mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-12-04 22:43:45 +00:00
475 lines
18 KiB
Python
475 lines
18 KiB
Python
import torch
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import torch.nn as nn
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import torch.nn.functional as F
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import math
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from opt_einsum import contract as einsum
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from rf2aa.util_module import init_lecun_normal
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class FeedForwardLayer(nn.Module):
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def __init__(self, d_model, r_ff, p_drop=0.1):
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super(FeedForwardLayer, self).__init__()
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self.norm = nn.LayerNorm(d_model)
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self.linear1 = nn.Linear(d_model, d_model*r_ff)
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self.dropout = nn.Dropout(p_drop)
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self.linear2 = nn.Linear(d_model*r_ff, d_model)
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self.reset_parameter()
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def reset_parameter(self):
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# initialize linear layer right before ReLu: He initializer (kaiming normal)
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nn.init.kaiming_normal_(self.linear1.weight, nonlinearity='relu')
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nn.init.zeros_(self.linear1.bias)
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# initialize linear layer right before residual connection: zero initialize
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nn.init.zeros_(self.linear2.weight)
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nn.init.zeros_(self.linear2.bias)
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def forward(self, src):
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src = self.norm(src)
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src = self.linear2(self.dropout(F.relu_(self.linear1(src))))
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return src
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class Attention(nn.Module):
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# calculate multi-head attention
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def __init__(self, d_query, d_key, n_head, d_hidden, d_out, p_drop=0.1):
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super(Attention, self).__init__()
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self.h = n_head
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self.dim = d_hidden
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#
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self.to_q = nn.Linear(d_query, n_head*d_hidden, bias=False)
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self.to_k = nn.Linear(d_key, n_head*d_hidden, bias=False)
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self.to_v = nn.Linear(d_key, n_head*d_hidden, bias=False)
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#
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self.to_out = nn.Linear(n_head*d_hidden, d_out)
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self.scaling = 1/math.sqrt(d_hidden)
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#
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# initialize all parameters properly
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_q.weight)
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nn.init.xavier_uniform_(self.to_k.weight)
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nn.init.xavier_uniform_(self.to_v.weight)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.to_out.weight)
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nn.init.zeros_(self.to_out.bias)
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def forward(self, query, key, value):
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B, Q = query.shape[:2]
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B, K = key.shape[:2]
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#
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query = self.to_q(query).reshape(B, Q, self.h, self.dim)
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key = self.to_k(key).reshape(B, K, self.h, self.dim)
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value = self.to_v(value).reshape(B, K, self.h, self.dim)
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#
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query = query * self.scaling
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attn = einsum('bqhd,bkhd->bhqk', query, key)
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attn = F.softmax(attn, dim=-1)
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#
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out = einsum('bhqk,bkhd->bqhd', attn, value)
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out = out.reshape(B, Q, self.h*self.dim)
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#
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out = self.to_out(out)
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return out
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# MSA Attention (row/column) from AlphaFold architecture
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class SequenceWeight(nn.Module):
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def __init__(self, d_msa, n_head, d_hidden, p_drop=0.1):
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super(SequenceWeight, self).__init__()
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self.h = n_head
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self.dim = d_hidden
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self.scale = 1.0 / math.sqrt(self.dim)
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self.to_query = nn.Linear(d_msa, n_head*d_hidden)
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self.to_key = nn.Linear(d_msa, n_head*d_hidden)
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self.dropout = nn.Dropout(p_drop)
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_query.weight)
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nn.init.xavier_uniform_(self.to_key.weight)
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def forward(self, msa):
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B, N, L = msa.shape[:3]
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tar_seq = msa[:,0]
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q = self.to_query(tar_seq).view(B, 1, L, self.h, self.dim)
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k = self.to_key(msa).view(B, N, L, self.h, self.dim)
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q = q * self.scale
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attn = einsum('bqihd,bkihd->bkihq', q, k)
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attn = F.softmax(attn, dim=1)
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return self.dropout(attn)
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class MSARowAttentionWithBias(nn.Module):
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def __init__(self, d_msa=256, d_pair=128, n_head=8, d_hidden=32):
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super(MSARowAttentionWithBias, self).__init__()
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self.norm_msa = nn.LayerNorm(d_msa)
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self.norm_pair = nn.LayerNorm(d_pair)
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#
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self.seq_weight = SequenceWeight(d_msa, n_head, d_hidden, p_drop=0.1)
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self.to_q = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_k = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_v = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_b = nn.Linear(d_pair, n_head, bias=False)
