Construction of Gene Networks With Hybrid Approach From Expression Profile and Gene Ontology

Gene regulatory networks have been long studied in model organisms as a means of identifying functional relationships among genes or their corresponding products. Despite many existing methods for genome-wide construction of such networks, solutions to the gene regulatory networks problem are however not trivial. Here, we present, a hybrid approach with gene expression profiles and gene ontology (HAEO). HAEO makes use of multimethods (overlapping clustering and reverse engineering methods) to effectively and efficiently construct gene regulatory networks from multisources (gene expression profiles and gene ontology). Application to yeast cell cycle dataset demonstrates HAEO’s ability to construct validated gene regulatory networks, such as some potential gene regulatory pairs, which cannot be discovered by general inferring methods and identifying cycles (i.e., feedback loops) between genes. We also experimentally study the efficiency of building networks and show that the proposed method, HAEO is much faster than Bayesian networks method.      

基于信息准则的基因选取方法及其在肿瘤诊断中的应用

大规模基因表达谱为肿瘤诊断提供了更为可靠和细致的生物数据,但相关基因的选取是对这些数据进行分析的关键。本文从Kullback-Leiber判别信息的角度对于肿瘤相关基因的选取进行了研究。根据肿瘤相关基因和无关基因的表达水平值分布的特性,我们提出了一种基于信息准则的基因选取方法。进一步,我们将这种方法应用到肿瘤诊断上,并根据支持向量机(SVM)对相关基因表达谱数据进行训练建立肿瘤诊断模型。实验结果表明这种方法是有效的,依此所建立的诊断模型可使得在结肠癌数据集和白血病数据集上的诊断(预测)正确率分别高达94.4%和100%石。     

Estimating the Number of Clusters via System Evolution for Cluster Analysis of Gene Expression Data

The estimation of the number of clusters (NC) is one of crucial problems in the cluster analysis of gene expression data. Most approaches available give their answers without the intuitive information about separable degrees between clusters. However, this information is useful for understanding cluster structures. To provide this information, we propose system evolution (SE) method to estimate NC based on partitioning around medoids (PAM) clustering algorithm. SE analyzes cluster structures of a dataset from the viewpoint of a pseudothermodynamics system. The system will go to its stable equilibrium state, at which the optimal NC is found, via its partitioning process and merging process. The experimental results on simulated and real gene expression data demonstrate that the SE works well on the data with well-separated clusters and the one with slightly overlapping clusters.     

基于ARMA模型的CFAR网络入侵检测方法研究

提出了一种基于ARMA网络流量模型的CFAR入侵检测系统。采用ARMA模型对网络流量进行预测,并运用雷达信号处理中的恒误警CFAR技术,选取检测阀值以判定是否存在入侵信号。利用林肯实验室DARPA数据对系统进行试验,结果表明,此方法与AR预测模型相比,具有更高的检测率和更低的误警率。     

Time-Varying Surrogate Data to Assess Nonlinearity in Nonstationary Time Series: Application to Heart Rate Variability

We propose a method to extend to time-varying (TV) systems the procedure for generating typical surrogate time series, in order to test the presence of nonlinear dynamics in potentially nonstationary signals. The method is based on fitting a TV autoregressive (AR) model to the original series and then regressing the model coefficients with random replacements of the model residuals to generate TV AR surrogate series. The proposed surrogate series were used in combination with a TV sample entropy (SE) discriminating statistic to assess nonlinearity in both simulated and experimental time series, in comparison with traditional time-invariant (TIV) surrogates combined with the TIV SE discriminating statistic. Analysis of simulated time series showed that using TIV surrogates, linear nonstationary time series may be erroneously regarded as nonlinear and weak TV nonlinearities may remain unrevealed, while the use of TV AR surrogates markedly increases the probability of a correct interpretation. Application to short (500 beats) heart rate variability (HRV) time series recorded at rest (R), after head-up tilt (T), and during paced breathing (PB) showed: (1) modifications of the SE statistic that were well interpretable with the known cardiovascular physiology; (2) significant contribution of nonlinear dynamics to HRV in all conditions, with significant increase during PB at 0.2 Hz respiration rate; and (3) a disagreement between TV AR surrogates and TIV surrogates in about a quarter of the series, suggesting that nonstationarity may affect HRV recordings and bias the outcome of the traditional surrogate-based nonlinearity test.     

