Network-based ranking methods for prediction of novel disease associated microRNAs

BackgroundMany studies have shown roles of microRNAs on human disease and a number of computational methods have been proposed to predict such associations by ranking candidate microRNAs according to their relevance to a disease. Among them, machine learning-based methods usually have a limitation in specifying non-disease microRNAs as negative training samples. Meanwhile, network-based methods are becoming dominant since they well exploit a “disease module” principle in microRNA functional similarity networks. Of which, random walk with restart (RWR) algorithm-based method is currently state-of-the-art. The use of this algorithm was inspired from its success in predicting disease gene because the “disease module” principle also exists in protein interaction networks. Besides, many algorithms designed for webpage ranking have been successfully applied in ranking disease candidate genes because web networks share topological properties with protein interaction networks. However, these algorithms have not yet been utilized for disease microRNA prediction.MethodsWe constructed microRNA functional similarity networks based on shared targets of microRNAs, and then we integrated them with a microRNA functional synergistic network, which was recently identified. After analyzing topological properties of these networks, in addition to RWR, we assessed the performance of (i) PRINCE (PRIoritizatioN and Complex Elucidation), which was proposed for disease gene prediction; (ii) PageRank with Priors (PRP) and K-Step Markov (KSM), which were used for studying web networks; and (iii) a neighborhood-based algorithm.ResultsAnalyses on topological properties showed that all microRNA functional similarity networks are small-worldness and scale-free. The performance of each algorithm was assessed based on average AUC values on 35 disease phenotypes and average rankings of newly discovered disease microRNAs. As a result, the performance on the integrated network was better than that on individual ones. In addition, the performance of PRINCE, PRP and KSM was comparable with that of RWR, whereas it was worst for the neighborhood-based algorithm. Moreover, all the algorithms were stable with the change of parameters. Final, using the integrated network, we predicted six novel miRNAs (i.e., hsa-miR-101, hsa-miR-181d, hsa-miR-192, hsa-miR-423-3p, hsa-miR-484 and hsa-miR-98) associated with breast cancer.ConclusionsNetwork-based ranking algorithms, which were successfully applied for either disease gene prediction or for studying social/web networks, can be also used effectively for disease microRNA prediction.     

Delay optimization and energy balancing algorithm for improving network lifetime in fixed wireless sensor networks

Since wireless in terms of energy-restricted processes, dispersion radii, processing power limitations, buffers, bandwidth-limited connections, active network topologies, and network stream of traffic outlines, sensor networks provide difficult design issues. The number of hops and latency are decreased if there is a relay mote because it interacts directly with relay motes that are closer to the destination mote. The tremendous intensive research in the area of Wireless Sensor Networks (WSN) has gained a lot of significance among the technical community and research. The job of WSN is to sense the data using sensor motes, pass on the data to the destination detection mote which is associated with a processing center and can be used in multiple spans of Internet of Things (IoT) applications. Wireless sensor network has a set of sensor motes. By making use of sensor mote placement strategy all the sensor motes are spread in an area with each mote having its own exceptional location. Internet of things applications are delay sensitive those applications have a challenge of forming the complete path at a lower delay constraint. The proposal is to modify the game theory energy balancing algorithm by making use of relay motes so that overall network lifetime is increased. It has been proved that modified GTEB is better with respect to existing algorithms in terms of delay, figure of hops, energy depletion, figure of alive motes, figure of dead motes, lifespan ratio, routing overhead and throughput.     

Energy-efficient beamforming optimization for MISO communication based on reconfigurable intelligent surface

Reconfigurable intelligent surface (RIS), a planar metasurface consisting of a large number of low-cost reflecting elements, has received much attention due to its ability to improve both the spectrum and energy efficiency (EE) by reconfiguring the wireless propagation environment. In this paper, we propose a base station (BS) beamforming and RIS phase shift optimization technique that maximizes the EE of a RIS-aided multiple-input–single-output system. In particular, considering the system circuits’ energy consumption, an EE maximization problem is formulated by jointly optimizing the active beamforming at the BS and the passive beamforming at the RIS, under the constraints of each user’ rate requirement, the BS’s maximal transmit power budget and unit-modulus constraint of the RIS phase shifts. Due to the coupling of optimization variables, this problem is a complex non-convex optimization problem, and it is challenging to solve it directly. To overcome this obstacle, we divide the problem into active and passive beamforming optimization subproblems. For the first subproblem, the active beamforming is given by the maximum ratio transmission optimal strategy. For the second subproblem, the optimal phase shift matrix at the RIS is obtained by exploiting sine cosine algorithm (SCA). Moreover, for this case where each reflection element’s working state is controlled by a circuit switch, each reflection element’s switch value is optimized with the aid of particle swarm optimization algorithm. Finally, numerical results verify the effectiveness of our proposed algorithm compared to other algorithms.     