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self.to_g = nn.Linear(d_msa, n_head*d_hidden)
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self.to_out = nn.Linear(n_head*d_hidden, d_msa)
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self.scaling = 1/math.sqrt(d_hidden)
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self.h = n_head
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self.dim = d_hidden
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_q.weight)
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nn.init.xavier_uniform_(self.to_k.weight)
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nn.init.xavier_uniform_(self.to_v.weight)
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# bias: normal distribution
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self.to_b = init_lecun_normal(self.to_b)
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# gating: zero weights, one biases (mostly open gate at the begining)
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nn.init.zeros_(self.to_g.weight)
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nn.init.ones_(self.to_g.bias)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.to_out.weight)
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nn.init.zeros_(self.to_out.bias)
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def forward(self, msa, pair): # TODO: make this as tied-attention
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B, N, L = msa.shape[:3]
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#
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msa = self.norm_msa(msa)
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pair = self.norm_pair(pair)
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#
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seq_weight = self.seq_weight(msa) # (B, N, L, h, 1)
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query = self.to_q(msa).reshape(B, N, L, self.h, self.dim)
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key = self.to_k(msa).reshape(B, N, L, self.h, self.dim)
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value = self.to_v(msa).reshape(B, N, L, self.h, self.dim)
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bias = self.to_b(pair) # (B, L, L, h)
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gate = torch.sigmoid(self.to_g(msa))
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#
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query = query * seq_weight.expand(-1, -1, -1, -1, self.dim)
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key = key * self.scaling
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attn = einsum('bsqhd,bskhd->bqkh', query, key)
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attn = attn + bias
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attn = F.softmax(attn, dim=-2)
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#
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out = einsum('bqkh,bskhd->bsqhd', attn, value).reshape(B, N, L, -1)
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out = gate * out
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#
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out = self.to_out(out)
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return out
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class MSAColAttention(nn.Module):
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def __init__(self, d_msa=256, n_head=8, d_hidden=32):
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super(MSAColAttention, self).__init__()
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self.norm_msa = nn.LayerNorm(d_msa)
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#
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self.to_q = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_k = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_v = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_g = nn.Linear(d_msa, n_head*d_hidden)
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self.to_out = nn.Linear(n_head*d_hidden, d_msa)
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self.scaling = 1/math.sqrt(d_hidden)
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self.h = n_head
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self.dim = d_hidden
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_q.weight)
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nn.init.xavier_uniform_(self.to_k.weight)
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nn.init.xavier_uniform_(self.to_v.weight)
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# gating: zero weights, one biases (mostly open gate at the begining)
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nn.init.zeros_(self.to_g.weight)
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nn.init.ones_(self.to_g.bias)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.to_out.weight)
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nn.init.zeros_(self.to_out.bias)
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def forward(self, msa):
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B, N, L = msa.shape[:3]
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#
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msa = self.norm_msa(msa)
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#
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query = self.to_q(msa).reshape(B, N, L, self.h, self.dim)
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key = self.to_k(msa).reshape(B, N, L, self.h, self.dim)
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value = self.to_v(msa).reshape(B, N, L, self.h, self.dim)
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gate = torch.sigmoid(self.to_g(msa))
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#
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query = query * self.scaling
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attn = einsum('bqihd,bkihd->bihqk', query, key)
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attn = F.softmax(attn, dim=-1)
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#
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out = einsum('bihqk,bkihd->bqihd', attn, value).reshape(B, N, L, -1)
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out = gate * out
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#
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out = self.to_out(out)
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return out
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class MSAColGlobalAttention(nn.Module):
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def __init__(self, d_msa=64, n_head=8, d_hidden=8):
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super(MSAColGlobalAttention, self).__init__()
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self.norm_msa = nn.LayerNorm(d_msa)
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#
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self.to_q = nn.Linear(d_msa, n_head*d_hidden, bias=False)
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self.to_k = nn.Linear(d_msa, d_hidden, bias=False)
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self.to_v = nn.Linear(d_msa, d_hidden, bias=False)
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self.to_g = nn.Linear(d_msa, n_head*d_hidden)
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self.to_out = nn.Linear(n_head*d_hidden, d_msa)
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self.scaling = 1/math.sqrt(d_hidden)
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self.h = n_head
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self.dim = d_hidden
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_q.weight)
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nn.init.xavier_uniform_(self.to_k.weight)
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nn.init.xavier_uniform_(self.to_v.weight)
