Inference of Molecular Regulatory Systems Using Statistical Path-Consistency Algorithm

One of the key challenges in systems biology and molecular sciences is how to infer regulatory relationships between genes and proteins using high-throughout omics datasets. Although a wide range of methods have been designed to reverse engineer the regulatory networks, recent studies show that the inferred network may depend on the variable order in the dataset. In this work, we develop a new algorithm, called the statistical path-consistency algorithm (SPCA), to solve the problem of the dependence of variable order. This method generates a number of different variable orders using random samples, and then infers a network by using the path-consistent algorithm based on each variable order. We propose measures to determine the edge weights using the corresponding edge weights in the inferred networks, and choose the edges with the largest weights as the putative regulations between genes or proteins. The developed method is rigorously assessed by the six benchmark networks in DREAM challenges, the mitogen-activated protein (MAP) kinase pathway, and a cancer-specific gene regulatory network. The inferred networks are compared with those obtained by using two up-to-date inference methods. The accuracy of the inferred networks shows that the developed method is effective for discovering molecular regulatory systems.     

State Sampling Dependence of Hopfield Network Inference

The fully connected Hopfield network is inferred based on observed magnetizations and pairwise correlations.We present the system in the glassy phase with low temperature and high memory load.We find that the inference error is very sensitive to the form of state sampling.When a single state is sampled to compute magnetizations and correlations,the inference error is almost indistinguishable irrespective of the sampled state.However,the error can be greatly reduced if the data is collected with state transitions.Our result holds for different disorder samples and accounts for the previously observed large fluctuations of inference error at low temperatures.     

An Adaptive Hierarchical Network Model for Studying the Structure of Economic Network

The interdependence of financial institutions is primarily responsible for creating a systemic hierarchy in the industry. In this paper, an Adaptive Hierarchical Network Model is proposed to study the problem of hierarchical relationships arising from different individuals in the economic domain. In the presented dynamically evolving network model, new directed edges are generated depending on the existing nodes and the hierarchical structures among the network, and these edges decay over time. When the preference of nodes in the network for higher ranks exceeds a certain threshold value, the equality state in the network becomes unstable and rank states emerge. Meanwhile, we select four real data sets for model evaluation and observe the resilience in the network hierarchy evolution and the differences formed by different patterns of hierarchy preference mechanisms, which help us better understand data science and network dynamics evolution.     

Granger-Causality Inference of the Existence of Unobserved Important Components in Network Analysis

Detecting causal interrelationships in multivariate systems, in terms of the Granger-causality concept, is of major interest for applications in many fields. Analyzing all the relevant components of a system is almost impossible, which contrasts with the concept of Granger causality. Not observing some components might, in turn, lead to misleading results, particularly if the missing components are the most influential and important in the system under investigation. In networks, the importance of a node depends on the number of nodes connected to this node. The degree of centrality is the most commonly used measure to identify important nodes in networks. There are two kinds of degree centrality, which are in-degree and out-degree. This manuscrpt is concerned with finding the highest out-degree among nodes to identify the most influential nodes. Inferring the existence of unobserved important components is critical in many multivariate interacting systems. The implications of such a situation are discussed in the Granger-causality framework. To this end, two of the most recent Granger-causality techniques, renormalized partial directed coherence and directed partial correlation, were employed. They were then compared in terms of their performance according to the extent to which they can infer the existence of unobserved important components. Sub-network analysis was conducted to aid these two techniques in inferring the existence of unobserved important components, which is evidenced in the results. By comparing the results of the two conducted techniques, it can be asserted that renormalized partial coherence outperforms directed partial correlation in the inference of existing unobserved important components that have not been included in the analysis. This measure of Granger causality and sub-network analysis emphasizes their ubiquitous successful applicability in such cases of the existence of hidden unobserved important components.     

基于贝叶斯网络推理的起落架系统故障诊断技术研究

民机起落架系统结构复杂,是典型的故障多发系统,实际诊断过程主要依赖于排故手册流程和工程经验积累,存在诸多不确定性因素。贝叶斯网络是用有向无环图的形式表达变量间因果关联关系,可以充分利用专家知识和试验信息进行基于概率的统计推断,适于处理复杂系统的不确定性问题。通过深入分析某型民机起落架技术资料,建立了基于贝叶斯网络的起落架系统诊断架构,结合专家知识和维护经验提出了基于贝叶斯网络的起落架系统故障诊断方法,并给出了网络推理流程,提升了起落架系统故障诊断效率和精度。     

Attack Vulnerability of Network with Duplication-Divergence Mechanism

We study the attack vulnerability of network with duplication-divergence mechanism. Numerical results have shown that the duplication-divergence network with larger retention probability a is more robust against target attack relatively. Furthermore, duplication-divergence network is broken down more quickly than its counterpart BA network under target attack. Such result is consistent with the fact of WWW and Internet networks under target attack. So duplication-divergence model is a more realistic one for us to investigate the characteristics of the world wide web in future. We also observe that the exponent γ of degree distribution and average degree are important parameters of networks, reflecting the performance of networks under target attack. Our results are helpful to the research on the security of network.     

