Context-aware Distance Measures for Dynamic Networks

Dynamic networks are widely used in the social, physical, and biological sciences as a concise mathematical representation of the evolving interactions in dynamic complex systems. Measuring distances between network snapshots is important for analyzing and understanding evolution processes of dynamic systems. To the best of our knowledge, however, existing network distance measures are designed for static networks. Therefore, when measuring the distance between any two snapshots in dynamic networks, valuable context structure information existing in other snapshots is ignored. To guide the construction of context-aware distance measures, we propose a context-aware distance paradigm, which introduces context information to enrich the connotation of the general definition of network distance measures. A Context-aware Spectral Distance (CSD) is then given as an instance of the paradigm by constructing a context-aware spectral representation to replace the core component of traditional Spectral Distance (SD). In a node-aligned dynamic network, the context effectively helps CSD gain mainly advantages over SD as follows: (1) CSD is not affected by isospectral problems; (2) CSD satisfies all the requirements of a metric, while SD cannot; and (3) CSD is computationally efficient. In order to process large-scale networks, we develop a kCSD that computes top- k eigenvalues to further reduce the computational complexity of CSD. Although kCSD is a pseudo-metric, it retains most of the advantages of CSD. Experimental results in two practical applications, i.e., event detection and network clustering in dynamic networks, show that our context-aware spectral distance performs better than traditional spectral distance in terms of accuracy, stability, and computational efficiency. In addition, context-aware spectral distance outperforms other baseline methods.

Analysing the distance decay of community similarity in river networks using Bayesian methods

The distance decay of community similarity (DDCS) is a pattern that is widely observed in terrestrial and aquatic environments. Niche-based theories argue that species are sorted in space according to their ability to adapt to new environmental conditions. The ecological neutral theory argues that community similarity decays due to ecological drift. The continuum hypothesis provides an intermediate perspective between niche-based theories and the neutral theory, arguing that niche and neutral factors are at the opposite ends of a continuum that ranges from competitive to stochastic exclusion. We assessed the association between niche-based and neutral factors and changes in community similarity measured by Sorensen’s index in riparian plant communities. We assessed the importance of neutral processes using network distances and flow connection and of niche-based processes using Strahler order differences and precipitation differences. We used a hierarchical Bayesian approach to determine which perspective is best supported by the results. We used dataset composed of 338 vegetation censuses from eleven river basins in continental Portugal. We observed that changes in Sorensen indices were associated with network distance, flow connection, Strahler order difference and precipitation difference but to different degrees. The results suggest that community similarity changes are associated with environmental and neutral factors, supporting the continuum hypothesis.

Advances in Regression Kriging-Based Methods for Estimating Statewide Winter Weather Collisions: An Empirical Investigation

Winter conditions create hazardous roads that municipalities work hard to maintain to ensure the safety of the travelling public. Targeting their efforts with effective network screening will help transportation managers address these problems. In our recent efforts, regression kriging was found to be a viable and effective network screening methodology. However, the study was constrained by its limited spatial extent making the reported results less conclusive and transferrable. In addition, our previous work implemented what has long been adopted in most of conventional studies—the Euclidean distance; however, use of the road network distance would, intuitively, result in further improving kriging estimates, especially when dealing with transportation problems. Therefore, this study improves upon our previous efforts by developing a more advanced kriging model; namely, network regression kriging using the entire state of Iowa with the significantly expanded road network. The transferability of the developed models is also explored to investigate its generalization potential. The findings based on various statistical measures suggest that the enhanced kriging model vastly improved the estimation performance at the cost of greater computational complexity and run times. The study also suggests that regional semivariograms better represent the true nature of the local variances, though an overall model may still function adequately if higher fidelity is not required.

Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes

A better fundamental understanding of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has the potential to advance applications ranging from drug discovery to cardiac repair. Automated quantitative analysis of beating hiPSC-CMs is an important and fast developing component of the hiPSC-CM research pipeline. Here we introduce “Sarc-Graph,” a computational framework to segment, track, and analyze sarcomeres in fluorescently tagged hiPSC-CMs. Our framework includes functions to segment z-discs and sarcomeres, track z-discs and sarcomeres in beating cells, and perform automated spatiotemporal analysis and data visualization. In addition to reporting good performance for sarcomere segmentation and tracking with little to no parameter tuning and a short runtime, we introduce two novel analysis approaches. First, we construct spatial graphs where z-discs correspond to nodes and sarcomeres correspond to edges. This makes measuring the network distance between each sarcomere (i.e., the number of connecting sarcomeres separating each sarcomere pair) straightforward. Second, we treat tracked and segmented components as fiducial markers and use them to compute the approximate deformation gradient of the entire tracked population. This represents a new quantitative descriptor of hiPSC-CM function. We showcase and validate our approach with both synthetic and experimental movies of beating hiPSC-CMs. By publishing Sarc-Graph, we aim to make automated quantitative analysis of hiPSC-CM behavior more accessible to the broader research community.