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# MIT License
# Copyright (c) 2022 Phil Wang
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
"""All code taken from https://github.com/lucidrains/VN-transformer"""
from collections import namedtuple
from functools import wraps
import torch
import torch.nn.functional as F
from einops import rearrange, reduce
from einops.layers.torch import Rearrange
from packaging import version
from torch import einsum, nn
# constants
FlashAttentionConfig = namedtuple(
"FlashAttentionConfig", ["enable_flash", "enable_math", "enable_mem_efficient"]
)
# helpers
def exists(val):
return val is not None
def once(fn):
called = False
@wraps(fn)
def inner(x):
nonlocal called
if called:
return
called = True
return fn(x)
return inner
print_once = once(print)
# main class
class Attend(nn.Module):
def __init__(self, dropout=0.0, flash=False, l2_dist=False):
super().__init__()
assert not (
flash and l2_dist
), "flash attention is not compatible with l2 distance"
self.l2_dist = l2_dist
self.dropout = dropout
self.attn_dropout = nn.Dropout(dropout)
self.flash = flash
assert not (
flash and version.parse(torch.__version__) < version.parse("2.0.0")
), "in order to use flash attention, you must be using pytorch 2.0 or above"
# determine efficient attention configs for cuda and cpu
self.cpu_config = FlashAttentionConfig(True, True, True)
self.cuda_config = None
if not torch.cuda.is_available() or not flash:
return
device_properties = torch.cuda.get_device_properties(torch.device("cuda"))
if device_properties.major == 8 and device_properties.minor == 0:
print_once(
"A100 GPU detected, using flash attention if input tensor is on cuda"
)
self.cuda_config = FlashAttentionConfig(True, False, False)
else:
print_once(
"Non-A100 GPU detected, using math or mem efficient attention if input tensor is on cuda"
)
self.cuda_config = FlashAttentionConfig(False, True, True)
def flash_attn(self, q, k, v, mask=None):
_, heads, q_len, _, _, is_cuda = (
*q.shape,
k.shape[-2],
q.is_cuda,
)
# Check if mask exists and expand to compatible shape
# The mask is B L, so it would have to be expanded to B H N L
if exists(mask):
mask = mask.expand(-1, heads, q_len, -1)
# Check if there is a compatible device for flash attention
config = self.cuda_config if is_cuda else self.cpu_config
# pytorch 2.0 flash attn: q, k, v, mask, dropout, softmax_scale
with torch.backends.cuda.sdp_kernel(**config._asdict()):
out = F.scaled_dot_product_attention(
q,
k,
v,
attn_mask=mask,
dropout_p=self.dropout if self.training else 0.0,
)
return out
def forward(self, q, k, v, mask=None):
"""
einstein notation
b - batch
h - heads
n, i, j - sequence length (base sequence length, source, target)
d - feature dimension
"""
scale = q.shape[-1] ** -0.5
if exists(mask) and mask.ndim != 4:
mask = rearrange(mask, "b j -> b 1 1 j")
if self.flash:
return self.flash_attn(q, k, v, mask=mask)
# similarity
sim = einsum("b h i d, b h j d -> b h i j", q, k) * scale
# l2 distance
if self.l2_dist:
# -cdist squared == (-q^2 + 2qk - k^2)
# so simply work off the qk above
q_squared = reduce(q**2, "b h i d -> b h i 1", "sum")
k_squared = reduce(k**2, "b h j d -> b h 1 j", "sum")
sim = sim * 2 - q_squared - k_squared
# key padding mask
if exists(mask):
sim = sim.masked_fill(~mask, -torch.finfo(sim.dtype).max)
# attention
attn = sim.softmax(dim=-1)
attn = self.attn_dropout(attn)
# aggregate values
out = einsum("b h i j, b h j d -> b h i d", attn, v)
return out
# helper
def exists(val): # noqa: F811
return val is not None
def default(val, d):
return val if exists(val) else d
def inner_dot_product(x, y, *, dim=-1, keepdim=True):
return (x * y).sum(dim=dim, keepdim=keepdim)
# layernorm
class LayerNorm(nn.Module):
def __init__(self, dim):
super().__init__()
self.gamma = nn.Parameter(torch.ones(dim))
self.register_buffer("beta", torch.zeros(dim))
def forward(self, x):
return F.layer_norm(x, x.shape[-1:], self.gamma, self.beta)
# equivariant modules
class VNLinear(nn.Module):
