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With multiple units, the naïve VCG protocol that runs several efficient protocols in sequence (one with all agents, and ones with an agent removed, for each agent) is asymptotically optimal for several parameter settings of the number of agents, commodities, and units.
However, the method showed less correlation to the intensity readouts (Supplementary Table S2 shows the results for several parameter settings).
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Several parameter settings are the same for all experiments and are adapted to simulate the behavior of our testbed environment.
Finally, automatic methods determine the number of modules completely automatically, usually by iterating over several parameter settings and selecting the one that optimizes some criterion of cluster quality.
It is used for running several parameter sets.
The best models for ML analysis were estimated using PhyML [ 49] by experimenting with a range of settings for several parameters (gamma parameter, substitution model, number of substitution rate categories) and choosing the ones that gave the highest likelihood.
Since each model has arbitrary parameters, we tested a number of data sets using several different parameter settings.
Although we tried several different parameter settings in each method, only the best results are shown for the comparison.
Several control parameter settings are compared regarding their influence on the optimizer performance.
All numbers are for best parameter settings.
Figure 7 Overall network performance for uniform parameter settings.
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