A Book of Generations – Writing at the Frontier

We address the problem of finding viewpoints that preserve the relational structure of a three-dimensional graph drawing under orthographic parallel projection. Previously, algorithms for finding the best viewpoints under two natural models of viewpoint “goodness” were proposed. Unfortunately, the inherent combinatorial complexity of the problem makes finding exact solutions is impractical. In this paper, we propose two approximation algorithms for the problem, commenting on their design, and presenting results on their performance

Design of chemical space networks incorporating compound distance relationships

Networks, in which nodes represent compounds and edges pairwise similarity relationships, are used as coordinate-free representations of chemical space. So-called chemical space networks (CSNs) provide intuitive access to structural relationships within compound data sets and can be annotated with activity information. However, in such similarity-based networks, distances between compounds are typically determined for layout purposes and clarity and have no chemical meaning. By contrast, inter-compound distances as a measure of dissimilarity can be directly obtained from coordinate-based representations of chemical space. Herein, we introduce a CSN variant that incorporates compound distance relationships and thus further increases the information content of compound networks. The design was facilitated by adapting the Kamada-Kawai algorithm. Kamada-Kawai networks are the first CSNs that are based on numerical similarity measures, but do not depend on chosen similarity threshold values

A statistical network analysis of the HIV/AIDS epidemics in Cuba

The Cuban contact-tracing detection system set up in 1986 allowed the reconstruction and analysis of the sexual network underlying the epidemic (5,389 vertices and 4,073 edges, giant component of 2,386 nodes and 3,168 edges), shedding light onto the spread of HIV and the role of contact-tracing. Clustering based on modularity optimization provides a better visualization and understanding of the network, in combination with the study of covariates. The graph has a globally low but heterogeneous density, with clusters of high intraconnectivity but low interconnectivity. Though descriptive, our results pave the way for incorporating structure when studying stochastic SIR epidemics spreading on social networks

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

"Meaning" as a sociological concept: A review of the modeling, mapping, and simulation of the communication of knowledge and meaning

The development of discursive knowledge presumes the communication of meaning as analytically different from the communication of information. Knowledge can then be considered as a meaning which makes a difference. Whereas the communication of information is studied in the information sciences and scientometrics, the communication of meaning has been central to Luhmann's attempts to make the theory of autopoiesis relevant for sociology. Analytical techniques such as semantic maps and the simulation of anticipatory systems enable us to operationalize the distinctions which Luhmann proposed as relevant to the elaboration of Husserl's "horizons of meaning" in empirical research: interactions among communications, the organization of meaning in instantiations, and the self-organization of interhuman communication in terms of symbolically generalized media such as truth, love, and power. Horizons of meaning, however, remain uncertain orders of expectations, and one should caution against reification from the meta-biological perspective of systems theory

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

Recognition of Crowd Behavior from Mobile Sensors with Pattern Analysis and Graph Clustering Methods

Mobile on-body sensing has distinct advantages for the analysis and understanding of crowd dynamics: sensing is not geographically restricted to a specific instrumented area, mobile phones offer on-body sensing and they are already deployed on a large scale, and the rich sets of sensors they contain allows one to characterize the behavior of users through pattern recognition techniques. In this paper we present a methodological framework for the machine recognition of crowd behavior from on-body sensors, such as those in mobile phones. The recognition of crowd behaviors opens the way to the acquisition of large-scale datasets for the analysis and understanding of crowd dynamics. It has also practical safety applications by providing improved crowd situational awareness in cases of emergency. The framework comprises: behavioral recognition with the user's mobile device, pairwise analyses of the activity relatedness of two users, and graph clustering in order to uncover globally, which users participate in a given crowd behavior. We illustrate this framework for the identification of groups of persons walking, using empirically collected data. We discuss the challenges and research avenues for theoretical and applied mathematics arising from the mobile sensing of crowd behaviors

The role of endogenous and exogenous mechanisms in the formation of R&D networks

We develop an agent-based model of strategic link formation in Research and Development (R&D)networks. Empirical evidence has shown that the growth of these networks is driven by mechanisms whichare both endogenous to the system (that is, depending on existing alliances patterns) and exogenous (that is, driven by an exploratory search for newcomer firms). Extant research to date has not investigated both mechanisms simultaneously in a comparative manner. To overcome this limitation, we develop a general modeling framework to shed light on the relative importance of these two mechanisms. We test our model against a comprehensive dataset, listing cross-country and cross-sectoral R&D alliances from 1984 to 2009. Our results show that by fitting only three macroscopic properties of the network topology, this framework is able to reproduce a number of micro-level measures, including the distributions of degree, local clustering, path length and component size, and the emergence of network clusters. Furthermore, by estimating the link probabilities towards newcomers and established firms from the data, we find that endogenous mechanisms are predominant over the exogenous ones in the network formation, thus quantifying the importance of existing structures in selecting partner firms