def __init__(self, dim_in, dim_out, bias_epsilon=0.0):
super().__init__()
self.weight = nn.Parameter(torch.randn(dim_out, dim_in))
self.bias = None
self.bias_epsilon = bias_epsilon
# in this paper, they propose going for quasi-equivariance with a small bias, controllable with epsilon, which they claim lead to better stability and results
if bias_epsilon > 0.0:
self.bias = nn.Parameter(torch.randn(dim_out))
def forward(self, x):
out = einsum("... i c, o i -> ... o c", x, self.weight)
if exists(self.bias):
bias = F.normalize(self.bias, dim=-1) * self.bias_epsilon
out = out + rearrange(bias, "... -> ... 1")
return out
class VNReLU(nn.Module):
def __init__(self, dim, eps=1e-6):
super().__init__()
self.eps = eps
self.W = nn.Parameter(torch.randn(dim, dim))
self.U = nn.Parameter(torch.randn(dim, dim))
def forward(self, x):
q = einsum("... i c, o i -> ... o c", x, self.W)
k = einsum("... i c, o i -> ... o c", x, self.U)
qk = inner_dot_product(q, k)
k_norm = k.norm(dim=-1, keepdim=True).clamp(min=self.eps)
q_projected_on_k = q - inner_dot_product(q, k / k_norm) * k
out = torch.where(qk >= 0.0, q, q_projected_on_k)
return out
class VNAttention(nn.Module):
def __init__(
self,
dim,
dim_head=64,
heads=8,
dim_coor=3,
bias_epsilon=0.0,
l2_dist_attn=False,
flash=False,
num_latents=None, # setting this would enable perceiver-like cross attention from latents to sequence, with the latents derived from VNWeightedPool
):
super().__init__()
assert not (
l2_dist_attn and flash
), "l2 distance attention is not compatible with flash attention"
self.scale = (dim_coor * dim_head) ** -0.5
dim_inner = dim_head * heads
self.heads = heads
self.to_q_input = None
if exists(num_latents):
self.to_q_input = VNWeightedPool(
dim, num_pooled_tokens=num_latents, squeeze_out_pooled_dim=False
)
self.to_q = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon)
self.to_k = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon)
self.to_v = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon)
self.to_out = VNLinear(dim_inner, dim, bias_epsilon=bias_epsilon)
if l2_dist_attn and not exists(num_latents):
# tied queries and keys for l2 distance attention, and not perceiver-like attention
self.to_k = self.to_q
self.attend = Attend(flash=flash, l2_dist=l2_dist_attn)
def forward(self, x, mask=None):
"""
einstein notation
b - batch
n - sequence
h - heads
d - feature dimension (channels)
c - coordinate dimension (3 for 3d space)
i - source sequence dimension
j - target sequence dimension
"""
c = x.shape[-1]
if exists(self.to_q_input):
q_input = self.to_q_input(x, mask=mask)
else:
q_input = x
q, k, v = self.to_q(q_input), self.to_k(x), self.to_v(x)
q, k, v = map(
lambda t: rearrange(t, "b n (h d) c -> b h n (d c)", h=self.heads),
(q, k, v),
)
out = self.attend(q, k, v, mask=mask)
out = rearrange(out, "b h n (d c) -> b n (h d) c", c=c)
return self.to_out(out)
def VNFeedForward(dim, mult=4, bias_epsilon=0.0):
dim_inner = int(dim * mult)
return nn.Sequential(
VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon),
VNReLU(dim_inner),
VNLinear(dim_inner, dim, bias_epsilon=bias_epsilon),
)
class VNLayerNorm(nn.Module):
def __init__(self, dim, eps=1e-6):
super().__init__()
self.eps = eps
self.ln = LayerNorm(dim)
def forward(self, x):
norms = x.norm(dim=-1)
x = x / rearrange(norms.clamp(min=self.eps), "... -> ... 1")
ln_out = self.ln(norms)
return x * rearrange(ln_out, "... -> ... 1")
class VNWeightedPool(nn.Module):
def __init__(
self, dim, dim_out=None, num_pooled_tokens=1, squeeze_out_pooled_dim=True
):
super().__init__()
dim_out = default(dim_out, dim)
self.weight = nn.Parameter(torch.randn(num_pooled_tokens, dim, dim_out))
self.squeeze_out_pooled_dim = num_pooled_tokens == 1 and squeeze_out_pooled_dim
def forward(self, x, mask=None):
if exists(mask):
mask = rearrange(mask, "b n -> b n 1 1")
x = x.masked_fill(~mask, 0.0)
numer = reduce(x, "b n d c -> b d c", "sum")
denom = mask.sum(dim=1)
mean_pooled = numer / denom.clamp(min=1e-6)
else:
