se3-denoise-sidechainnet.py

import torch
import torch.nn.functional as F
from torch.optim import Adam

from einops import rearrange, repeat
import sidechainnet as scn
from se3_transformer_pytorch.se3_transformer_pytorch import SE3Transformer

torch.set_default_dtype(torch.float64)

BATCH_SIZE = 1
GRADIENT_ACCUMULATE_EVERY = 16

def cycle(loader, len_thres = 500):
    while True:
        for data in loader:
            if data.seqs.shape[1] > len_thres:
                continue
            yield data

def test_sequence():
    # Move this to a config
    transformer = SE3Transformer(
        num_tokens = 24,
        dim = 8,
        dim_head = 8,
        heads = 2,
        depth = 2,
        num_neighbors = 12,
        attend_self = True,
        input_degrees = 1,
        output_degrees = 2,
        reduce_dim_out = True,
        differentiable_coors = True
    )

    data = scn.load(
        casp_version = 12,
        thinning = 30,
        with_pytorch = 'dataloaders',
        batch_size = BATCH_SIZE,
        dynamic_batching = False
    )
    # Add gaussian noise to the coords
    # Testing the refinement algorithm

    dl = cycle(data['train'])
    optim = Adam(transformer.parameters(), lr=1e-4)
    transformer = transformer.cuda()

    for _ in range(10000):
        for _ in range(GRADIENT_ACCUMULATE_EVERY):
            batch = next(dl)
            seqs, coords, masks = batch.seqs, batch.crds, batch.msks

            seqs = seqs.cuda().argmax(dim = -1)
            coords = coords.cuda().type(torch.float64)
            masks = masks.cuda().bool()

            l = seqs.shape[1]
            coords = rearrange(coords, 'b (l s) c -> b l s c', s=14)

            # Keeping only the backbone coordinates
            coords = coords[:, :, 0:4, :]
            coords = rearrange(coords, 'b l s c -> b (l s) c')

            seq = repeat(seqs, 'b n -> b (n c)', c = 4)
            masks = repeat(masks, 'b n -> b (n c)', c = 4)

            noised_coords = coords + torch.randn_like(coords).cuda()

            out = transformer(
                seq,
                noised_coords,
                mask = masks,
                return_type = 1
            )

            denoised_coords = noised_coords + out

            loss = F.mse_loss(denoised_coords[masks], coords[masks]) 
            (loss / GRADIENT_ACCUMULATE_EVERY).backward()

        print('loss:', loss.item())
        optim.step()
        optim.zero_grad()

if __name__ == '__main__':
    # This starts to NaN after the first iteration
    test_sequence()