一种基于AR模型的矩阵CFAR检测器

矩阵恒虚警（Constant False Alarm Rate,CFAR）检测器是根据信息几何理论利用检测单元相关矩阵与参考单元矩阵黎曼均值间的测地线距离作为检测统计量进行检测.本文根据尤尔-沃克方程中相关矩阵与自回归（Auto-Regressive,AR）谱之间的一一对应关系,将矩阵CFAR检测器中两矩阵间的距离转化为两AR谱之间的距离,提出了一种基于AR模型的矩阵CFAR检测器,该检测器能利用分辨率更高的AR模型进行谱估计,并将功率谱整体进行检测,能充分利用回波的多普勒信息,非常适用于频域扩展目标的检测,通过利用具有频域扩展特性的尾流实测数据对该方法和传统方法的检测性能进行比较分析,验证了本文所提检测器的有效性.     

Security anomaly detection in software‐defined networking based on a prediction technique

Nowadays, software‐defined networking (SDN) is regarded as the best solution for the centralized handling and monitoring of large networks. However, it should be noted that SDN architecture suffers from the same security issues, which are the case with common networks. As a case in point, one of the shortcomings of SDNs is related to its high vulnerability to distributed denial of service (DDoS) attacks and other similar ones. Indeed, anomaly detection systems have been considered to deal with these attacks. The challenges are related to designing these systems including gathering data, extracting effective features, and selecting the best model for anomaly detection. In this paper, a novel combined approach is proposed; this method uses NetFlow protocol for gathering information and generating dataset, information gain ratio (IGR), in order to select the effective and relevant features and ensemble learning scheme (Stacking) for developing a structure with desirable performance and efficiency for detecting anomaly in SDN environment. The results obtained from the experiments revealed that the proposed method performs better than other methods in terms of enhancing accuracy (AC) and detection rate (DR) and reducing classification error (CE) and false alarm rate (FAR). The AC, DR, CE, and FAR of the proposed model were measured as 99.92%, 99.83%, 0.08%, and 0.03%, respectively. Furthermore, the proposed method prevents the occurrence of excessive overload on the controller and OpenFlow.     

基于相关向量机的网络入侵检测算法

针对支持向量机理论中存在的问题：训练样本数量多以及必须满足MerCer条件等,提出了一种基于相关向量机（RVM）的网络入侵检测方法。首先采用“删除特征”法对KDD99数据集中的41个特征进行评级,筛选出针对不同入侵类型的重要特征和非重要特征,然后只选择重要特征进行匹配。结果表明,这种方法与基于支持向量机（SVM）的入侵检测模型相比,具有更高的检测率和更低的误警率。     

基于网络流量预测模型的CFAR入侵检测方法研究

论文提出了一种基于网络流量预测模型的CFAR入侵检测系统。采用AR模型对网络流量进行预测,并运用雷达信号处理中的恒误警CFAR技术,选取检测阀值以判定是否存在入侵信号。利用林肯实验室DARPA数据对系统进千亍试验,通过对不同的CFAR检测进行比较分析,最后提出三种CFAR联合检测,使得系统具有更高的检测率和更低的误警率。     

基于基因表达谱的肿瘤亚型识别与分类特征基因选取研究

利用肿瘤基因表达谱建立有效的"预测性"分类模型,对肿瘤的不同亚型进行准确判别并找出决定样本类别的一组特征基因是当前生物信息学研究的重要课题.本文在分析肿瘤基因表达谱特征的基础上,以急性白血病的基因表达谱为例,研究了肿瘤亚型识别与分类特征基因选取问题.在类别可分离性判据的问题上,修正了已有的"信噪比"指标,据此进行无关基因的剔除,并以支持向量机作为分类器进行肿瘤亚型的识别.在特征基因选取问题上,本文从生物学分析出发,首先剔除无关基因和具有较强相关性的冗余基因,然后采用顺序浮动搜索算法进行分类特征基因的选取.实验结果表明了上述方法的可行性和有效性.     

