def forward(self,
feats,
coors,
mask=None,
adj_mat=None,
edges=None,
return_type=None,
return_pooled=False):
_mask = mask
if self.output_degrees == 1:
return_type = 0
if exists(self.token_emb):
feats = self.token_emb(feats)
assert not (
self.attend_sparse_neighbors and not exists(adj_mat)
), 'adjacency matrix (adjacency_mat) or edges (edges) must be passed in'
assert not (
exists(edges) and not exists(self.edge_emb)
), 'edge embedding (num_edge_tokens & edge_dim) must be supplied if one were to train on edge types'
if torch.is_tensor(feats):
feats = {'0': feats[..., None]}
b, n, d, *_, device = *feats['0'].shape, feats['0'].device
assert d == self.dim, f'feature dimension {d} must be equal to dimension given at init {self.dim}'
assert set(map(int, feats.keys())) == set(
range(self.input_degrees
)), f'input must have {self.input_degrees} degree'
num_degrees, neighbors, max_sparse_neighbors, valid_radius = self.num_degrees, self.num_neighbors, self.max_sparse_neighbors, self.valid_radius
assert self.attend_sparse_neighbors or neighbors > 0, 'you must either attend to sparsely bonded neighbors, or set number of locally attended neighbors to be greater than 0'
# create N-degrees adjacent matrix from 1st degree connections
if exists(self.num_adj_degrees):
if len(adj_mat.shape) == 2:
adj_mat = repeat(adj_mat.clone(), 'i j -> b i j', b=b)
adj_indices = adj_mat.clone().long()
for ind in range(self.num_adj_degrees - 1):
degree = ind + 2
next_degree_adj_mat = (adj_mat.float() @ adj_mat.float()) > 0
next_degree_mask = (next_degree_adj_mat.float() -
adj_mat.float()).bool()
adj_indices.masked_fill_(next_degree_mask, degree)
adj_mat = next_degree_adj_mat.clone()
# se3 transformer by default cannot have a node attend to itself
exclude_self_mask = rearrange(
~torch.eye(n, dtype=torch.bool, device=device), 'i j -> () i j')
# calculate sparsely connected neighbors
sparse_neighbor_mask = None
num_sparse_neighbors = 0
if self.attend_sparse_neighbors:
assert exists(
adj_mat
), 'adjacency matrix must be passed in (keyword argument adj_mat)'
if exists(adj_mat):
if len(adj_mat) == 2:
adj_mat = repeat(adj_mat, 'i j -> b i j', b=b)
adj_mat = adj_mat.masked_select(exclude_self_mask).reshape(
b, n, n - 1)
adj_mat_values = adj_mat.float()
adj_mat_max_neighbors = adj_mat_values.sum(dim=-1).max().item()
if max_sparse_neighbors < adj_mat_max_neighbors:
noise = torch.empty_like(adj_mat_values).uniform_(-0.01, 0.01)
adj_mat_values += noise
num_sparse_neighbors = int(
min(max_sparse_neighbors, adj_mat_max_neighbors))
values, indices = adj_mat_values.topk(num_sparse_neighbors, dim=-1)
sparse_neighbor_mask = torch.zeros_like(adj_mat_values).scatter_(
-1, indices, values)
sparse_neighbor_mask = sparse_neighbor_mask > 0.5
# exclude edge of token to itself
indices = repeat(torch.arange(n, device=device),
'i -> b i j',
b=b,
j=n)
rel_pos = rearrange(coors, 'b n d -> b n () d') - rearrange(
coors, 'b n d -> b () n d')
indices = indices.masked_select(exclude_self_mask).reshape(b, n, n - 1)
rel_pos = rel_pos.masked_select(exclude_self_mask[..., None]).reshape(
b, n, n - 1, 3)
if exists(mask):
mask = rearrange(mask, 'b i -> b i ()') * rearrange(
mask, 'b j -> b () j')
mask = mask.masked_select(exclude_self_mask).reshape(b, n, n - 1)
if exists(edges):
edges = self.edge_emb(edges)
edges = edges.masked_select(exclude_self_mask[..., None]).reshape(
b, n, n - 1, -1)
if exists(self.adj_emb):
adj_emb = self.adj_emb(adj_indices)
edges = torch.cat(
(edges, adj_emb), dim=-1) if exists(edges) else adj_emb
rel_dist = rel_pos.norm(dim=-1)
# use sparse neighbor mask to assign priority of bonded
modified_rel_dist = rel_dist
if exists(sparse_neighbor_mask):
modified_rel_dist.masked_fill_(sparse_neighbor_mask, 0.)
