A Regularized Graph Layout Framework for Dynamic Network Visualization

Many real-world networks, including social and information networks, are dynamic structures that evolve over time. Such dynamic networks are typically visualized using a sequence of static graph layouts. In addition to providing a visual representation of the network structure at each time step, the sequence should preserve the mental map between layouts of consecutive time steps to allow a human to interpret the temporal evolution of the network. In this paper, we propose a framework for dynamic network visualization in the on-line setting where only present and past graph snapshots are available to create the present layout. The proposed framework creates regularized graph layouts by augmenting the cost function of a static graph layout algorithm with a grouping penalty, which discourages nodes from deviating too far from other nodes belonging to the same group, and a temporal penalty, which discourages large node movements between consecutive time steps. The penalties increase the stability of the layout sequence, thus preserving the mental map. We introduce two dynamic layout algorithms within the proposed framework, namely dynamic multidimensional scaling (DMDS) and dynamic graph Laplacian layout (DGLL). We apply these algorithms on several data sets to illustrate the importance of both grouping and temporal regularization for producing interpretable visualizations of dynamic networks.Comment: To appear in Data Mining and Knowledge Discovery, supporting material (animations and MATLAB toolbox) available at http://tbayes.eecs.umich.edu/xukevin/visualization_dmkd_201

Community evolution in patent networks: technological change and network dynamics

When studying patent data as a way to understand innovation and technological change, the conventional indicators might fall short, and categorizing technologies based on the existing classification systems used by patent authorities could cause inaccuracy and misclassification, as shown in literature. Gao et al. (International Workshop on Complex Networks and their Applications, 2017) have established a method to analyze patent classes of similar technologies as network communities. In this paper, we adopt the stabilized Louvain method for network community detection to improve consistency and stability. Incorporating the overlapping community mapping algorithm, we also develop a new method to identify the central nodes based on the temporal evolution of the network structure and track the changes of communities over time. A case study of Germany’s patent data is used to demonstrate and verify the application of the method and the results. Compared to the non-network metrics and conventional network measures, we offer a heuristic approach with a dynamic view and more stable results

Community evolution in patent networks: technological change and network dynamics

When studying patent data as a way to understand innovation and technological change, the conventional indicators might fall short, and categorizing technologies based on the existing classification systems used by patent authorities could cause inaccuracy and misclassification, as shown in literature. Gao et al. (International Workshop on Complex Networks and their Applications, 2017) have established a method to analyze patent classes of similar technologies as network communities. In this paper, we adopt the stabilized Louvain method for network community detection to improve consistency and stability. Incorporating the overlapping community mapping algorithm, we also develop a new method to identify the central nodes based on the temporal evolution of the network structure and track the changes of communities over time. A case study of Germany’s patent data is used to demonstrate and verify the application of the method and the results. Compared to the non-network metrics and conventional network measures, we offer a heuristic approach with a dynamic view and more stable results

Intra- and inter-individual genetic differences in gene expression

Genetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences are essentially tissue specific and consequently the same genetic variations in the one animal may up-regulate a CGG in one tissue but down-regulate the same CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. The implication of this study is that this class of genetic variation can result in complex inter- and intra-individual and tissue differences and that this will create substantial challenges to the investigation of phenotypic outcomes, particularly in humans where multiple tissues are not readily available.

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A unified data representation theory for network visualization, ordering and coarse-graining

Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form.Comment: 13 pages, 5 figure

Link-Prediction to Tackle the Boundary Specification Problem in Social Network Surveys

Diffusion processes in social networks often cause the emergence of global phenomena from individual behavior within a society. The study of those global phenomena and the simulation of those diffusion processes frequently require a good model of the global network. However, survey data and data from online sources are often restricted to single social groups or features, such as age groups, single schools, companies, or interest groups. Hence, a modeling approach is required that extrapolates the locally restricted data to a global network model. We tackle this Missing Data Problem using Link-Prediction techniques from social network research, network generation techniques from the area of Social Simulation, as well as a combination of both. We found that techniques employing less information may be more adequate to solve this problem, especially when data granularity is an issue. We validated the network models created with our techniques on a number of real-world networks, investigating degree distributions as well as the likelihood of links given the geographical distance between two nodes

Analysis of gene expression in the nervous system identifies key genes and novel candidates for health and disease

The incidence of neurodegenerative diseases in the developed world has risen over the last century, concomitant with an increase in average human lifespan. A major challenge is therefore to identify genes that control neuronal health and viability with a view to enhancing neuronal health during ageing and reducing the burden of neurodegeneration. Analysis of gene expression data has recently been used to infer gene functions for a range of tissues from co-expression networks. We have now applied this approach to transcriptomic datasets from the mammalian nervous system available in the public domain. We have defined the genes critical for influencing neuronal health and disease in different neurological cell types and brain regions. The functional contribution of genes in each co-expression cluster was validated using human disease and knockout mouse phenotypes, pathways and gene ontology term annotation. Additionally a number of poorly annotated genes were implicated by this approach in nervous system function. Exploiting gene expression data available in the public domain allowed us to validate key nervous system genes and, importantly, to identify additional genes with minimal functional annotation but with the same expression pattern. These genes are thus novel candidates for a role in neurological health and disease and could now be further investigated to confirm their function and regulation during ageing and neurodegeneration. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10048-017-0509-5) contains supplementary material, which is available to authorized users