Real-world network datasets are typically obtained in ways that fail to capture all edges. The patterns of missing data are often non-uniform as they reflect biases and other shortcomings of different data collection methods. Nevertheless, uniform missing data is a common assumption made when no additional information is available about the underlying missing-edge pattern, and link prediction methods are frequently tested against uniformly missing edges. To investigate the impact of different missing-edge patterns on link prediction accuracy, we employ 9 link prediction algorithms from 4 different families to analyze 20 different missing-edge patterns that we categorize into 5 groups. Our comparative simulation study, spanning 250 real-world network datasets from 6 different domains, provides a detailed picture of the significant variations in the performance of different link prediction algorithms in these different settings. With this study, we aim to provide a guide for future researchers to help them select a link prediction algorithm that is well suited to their sampled network data, considering the data collection process and application domain.

Link prediction algorithms are indispensable tools in many scientific applications by speeding up network data collection and imputing missing connections. However, in many systems, links change over time and it remains unclear how to optimally exploit such temporal information for link predictions in such networks. Here, we show that many temporal topological features, in addition to having high computational cost, are less accurate in temporal link prediction than sequentially stacked static network features. This sequential stacking link prediction method uses 41 static network features that avoid detailed feature engineering choices and is capable of learning a highly accurate predictive distribution of future connections from historical data. We demonstrate that this algorithm works well for both partially observed and completely unobserved target layers, and on two temporal stochastic block models achieves near-oracle-level performance when combined with other single predictor methods as an ensemble learning method. Finally, we empirically illustrate that stacking multiple predictive methods together further improves performance on 19 real-world temporal networks from different domains.

Cancer cells alter the expression levels of metabolic enzymes to fuel proliferation. The mitochondrion is a central hub of metabolic reprogramming, where chaperones service hundreds of clients, forming chaperone-client interaction networks. How network structure affects its robustness to chaperone targeting is key to developing cancer-specific drug therapy. However, few studies have assessed how structure and robustness vary across different cancer tissues. Here, using ecological network analysis, we reveal a non-random, hierarchical pattern whereby the cancer type modulates the chaperones’ ability to realize their potential client interactions. Despite the low similarity between the chaperone-client interaction networks, we highly accurately predict links in one cancer type based on another. Moreover, we identify groups of chaperones that interact with similar clients. Simulations of network robustness show that this group structure affects cancer-specific response to chaperone removal. Our results open the door for new hypotheses regarding the ecology and evolution of chaperone-client interaction networks and can inform cancer-specific drug development strategies.

An active area of research in computational science is the design of algorithms for solving the subgraph matching problem to find copies of a given template graph in a larger world graph. Prior works have largely addressed single-channel networks using a variety of approaches. We present a suite of filtering methods for subgraph isomorphisms for multiplex networks (with different types of edges between nodes and more than one edge within each channel type). We aim to understand the entire solution space rather than focusing on finding one isomorphism. Results are shown on several classes of datasets: (a) Sudoku puzzles mapped to the subgraph isomorphism problem, (b) Erdos-Renyi multigraphs, (c) real-world datasets from Twitter and transportation networks, (d) synthetic data created for the DARPA MAA program.

We address the problem of finding noisy subgraph isomorphisms on large multiplex networks. Our goal is to find as many subgraph matches as possible within a noise tolerance. We propose a novel approach based on the well-known A* search algorithm. Our approach employs new heuristics to estimate the number of missing edges of subgraph matches. This method is verified on one of the synthetic multiplex networks from the Modeling Adversarial Activity program of the Defense Advanced Research Projects Agency.