Higher-Order Visualization of Causal Structures in Dynamics Graphs

Graph or network representations are an important foundation for data mining and machine learning tasks in relational data. Many tools of network analysis, like centrality measures, information ranking, or cluster detection rest on the assumption that links capture direct influence, and that paths represent possible indirect influence. This assumption is invalidated in time-stamped network data capturing, e.g., dynamic social networks, biological sequences or financial transactions. In such data, for two time-stamped links (A,B) and (B,C) the chronological ordering and timing determines whether a causal path from node A via B to C exists. A number of works has shown that for that reason network analysis cannot be directly applied to time-stamped network data. Existing methods to address this issue require statistics on causal paths, which is computationally challenging for big data sets. Addressing this problem, we develop an efficient algorithm to count causal paths in time-stamped network data. Applying it to empirical data, we show that our method is more efficient than a baseline method implemented in an OpenSource data analytics package. Our method works efficiently for different values of the maximum time difference between consecutive links of a causal path and supports streaming scenarios. With it, we are closing a gap that hinders an efficient analysis of big time series data on complex networks

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Principal Patterns on Graphs: Discovering Coherent Structures in Datasets

Graphs are now ubiquitous in almost every field of research. Recently, new research areas devoted to the analysis of graphs and data associated to their vertices have emerged. Focusing on dynamical processes, we propose a fast, robust and scalable framework for retrieving and analyzing recurring patterns of activity on graphs. Our method relies on a novel type of multilayer graph that encodes the spreading or propagation of events between successive time steps. We demonstrate the versatility of our method by applying it on three different real-world examples. Firstly, we study how rumor spreads on a social network. Secondly, we reveal congestion patterns of pedestrians in a train station. Finally, we show how patterns of audio playlists can be used in a recommender system. In each example, relevant information previously hidden in the data is extracted in a very efficient manner, emphasizing the scalability of our method. With a parallel implementation scaling linearly with the size of the dataset, our framework easily handles millions of nodes on a single commodity server

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

We introduce the \texttt{pyunicorn} (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. \texttt{pyunicorn} is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics or network surrogates. Additionally, \texttt{pyunicorn} provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis (RQA), recurrence networks, visibility graphs and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.Comment: 28 pages, 17 figure