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"""All code taken from https://github.com/lucidrains/VN-transformer""" |
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from collections import namedtuple |
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from functools import wraps |
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import torch |
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import torch.nn.functional as F |
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from einops import rearrange, reduce |
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from einops.layers.torch import Rearrange |
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from packaging import version |
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from torch import einsum, nn |
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FlashAttentionConfig = namedtuple( |
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"FlashAttentionConfig", ["enable_flash", "enable_math", "enable_mem_efficient"] |
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) |
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def exists(val): |
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return val is not None |
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def once(fn): |
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called = False |
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@wraps(fn) |
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def inner(x): |
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nonlocal called |
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if called: |
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return |
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called = True |
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return fn(x) |
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return inner |
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print_once = once(print) |
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class Attend(nn.Module): |
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def __init__(self, dropout=0.0, flash=False, l2_dist=False): |
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super().__init__() |
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assert not ( |
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flash and l2_dist |
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), "flash attention is not compatible with l2 distance" |
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self.l2_dist = l2_dist |
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self.dropout = dropout |
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self.attn_dropout = nn.Dropout(dropout) |
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self.flash = flash |
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assert not ( |
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flash and version.parse(torch.__version__) < version.parse("2.0.0") |
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), "in order to use flash attention, you must be using pytorch 2.0 or above" |
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self.cpu_config = FlashAttentionConfig(True, True, True) |
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self.cuda_config = None |
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if not torch.cuda.is_available() or not flash: |
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return |
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device_properties = torch.cuda.get_device_properties(torch.device("cuda")) |
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if device_properties.major == 8 and device_properties.minor == 0: |
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print_once( |
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"A100 GPU detected, using flash attention if input tensor is on cuda" |
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) |
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self.cuda_config = FlashAttentionConfig(True, False, False) |
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else: |
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print_once( |
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"Non-A100 GPU detected, using math or mem efficient attention if input tensor is on cuda" |
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) |
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self.cuda_config = FlashAttentionConfig(False, True, True) |
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def flash_attn(self, q, k, v, mask=None): |
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_, heads, q_len, _, _, is_cuda = ( |
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*q.shape, |
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k.shape[-2], |
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q.is_cuda, |
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) |
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if exists(mask): |
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mask = mask.expand(-1, heads, q_len, -1) |
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config = self.cuda_config if is_cuda else self.cpu_config |
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with torch.backends.cuda.sdp_kernel(**config._asdict()): |
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out = F.scaled_dot_product_attention( |
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q, |
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k, |
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v, |
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attn_mask=mask, |
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dropout_p=self.dropout if self.training else 0.0, |
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) |
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return out |
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def forward(self, q, k, v, mask=None): |
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""" |
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einstein notation |
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b - batch |
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h - heads |
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n, i, j - sequence length (base sequence length, source, target) |
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d - feature dimension |
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""" |
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scale = q.shape[-1] ** -0.5 |
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if exists(mask) and mask.ndim != 4: |
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mask = rearrange(mask, "b j -> b 1 1 j") |
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if self.flash: |
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return self.flash_attn(q, k, v, mask=mask) |
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sim = einsum("b h i d, b h j d -> b h i j", q, k) * scale |
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if self.l2_dist: |
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q_squared = reduce(q**2, "b h i d -> b h i 1", "sum") |
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k_squared = reduce(k**2, "b h j d -> b h 1 j", "sum") |
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sim = sim * 2 - q_squared - k_squared |
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if exists(mask): |
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sim = sim.masked_fill(~mask, -torch.finfo(sim.dtype).max) |
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attn = sim.softmax(dim=-1) |
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attn = self.attn_dropout(attn) |
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out = einsum("b h i j, b h j d -> b h i d", attn, v) |
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return out |
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def exists(val): |
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return val is not None |
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def default(val, d): |
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return val if exists(val) else d |
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def inner_dot_product(x, y, *, dim=-1, keepdim=True): |
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return (x * y).sum(dim=dim, keepdim=keepdim) |
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class LayerNorm(nn.Module): |
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def __init__(self, dim): |
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super().__init__() |
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self.gamma = nn.Parameter(torch.ones(dim)) |
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self.register_buffer("beta", torch.zeros(dim)) |
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def forward(self, x): |
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return F.layer_norm(x, x.shape[-1:], self.gamma, self.beta) |
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class VNLinear(nn.Module): |
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def __init__(self, dim_in, dim_out, bias_epsilon=0.0): |
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super().__init__() |
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self.weight = nn.Parameter(torch.randn(dim_out, dim_in)) |
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self.bias = None |
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self.bias_epsilon = bias_epsilon |
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if bias_epsilon > 0.0: |
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self.bias = nn.Parameter(torch.randn(dim_out)) |
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def forward(self, x): |
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out = einsum("... i c, o i -> ... o c", x, self.weight) |
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if exists(self.bias): |
