     

水晶梨病虫害防治预测模型

[目的]为提高水晶梨病虫害防治工作效率,进一步提升病虫害的预测效果和精度。[方法]深入研究了灰色模型(GM),利用GM对水晶梨环境因子数据进行建模得到病虫害预测公式,通过差分方程推导出时间响应式和参数估计,建立了优化初始值的灰色模型(OIVGM),将OIVGM与BP神经网络预测模型(BP)进行组合,建立了优化初始值的灰色BP神经网络预测组合模型(OIVGM-BP)。[结果]通过单位根检验法测量模型的稳定性,OIVGM-BP一阶差分处理后,T统计量(-5.487654)小于5%临界值(-2.878073),数据序列表明平稳,OIVGM-BP可以稳定进行预测。通过白噪声检验方法测量OIVGM-BP的适应性,OIVGM-BP的残差P值从第二阶开始,均大于0.05,说明OIVGM-BP的适应性较好,各阶均通过了白噪声检验。LRM、GM、TSM、BP、OIVGM-BP对梨锈病、白粉病、腐烂病、梨黄粉蚜、梨二叉蚜、梨木虱6种病虫害的预测准确率的平均值分别为70.81%、70.09%、69.74%、65.64%、83.01%,OIVGM-BP的预测准确率优于其他4种预测模型。[结论]OIVGM-BP能够对水晶梨病虫害进行有效预测,能够更好地指导农业生产。     

基于位置特异性谱和输入加权神经网络的蛋白质亚细胞定位预测

蛋白质必须处于正确的亚细胞位置才能行使其功能。文章利用PSI-BLAST工具搜索蛋白质序列,提取位点特异性谱中的位点特异性得分矩阵作为蛋白质的一类特征,并计算4等分序列的氨基酸含量以及1～7阶二肽含量作为另外两类特征,由这三类特征一共得到蛋白质序列的12个特征向量。通过设计一个简单加权函数对各类特征向量加权处理,作为神经网络预测器的输入,并使用Levenberg-Marquardt算法代替传统的EBP算法来调整网络权值和阈值,大大提高了训练速度。对具有4类亚细胞位置和12类亚细胞位置的两种蛋白质数据集分别进行＂留一法＂测试和5倍交叉验证测试,总体预测精度分别达到88.4%和83.3%。其中,对4类亚细胞位置数据集的预测效果优于普通BP神经网络、隐马尔可夫模型、模糊K邻近等预测方法,对12类亚细胞位置数据集的预测效果优于支持向量机分类方法。最后还对三类特征采取不同加权比例对预测精度的影响进行了讨论,对选择的八种加权比例的预测结果表明,分别给予三类特征合适的权值系数可以进一步提高预测精度。     

基于贝叶斯网络和相互作用可信度的蛋白质功能预测方法

蛋白质功能注释是后基因组时代研究的核心内容之一,基于蛋白质相互作用网络的蛋白质功能预测方法越来越受到研究者们的关注.提出了一种基于贝叶斯网络和蛋白质相互作用可信度的蛋白质功能预测方法.该方法在功能预测过程中为待注释的蛋白质建立贝叶斯网络预测模型,并充分考虑了蛋白质相互作用的可信度问题.在构建的芽殖酵母数据集上的三重交叉验证测试表明,在功能预测过程中考虑蛋白质可信度能够有效地提高功能预测的性能.与现有一些算法相比,该方法能够给出令人满意的预测效果.     

基于神经网络数据挖掘的红色籽用西瓜亲本选择方法研究

根据多年来红色籽用西瓜自交系育种过程中,积累的多代性状复杂、数量庞大的种质资源及数据,利用数据挖掘中的反向传播（Back propagation,BP）神经网络方法,建立红色籽用西瓜BP神经网络模型。以红籽瓜数量性状作为预测依据,选择出具有丰产性状的红籽瓜亲本材料,为育种工作者进行亲本选择时提供一种新的途径和方法。     

基于小波神经网络的麦蚜发生程度预测模型

【目的】建立基于小波神经网络病虫害预测预报模型,对提前采取防病防虫措施、减少农作物病虫害损失、提高农作物产量与质量具有重要意义。【方法】本研究以山西省运城市芮城县1980-2014年麦蚜发生程度和气象因子数据为基础,采用主成分分析法从40个基础气象因子中整合形成9个新的自变量输入模型,采用试凑法筛选隐含层节点数,用1980-2009年的数据进行网络训练,对2010-2014年麦蚜发生程度进行回测,建立了以Morlet小波函数为传递函数的小波神经网络模型,并与以Sigmoid函数为传递函数的BP神经网络模型进行了比较。【结果】小波和BP神经网络两种模型对训练样本的平均拟合精度均有10年以上超过80%,两者MAPE 值分别为 89.83% 和83.07%,MSE 值分别为0.0578和0.6192。【结论】两个模型都能较好地描述麦蚜发生程度;从预测精度和模型的稳定性来看,小波神经网络好于BP神经网络。     

