A genetic programming method for protein motif discovery and protein classification

Proteins can be grouped into families according to some features such as hydrophobicity, composition or structure, aiming to establish common biological functions. This paper presents MAHATMA—memetic algorithm-based highly adapted tool for motif ascertainment—a system that was conceived to discover features (particular sequences of amino acids, or motifs) that occur very often in proteins of a given family but rarely occur in proteins of other families. These features can be used for the classification of unknown proteins, that is, to predict their function by analyzing their primary structure. Experiments were done with a set of enzymes extracted from the Protein Data Bank. The heuristic method used was based on genetic programming using operators specially tailored for the target problem. The final performance was measured using sensitivity, specificity and hit rate. The best results obtained for the enzyme dataset suggest that the proposed evolutionary computation method is effective in finding predictive features (motifs) for protein classification.     

Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization

The MEME algorithm extends the expectation maximization (EM) algorithm for identifying motifs in unaligned biopolymer sequences. The aim of MEME is to discover new motifs in a set of biopolymer sequences where little or nothing is known in advance about any motifs that may be present. MEME innovations expand the range of problems which can be solved using EM and increase the chance of finding good solutions. First, subsequences which actually occur in the biopolymer sequences are used as starting points for the EM algorithm to increase the probability of finding globally optimal motifs. Second, the assumption that each sequence contains exactly one occurrence of the shared motif is removed. This allows multiple appearances of a motif to occur in any sequence and permits the algorithm to ignore sequences with no appearance of the shared motif, increasing its resistance to noisy data. Third, a method for probabilistically erasing shared motifs after they are found is incorporated so that several distinct motifs can be found in the same set of sequences, both when different motifs appear in different sequences and when a single sequence may contain multiple motifs. Experiments show that MEME can discover both the CRP and LexA binding sites from a set of sequences which contain one or both sites, and that MEME can discover both the –10 and –35 promoter regions in a set of E. coli sequences.     

基于迭代神经网络的图像结构表示和分类

由于缺少结构化的表示,基于内容的图像分类存在一定的问题,据此提出了一种基于迭 代神经网络的自然图像表示和分类的方法。利用Berkeley分割算法将图像分割成不同的区域,采用 基于人工的多叉树或基于邻接区域的二叉树的方法进行区域合并,同时提取区域统计特征,得到图像 的树型结构表示。根据BPTS算法对网络进行训练,训练好的网络就具备了图像分类的功能。实验 结果表明,基于迭代神经网络的结构表示和分类方法具有很强的结构学习能力,同时人工生成的多叉 树涵盖更多的语义信息且能得到较好的分类结果。     

Design of neural network-based estimator for tool wear modeling in hard turning

Hard turning with cubic boron nitride (CBN) tools has been proven to be more effective and efficient than traditional grinding operations in machining hardened steels. However, rapid tool wear is still one of the major hurdles affecting the wide implementation of hard turning in industry. Better prediction of the CBN tool wear progression helps to optimize cutting conditions and/or tool geometry to reduce tool wear, which further helps to make hard turning a viable technology. The objective of this study is to design a novel but simple neural network-based generalized optimal estimator for CBN tool wear prediction in hard turning. The proposed estimator is based on a fully forward connected neural network with cutting conditions and machining time as the inputs and tool flank wear as the output. Extended Kalman filter algorithm is utilized as the network training algorithm to speed up the learning convergence. Network neuron connection is optimized using a destructive optimization algorithm. Besides performance comparisons with the CBN tool wear measurements in hard turning, the proposed tool wear estimator is also evaluated against a multilayer perceptron neural network modeling approach and/or an analytical modeling approach, and it has been proven to be faster, more accurate, and more robust. Although this neural network-based estimator is designed for CBN tool wear modeling in this study, it is expected to be applicable to other tool wear modeling applications.     