mean_pooled = reduce(x, "b n d c -> b d c", "mean")
out = einsum("b d c, m d e -> b m e c", mean_pooled, self.weight)
if not self.squeeze_out_pooled_dim:
return out
out = rearrange(out, "b 1 d c -> b d c")
return out
# equivariant VN transformer encoder
class VNTransformerEncoder(nn.Module):
def __init__(
self,
dim,
*,
depth,
dim_head=64,
heads=8,
dim_coor=3,
ff_mult=4,
final_norm=False,
bias_epsilon=0.0,
l2_dist_attn=False,
flash_attn=False,
):
super().__init__()
self.dim = dim
self.dim_coor = dim_coor
self.layers = nn.ModuleList([])
for _ in range(depth):
self.layers.append(
nn.ModuleList(
[
VNAttention(
dim=dim,
dim_head=dim_head,
heads=heads,
bias_epsilon=bias_epsilon,
l2_dist_attn=l2_dist_attn,
flash=flash_attn,
),
VNLayerNorm(dim),
VNFeedForward(dim=dim, mult=ff_mult, bias_epsilon=bias_epsilon),
VNLayerNorm(dim),
]
)
)
self.norm = VNLayerNorm(dim) if final_norm else nn.Identity()
def forward(self, x, mask=None):
*_, d, c = x.shape
assert (
x.ndim == 4 and d == self.dim and c == self.dim_coor
), "input needs to be in the shape of (batch, seq, dim ({self.dim}), coordinate dim ({self.dim_coor}))"
for attn, attn_post_ln, ff, ff_post_ln in self.layers:
x = attn_post_ln(attn(x, mask=mask)) + x
x = ff_post_ln(ff(x)) + x
return self.norm(x)
# invariant layers
class VNInvariant(nn.Module):
def __init__(
self,
dim,
dim_coor=3,
):
super().__init__()
self.mlp = nn.Sequential(
VNLinear(dim, dim_coor), VNReLU(dim_coor), Rearrange("... d e -> ... e d")
)
def forward(self, x):
return einsum("b n d i, b n i o -> b n o", x, self.mlp(x))
# main class
class VNTransformer(nn.Module):
def __init__(
self,
*,
dim,
depth,
num_tokens=None,
dim_feat=None,
dim_head=64,
heads=8,
dim_coor=3,
reduce_dim_out=True,
bias_epsilon=0.0,
l2_dist_attn=False,
flash_attn=False,
translation_equivariance=False,
translation_invariant=False,
):
super().__init__()
self.token_emb = nn.Embedding(num_tokens, dim) if exists(num_tokens) else None
dim_feat = default(dim_feat, 0)
self.dim_feat = dim_feat
self.dim_coor_total = dim_coor + dim_feat
assert (int(translation_equivariance) + int(translation_invariant)) <= 1
self.translation_equivariance = translation_equivariance
self.translation_invariant = translation_invariant
self.vn_proj_in = nn.Sequential(
Rearrange("... c -> ... 1 c"), VNLinear(1, dim, bias_epsilon=bias_epsilon)
)
self.encoder = VNTransformerEncoder(
dim=dim,
depth=depth,
dim_head=dim_head,
heads=heads,
bias_epsilon=bias_epsilon,
dim_coor=self.dim_coor_total,
l2_dist_attn=l2_dist_attn,
flash_attn=flash_attn,
)
if reduce_dim_out:
self.vn_proj_out = nn.Sequential(
VNLayerNorm(dim),
VNLinear(dim, 1, bias_epsilon=bias_epsilon),
Rearrange("... 1 c -> ... c"),
)
else:
self.vn_proj_out = nn.Identity()
def forward(
self, coors, *, feats=None, mask=None, return_concatted_coors_and_feats=False
):
if self.translation_equivariance or self.translation_invariant:
coors_mean = reduce(coors, "... c -> c", "mean")
coors = coors - coors_mean
x = coors # [batch, num_points, 3]
if exists(feats):
if feats.dtype == torch.long:
assert exists(
self.token_emb
), "num_tokens must be given to the VNTransformer (to build the Embedding), if the features are to be given as indices"
feats = self.token_emb(feats)
assert (
feats.shape[-1] == self.dim_feat
), f"dim_feat should be set to {feats.shape[-1]}"
x = torch.cat((x, feats), dim=-1) # [batch, num_points, 3 + dim_feat]
assert x.shape[-1] == self.dim_coor_total
x = self.vn_proj_in(x) # [batch, num_points, hidden_dim, 3 + dim_feat]
x = self.encoder(x, mask=mask) # [batch, num_points, hidden_dim, 3 + dim_feat]
x = self.vn_proj_out(x) # [batch, num_points, 3 + dim_feat]
coors_out, feats_out = (
x[..., :3],
x[..., 3:],
) # [batch, num_points, 3], [batch, num_points, dim_feat]
if self.translation_equivariance:
coors_out = coors_out + coors_mean
if not exists(feats):
return coors_out
if return_concatted_coors_and_feats:
return torch.cat((coors_out, feats_out), dim=-1)
return coors_out, feats_out
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