Selecting neural networks for a committee decision

To improve recognition results, decisions of multiple neural networks can be aggregated into a committee decision. In contrast to the ordinary approach of utilizing all neural networks available to make a committee decision, we propose creating adaptive committees, which are specific for each input data point. A prediction network is used to identify classification neural networks to be fused for making a committee decision about a given input data point. The jth output value of the prediction network expresses the expectation level that the jth classification neural network will make a correct decision about the class label of a given input data point. The proposed technique is tested in three aggregation schemes, namely majority vote, averaging, and aggregation by the median rule and compared with the ordinary neural networks fusion approach. The effectiveness of the approach is demonstrated on two artificial and three real data sets.     

Prediction of beta-turns in proteins using neural networks

The use of neural networks to improve empirical secondary structure prediction is explored with regard to the identification of the position and conformational class of beta-turns, a four-residue chain reversal. Recently an algorithm was developed for beta-turn predictions based on the empirical approach of Chou and Fasman using different parameters for three classes (I, II and non-specific) of beta-turns. In this paper, using the same data, an alternative approach to derive an empirical prediction method is used based on neural networks which is a general learning algorithm extensively used in artificial intelligence. Thus the results of the two approaches can be compared. The most severe test of prediction accuracy is the percentage of turn predictions that are correct and the neural network gives an overall improvement from 20.6% to 26.0%. The proportion of correctly predicted residues is 71%, compared to a chance level of about 58%. Thus neural networks provide a method of obtaining more accurate predictions from empirical data than a simpler method of deriving propensities.     

Financial Time Series Prediction Using Spiking Neural Networks

In this paper a novel application of a particular type of spiking neural network, a Polychronous Spiking Network, was used for financial time series prediction. It is argued that the inherent temporal capabilities of this type of network are suited to non-stationary data such as this. The performance of the spiking neural network was benchmarked against three systems: two “traditional”, rate-encoded, neural networks; a Multi-Layer Perceptron neural network and a Dynamic Ridge Polynomial neural network, and a standard Linear Predictor Coefficients model. For this comparison three non-stationary and noisy time series were used: IBM stock data; US/Euro exchange rate data, and the price of Brent crude oil. The experiments demonstrated favourable prediction results for the Spiking Neural Network in terms of Annualised Return and prediction error for 5-Step ahead predictions. These results were also supported by other relevant metrics such as Maximum Drawdown and Signal-To-Noise ratio. This work demonstrated the applicability of the Polychronous Spiking Network to financial data forecasting and this in turn indicates the potential of using such networks over traditional systems in difficult to manage non-stationary environments.     

Resolution of binary mixtures of microorganisms using electrochemical impedance spectroscopy and artificial neural networks

This work describes the resolution of binary mixtures of microorganisms using electrochemical impedance spectroscopy (EIS) and artificial neural networks (ANNs) for the processing of data. Pseudomonas aeruginosa, Staphylococcus aureus and Saccharomyces cerevisiae were chosen as models for Gram-negative bacteria, Gram-positive bacteria and yeasts, respectively. In this study, best results were obtained when entering the imaginary component of the impedance at each frequency (strongly related to the capacitive elements of the electrical equivalent circuit) into backpropagation neural networks made up by two hidden layers. The optimal configuration of these layers respectively used the radbas and the logsig transfer functions with 4 or 6 neurons in the first hidden layer and 10 neurons in the second one. In all cases, good prediction ability was obtained with correlation coefficients better than 0.989 when comparing the predicted and the expected values for a set of six external test samples not used in the training process.     

Neural network models for earthquake magnitude prediction using multiple seismicity indicators

Neural networks are investigated for predicting the magnitude of the largest seismic event in the following month based on the analysis of eight mathematically computed parameters known as seismicity indicators. The indicators are selected based on the Gutenberg-Richter and characteristic earthquake magnitude distribution and also on the conclusions drawn by recent earthquake prediction studies. Since there is no known established mathematical or even empirical relationship between these indicators and the location and magnitude of a succeeding earthquake in a particular time window, the problem is modeled using three different neural networks: a feed-forward Levenberg-Marquardt backpropagation (LMBP) neural network, a recurrent neural network, and a radial basis function (RBF) neural network. Prediction accuracies of the models are evaluated using four different statistical measures: the probability of detection, the false alarm ratio, the frequency bias, and the true skill score or R score. The models are trained and tested using data for two seismically different regions: Southern California and the San Francisco bay region. Overall the recurrent neural network model yields the best prediction accuracies compared with LMBP and RBF networks. While at the present earthquake prediction cannot be made with a high degree of certainty this research provides a scientific approach for evaluating the short-term seismic hazard potential of a region.     