Efficient automatic exact motif discovery algorithms for biological sequences

ObjectiveThis paper presents an algorithm for the solution of the motif discovery problem (MDP).Methods and materialsMotif discovery problem can be considered in two cases: motifs with insertions/deletions, and motifs without insertions/deletions. The first group motifs can be found by stochastic and approximated methods. The second group can be found by using stochastic and approximated methods, but also deterministic method. We proved that the second group motifs can be found with a deterministic algorithm, and so, it can be said that the second motifs finding is a P-type problem as proved in this paper.Results and conclusionsAn algorithm was proposed in this paper for motif discovery problem. The proposed algorithm finds all motifs which are occurred in the sequence at least two times, and it also finds motifs of various sizes. Due to this case, this algorithm is regarded as Automatic Exact Motif Discovery Algorithm. All motifs of different sizes can be found with this algorithm, and this case was proven in this paper. It shown that automatic exact motif discovery is a P-type problem in this paper. The application of the proposed algorithm has been shown that this algorithm is superior to MEME, MEME3, Motif Sampler, WEEDER, CONSENSUS, AlignACE.     

基于不同算法的Motif预测比较分析与优化

研究转录因子结合位点（TFBs）的主要预测模型及其预测的算法,通过基于调控元件预测的3种代表性的算法MEME、Gibbs采样和Weeder预测拟南芥基因组。比较结果表明,Gibbs采样算法和Weeder算法预测长、短motif效率较高。重点分析MEME算法,提出结合不同算法查找motif的优化方法,并以实验验证该方法能有效提高预测效率。     

Classification of bioinformatics dataset using finite impulse response extreme learning machine for cancer diagnosis

In this paper, the classification of the two binary bioinformatics datasets, leukemia and colon tumor, is further studied by using the recently developed neural network-based finite impulse response extreme learning machine (FIR-ELM). It is seen that a time series analysis of the microarray samples is first performed to determine the filtering properties of the hidden layer of the neural classifier with FIR-ELM for feature identification. The linear separability of the data patterns in the microarray datasets is then studied. For improving the robustness of the neural classifier against noise and errors, a frequency domain gene feature selection algorithm is also proposed. It is shown in the simulation results that the FIR-ELM algorithm has an excellent performance for the classification of bioinformatics data in comparison with many existing classification algorithms.     

Accurate and robust image registration based on radial basis neural networks

Neural network-based image registration using global image features is relatively a new research subject, and the schemes devised so far use a feedforward neural network to find the geometrical transformation parameters. In this work, we propose to use a radial basis function neural network instead of feedforward neural network to overcome lengthy pre-registration training stage. This modification has been tested on the neural network-based registration approach using discrete cosine transformation features in the presence of noise. The experimental registration work is conducted in two different levels: estimation of transformation parameters from a local range for fine registration and from a medium range for coarse registration. For both levels, the performances of the feedforward neural network-based and radial basis function neural network-based schemes have been obtained and compared to each other. The proposed scheme does not only speed up the training stage enormously but also increases the accuracy and gives robust results in the presence of additive Gaussian noise owing to the better generalization ability of the radial basis function neural networks.     

Static hand gesture recognition using neural networks

This paper presents a novel technique for hand gesture recognition through human–computer interaction based on shape analysis. The main objective of this effort is to explore the utility of a neural network-based approach to the recognition of the hand gestures. A unique multi-layer perception of neural network is built for classification by using back-propagation learning algorithm. The goal of static hand gesture recognition is to classify the given hand gesture data represented by some features into some predefined finite number of gesture classes. The proposed system presents a recognition algorithm to recognize a set of six specific static hand gestures, namely: Open, Close, Cut, Paste, Maximize, and Minimize. The hand gesture image is passed through three stages, preprocessing, feature extraction, and classification. In preprocessing stage some operations are applied to extract the hand gesture from its background and prepare the hand gesture image for the feature extraction stage. In the first method, the hand contour is used as a feature which treats scaling and translation of problems (in some cases). The complex moment algorithm is, however, used to describe the hand gesture and treat the rotation problem in addition to the scaling and translation. The algorithm used in a multi-layer neural network classifier which uses back-propagation learning algorithm. The results show that the first method has a performance of 70.83% recognition, while the second method, proposed in this article, has a better performance of 86.38% recognition rate.     