# if number of local neighbors by distance is set to 0, then only fetch the sparse neighbors defined by adjacency matrix
if neighbors == 0:
valid_radius = 0
# get neighbors and neighbor mask, excluding self
neighbors = int(min(neighbors, n - 1))
total_neighbors = int(neighbors + num_sparse_neighbors)
assert total_neighbors > 0, 'you must be fetching at least 1 neighbor'
total_neighbors = int(
min(total_neighbors, n - 1)
) # make sure total neighbors does not exceed the length of the sequence itself
dist_values, nearest_indices = modified_rel_dist.topk(total_neighbors,
dim=-1,
largest=False)
neighbor_mask = dist_values <= valid_radius
neighbor_rel_dist = batched_index_select(rel_dist,
nearest_indices,
dim=2)
neighbor_rel_pos = batched_index_select(rel_pos,
nearest_indices,
dim=2)
neighbor_indices = batched_index_select(indices,
nearest_indices,
dim=2)
if exists(mask):
neighbor_mask = neighbor_mask & batched_index_select(
mask, nearest_indices, dim=2)
if exists(edges):
edges = batched_index_select(edges, nearest_indices, dim=2)
# calculate basis
basis = get_basis(neighbor_rel_pos,
num_degrees - 1,
differentiable=self.differentiable_coors)
# main logic
edge_info = (neighbor_indices, neighbor_mask, edges)
x = feats
# project in
x = self.conv_in(x, edge_info, rel_dist=neighbor_rel_dist, basis=basis)
# transformer layers
x = self.net(x,
edge_info=edge_info,
rel_dist=neighbor_rel_dist,
basis=basis)
# project out
x = self.conv_out(x,
edge_info,
rel_dist=neighbor_rel_dist,
basis=basis)
# norm
x = self.norm(x)
# reduce dim if specified
if exists(self.linear_out):
x = self.linear_out(x)
x = map_values(lambda t: t.squeeze(dim=2), x)
if return_pooled:
mask_fn = (lambda t: masked_mean(t, _mask, dim=1)
) if exists(_mask) else (lambda t: t.mean(dim=1))
x = map_values(mask_fn, x)
if '0' in x:
x['0'] = x['0'].squeeze(dim=-1)
if exists(return_type):
return x[str(return_type)]
return x
def test_basis():
max_degree = 3
x = torch.randn(2, 1024, 3)
basis = get_basis(x, max_degree)
assert len(basis.keys()) == (max_degree +
1)**2, 'correct number of basis kernels'
def forward(
self,
feats,
coors,
mask = None,
adj_mat = None,
edges = None,
return_type = None,
return_pooled = False,
neighbor_mask = None,
global_feats = None
):
assert not (self.accept_global_feats ^ exists(global_feats)), 'you cannot pass in global features unless you init the class correctly'
_mask = mask
if self.output_degrees == 1:
return_type = 0
if exists(self.token_emb):
feats = self.token_emb(feats)
assert not (self.attend_sparse_neighbors and not exists(adj_mat)), 'adjacency matrix (adjacency_mat) or edges (edges) must be passed in'
assert not (self.has_edges and not exists(edges)), 'edge embedding (num_edge_tokens & edge_dim) must be supplied if one were to train on edge types'
if torch.is_tensor(feats):
feats = {'0': feats[..., None]}
if torch.is_tensor(global_feats):
global_feats = {'0': global_feats[..., None]}
b, n, d, *_, device = *feats['0'].shape, feats['0'].device
assert d == self.dim_in[0], f'feature dimension {d} must be equal to dimension given at init {self.dim_in[0]}'
assert set(map(int, feats.keys())) == set(range(self.input_degrees)), f'input must have {self.input_degrees} degree'
num_degrees, neighbors, max_sparse_neighbors, valid_radius = self.num_degrees, self.num_neighbors, self.max_sparse_neighbors, self.valid_radius