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# gating: zero weights, one biases (mostly open gate at the begining)
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nn.init.zeros_(self.to_g.weight)
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nn.init.ones_(self.to_g.bias)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.to_out.weight)
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nn.init.zeros_(self.to_out.bias)
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def forward(self, msa):
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B, N, L = msa.shape[:3]
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#
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msa = self.norm_msa(msa)
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#
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query = self.to_q(msa).reshape(B, N, L, self.h, self.dim)
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query = query.mean(dim=1) # (B, L, h, dim)
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key = self.to_k(msa) # (B, N, L, dim)
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value = self.to_v(msa) # (B, N, L, dim)
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gate = torch.sigmoid(self.to_g(msa)) # (B, N, L, h*dim)
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#
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query = query * self.scaling
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attn = einsum('bihd,bkid->bihk', query, key) # (B, L, h, N)
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attn = F.softmax(attn, dim=-1)
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#
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out = einsum('bihk,bkid->bihd', attn, value).reshape(B, 1, L, -1) # (B, 1, L, h*dim)
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out = gate * out # (B, N, L, h*dim)
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#
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out = self.to_out(out)
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return out
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# TriangleAttention & TriangleMultiplication from AlphaFold architecture
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class TriangleAttention(nn.Module):
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def __init__(self, d_pair, n_head=4, d_hidden=32, p_drop=0.1, start_node=True):
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super(TriangleAttention, self).__init__()
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self.norm = nn.LayerNorm(d_pair)
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self.to_q = nn.Linear(d_pair, n_head*d_hidden, bias=False)
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self.to_k = nn.Linear(d_pair, n_head*d_hidden, bias=False)
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self.to_v = nn.Linear(d_pair, n_head*d_hidden, bias=False)
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self.to_b = nn.Linear(d_pair, n_head, bias=False)
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self.to_g = nn.Linear(d_pair, n_head*d_hidden)
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self.to_out = nn.Linear(n_head*d_hidden, d_pair)
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self.scaling = 1/math.sqrt(d_hidden)
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self.h = n_head
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self.dim = d_hidden
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self.start_node=start_node
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_q.weight)
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nn.init.xavier_uniform_(self.to_k.weight)
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nn.init.xavier_uniform_(self.to_v.weight)
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# bias: normal distribution
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self.to_b = init_lecun_normal(self.to_b)
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# gating: zero weights, one biases (mostly open gate at the begining)
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nn.init.zeros_(self.to_g.weight)
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nn.init.ones_(self.to_g.bias)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.to_out.weight)
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nn.init.zeros_(self.to_out.bias)
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def forward(self, pair):
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B, L = pair.shape[:2]
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pair = self.norm(pair)
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# input projection
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query = self.to_q(pair).reshape(B, L, L, self.h, -1)
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key = self.to_k(pair).reshape(B, L, L, self.h, -1)
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value = self.to_v(pair).reshape(B, L, L, self.h, -1)
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bias = self.to_b(pair) # (B, L, L, h)
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gate = torch.sigmoid(self.to_g(pair)) # (B, L, L, h*dim)
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# attention
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query = query * self.scaling
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if self.start_node:
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attn = einsum('bijhd,bikhd->bijkh', query, key)
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else:
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attn = einsum('bijhd,bkjhd->bijkh', query, key)
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attn = attn + bias.unsqueeze(1).expand(-1,L,-1,-1,-1) # (bijkh)
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attn = F.softmax(attn, dim=-2)
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if self.start_node:
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out = einsum('bijkh,bikhd->bijhd', attn, value).reshape(B, L, L, -1)
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else:
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out = einsum('bijkh,bkjhd->bijhd', attn, value).reshape(B, L, L, -1)
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out = gate * out # gated attention
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# output projection
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out = self.to_out(out)
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return out
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class TriangleMultiplication(nn.Module):
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def __init__(self, d_pair, d_hidden=128, outgoing=True):
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super(TriangleMultiplication, self).__init__()
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self.norm = nn.LayerNorm(d_pair)
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self.left_proj = nn.Linear(d_pair, d_hidden)
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self.right_proj = nn.Linear(d_pair, d_hidden)
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self.left_gate = nn.Linear(d_pair, d_hidden)
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self.right_gate = nn.Linear(d_pair, d_hidden)
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#
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self.gate = nn.Linear(d_pair, d_pair)
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self.norm_out = nn.LayerNorm(d_hidden)
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self.out_proj = nn.Linear(d_hidden, d_pair)
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self.outgoing = outgoing
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self.reset_parameter()
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def reset_parameter(self):
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# normal distribution for regular linear weights
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self.left_proj = init_lecun_normal(self.left_proj)