A comparative study of AR order selection methods

Autoregressive (AR) modelling has assumed an important role in many application areas of signal processing. When fitting an AR model to an observed data sequence the selection of the model order is of great importance. Many criteria for selecting the AR model order have been proposed. However, these are scattered throughout the literature and little analysis of their relative performance is available. The principle aim of this paper is to compare the performance of some of the more recent methods of AR model order selection so that a broad perspective of the subject may be obtained. We compare the order selection methods using both narrowband and wideband data, with and without additive noise. The results of the study allow some basic recommendations to be made about the best types of method to be used in each case. It is observed that methods using the observed data perform best in the case of narrowband signal with no noise. Methods which employ the autocorrelation (second-order cumulant) sequence of the data show promise when used with wideband or noisy signals.     

基于直线邻近平行性和GBVS显著性的遥感图像机场目标检测

现有的全色遥感图像机场目标检测方法,对机场目标的直线特征利用得非常有限.提出一种同时利用自顶向下和自底向上显著性机制的新方法.利用线段检测算法检测直线,通过跑道线段间邻近、平行且长度范围一定的特点,提出了邻近平行性的概念,可以深度挖掘机场跑道几何关系的先验知识.同时使用简化的基于图的视觉显著性模型,提取自底向上的显著性.两者协同得到机场的候选位置.最后,通过尺度不变特征变换提取特征,利用支撑向量机进行判决,可以精确定位机场目标.在具有各种类型的机场图像数据库上的实验结果表明,相对于其他方法,所提议算法具有速度快、识别率高、虚警率低的优势,同时对于复杂背景具有更强的鲁棒性.     

Effect of spatial distribution of generation rate on bulk heterojunction organic solar cell performance: A novel semi-analytical approach

We present a physics-based semi-analytical model of bulk heterojunction (BHJ) organic solar cell (OSC) for predicting the electrical characteristics of the device, taking into account the space dependency of generation rate profiles. The model enables us to derive the J-V characteristics of BHJ OSC without the need of a closed form expression of arbitrary carrier generation rate (which may not exist), hence avoiding the cumbersome numerical fitting method employed in literature previously. Using the proposed model, we perform an extensive analysis to study the effect of spatial distribution of generation rate profiles on the device performance. For this purpose, we use Gaussian shaped profiles that have a common average value thus retaining the total number of generated carriers same. We vary the position of the generation peak and its sharpness (width of the Gaussian peak) as well as number of peaks to analyze their effects on device efficiency. For the considered profiles, results show that the optimized profile has a peak carrier generation rate exactly halfway through the active layer and falls off sharply on either side. In the end, we propose methods of controlling the generation profiles by modifying the device structure and perform optical simulation to show the corresponding generation profiles. Thus, we show the usefulness of our derived model in finding the spatial distribution of a given number of carriers along the active layer that yields the best device performance.     

一种肿瘤基因表达数据的知识提取方法

本文以多发性骨髓瘤的基因表达数据为例,利用数据挖掘技术,提出了一种针对基因表达数据进行知识发现的方法.该方法通过计算基因的信息增益,结合神经网络,找出了特征基因集合,最后利用决策树进行特征规则的提取,给出了基于多发性骨髓瘤数据样本的产生式规则,为生物医学研究提供了一种分析和研究基因表达数据的参考方法.实验结果表明了该方法的有效性.     