assert self.attend_sparse_neighbors or neighbors > 0, 'you must either attend to sparsely bonded neighbors, or set number of locally attended neighbors to be greater than 0'
# se3 transformer by default cannot have a node attend to itself
exclude_self_mask = rearrange(~torch.eye(n, dtype = torch.bool, device = device), 'i j -> () i j')
remove_self = lambda t: t.masked_select(exclude_self_mask).reshape(b, n, n - 1)
get_max_value = lambda t: torch.finfo(t.dtype).max
# create N-degrees adjacent matrix from 1st degree connections
if exists(self.num_adj_degrees):
if len(adj_mat.shape) == 2:
adj_mat = repeat(adj_mat.clone(), 'i j -> b i j', b = b)
adj_indices = adj_mat.clone().long()
for ind in range(self.num_adj_degrees - 1):
degree = ind + 2
next_degree_adj_mat = (adj_mat.float() @ adj_mat.float()) > 0
next_degree_mask = (next_degree_adj_mat.float() - adj_mat.float()).bool()
adj_indices.masked_fill_(next_degree_mask, degree)
adj_mat = next_degree_adj_mat.clone()
adj_indices = adj_indices.masked_select(exclude_self_mask).reshape(b, n, n - 1)
# calculate sparsely connected neighbors
sparse_neighbor_mask = None
num_sparse_neighbors = 0
if self.attend_sparse_neighbors:
assert exists(adj_mat), 'adjacency matrix must be passed in (keyword argument adj_mat)'
if exists(adj_mat):
if len(adj_mat.shape) == 2:
adj_mat = repeat(adj_mat, 'i j -> b i j', b = b)
adj_mat = remove_self(adj_mat)
adj_mat_values = adj_mat.float()
adj_mat_max_neighbors = adj_mat_values.sum(dim = -1).max().item()
if max_sparse_neighbors < adj_mat_max_neighbors:
noise = torch.empty_like(adj_mat_values).uniform_(-0.01, 0.01)
adj_mat_values += noise
num_sparse_neighbors = int(min(max_sparse_neighbors, adj_mat_max_neighbors))
values, indices = adj_mat_values.topk(num_sparse_neighbors, dim = -1)
sparse_neighbor_mask = torch.zeros_like(adj_mat_values).scatter_(-1, indices, values)
sparse_neighbor_mask = sparse_neighbor_mask > 0.5
# exclude edge of token to itself
indices = repeat(torch.arange(n, device = device), 'i -> b i j', b = b, j = n)
rel_pos = rearrange(coors, 'b n d -> b n () d') - rearrange(coors, 'b n d -> b () n d')
indices = indices.masked_select(exclude_self_mask).reshape(b, n, n - 1)
rel_pos = rel_pos.masked_select(exclude_self_mask[..., None]).reshape(b, n, n - 1, 3)
if exists(mask):
mask = rearrange(mask, 'b i -> b i ()') * rearrange(mask, 'b j -> b () j')
mask = mask.masked_select(exclude_self_mask).reshape(b, n, n - 1)
if exists(edges):
if exists(self.edge_emb):
edges = self.edge_emb(edges)
edges = edges.masked_select(exclude_self_mask[..., None]).reshape(b, n, n - 1, -1)
if exists(self.adj_emb):
adj_emb = self.adj_emb(adj_indices)
edges = torch.cat((edges, adj_emb), dim = -1) if exists(edges) else adj_emb
rel_dist = rel_pos.norm(dim = -1)
# rel_dist gets modified using adjacency or neighbor mask
modified_rel_dist = rel_dist.clone()
max_value = get_max_value(modified_rel_dist) # for masking out nodes from being considered as neighbors
# neighbors
if exists(neighbor_mask):
neighbor_mask = remove_self(neighbor_mask)
max_neighbors = neighbor_mask.sum(dim = -1).max().item()
if max_neighbors > neighbors:
print(f'neighbor_mask shows maximum number of neighbors as {max_neighbors} but specified number of neighbors is {neighbors}')
modified_rel_dist.masked_fill_(~neighbor_mask, max_value)
# use sparse neighbor mask to assign priority of bonded
if exists(sparse_neighbor_mask):
modified_rel_dist.masked_fill_(sparse_neighbor_mask, 0.)
