The Louvain algorithm (Reichardt and Bornholdt, 2006; Blondel et al., 2008; Ronhovde and Nussinov, 2009; Sun et al., 2009) is a fast, heuristic, agglomerative community detection algorithm, that finds the optimal partition structure of the nodes into communities, by maximizing a measure of partition quality; the modularity index Q (Newman and Girvan, 2004), example in Figure 3B. The Louvain algorithm in this work used an adapted modularity index suitable for directed weighted networks (Rubinov and Sporns, 2010a,b, 2011). It uses a greedy optimization phase which randomly selects the starting node, leads to an inherent variability of the Louvain algorithm. To overcome this, consensus clustering was done (Rubinov and Sporns, 2011; Lancichinetti and Fortunato, 2012; Dwyer et al., 2014), where the algorithm was run R = 100 times, and an R × R module allegiance matrix (Bassett et al., 2013, 2015) was created. The community detection algorithm was then run for a second time on this module allegiance matrix, which revealed the most robust partition of the data (Lancichinetti and Fortunato, 2012). The number of communities in each graph was determined by the output of the algorithm. The Louvain communities in three windows for a patient are shown in Figure 5C.

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