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bias = F.normalize(self.bias, dim=-1) * self.bias_epsilon |
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out = out + rearrange(bias, "... -> ... 1") |
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return out |
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class VNReLU(nn.Module): |
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def __init__(self, dim, eps=1e-6): |
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super().__init__() |
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self.eps = eps |
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self.W = nn.Parameter(torch.randn(dim, dim)) |
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self.U = nn.Parameter(torch.randn(dim, dim)) |
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def forward(self, x): |
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q = einsum("... i c, o i -> ... o c", x, self.W) |
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k = einsum("... i c, o i -> ... o c", x, self.U) |
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qk = inner_dot_product(q, k) |
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k_norm = k.norm(dim=-1, keepdim=True).clamp(min=self.eps) |
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q_projected_on_k = q - inner_dot_product(q, k / k_norm) * k |
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out = torch.where(qk >= 0.0, q, q_projected_on_k) |
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return out |
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class VNAttention(nn.Module): |
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def __init__( |
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self, |
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dim, |
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dim_head=64, |
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heads=8, |
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dim_coor=3, |
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bias_epsilon=0.0, |
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l2_dist_attn=False, |
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flash=False, |
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num_latents=None, |
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): |
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super().__init__() |
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assert not ( |
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l2_dist_attn and flash |
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), "l2 distance attention is not compatible with flash attention" |
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self.scale = (dim_coor * dim_head) ** -0.5 |
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dim_inner = dim_head * heads |
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self.heads = heads |
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self.to_q_input = None |
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if exists(num_latents): |
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self.to_q_input = VNWeightedPool( |
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dim, num_pooled_tokens=num_latents, squeeze_out_pooled_dim=False |
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) |
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self.to_q = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon) |
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self.to_k = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon) |
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self.to_v = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon) |
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self.to_out = VNLinear(dim_inner, dim, bias_epsilon=bias_epsilon) |
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if l2_dist_attn and not exists(num_latents): |
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self.to_k = self.to_q |
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self.attend = Attend(flash=flash, l2_dist=l2_dist_attn) |
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def forward(self, x, mask=None): |
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""" |
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einstein notation |
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b - batch |
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n - sequence |
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h - heads |
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d - feature dimension (channels) |
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c - coordinate dimension (3 for 3d space) |
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i - source sequence dimension |
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j - target sequence dimension |
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""" |
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c = x.shape[-1] |
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if exists(self.to_q_input): |
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q_input = self.to_q_input(x, mask=mask) |
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else: |
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q_input = x |
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q, k, v = self.to_q(q_input), self.to_k(x), self.to_v(x) |
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q, k, v = map( |
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lambda t: rearrange(t, "b n (h d) c -> b h n (d c)", h=self.heads), |
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(q, k, v), |
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) |
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out = self.attend(q, k, v, mask=mask) |
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out = rearrange(out, "b h n (d c) -> b n (h d) c", c=c) |
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return self.to_out(out) |
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def VNFeedForward(dim, mult=4, bias_epsilon=0.0): |
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dim_inner = int(dim * mult) |
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return nn.Sequential( |
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VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon), |
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VNReLU(dim_inner), |
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VNLinear(dim_inner, dim, bias_epsilon=bias_epsilon), |
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) |
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class VNLayerNorm(nn.Module): |
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def __init__(self, dim, eps=1e-6): |
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super().__init__() |
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self.eps = eps |
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self.ln = LayerNorm(dim) |
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def forward(self, x): |
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norms = x.norm(dim=-1) |
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x = x / rearrange(norms.clamp(min=self.eps), "... -> ... 1") |
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ln_out = self.ln(norms) |
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return x * rearrange(ln_out, "... -> ... 1") |
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class VNWeightedPool(nn.Module): |
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def __init__( |
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self, dim, dim_out=None, num_pooled_tokens=1, squeeze_out_pooled_dim=True |
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): |
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super().__init__() |
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dim_out = default(dim_out, dim) |
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self.weight = nn.Parameter(torch.randn(num_pooled_tokens, dim, dim_out)) |
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self.squeeze_out_pooled_dim = num_pooled_tokens == 1 and squeeze_out_pooled_dim |
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def forward(self, x, mask=None): |
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if exists(mask): |
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mask = rearrange(mask, "b n -> b n 1 1") |
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x = x.masked_fill(~mask, 0.0) |
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numer = reduce(x, "b n d c -> b d c", "sum") |
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denom = mask.sum(dim=1) |
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mean_pooled = numer / denom.clamp(min=1e-6) |
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else: |
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mean_pooled = reduce(x, "b n d c -> b d c", "mean") |
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out = einsum("b d c, m d e -> b m e c", mean_pooled, self.weight) |
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if not self.squeeze_out_pooled_dim: |
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return out |
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out = rearrange(out, "b 1 d c -> b d c") |
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return out |
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class VNTransformerEncoder(nn.Module): |
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def __init__( |
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self, |
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dim, |
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*, |
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depth, |
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dim_head=64, |
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heads=8, |
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dim_coor=3, |
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ff_mult=4, |
