动态网络社团结构挖掘有助于获取整体网络特性和发展规律。由于动态网络具有多个时刻,传统静态网络社团挖掘算法不仅容易在相邻时刻产生具有较大差异的社团划分结果,而且导致较高时间复杂度。虽然最近受到广泛关注的动态网络增量算法可以一定程度上降低算法时间复杂度,但普遍存在人工设定参数、可扩展性差等局限性。该文提出一种随机游走与增量相关节点相结合的社团挖掘算法(RWIV)进行动态网络社团挖掘。利用动态网络时间局部性即相邻采样时刻网络变化不大的特点,通过对增量相关节点进行随机游走聚类后社团划分,避免了对整个网络中的节点全部重新划分。实验结果和分析表明:RWIV算法可有效解决IC(Incremental algorithm for Community identification)和IDCM(Increment and Density based Community detection Method)判定参数难以选定、累积误差及网络突变等问题,其社团挖掘效率高于现有IC和IDCM算法。
动脉粥样硬化是因脂质堆积在血管壁上并受到多种遗传和环境因素影响的一种复杂的病理生理疾病。动脉粥样硬化风险疾病基因的辨识可以增进对该疾病机理的了解,并对该疾病的诊断和治疗起到指导性作用。虽然在风险疾病基因的辨识方面已经提出了很多计算方法,但仍存在着推论准确性和计算效率方面的问题。一种命名为基于熵聚类和双重筛选(Entropy-based clustering and double screening,ECDS)的新方法被用来辨识该疾病的风险疾病基因。该方法将功能基因组信息和蛋白质相互作用网络拓扑结构信息进行整合,运用于基于熵聚类的方法中,之后,使用双重筛选策略(即支持向量机和相似性得分)进行风险疾病基因挖掘。运用该方法,从巨噬细胞样本和泡沫细胞样本中分别辨识出79个和113个风险疾病基因。该结果表明ECDS在辨识动脉粥样硬化风险疾病基因方面非常有效。此外,该方法也很易于扩展应用到其它复杂疾病的风险基因辨识中。
The sequencing revolution driven by high-throughput technologies has generated a huge amount of marine microbial sequences which hide the interaction patterns among microbial species and environment factors. Exploring these patterns is helpful for exploiting the marine resources. In this paper, we use the complex network approach to mine and analyze the interaction patterns of marine taxa and environments in spring, summer, fall and winter seasons. With the 16S rRNA pyrosequencing data of 76 time point taken monthly over 6 years, we first use our MtHc clustering algorithm to generate the operational taxonomic units （OTUs）. Then, employ the k-means method to divide 76 time point samples into four seasonal groups, and utilize mutual information （MI） to construct the four correlation networks among microbial species and environment factors. Finally, we adopt the symmetrical non-negative matrix factorization method to detect the interaction patterns, and analysis the relationship between marine species and environment factors. The results show that the four seasonal microbial interaction networks have the characters of complex networks, and interaction patterns are related with the seasonal variability; the same environmental factor influences different species in the four seasons; the four environmental factors of day length, photosynthetically active radiation, NO2＋ NO3 and silicate may have stronger influences on microbes than other environment factors.
