Distogram prediction head of AlphaFold

Supplement section 1.9.8 of Jumper et al. (2021), p. 39. The pair representation is symmetrised, projected to distance bins and passed through a softmax. Symmetrising is the point: a distance is symmetric, and feeding the head z_ij + z_ji guarantees the prediction respects that whatever the trunk produced.

Usage

Alfdgram(z, w, bins = NULL, dtrue = NULL)

Arguments

z

Pair representation, an n x n x cz array.

w

Projection to the bin logits.

bins

Bin centres; defaults to 64 bins from 2 to 22 angstrom.

dtrue

Optional ground-truth distances, giving the cross-entropy of equation (41).

Value

A list with the distributions p, expected distances dist, the loss, estimate, n and method.

References

Jumper et al (2021) Nature 596:583-589, Suppl. section 1.9.8

Examples

set.seed(12)
n <- 4; cz <- 3
z <- array(rnorm(n * n * cz), c(n, n, cz))
w <- matrix(rnorm(64 * cz), 64, cz)
dim(Alfdgram(z, w)$p)
#> [1]  4  4 64