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final_norm=False, |
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bias_epsilon=0.0, |
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l2_dist_attn=False, |
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flash_attn=False, |
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): |
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super().__init__() |
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self.dim = dim |
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self.dim_coor = dim_coor |
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self.layers = nn.ModuleList([]) |
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for _ in range(depth): |
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self.layers.append( |
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nn.ModuleList( |
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[ |
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VNAttention( |
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dim=dim, |
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dim_head=dim_head, |
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heads=heads, |
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bias_epsilon=bias_epsilon, |
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l2_dist_attn=l2_dist_attn, |
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flash=flash_attn, |
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), |
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VNLayerNorm(dim), |
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VNFeedForward(dim=dim, mult=ff_mult, bias_epsilon=bias_epsilon), |
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VNLayerNorm(dim), |
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] |
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) |
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) |
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self.norm = VNLayerNorm(dim) if final_norm else nn.Identity() |
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def forward(self, x, mask=None): |
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*_, d, c = x.shape |
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assert ( |
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x.ndim == 4 and d == self.dim and c == self.dim_coor |
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), "input needs to be in the shape of (batch, seq, dim ({self.dim}), coordinate dim ({self.dim_coor}))" |
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for attn, attn_post_ln, ff, ff_post_ln in self.layers: |
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x = attn_post_ln(attn(x, mask=mask)) + x |
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x = ff_post_ln(ff(x)) + x |
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return self.norm(x) |
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class VNInvariant(nn.Module): |
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def __init__( |
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self, |
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dim, |
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dim_coor=3, |
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): |
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super().__init__() |
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self.mlp = nn.Sequential( |
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VNLinear(dim, dim_coor), VNReLU(dim_coor), Rearrange("... d e -> ... e d") |
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) |
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def forward(self, x): |
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return einsum("b n d i, b n i o -> b n o", x, self.mlp(x)) |
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class VNTransformer(nn.Module): |
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def __init__( |
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self, |
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*, |
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dim, |
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depth, |
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num_tokens=None, |
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dim_feat=None, |
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dim_head=64, |
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heads=8, |
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dim_coor=3, |
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reduce_dim_out=True, |
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bias_epsilon=0.0, |
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l2_dist_attn=False, |
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flash_attn=False, |
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translation_equivariance=False, |
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translation_invariant=False, |
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): |
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super().__init__() |
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self.token_emb = nn.Embedding(num_tokens, dim) if exists(num_tokens) else None |
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dim_feat = default(dim_feat, 0) |
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self.dim_feat = dim_feat |
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self.dim_coor_total = dim_coor + dim_feat |
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assert (int(translation_equivariance) + int(translation_invariant)) <= 1 |
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self.translation_equivariance = translation_equivariance |
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self.translation_invariant = translation_invariant |
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self.vn_proj_in = nn.Sequential( |
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Rearrange("... c -> ... 1 c"), VNLinear(1, dim, bias_epsilon=bias_epsilon) |
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) |
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self.encoder = VNTransformerEncoder( |
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dim=dim, |
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depth=depth, |
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dim_head=dim_head, |
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heads=heads, |
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bias_epsilon=bias_epsilon, |
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dim_coor=self.dim_coor_total, |
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l2_dist_attn=l2_dist_attn, |
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flash_attn=flash_attn, |
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) |
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if reduce_dim_out: |
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self.vn_proj_out = nn.Sequential( |
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VNLayerNorm(dim), |
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VNLinear(dim, 1, bias_epsilon=bias_epsilon), |
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Rearrange("... 1 c -> ... c"), |
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) |
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else: |
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self.vn_proj_out = nn.Identity() |
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def forward( |
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self, coors, *, feats=None, mask=None, return_concatted_coors_and_feats=False |
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): |
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if self.translation_equivariance or self.translation_invariant: |
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coors_mean = reduce(coors, "... c -> c", "mean") |
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coors = coors - coors_mean |
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x = coors |
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if exists(feats): |
|
if feats.dtype == torch.long: |
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assert exists( |
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self.token_emb |
|
), "num_tokens must be given to the VNTransformer (to build the Embedding), if the features are to be given as indices" |
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feats = self.token_emb(feats) |
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|
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assert ( |
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feats.shape[-1] == self.dim_feat |
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), f"dim_feat should be set to {feats.shape[-1]}" |
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x = torch.cat((x, feats), dim=-1) |
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assert x.shape[-1] == self.dim_coor_total |
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x = self.vn_proj_in(x) |
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x = self.encoder(x, mask=mask) |
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x = self.vn_proj_out(x) |
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coors_out, feats_out = ( |
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x[..., :3], |
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x[..., 3:], |
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) |
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if self.translation_equivariance: |
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coors_out = coors_out + coors_mean |
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|
|
if not exists(feats): |
|
return coors_out |
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|
if return_concatted_coors_and_feats: |
|
return torch.cat((coors_out, feats_out), dim=-1) |
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|
return coors_out, feats_out |
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