Protein interaction networks: centrality,modularity, dynamics,and applications

In the post-genomic era, proteomics has achieved significant theoretical and practical advances with the development of high-throughput technologies. Especially the rapid accumulation of protein-protein interactions (PPIs) provides a foundation for constructing protein interaction networks (PINs), which can furnish a new perspective for understanding cellular organizations, processes, and functions at network level. In this paper, we present a comprehensive survey on three main characteristics of PINs: centrality, modularity, and dynamics. 1) Different centrality measures, which are used to calculate the importance of proteins, are summarized based on the structural characteristics of PINs or on the basis of its integrated biological information; 2) Different modularity definitions and various clustering algorithms for predicting protein complexes or identifying functional modules are introduced; 3) The dynamics of proteins, PPIs and sub-networks are discussed, respectively. Finally, the main applications of PINs in the complex diseases are reviewed, and the challenges and future research directions are also discussed.     

基于加权网络和局部适应度的蛋白质复合物识别算法

蛋白质复合物识别对分析蛋白质网络的结构特征和模块功能具有重要意义。通常在蛋白质网络中挖掘稠密子图或模块来识别其中的蛋白质复合物,限制了其应用范围和识别的准确性。针对该问题,提出了一种基于加权网络和局部适应度的蛋白质复合物识别算法,该算法综合稠密子图的密度指标和模块性定义了新的局部适应度函数,并基于边聚集系数构建加权的蛋白质网络,根据权值选择边,在加权蛋白质网络中将种子边不断聚类扩展,从而获取具有最大综合适应度的子图作为蛋白质复合物。在酵母蛋白质等多个实际网络中试验表明,该算法能够有效提升蛋白质复合物识别的准确性。     

动态社会网络的社团结构检测与分析

真实社会网络如邮件、科学合作、对等网络等均可以用图进行建模. 近年来, 基于图的社团挖掘吸引了人们越来越多的研究兴趣, 它不仅可以帮助识别网络的整体结构, 还可以发现社团演变的隐藏规律. 尽管使用静态图进行社团挖掘已经被广泛采用, 但基于动态图的研究还比较少. 通过使用时间序列, 对动态图上的社团挖掘包括社团检测与分析进行研究, 提出了一个新的动态社团结构检测模型, 并采用真实网络数据集进行了实验. 实验结果显示该模型在社团结构发现的有效性和效率性方面均有着良好的表现.     

Task-dependent evolution of modularity in neural networks

There exist many ideas and assumptions about the development and meaning of modularity in biological and technical neural systems. We empirically study the evolution of connectionist models in the context of modular problems. For this purpose, we define quantitative measures for the degree of modularity and monitor them during evolutionary processes under different constraints. It turns out that the modularity of the problem is reflected by the architecture of adapted systems, although learning can counterbalance some imperfection of the architecture. The demand for fast learning systems increases the selective pressure towards modularity.     

Connectionist simulation of quantification skills

The study of numerical abilities, and how they are acquired, is being used to explore the continuity between ontogenesis and environmental learning. One technique that proves useful in this exploration is the artificial simulation of numerical abilities with neural networks, using different learning paradigms to explore development. A neural network simulation of subitization, sometimes referred to as visual enumeration, and of counting, a recurrent operation, has been developed using the so-called multi-net architecture. Our numerical ability simulations use two or more neural networks combining supervised and unsupervised learning techniques to model subitization and counting. Subitization has been simulated using networks employing unsupervised self-organizing learning, the results of which agree with infant subitization experiments and are comparable with supervised neural network simulations of subitization reported in the literature. Counting has been simulated using a multi-net system of supervised static and recurrent backpropagation networks that learn their individual tasks within an unsupervised, competitive framework. The developmental profile of the counting simulation shows similarities to that of children learning to count and demonstrates how neural networks can learn how to be combined together in a process modelling development.     

基于模块度的社交网络分形维度计算方法

社交网络是由个体或组织以及它们之间的关系所组成的社会结构。利用社交网络的分形结构来解释和预测社交网络的行为是目前的一个研究热点。分形维度是对社交网络中分形结构的度量,为了更准确地对社交网络分形结构进行度量,提出了一种基于模块度的盒子覆盖算法来计算分形维度。该算法利用分形维度和模块度互斥的性质,基于模块度最小的原则来构建盒子,再对盒子进行计数来计算社交网络的分形维度。仿真实验表明：基于模块度的盒子覆盖法比传统的盒覆盖算法得到更为精确的分形维度。     

Detecting Overlapping Community Structures in Networks

Community structure has been recognized as an important statistical feature of networked systems over the past decade. A lot of work has been done to discover isolated communities from a network, and the focus was on developing of algorithms with high quality and good performance. However, there is less work done on the discovery of overlapping community structure, even though it could better capture the nature of network in some real-world applications. For example, people are always provided with varying characteristics and interests, and are able to join very different communities in their social network. In this context, we present a novel overlapping community structures detecting algorithm which first finds the seed sets by the spectral partition and then extends them with a special random walks technique. At every expansion step, the modularity function Q is chosen to measure the expansion structures. The function has become one of the popular standards in community detecting and is defined in Newman and Girvan (Phys. Rev. 69:026113, 2004). We also give a theoretic analysis to the whole expansion process and prove that our algorithm gets the best community structures greedily. Extensive experiments are conducted in real-world networks with various sizes. The results show that overlapping is important to find the complete community structures and our method outperforms the C-means in quality.     

复杂网络强社团结构探测

社团结构是反映复杂网络整体性质的重要特征,本文从强社团结构定义出发提出简单启发式强社团结构探测算法,受启发因素为度-度负相关性和簇-度负相关性.利用该算法对空手道俱乐部成员关系网络和美国大学橄榄球队网络进行社团结构探测,验证了该算法能正确探测出网络的强社团结构.并将划分结果与传统划分进行比较分析,该算法未引入其它量化指标或中间变量,降低了计算复杂度,在采用方法上不同于单纯的分裂或聚合,有效地提高了探测速度,更适合大规模复杂网络社团结构探测.     

基于模块度优化的标签传播社区发现算法

标签传播算法（LPA）是一种快速高效的社区发现算法,算法无需社区数量等先验信息,但存在大量随机性,稳定性较差. 为了提高标签传播算法的稳定性,提出了一种改进的标签传播算法（LPAMP）. 该算法分为两个阶段,第一阶段以模块度贪婪为依据,进行节点粗聚类;第二阶段在粗聚类的基础上,进行节点标签传播. 实验结果表明,所提算法降低了标签传播算法的随机性,增强了稳定性,并且提高了准确率.