# mask out future nodes to high distance if causal turned on
if self.causal:
causal_mask = torch.ones(n, n - 1, device = device).triu().bool()
modified_rel_dist.masked_fill_(causal_mask[None, ...], max_value)
# if number of local neighbors by distance is set to 0, then only fetch the sparse neighbors defined by adjacency matrix
if neighbors == 0:
valid_radius = 0
# get neighbors and neighbor mask, excluding self
neighbors = int(min(neighbors, n - 1))
total_neighbors = int(neighbors + num_sparse_neighbors)
assert total_neighbors > 0, 'you must be fetching at least 1 neighbor'
total_neighbors = int(min(total_neighbors, n - 1)) # make sure total neighbors does not exceed the length of the sequence itself
dist_values, nearest_indices = modified_rel_dist.topk(total_neighbors, dim = -1, largest = False)
neighbor_mask = dist_values <= valid_radius
neighbor_rel_dist = batched_index_select(rel_dist, nearest_indices, dim = 2)
neighbor_rel_pos = batched_index_select(rel_pos, nearest_indices, dim = 2)
neighbor_indices = batched_index_select(indices, nearest_indices, dim = 2)
if exists(mask):
neighbor_mask = neighbor_mask & batched_index_select(mask, nearest_indices, dim = 2)
if exists(edges):
edges = batched_index_select(edges, nearest_indices, dim = 2)
# calculate rotary pos emb
rotary_pos_emb = None
rotary_query_pos_emb = None
rotary_key_pos_emb = None
if self.rotary_position:
seq = torch.arange(n, device = device)
seq_pos_emb = self.rotary_pos_emb(seq)
self_indices = torch.arange(neighbor_indices.shape[1], device = device)
self_indices = repeat(self_indices, 'i -> b i ()', b = b)
neighbor_indices_with_self = torch.cat((self_indices, neighbor_indices), dim = 2)
pos_emb = batched_index_select(seq_pos_emb, neighbor_indices_with_self, dim = 0)
rotary_key_pos_emb = pos_emb
rotary_query_pos_emb = repeat(seq_pos_emb, 'n d -> b n d', b = b)
if self.rotary_rel_dist:
neighbor_rel_dist_with_self = F.pad(neighbor_rel_dist, (1, 0), value = 0) * 1e2
rel_dist_pos_emb = self.rotary_pos_emb(neighbor_rel_dist_with_self)
rotary_key_pos_emb = safe_cat(rotary_key_pos_emb, rel_dist_pos_emb, dim = -1)
query_dist = torch.zeros(n, device = device)
query_pos_emb = self.rotary_pos_emb(query_dist)
query_pos_emb = repeat(query_pos_emb, 'n d -> b n d', b = b)
rotary_query_pos_emb = safe_cat(rotary_query_pos_emb, query_pos_emb, dim = -1)
if exists(rotary_query_pos_emb) and exists(rotary_key_pos_emb):
rotary_pos_emb = (rotary_query_pos_emb, rotary_key_pos_emb)
# calculate basis
basis = get_basis(neighbor_rel_pos, num_degrees - 1, differentiable = self.differentiable_coors)
# main logic
edge_info = (neighbor_indices, neighbor_mask, edges)
x = feats
# project in
x = self.conv_in(x, edge_info, rel_dist = neighbor_rel_dist, basis = basis)
# preconvolution layers
for conv, nonlin in self.convs:
x = nonlin(x)
x = conv(x, edge_info, rel_dist = neighbor_rel_dist, basis = basis)
# transformer layers
x = self.net(x, edge_info = edge_info, rel_dist = neighbor_rel_dist, basis = basis, global_feats = global_feats, pos_emb = rotary_pos_emb)
# project out
x = self.conv_out(x, edge_info, rel_dist = neighbor_rel_dist, basis = basis)
