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In short, the Geithner agenda was to allow the Wall Street banks to feed at the public trough until they were returned to their prior strength.
Although the organization is certainly weaker than it was at its peak five years ago and is unlikely to regain its prior strength, American and Iraqi analysts said the Qaeda franchise is shifting its tactics and strategies — like attacking Iraqi security forces in small squads — to exploit gaps left by the departing American troops and to try to reignite sectarian violence in the country.
Prior strength M = 100 seems to provide good results and this value was used in all our simulations for consistency.
For simplicity, we use the same prior strength for all the motif models, although this does not need to be the case in general.
We instead use a version that incorporates a so-called prior strength term M, i.e., <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0001820.e039.PNG" class= inline-graphic"/> This prevents a (single) sequence to have too strong of an influence on the posterior parameter values.
The error is relatively insensitive to variations in κ as the final error is in the range of 5.6 6.1 for different κ values, although the connectivity increases with increasing prior strength in the cost function.
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Figure 3 shows the ROC results for the likelihood and Bayesian methods with varying prior strengths (see 'Materials and Methods' Section for more details).
Figure 4 shows histograms of the estimated binding probabilities for the likelihood and Bayesian methods for prior strengths M = 50 and M = 100.
In terms of ROC curves and AUC measures, proposed methods are insensitive to small deviations in prior strengths (within a range of reasonable values).
Typically, smaller prior strengths also bias overall posterior probabilities towards higher values, especially for the negative set (compare blue bars in Figures 4 (a b) with the ones in (c d)).
Smaller prior strengths correspond to more uncertain motif models and that, in turn, allows the data (i.e., promoter sequence) to have a stronger effect on the posterior motif model.
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