Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Results: Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. Conclusions: Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks

Application of Random Matrix Theory to Biological Networks

We show that spectral fluctuation of interaction matrices of yeast a core protein interaction network and a metabolic network follows the description of the Gaussian orthogonal ensemble (GOE) of random matrix theory (RMT). Furthermore, we demonstrate that while the global biological networks evaluated belong to GOE, removal of interactions between constituents transitions the networks to systems of isolated modules described by the Poisson statistics of RMT. Our results indicate that although biological networks are very different from other complex systems at the molecular level, they display the same statistical properties at large scale. The transition point provides a new objective approach for the identification of functional modules.Comment: 3 pages, 2 figure

Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Models of Social Groups in Blogosphere Based on Information about Comment Addressees and Sentiments

This work concerns the analysis of number, sizes and other characteristics of groups identified in the blogosphere using a set of models identifying social relations. These models differ regarding identification of social relations, influenced by methods of classifying the addressee of the comments (they are either the post author or the author of a comment on which this comment is directly addressing) and by a sentiment calculated for comments considering the statistics of words present and connotation. The state of a selected blog portal was analyzed in sequential, partly overlapping time intervals. Groups in each interval were identified using a version of the CPM algorithm, on the basis of them, stable groups, existing for at least a minimal assumed duration of time, were identified.Comment: Gliwa B., Ko\'zlak J., Zygmunt A., Models of Social Groups in Blogosphere Based on Information about Comment Addressees and Sentiments, in the K. Aberer et al. (Eds.): SocInfo 2012, LNCS 7710, pp. 475-488, Best Paper Awar

Learning Particle Dynamics for Manipulating Rigid Bodies, Deformable Objects, and Fluids

Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been developed to model the dynamics of these complex scenes; however, relying on approximation techniques, their simulation often deviates from real-world physics, especially in the long term. In this paper, we propose to learn a particle-based simulator for complex control tasks. Combining learning with particle-based systems brings in two major benefits: first, the learned simulator, just like other particle-based systems, acts widely on objects of different materials; second, the particle-based representation poses strong inductive bias for learning: particles of the same type have the same dynamics within. This enables the model to quickly adapt to new environments of unknown dynamics within a few observations. We demonstrate robots achieving complex manipulation tasks using the learned simulator, such as manipulating fluids and deformable foam, with experiments both in simulation and in the real world. Our study helps lay the foundation for robot learning of dynamic scenes with particle-based representations.Comment: Accepted to ICLR 2019. Project Page: http://dpi.csail.mit.edu Video: https://www.youtube.com/watch?v=FrPpP7aW3L