Three Decades in Econophysics—From Microscopic Modelling to Macroscopic Complexity and Back

We explore recent contributions to research in Econophysics, switching between Macroscopic complexity and microscopic modelling, showing how each leads to the other and detailing the everyday applicability of both approaches and the tools they help develop. Over the past decades, the world underwent several major crises, leading to significant increase in interdependence and, thus, complexity. We show here that from the perspective of network science, these processes become more understandable and, to some extent, also controllable.     

Network dynamics and its relationships to topology and coupling structure in excitable complex networks

All dynamic complex networks have two important aspects, pattern dynamics and network topology. Discovering different types of pattern dynamics and exploring how these dynamics depend or/network topologies are tasks of both great theoretical importance and broad practical significance. In this paper we study the oscillatory behaviors of excitable complex networks （ECNs） and find some interesting dynamic behaviors of ECNs in oscillatory probability, the multiplicity of oscillatory attractors, period distribution, and different types of oscillatory patterns （e.g., periodic, quasiperiodic, and chaotic）. In these aspects, we further explore strikingly sharp differences among network dynamics induced by different topologies （random or scale-free topologies） and different interaction structures （symmetric or asymmetric couplings）. The mechanisms behind these differences are explained physically.     

Complex Network Analysis of Mass Violation,Specifically Mass Killing

News reports in media contain news about society’s social and political conditions. With the help of publicly available digital datasets of events, it is possible to study a complex network of mass violations, i.e., Mass Killings. Multiple approaches have been applied to bring essential insights into the events and involved actors. Power law distribution behavior finds in the tail of actor mention, co-actor mention, and actor degree tells us about the dominant behavior of influential actors that grows their network with time. The United States, France, Israel, and a few other countries have been identified as major players in the propagation of Mass Killing throughout the past 20 years. It is demonstrated that targeting the removal of influential actors may stop the spreading of such conflicting events and help policymakers and organizations. This paper aims to identify and formulate the conflicts with the actor’s perspective at a global level for a period of time. This process is a generalization to be applied to any level of news, i.e., it is not restricted to only the global level.     

Clarifying How Degree Entropies and Degree-Degree Correlations Relate to Network Robustness

It is often claimed that the entropy of a network’s degree distribution is a proxy for its robustness. Here, we clarify the link between degree distribution entropy and giant component robustness to node removal by showing that the former merely sets a lower bound to the latter for randomly configured networks when no other network characteristics are specified. Furthermore, we show that, for networks of fixed expected degree that follow degree distributions of the same form, the degree distribution entropy is not indicative of robustness. By contrast, we show that the remaining degree entropy and robustness have a positive monotonic relationship and give an analytic expression for the remaining degree entropy of the log-normal distribution. We also show that degree-degree correlations are not by themselves indicative of a network’s robustness for real networks. We propose an adjustment to how mutual information is measured which better encapsulates structural properties related to robustness.     

复杂网络中节点重要性排序的研究进展

如何用定量分析的方法识别超大规模网络中哪些节点最重要, 或者评价某个节点相对于其他一个或多个节点的重要程度, 这是复杂网络研究中亟待解决的重要问题之一. 本文分别从网络结构和传播动力学的角度, 对现有的复杂网络中节点重要性排序方法进行了系统的回顾,总结了节点重要性排序方法的最新研究进展, 并对不同的节点重要性排序指标的优缺点以及适用环境进行了分析, 最后指出了这一领域中几个有待解决的问题及可能的发展方向. 关键词： 复杂网络 节点重要性 网络结构 传播动力学     

The effects of degree correlations on network topologies and robustness

Complex networks have been applied to model numerous interactive nonlinear systems in the real world. Knowledge about network topology is crucial to an understanding of the function, performance and evolution of complex systems. In the last few years, many network metrics and models have been proposed to investigate the network topology, dynamics and evolution. Since these network metrics and models are derived from a wide range of studies, a systematic study is required to investigate the correlations among them. The present paper explores the effect of degree correlation on the other network metrics through studying an ensemble of graphs where the degree sequence (set of degrees) is fixed. We show that to some extent, the characteristic path length, clustering coefficient, modular extent and robustness of networks are directly influenced by the degree correlation.     

Sensing Enhancement on Social Networks: The Role of Network Topology

Sensing and processing information from dynamically changing environments is essential for the survival of animal collectives and the functioning of human society. In this context, previous work has shown that communication between networked agents with some preference towards adopting the majority opinion can enhance the quality of error-prone individual sensing from dynamic environments. In this paper, we compare the potential of different types of complex networks for such sensing enhancement. Numerical simulations on complex networks are complemented by a mean-field approach for limited connectivity that captures essential trends in dependencies. Our results show that, whilst bestowing advantages on a small group of agents, degree heterogeneity tends to impede overall sensing enhancement. In contrast, clustering and spatial structure play a more nuanced role depending on overall connectivity. We find that ring graphs exhibit superior enhancement for large connectivity and that random graphs outperform for small connectivity. Further exploring the role of clustering and path lengths in small-world models, we find that sensing enhancement tends to be boosted in the small-world regime.     