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self.right_proj = init_lecun_normal(self.right_proj)
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# Set Bias of Linear layers to zeros
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nn.init.zeros_(self.left_proj.bias)
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nn.init.zeros_(self.right_proj.bias)
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# gating: zero weights, one biases (mostly open gate at the begining)
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nn.init.zeros_(self.left_gate.weight)
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nn.init.ones_(self.left_gate.bias)
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nn.init.zeros_(self.right_gate.weight)
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nn.init.ones_(self.right_gate.bias)
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nn.init.zeros_(self.gate.weight)
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nn.init.ones_(self.gate.bias)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.out_proj.weight)
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nn.init.zeros_(self.out_proj.bias)
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def forward(self, pair):
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B, L = pair.shape[:2]
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pair = self.norm(pair)
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left = self.left_proj(pair) # (B, L, L, d_h)
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left_gate = torch.sigmoid(self.left_gate(pair))
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left = left_gate * left
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right = self.right_proj(pair) # (B, L, L, d_h)
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right_gate = torch.sigmoid(self.right_gate(pair))
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right = right_gate * right
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if self.outgoing:
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out = einsum('bikd,bjkd->bijd', left, right/float(L))
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else:
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out = einsum('bkid,bkjd->bijd', left, right/float(L))
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out = self.norm_out(out)
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out = self.out_proj(out)
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gate = torch.sigmoid(self.gate(pair)) # (B, L, L, d_pair)
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out = gate * out
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return out
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# Instead of triangle attention, use Tied axail attention with bias from coordinates..?
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class BiasedAxialAttention(nn.Module):
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def __init__(self, d_pair, d_bias, n_head, d_hidden, p_drop=0.1, is_row=True):
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super(BiasedAxialAttention, self).__init__()
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#
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self.is_row = is_row
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self.norm_pair = nn.LayerNorm(d_pair)
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self.norm_bias = nn.LayerNorm(d_bias)
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self.to_q = nn.Linear(d_pair, n_head*d_hidden, bias=False)
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self.to_k = nn.Linear(d_pair, n_head*d_hidden, bias=False)
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self.to_v = nn.Linear(d_pair, n_head*d_hidden, bias=False)
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self.to_b = nn.Linear(d_bias, n_head, bias=False)
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self.to_g = nn.Linear(d_pair, n_head*d_hidden)
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self.to_out = nn.Linear(n_head*d_hidden, d_pair)
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self.scaling = 1/math.sqrt(d_hidden)
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self.h = n_head
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self.dim = d_hidden
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# initialize all parameters properly
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self.reset_parameter()
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def reset_parameter(self):
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# query/key/value projection: Glorot uniform / Xavier uniform
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nn.init.xavier_uniform_(self.to_q.weight)
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nn.init.xavier_uniform_(self.to_k.weight)
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nn.init.xavier_uniform_(self.to_v.weight)
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# bias: normal distribution
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self.to_b = init_lecun_normal(self.to_b)
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# gating: zero weights, one biases (mostly open gate at the begining)
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nn.init.zeros_(self.to_g.weight)
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nn.init.ones_(self.to_g.bias)
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# to_out: right before residual connection: zero initialize -- to make it sure residual operation is same to the Identity at the begining
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nn.init.zeros_(self.to_out.weight)
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nn.init.zeros_(self.to_out.bias)
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def forward(self, pair, bias):
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# pair: (B, L, L, d_pair)
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B, L = pair.shape[:2]
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if self.is_row:
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pair = pair.permute(0,2,1,3)
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bias = bias.permute(0,2,1,3)
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pair = self.norm_pair(pair)
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bias = self.norm_bias(bias)
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query = self.to_q(pair).reshape(B, L, L, self.h, self.dim)
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key = self.to_k(pair).reshape(B, L, L, self.h, self.dim)
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value = self.to_v(pair).reshape(B, L, L, self.h, self.dim)
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bias = self.to_b(bias) # (B, L, L, h)
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gate = torch.sigmoid(self.to_g(pair)) # (B, L, L, h*dim)
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|
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query = query * self.scaling
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key = key / L # normalize for tied attention
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attn = einsum('bnihk,bnjhk->bijh', query, key) # tied attention
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attn = attn + bias # apply bias
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attn = F.softmax(attn, dim=-2) # (B, L, L, h)
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|
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out = einsum('bijh,bnjhd->bnihd', attn, value).reshape(B, L, L, -1)
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out = gate * out
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out = self.to_out(out)
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if self.is_row:
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out = out.permute(0,2,1,3)
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return out
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