A deep dense inception network for protein beta-turn prediction

Beta-turn prediction is useful in protein function studies and experimental design. Although recent approaches using machine-learning techniques such as support vector machine (SVM), neural networks, and K nearest neighbor have achieved good results for beta-turn prediction, there is still significant room for improvement. As previous predictors utilized features in a sliding window of 4-20 residues to capture interactions among sequentially neighboring residues, such feature engineering may result in incomplete or biased features and neglect interactions among long-range residues. Deep neural networks provide a new opportunity to address these issues. Here, we proposed a deep dense inception network (DeepDIN) for beta-turn prediction, which takes advantage of the state-of-the-art deep neural network design of dense networks and inception networks. A test on a recent BT6376 benchmark data set shows that DeepDIN outperformed the previous best tool BetaTPred3 significantly in both the overall prediction accuracy and the nine-type beta-turn classification accuracy. A tool, called MUFold-BetaTurn, was developed, which is the first beta-turn prediction tool utilizing deep neural networks. The tool can be downloaded at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldBetaTurn/download.html .     

Prediction of continuous B-cell epitopes in an antigen using recurrent neural network

B-cell epitopes play a vital role in the development of peptide vaccines, in diagnosis of diseases, and also for allergy research. Experimental methods used for characterizing epitopes are time consuming and demand large resources. The availability of epitope prediction method(s) can rapidly aid experimenters in simplifying this problem. The standard feed-forward (FNN) and recurrent neural network (RNN) have been used in this study for predicting B-cell epitopes in an antigenic sequence. The networks have been trained and tested on a clean data set, which consists of 700 non-redundant B-cell epitopes obtained from Bcipep database and equal number of non-epitopes obtained randomly from Swiss-Prot database. The networks have been trained and tested at different input window length and hidden units. Maximum accuracy has been obtained using recurrent neural network (Jordan network) with a single hidden layer of 35 hidden units for window length of 16. The final network yields an overall prediction accuracy of 65.93% when tested by fivefold cross-validation. The corresponding sensitivity, specificity, and positive prediction values are 67.14, 64.71, and 65.61%, respectively. It has been observed that RNN (JE) was more successful than FNN in the prediction of B-cell epitopes. The length of the peptide is also important in the prediction of B-cell epitopes from antigenic sequences. The webserver ABCpred is freely available at www.imtech.res.in/raghava/abcpred/.     

Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks

MOTIVATION: Apoptosis has drawn the attention of researchers because of its importance in treating some diseases through finding a proper way to block or slow down the apoptosis process. Having understood that caspase cleavage is the key to apoptosis, we find novel methods or algorithms are essential for studying the specificity of caspase cleavage activity and this helps the effective drug design. As bio-basis function neural networks have proven to outperform some conventional neural learning algorithms, there is a motivation, in this study, to investigate the application of bio-basis function neural networks for the prediction of caspase cleavage sites. RESULTS: Thirteen protein sequences with experimentally determined caspase cleavage sites were downloaded from NCBI. Bayesian bio-basis function neural networks are investigated and the comparisons with single-layer perceptrons, multilayer perceptrons, the original bio-basis function neural networks and support vector machines are given. The impact of the sliding window size used to generate sub-sequences for modelling on prediction accuracy is studied. The results show that the Bayesian bio-basis function neural network with two Gaussian distributions for model parameters (weights) performed the best and the highest prediction accuracy is 97.15 +/- 1.13%. AVAILABILITY: The package of Bayesian bio-basis function neural network can be obtained by request to the author.     

基于 RBF 神经网络的蛋白质二级结构预测

蛋白质二级结构对于研究其功能具有重要作用。采用主成分分析方法对氨基酸的基本物化属性及其二级结构倾向性进行降维降噪处理,使用径向基神经网络对蛋白质二级结构进行预测。主成分分析使得之前 20 ×12 矩阵变为 20 ×4 矩阵,极大地减少了神经网络输入端的维数。在仿真过程中,当窗口大小为 21,扩展函数为 7 时,预测精确度达到了 71. 81%。实验结果表明 RBF 神经网络可以有效的用于蛋白质二级结构的预测。