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The maximum depth of the graphs; 5.
Number of branch constructions; Number of join constructions; Number of loop constructions; The maximum depth of the graphs; The number of graphs to generate.
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The network is generated as four joint small-world graphs with 30 nodes (to limit the depth of the graph) and rewiring probability p=0.4 (see also details in [16]).
Although these statistics provide good feedback regarding multiple aspects of a predictor's performance, they do not always address node dependency or the problem of unequal specificity of functional annotations found at the same depth of the graph.
The lower bounds L A and L d for the A-cost and the A-depth of the graph for c, respectively, are given in [12] as L A = L d = log 2 S c (2).
In such case r needs to be at least equal to q + 1 in order to achieve n > 3 × 2p − 2 + 2Ω c) + q − 2. On the other hand, if r ≤ q holds, the value s should be at least equal to 1 in order to achieve n > 3 × 2p − 2 + 2Ω c) + q − 2, implying that the A-depth of the overall graph is at least equal to p + 1.
Such methods rely on depth-first walks of the graph to identify closing bifurcations.
Articulation nodes can be detected during a depth-first traversal of the graph, by calculating the "lowpoint" values of every node (cf. [ 48]).
That may prove to be a wise gambit if Facebook can bring to bear its most powerful resource: the depth of their social graph, a vast network of users that includes a huge chunk of the planet's population.
Since similar sequences are directly connected in our graphs, the larger the environmental distribution of ciliates with similar sequences, the lower the assortativity of sequences from a given location or from a given depth in the graph (since ciliates from different locations/depths with similar sequences directly connected in the graph display different labels, Figure 2B).
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