Fixed-Time Synchronization Control of Delayed Dynamical Complex Networks

Fixed-time synchronization problem for delayed dynamical complex networks is explored in this paper. Compared with some correspondingly existed results, a few new results are obtained to guarantee fixed-time synchronization of delayed dynamical networks model. Moreover, by designing adaptive controller and discontinuous feedback controller, fixed-time synchronization can be realized through regulating the main control parameter. Additionally, a new theorem for fixed-time synchronization is used to reduce the conservatism of the existing work in terms of conditions and the estimate of synchronization time. In particular, we obtain some fixed-time synchronization criteria for a type of coupled delayed neural networks. Finally, the analysis and comparison of the proposed controllers are given to demonstrate the validness of the derived results from one numerical example.     

直膨式空调人工神经网络在线自适应控制器应用研究

直接膨胀式空调系统人工神经网络控制器已经有了一些研究成果,为了解决控制器控制范围和精度的问题,引入在线自适应控制系统。该控制器的控制能力测试采用直接膨胀式空调系统实验装置进行。试验结果表明,基于人工神经网络动态模型的在线自适应控制器进行训练的前提下,该控制器能够将室内空气的干球和湿球温度控制在一定范围内,具有较高的控制精度。     

加速神经网络势能面的构建:一种杂化的训练算法

Machine learning approaches have been promising in constructing high-dimensional potential energy surfaces (PESs) for molecules and materials. Neural networks (NNs) are one of the most popular such tools because of its simplicity and efficiency. The training algorithm for NNs becomes essential to achieve a fast and accurate fit with numerous data. The Levenberg-Marquardt (LM) algorithm has been recognized as one of the fastest and robust algorithms to train medium sized NNs and widely applied in recent NN based high quality PESs. However, when the number of ab initio data becomes large, the efficiency of LM is limited, making the training time consuming. Extreme learning machine (ELM) is a recently proposed algorithm which determines the weights and biases of a single hidden layer NN by a linear solution and is thus extremely fast. It, however, does not produce sufficiently small fitting error because of its random nature. Taking advantages of both algorithms, we report a generalized hybrid algorithm in training multilayer NNs. Tests on H+H₂ and CH₄+Ni(111) systems demonstrate the much higher efficiency of this hybrid algorithm (ELM-LM) over the original LM. We expect that ELM-LM will find its widespread applications in building up high-dimensional NN based PESs.     

Small-world and the growing properties of the Chinese railway network

By using the tools of statistical physics and recent investigations of the scaling properties of different complex networks, the structural and evolving properties of the Chinese railway network (CRN) is studied. It has been verified that the CRN has the same small-world properties of the Indian railway network (IRN). According to the class of small-world networks, we believe the CRN is a single scale. In addition, a novel result is obtained. Measurements on the CRN indicate that the rate at which nodes acquire links depends on the node’s degree and follows a power law.      

水下航行器网络控制系统仿真

传统控制系统的设计方法中忽略了通信网络中的时延和数据包丢失等问题,仅通过传统方法设计的控制器来降低其对控制系统产生的不利影响,严重影响了系统的稳定性。对于水下航行器等对系统性能要求较高的水下控制平台,突破传统使其在网络环境下能够稳定运行显得尤为重要。在此背景下,提出了网络控制系统的设计方案,以水下航行器为控制平台,进行系统建模,设计反馈控制器,使用MATLAB仿真工具TrueTime,研究分析了网络体系结构下时延和丢包对传统控制系统动静态性能的影响。仿真结果表明该设计方法优化了系统性能,为系统在发生网络诱导时延和数据包丢失时能够稳定运行,提供了可靠的参考依据。该设计结果具有普适性,也可以用于导弹、坦克等航行器。     

动车组网络控制系统及技术分析

动车组的网络控制系统相当于人的大脑和神经,它在保证列车的行车安全、可靠性、舒适性方面具有至关重要的作用。为了给相关产品的网络控制系统设计提供借鉴,通过梳理中车已有典型动车组产品的网络控制系统,提取共性特征,总结归纳了动车组网络控制系统的组成、系统功能、拓扑功能、主要参数等内容。同时,乘客需求的提升以及轨道交通装备技术的不断升级,对动车组在速度、舒适性、智能化等方面提出了更高要求,为了明确动车组列车网络控制系统的发展方向,通过查询专利文献等途径,得出动车组网络控制系统新技术研究多集中在多网融合、列车冗余优化设计、列车自动驾驶、无线通信等方向,可以为轨道交通技术特别是网络控制系统技术的相关研究提供参考。