# norm
x = self.norm(x)
# reduce dim if specified
if exists(self.linear_out):
x = self.linear_out(x)
x = map_values(lambda t: t.squeeze(dim = 2), x)
if return_pooled:
mask_fn = (lambda t: masked_mean(t, _mask, dim = 1)) if exists(_mask) else (lambda t: t.mean(dim = 1))
x = map_values(mask_fn, x)
if '0' in x:
x['0'] = x['0'].squeeze(dim = -1)
if exists(return_type):
return x[str(return_type)]
return x
def forward(self, feats, coors, mask=None, edges=None, return_type=None):
if exists(self.token_emb):
feats = self.token_emb(feats)
assert not (
exists(edges) and not exists(self.edge_emb)
), 'edge embedding (num_edge_tokens & edge_dim) must be supplied if one were to train on edge types'
if exists(edges):
edges = self.edge_emb(edges)
if torch.is_tensor(feats):
feats = {'0': feats[..., None]}
b, n, d, *_, device = *feats['0'].shape, feats['0'].device
assert d == self.dim, f'feature dimension {d} must be equal to dimension given at init {self.dim}'
assert set(map(int, feats.keys())) == set(
range(self.input_degrees
)), f'input must have {self.input_degrees} degree'
num_degrees, neighbors = self.num_degrees, self.num_neighbors
neighbors = min(neighbors, n - 1)
# exclude edge of token to itself
exclude_self_mask = rearrange(
~torch.eye(n, dtype=torch.bool, device=device), 'i j -> () i j')
indices = repeat(torch.arange(n, device=device),
'i -> b i j',
b=b,
j=n)
rel_pos = rearrange(coors, 'b n d -> b n () d') - rearrange(
coors, 'b n d -> b () n d')
indices = indices.masked_select(exclude_self_mask).reshape(b, n, n - 1)
rel_pos = rel_pos.masked_select(exclude_self_mask[..., None]).reshape(
b, n, n - 1, 3)
if exists(mask):
mask = rearrange(mask, 'b i -> b i ()') * rearrange(
mask, 'b j -> b () j')
mask = mask.masked_select(exclude_self_mask).reshape(b, n, n - 1)
if exists(edges):
edges = edges.masked_select(exclude_self_mask[..., None]).reshape(
b, n, n - 1, -1)
rel_dist = rel_pos.norm(dim=-1)
# get neighbors and neighbor mask, excluding self
neighbor_rel_dist, nearest_indices = rel_dist.topk(neighbors,
dim=-1,
largest=False)
neighbor_rel_pos = batched_index_select(rel_pos,
nearest_indices,
dim=2)
neighbor_indices = batched_index_select(indices,
nearest_indices,
dim=2)
basis = get_basis(neighbor_rel_pos,
num_degrees - 1,
differentiable=self.differentiable_coors)
neighbor_mask = neighbor_rel_dist <= self.valid_radius
if exists(mask):
neighbor_mask = neighbor_mask & batched_index_select(
mask, nearest_indices, dim=2)
if exists(edges):
edges = batched_index_select(edges, nearest_indices, dim=2)
# main logic
edge_info = (neighbor_indices, neighbor_mask, edges)
x = feats
# project in
x = self.conv_in(x, edge_info, rel_dist=neighbor_rel_dist, basis=basis)
# transformer layers
x = self.net(x,
edge_info=edge_info,
rel_dist=neighbor_rel_dist,
basis=basis)
# project out
x = self.conv_out(x,
edge_info,
rel_dist=neighbor_rel_dist,
basis=basis)
# norm
x = self.norm(x)
# reduce dim if specified
if exists(self.linear_out):
x = self.linear_out(x)
x = {k: v.squeeze(dim=2) for k, v in x.items()}
if exists(return_type):
return x[str(return_type)]
return x