Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
(A) A generative process for the univariate leaf distribution. Here, the hidden variable I takes on a value of 0, 1 or −1 depending on whether selection pressure is absent, positive, or negative. (The subscript i, denoting a particular individual, is suppressed for simplicity.) The result is copied to Σ, which determines the result of the selection pressure. (B) The function that maps Σ and H to Y. (C) A generative process for the multivariate Noisy Add leaf distribution. (D) The grouping of the multivariate Noisy Add leaf distribution into a series of summations, grouped as Σ2 = I1+I2, Σ3 = Σ2+I3, and so on. This grouping makes inference much faster.