Segmentation of Assamese phonemes using hybrid soft-computational approach

Phonemes are the smallest distinguishable unit of speech signal. Segmentation of a phoneme from its word counterpart is a fundamental and crucial part in speech processing because an initial phoneme is used to activate words starting with that phoneme. This work describes an artificial neural network-based algorithm developed for segmentation and classification of consonant phoneme of the Assamese language. The algorithm uses weight vectors, obtained by training self-organising map (SOM) with different number of iterations, as a segment of different phonemes constituting the word whose linear prediction coefficients samples are used for training. The algorithm shows an abrupt rise in success rate than the conventional discrete wavelet-based speech segmentation. A two-class probabilistic neural network problem carried out with clean Assamese phoneme is used to identify phoneme segment. The classification of the phoneme segment is alone as per the consonant phoneme structure of the Assamese language which consists of six phoneme families. Experimental results establish the superiority of the SOM-based segmentation over the discrete wavelet transform-based approach.     

一种关于蛋白质模体的自动识别算法

随着生物信息学的发展，模体识别已经成为一种能够从生物序列中提取有用生物信息的方法。文中介绍了有关模体的一些概念，讨论了模体识别算法(MEME)的基础，即EM(expectation maximization)算法，由于MEME算法是建立在EM算法的基础上的，所以又由此引出了MEME算法，并对MEME算法的一些基本问题比如时间复杂度、算法性能等进行了详细讨论，对算法的局限性和有待改进的地方作了说明。实践证明，MEME是一个较好的模体识别算法，它能够识别出蛋白质或者DNA序列中单个或多个模体，具有很大的灵活性。     

CNN-ELM混合短文本分类模型

针对目前自然语言处理研究中,使用卷积神经网络（CNN）进行短文本分类任务时可以结合不同神经网络结构与分类算法以提高分类性能的问题,提出了一种结合卷积神经网络与极速学习机的CNN-ELM混合短文本分类模型。使用词向量训练构成文本矩阵作为输入数据,然后使用卷积神经网络提取特征并使用Highway网络进行特征优化,最后使用误差最小化极速学习机(EM-ELM)作为分类器完成短文本分类任务。与其他模型相比,该混合模型能够提取更具代表性的特征并能快速准确地输出分类结果。在多种英文数据集上的实验结果表明提出的CNN-ELM混合短文本分类模型比传统机器学习模型与深度学习模型更适合完成短文本分类任务。     

基于VGGNet的恶意代码变种分类

针对代码复用在同一恶意家族样本中普遍存在的现象,提出了一种利用代码复用特征的恶意样本分类方法。首先将文件的二进制序列分割成RGB三色通道的值,从而将恶意样本转换为彩色图;然后用这些图片基于VGG卷积神经网络生成恶意样本分类模型;最后在模型训练阶段利用随机失活算法解决过拟合和梯度消失问题以及降低神经网络计算开销。该方法使用Malimg数据集25个族的9342个样本进行评估,平均分类准确率达96.16%,能有效地分类恶意代码样本。实验结果表明,与灰度图相比,所提方法将二进制文件转换为彩色图能更明显地强调图像特征,尤其是对于二进制序列中含有重复短数据片段的文件,而且利用特征更明显的训练集,神经网络能生成分类效果更好的分类模型。所提方法预处理操作简单,分类结果响应较快,因此适用于大规模恶意样本的快速分类等即时性要求较高的场景。     

Adaptive network-based fuzzy inference system vs. other classification algorithms for warped LPC-based speech/music discrimination

