Algorithm 10 of the Supplementary Information to Jumper et al. (2021),
p. 17. This is the only path by which the MSA stack writes into the
pair stack. Rows i and j of the MSA representation are
projected, their outer product is averaged over sequences, flattened and
projected to the pair channel width.
Usage
Alfopm(m, wa, wb, wo, layernorm = TRUE)
Arguments
- m
MSA representation, an s x n x cm array.
- wa, wb
The two projections of line 2, each c x cm.
- wo
Output projection, cz x (c * c) (line 4).
- layernorm
Apply the layer normalisation of line 1. FALSE exposes
the degenerate single-channel reduction to a Gram matrix.
Value
A list with the pair update z, the flattened outer product
means o, estimate, n and method.
References
Jumper et al (2021) Nature 596:583-589, Suppl. Algorithm 10
Examples
set.seed(6)
m <- array(rnorm(2 * 3 * 4), c(2, 3, 4)) # 2 sequences, 3 residues, cm = 4
r <- Alfopm(m, wa = matrix(rnorm(8), 2, 4), wb = matrix(rnorm(8), 2, 4), wo = matrix(rnorm(12), 3, 4))
dim(r$z)
#> [1] 3 3 3
