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We present EASEE (Edge Advertisements into Snapshots using Evolving Expectations) for partitioning streaming communication data into static graph snapshots. Given streaming communication events (A talks to B), EASEE identifies when events suffice for a static graph (a snapshot ). EASEE uses combinatorial statistical models to adaptively find when a snapshot is stable, while watching for significant data shifts – indicating a new snapshot should begin. If snapshots are not found carefully, they poorly represent the underlying data – and downstream graph analytics fail: We show a community detection example. We demonstrate EASEE's strengths against several real-world datasets, and its accuracy against known-answer synthetic datasets. Synthetic datasets' results show that (1) EASEE finds known-answer data shifts very quickly; and (2) ignoring these shifts drastically affects analytics on resulting snapshots. We show that previous work misses these shifts. Further, we evaluate EASEE against seven real-world datasets (330 K to 2.5B events), and find snapshot-over-time behaviors missed by previous works. Finally, we show that the resulting snapshots' measured properties (e.g., graph density) are altered by how snapshots are identified from the communication event stream. In particular, EASEE's snapshots do not generally “densify” over time, contradicting previous influential results that used simpler partitioning methods. 

We propose a novel method which we call the Probabilistic Infection Model (PIM). Instead of stochastically assigning exactly one state to each agent at a time, PIM tracks the likelihood of each agent being in a particular state. Thus, a particular agent can exist in multiple disease states concurrently. Our model gives an improved resolution of transitions between states, and allows for a more comprehensive view of outbreak dynamics at the individual level. Moreover, by using a probabilistic approach, our model gives a representative understanding of the overall trajectories of simulated outbreaks without the need for numerous (order of hundreds) of repeated Monte Carlo simulations. We simulate our model over a contact network constructed using registration data of university students. We model three diseases; measles and two strains of influenza. We compare the results obtained by PIM with those obtained by simulating stochastic SEIR models over the same the contact network. The results demonstrate that the PIM can successfully replicate the averaged results from numerous simulations of a stochastic model in a single deterministic simulation. Keywords: Computational epidemics, Outbreak simulation, SEIR model 

Leveraging protein-protein interaction networks to identify groups of proteins and their common functionality is an important problem in bioinformatics. Systems-level analysis of protein-protein interactions is made possible through network science and modeling of high-throughput data. From these analyses, small protein complexes are traditionally represented graphically as complete graphs or dense clusters of nodes. However, there are certain graph theoretic properties that have not been extensively studied in PPI networks, especially as they pertain to cluster discovery, such as planarity. Planarity of graphs have been used to reflect the physical constraints of real-world systems outside of bioinformatics, in areas such as mapping and imaging. Here, we investigate the planarity property in network models of protein complexes. We hypothesize that complexes represented as PPI subgraphs will tend to be planar, reflecting the actual physical interface and limits of components in the complex. When testing the planarity of known complex subgraphs in S. cerevisiae and selected mammalian PPIs, we find that a majority of validated complexes possess this planar property. We discuss the biological motivation of planar versus nonplanar subgraphs, observing that planar subgraphs tend to have longer protein components. Functional classification of planar versus nonplanar complex subgraphs reveals differences in annotation of these groups relating to cellular component organization, structural molecule activity, catalytic activity, and nucleic acid binding. These results provide a new quantitative and biologically motivated measure of real protein complexes in the network model, important for the development of future complex-finding algorithms in PPIs. Accounting for this property paves the way to new means for discovering new protein complexes and uncovering the functionality of unknown or novel proteins. s 

Computing single-source shortest paths (SSSP) is one of the fundamental problems in graph theory. There are many applications of SSSP including finding routes in GPS systems and finding high centrality vertices for effective vaccination. In this paper, we focus on calculating SSSP on big dynamic graphs, which change with time. We propose a novel distributed computing approach, SSSPIncJoint, to update SSSP on big dynamic graphs using GraphX. Our approach considerably speeds up the recomputation of the SSSP tree by reducing the number of map-reduce operations required for implementing SSSP in the gather-apply- scatter programming model used by GraphX. 

Computing the single-source shortest path (SSSP) is one of the fundamental graph algorithms, and is used in many applications. Here, we focus on computing SSSP on large dynamic graphs, i.e. graphs whose structure evolves with time. We posit that instead of recomputing the SSSP for each set of changes on the dynamic graphs, it is more efficient to update the results based only on the region of change. To this end, we present a novel two-step shared-memory algorithm for updating SSSP on weighted large-scale graphs. The key idea of our algorithm is to identify changes, such as vertex/edge addition and deletion, that affect the shortest path computations and update only the parts of the graphs affected by the change. We provide the proof of correctness of our proposed algorithm. Our experiments on real and synthetic networks demonstrate that our algorithm is as much as 4X faster compared to computing SSSP with Galois, a state-of-the-art parallel graph analysis software for shared memory architectures. We also demonstrate how increasing the asynchrony can lead to even faster updates. To the best of our knowledge, this is one of the first practical parallel algorithms for updating networks on shared-memory systems, that is also scalable to large networks. 

In this paper, we present a network-based template for analyzing large-scale dynamic data. Specifically, we present a novel shared-memory parallel algorithm for updating treebased structures, including connected components (CC) and the minimum spanning tree (MST) on dynamic networks. We propose a rooted tree-based data structure to store the edges that are most relevant to the analysis. Our algorithm is based on updating the information stored in this rooted tree.In this paper, we present a network-based template for analyzing large-scale dynamic data. Specifically, we present a novel shared-memory parallel algorithm for updating tree-based structures, including connected components (CC) and the minimum spanning tree (MST) on dynamic networks. We propose a rooted tree-based data structure to store the edges that are most relevant to the analysis. Our algorithm is based on updating the information stored in this rooted tree.