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ItemHyperGraphs.jl: representing higher-order relationships in Julia.Diaz, LPM ; Stumpf, MPH ; Martelli, PL (Oxford University Press (OUP), 2022-07-11)SUMMARY: HyperGraphs.jl is a Julia package that implements hypergraphs. These are a generalization of graphs that allow us to represent n-ary relationships and not just binary, pairwise relationships. High-order interactions are commonplace in biological systems and are of critical importance to their dynamics; hypergraphs thus offer a natural way to accurately describe and model these systems. AVAILABILITY AND IMPLEMENTATION: HyperGraphs.jl is freely available under the MIT license. Source code and documentation can be found at https://github.com/lpmdiaz/HyperGraphs.jl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
ItemGaining confidence in inferred networksDiaz, LPM ; Stumpf, MPH (NATURE PORTFOLIO, 2022-02-14)Network inference is a notoriously challenging problem. Inferred networks are associated with high uncertainty and likely riddled with false positive and false negative interactions. Especially for biological networks we do not have good ways of judging the performance of inference methods against real networks, and instead we often rely solely on the performance against simulated data. Gaining confidence in networks inferred from real data nevertheless thus requires establishing reliable validation methods. Here, we argue that the expectation of mixing patterns in biological networks such as gene regulatory networks offers a reasonable starting point: interactions are more likely to occur between nodes with similar biological functions. We can quantify this behaviour using the assortativity coefficient, and here we show that the resulting heuristic, functional assortativity, offers a reliable and informative route for comparing different inference algorithms.