Identifying gene network rewiring by combining gene expression and gene mutation data

Multi-Attribute Decision Making Method for Node Importance Metric in Complex Network

Correctly measuring the importance of nodes in a complex network is critical for studying the robustness of the network, and designing a network security policy based on these highly important nodes can effectively improve security aspects of the network, such as the security of important data nodes on the Internet or the hardening of critical traffic hubs. Currently included are degree centrality, closeness centrality, clustering coefficient, and H-index. Although these indicators can identify important nodes to some extent, they are influenced by a single evaluation perspective and have limitations, so most of the existing evaluation methods cannot fully reflect the node importance information. In this paper, we propose a multi-attribute critic network decision indicator (MCNDI) based on the CRITIC method, considering the H-index, closeness centrality, k-shell indicator, and network constraint coefficient. This method integrates the information of network attributes from multiple perspectives and provides a more comprehensive measure of node importance. An experimental analysis of the Chesapeake Bay network and the contiguous USA network shows that MCNDI has better ranking monotonicity, more stable metric results, and is highly adaptable to network topology. Additionally, deliberate attack simulations on real networks showed that the method exhibits high convergence speed in attacks on USAir97 networks and technology routes networks.

A Novel Cox Proportional Hazards Model for High-Dimensional Genomic Data in Cancer Prognosis

The Cox proportional hazards model is a popular method to study the connection between feature and survival time. Because of the high-dimensionality of genomic data, existing Cox models trained on any specific dataset often generalize poorly to other independent datasets. In this paper, we suggest a novel strategy for the Cox model. This strategy is included a new learning technique, self-paced learning (SPL), and a new gene selection method, SCAD-Net penalty. The SPL method is adopted to aid to build a more accurate prediction with its built-in mechanism of learning from easy samples first and adaptively learning from hard samples. The SCAD-Net penalty has fixed the problem of the SCAD method without an inherent mechanism to fuse the prior graphical information. We combined the SPL with the SCAD-Net penalty to the Cox model (SSNC). The simulation shows that the SSNC outperforms the benchmark in terms of prediction and gene selection. The analysis of a large-scale experiment across several cancer datasets shows that the SSNC method not only results in higher prediction accuracies but also identifies markers that satisfactory stability across another validation dataset. The demo code for the proposed method is provided in supplemental file.

Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate t-Distribution

Identifying gene network rewiring under different biological conditions is important for understanding the mechanisms underlying complex diseases. Gaussian graphical models, which assume the data follow the multivariate normal distribution, are widely used to identify gene network rewiring. However, the normality assume often fails in reality since the data are contaminated by extreme outliers in general. In this study, we propose a new robust differential graphical model to identify gene network rewiring between two conditions based on the multivariate t-distribution. The multivariate t-distribution is more robust to outliers than the normal distribution since it has heavy tails and allows values far from the mean. A fused lasso penalty is used to borrow information across conditions to improve the results. We develop an expectation maximization algorithm to solve the optimization model. Experiment results on simulated data show that our method outperforms the state-of-the-art methods. Our method is also applied to identify gene network rewiring between luminal A and basal-like subtypes of breast cancer, and gene network rewiring between the proneural and mesenchymal subtypes of glioblastoma. Several key genes which drive gene network rewiring are discovered.