Automatic discrimination of speech and music is an important tool in many multimedia applications. The paper presents an effective approach based on an adaptive network-based fuzzy inference system (ANFIS) for the classification stage required in a speech/music discrimination system. A new simple feature, called warped LPC-based spectral centroid (WLPC-SC), is also proposed. Comparison between WLPC-SC and the classical features proposed in the literature for audio classification is performed, aiming to assess the good discriminatory power of the proposed feature. The vector length used to describe the proposed psychoacoustic-based feature is reduced to a few statistical values (mean, variance and skewness). With the aim of increasing the classification accuracy percentage, the feature space is then transformed to a new feature space by LDA. The classification task is performed applying ANFIS to the features in the transformed space. To evaluate the performance of the ANFIS system for speech/music discrimination, comparison to other commonly used classifiers is reported. The classification results for different types of music and speech signals show the good discriminating power of the proposed approach.     

基于自联想记忆与卷积神经网络的跨语言情感分类

该文提出了一种以商品评论为对象的基于语义融合的跨语言情感分类算法。该算法首先从短文本语义表示的角度出发,基于开源工具Word2Vec预先生成词嵌入向量来获得不同语言下的信息表示;其次,根据不同语种之间的词向量的统计关联性提出使用自联想记忆关系来融合提取跨语言文档语义;然后利用卷积神经网络的局部感知性和权值共享理论,融合自联想记忆模型下的复杂语义表达,从而获得不同长度的短语融合特征。深度神经网络将能够学习到任意语种语义的高层特征致密组合,并且输出分类预测。为了验证算法的有效性,将该模型与最新几种模型方法的实验结果进行了对比。实验结果表明,此模型适用于跨语言情感语料正负面情感分类,实验效果明显优于现有的其他算法。     

基于感知哈希算法和特征融合的恶意代码检测方法

在当前的恶意代码家族检测中,通过恶意代码灰度图像提取的局部特征或全局特征无法全面描述恶意代码,针对这个问题并为提高检测效率,提出了一种基于感知哈希算法和特征融合的恶意代码检测方法。首先,通过感知哈希算法对恶意代码灰度图样本进行检测,快速划分出具体恶意代码家族和不确定恶意代码家族的样本,实验测试表明约有67%的恶意代码能够通过感知哈希算法检测出来。然后,对于不确定恶意代码家族样本再进一步提取局部特征局部二值模式（LBP）与全局特征Gist,并利用二者融合后的特征通过机器学习算法对恶意代码样本进行分类检测。最后,对于25类恶意代码家族检测的实验结果表明,相较于仅用单一特征,使用LBP与Gist的融合特征时的检测准确率更高,并且所提方法与仅采用机器学习的检测算法相比分类检测效率更高,检测速度提高了93.5%。     

基于TSNE和多尺度稀疏自编码的高光谱图像分类

针对高光谱图像存在维数“灾难”、特征以及空间信息利用不足的问题,结合深度学习、流形学习及多尺度空间特征的最新进展,提出了一种TSNE和多尺度稀疏自编码网络的高光谱图像分类算法。利用TSNE算法对高光谱图像进行降维,再对每个像元的邻域进行多尺度空间特征提取,利用加入空谱联合信息的像元训练稀疏自编码网络模型并通过softmax分类器进行分类,减少计算复杂度,提高分类精确度。通过对Indian Pines及Pavia University两组数据进行实验,结果表明,提出的算法与其他五种算法相比分类效果更好。     

Parallel memetic algorithm for training recurrent neural networks for the energy efficiency problem

In our state-of-the-art study, we improve neural network-based models for predicting energy consumption in buildings by parallelizing the CHC adaptive search algorithm. We compared the sequential implementation of the evolutionary algorithm with the new parallel version to obtain predictors and found that this new version of our software tool halved the execution time of the sequential version. New predictors based on various classes of neural networks have been developed and the obtained results support the validity of the proposed approaches with an average improvement of 75% of the average execution time in relation to previous sequential implementations.