基于麻雀搜索算法结合深度前馈神经网络的近红外模型转移方法研究

该文提出了一种基于麻雀搜索算法结合深度前馈神经网络（SSA－DFN）的近红外光谱模型转移方法。使用深度前馈神经网络拟合不同仪器采集到的光谱之间的非线性函数映射,并将麻雀搜索算法用于网络各层连接权值和阈值的初始化,通过种群中个体位置的迭代更新,求得连接权值和阈值的最优初始值;通过多次调整深度前馈神经网络模型的超参数,使网络拟合效果趋于最优,最终确定转移函数。为验证方法的有效性,分别从烟叶近红外光谱谱图、主成分投影和预测结果的角度,将SSA－DFN方法与分段直接校正算法（PDS）、典型相关性分析算法（CCA）转移前后的效果进行了对比。结果表明SSA－DFN方法转移后的从机光谱与原主机光谱重合度最高,转移后主、从机总糖、烟碱含量的预测结果差异不显著,预测平均误差从8.32%、9.15%分别降至4.65%、4.82%,预测均方根误差（RMSEP）和决定系数（R2）等指标均优于PDS和CCA,取得了最佳的转移效果,可满足企业需求。结果表明该方法是一种有效的模型转移方法。     

基于改进免疫遗传算法的近红外光谱变量选择方法

该文在免疫遗传算法（IGA）的基础上,提出一种改进免疫遗传算法（iIGA）用于近红外光谱波长变量的选择。该算法舍去了原算法中固定抗体相似度阈值的思想,取而代之的是抗体相似度阈值自适应,同时引入精英保留策略和贪心算法思想,使得算法朝着正确的方向进行局部性探优。将该算法在玉米的淀粉和蛋白质含量数据集上进行实验测试,建立偏最小二乘（PLS）分析模型,并与IGA、遗传算法（GA）以及全谱方法进行了对比。结果表明,在玉米淀粉含量的预测上,iIGA相较于原IGA算法,预测集均方根误差（RMSEP）从0.312 0降至0.298 0,预测集预测精度提升4.5%;在玉米蛋白质含量的预测上,RMSEP从0.124 4降至0.110 3,预测集预测精度提升11.3%。分别对预测淀粉和蛋白质模型的RMSEP值进行显著性检验,F值分别为165.22和182.05,P值分别为9.5 × 10－23和4.5 × 10－24,P值均小于0.05,因此,iIGA能显著提升模型预测精度。     

基于内源性致香物质和化学计量学的烟草感官评价研究

采用主成分分析法结合遗传算法和神经网络,建立了基于烟草内源性致香物质的感官质量评价预测模型。利用气相色谱-质谱(GC-MS)技术对超临界萃取-分子蒸馏所得烟草精油中的内源性致香组分进行定性定量分析,汇总各类致香指标后,对其进行主成分分析;以提取所得5个主成分的得分作为输入变量,感官评吸分数作为输出变量,分别使用标准BP神经网络和遗传算法(GA)优化的BP神经网络建立预测模型。对比实验结果表明,GA优化后的模型预测效果更优,其预测值与实验值间的相关系数为0.96,预测均方根误差为1.81,说明GA-BP模型具有更好的拟合能力和预测能力,该模型能有效地预测烟草精油的感官品质。     

基于高通量解析算法的复杂样品重叠气相色谱-质谱信号的快速分析

化学计量学算法为重叠气相色谱-质谱(GC-MS)信号的解析提供了有效手段,但其在计算过程中一般需要将数据进行分段处理,然后只对信号的某些区间进行解析,难以实现真正意义上的高通量分析。该文结合移动窗口目标转换因子分析(MWTTFA)和非负免疫算法(NNIA),建立了一种高通量解析方法。首先,根据所有可能存在的目标组分的标准质谱信息,利用MWTTFA检验复杂信号中存在的组分,并确定目标组分的质谱信息和洗脱时间区域。以得到的质谱信息作为后续计算的输入值,利用NNIA解析得到相应的色谱信息。采用快速升温程序对17种和42种农药混合标准样品的GC-MS信号进行分析,利用所建立的方法可在10 min内得到全部组分的色谱和质谱信息。     

Local and parallel finite element algorithm for stationary incompressible magnetohydrodynamics

This article presents a local and parallel finite element method for the stationary incompressible magnetohydrodynamics problem. The key idea of this algorithm comes from the two‐grid discretization technique. Specifically, we solve the nonlinear system on a global coarse mesh, and then solve a series of linear problems on several subdomains in parallel. Furthermore, local a priori estimates are obtained on a general shape regular grid. The efficiency of the algorithm is also illustrated by some numerical experiments.© 2017 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 33: 1513–1539, 2017     

Disjoint Paths in Decomposable Digraphs

The k‐linkage problem is as follows: given a digraph and a collection of k terminal pairs such that all these vertices are distinct; decide whether D has a collection of vertex disjoint paths such that is from to for . A digraph is k‐linked if it has a k‐linkage for every choice of 2k distinct vertices and every choice of k pairs as above. The k‐linkage problem is NP‐complete already for [11] and there exists no function such that every ‐strong digraph has a k‐linkage for every choice of 2k distinct vertices of D [17]. Recently, Chudnovsky et al. [9] gave a polynomial algorithm for the k‐linkage problem for any fixed k in (a generalization of) semicomplete multipartite digraphs. In this article, we use their result as well as the classical polynomial algorithm for the case of acyclic digraphs by Fortune et al. [11] to develop polynomial algorithms for the k‐linkage problem in locally semicomplete digraphs and several classes of decomposable digraphs, including quasi‐transitive digraphs and directed cographs. We also prove that the necessary condition of being ‐strong is also sufficient for round‐decomposable digraphs to be k‐linked, obtaining thus a best possible bound that improves a previous one of . Finally we settle a conjecture from [3] by proving that every 5‐strong locally semicomplete digraph is 2‐linked. This bound is also best possible (already for tournaments) [1].     

一种新的求非线性方程组的数值延拓法

针对迭代过程中的Jacobi奇异问题,本文提出了一种新的数值延拓法.通过构造双参数同伦算子,采用可控条件和适当选取参数的方式克服Jacobi奇异性,并分析了方法的收敛性.最后,通过数值实验对比,验证了方法的可行性和优越性.特别是具有可调控越过Jacobi奇异(点、线、面)的优势,从而也在某种程度上解决了数值延拓法严重依赖于初值的问题.