基于小波包-FastICA在阿尔茨海默症中的应用及其生物学分析

阿尔茨海默症(Alzheimer’s disease,AD)基因表达谱数据具有高维性、高噪声、高冗余性等特点,使得AD特异性基因的搜索空间巨大,搜索算法时间长,降低了算法的挖掘性能及其生物学分析。因此对其基因表达谱数据进行去噪和降维预处理是十分必要的。文中首先利用小波包变换-SAM方法对数据进行降维去噪,实验结果证明了小波包方法能较好地提取基因表达谱有用信息;然后应用快速独立成分分析(FastICA)算法对预处理后的数据进行矩阵分解分析,并根据独立分量选取特异性基因。在此基础上的样本分类实验表明,FastICA提取的特异性基因具有较高的显著性,能够提高样本的分类结果。同时,通过所提取特异性基因的富集性分析,文中给出了这些基因在阿尔茨海默症数据集中聚类情况及其基因表达情况,为AD的生物学及医学病理分析提供有利的依据。     

Fisher分布下基于白化滤波的极化SAR图像CFAR检测方法

在已有的极化合成孔径雷达（SAR）图像恒虚警（CFAR）检测方法中,存在着高分辨下杂波模型适用性差的难题.为此提出了一种Fisher分布下具有虚警概率解析表达形式的CFAR检测方法.首先,在乘积模型框架下,引入Fisher纹理变量,推导出了极化白化滤波（PWF）检测量的概率密度函数（PDF）.然后,对PDF积分得到了虚警概率关于检测门限的解析表达形式,并设计了相应的CFAR检测算法流程.最后,通过机载合成孔径雷达（AIRSAR）实测数据比较了新方法和双参数恒虚警（2P-CFAR）算法及已有的基于K分布、G₀分布、Wishart分布的CFAR检测方法的检测性能.结果表明新方法能有效检测出目标,且鲁棒性较强,相比于其他检测方法,品质因数平均高出32.66%.     

Intrusion Detection System in Wireless Sensor Network Using Conditional Generative Adversarial Network

Wireless communication networks have much data to sense, process, and transmit. It tends to develop a security mechanism to care for these needs for such modern-day systems. An intrusion detection system (IDS) is a solution that has recently gained the researcher’s attention with the application of deep learning techniques in IDS. In this paper, we propose an IDS model that uses a deep learning algorithm, conditional generative adversarial network (CGAN), enabling unsupervised learning in the model and adding an eXtreme gradient boosting (XGBoost) classifier for faster comparison and visualization of results. The proposed method can reduce the need to deploy extra sensors to generate fake data to fool the intruder 1.2–2.6%, as the proposed system generates this fake data. The parameters were selected to give optimal results to our model without significant alterations and complications. The model learns from its dataset samples with the multiple-layer network for a refined training process. We aimed that the proposed model could improve the accuracy and thus, decrease the false detection rate and obtain good precision in the cases of both the datasets, NSL-KDD and the CICIDS2017, which can be used as a detector for cyber intrusions. The false alarm rate of the proposed model decreases by about 1.827%.

     

Interference rejection using the time-dependent constant modulusalgorithm (CMA) and the hybrid CMA/spectral correlation discriminator

Two new blind adaptive filtering algorithms for interference rejection using time-dependent filtering structures are presented. The time-dependent structure allows the adaptive filter to outperform the conventional adaptive filter implemented with a time-independent structure for filtering of cyclostationary communication signals. At the same time, the blind adaption algorithms allow the filters to operate without the use of an external training signal. The first algorithm applies the CMA to an unconstrained time-dependent filtering structure. The second algorithm applies the CMA to a spectral correlation discriminator, which is constrained to select signals with unique spectral correlation characteristics. Using computer simulations, it is shown that the blind time-dependent filtering algorithms can provide mean-square errors (MSEs) and bit error rates (BERs) that are significantly lower than the MSEs and BERs provided using conventional time-independent adaptive filters. It is also shown that these processors can outperform the nonblind training-sequence directed time-independent adaptive filter