En transformer
1.6.6
E(n)-Equivariant Transformer 的实现，它通过注意力机制和 Transformer 架构的思想扩展了 Welling 的 E(n)-Equivariant 图神经网络的思想。
更新：用于设计抗体中的 CDR 环！
$ pip install En-transformer import torch
from en_transformer import EnTransformer
model = EnTransformer (
dim = 512 ,
depth = 4 , # depth
dim_head = 64 , # dimension per head
heads = 8 , # number of heads
edge_dim = 4 , # dimension of edge feature
neighbors = 64 , # only do attention between coordinates N nearest neighbors - set to 0 to turn off
talking_heads = True , # use Shazeer's talking heads https://arxiv.org/abs/2003.02436
checkpoint = True , # use checkpointing so one can increase depth at little memory cost (and increase neighbors attended to)
use_cross_product = True , # use cross product vectors (idea by @MattMcPartlon)
num_global_linear_attn_heads = 4 # if your number of neighbors above is low, you can assign a certain number of attention heads to weakly attend globally to all other nodes through linear attention (https://arxiv.org/abs/1812.01243)
)
feats = torch . randn ( 1 , 1024 , 512 )
coors = torch . randn ( 1 , 1024 , 3 )
edges = torch . randn ( 1 , 1024 , 1024 , 4 )
mask = torch . ones ( 1 , 1024 ). bool ()
feats , coors = model ( feats , coors , edges , mask = mask ) # (1, 1024, 512), (1, 1024, 3)让网络同时处理原子和键类型嵌入
import torch
from en_transformer import EnTransformer
model = EnTransformer (
num_tokens = 10 , # number of unique nodes, say atoms
rel_pos_emb = True , # set this to true if your sequence is not an unordered set. it will accelerate convergence
num_edge_tokens = 5 , # number of unique edges, say bond types
dim = 128 ,
edge_dim = 16 ,
depth = 3 ,
heads = 4 ,
dim_head = 32 ,
neighbors = 8
)
atoms = torch . randint ( 0 , 10 , ( 1 , 16 )) # 10 different types of atoms
bonds = torch . randint ( 0 , 5 , ( 1 , 16 , 16 )) # 5 different types of bonds (n x n)
coors = torch . randn ( 1 , 16 , 3 ) # atomic spatial coordinates
feats_out , coors_out = model ( atoms , coors , edges = bonds ) # (1, 16, 512), (1, 16, 3)如果您只想关注由邻接矩阵（例如原子）定义的稀疏邻居，则必须再设置一个标志，然后传入N x N邻接矩阵。
import torch
from en_transformer import EnTransformer
model = EnTransformer (
num_tokens = 10 ,
dim = 512 ,
depth = 1 ,
heads = 4 ,
dim_head = 32 ,
neighbors = 0 ,
only_sparse_neighbors = True , # must be set to true
num_adj_degrees = 2 , # the number of degrees to derive from 1st degree neighbors passed in
adj_dim = 8 # whether to pass the adjacency degree information as an edge embedding
)
atoms = torch . randint ( 0 , 10 , ( 1 , 16 ))
coors = torch . randn ( 1 , 16 , 3 )
# naively assume a single chain of atoms
i = torch . arange ( atoms . shape [ 1 ])
adj_mat = ( i [:, None ] <= ( i [ None , :] + 1 )) & ( i [:, None ] >= ( i [ None , :] - 1 ))
# adjacency matrix must be passed in
feats_out , coors_out = model ( atoms , coors , adj_mat = adj_mat ) # (1, 16, 512), (1, 16, 3) 如果需要传入连续的边
import torch
from en_transformer import EnTransformer
from en_transformer . utils import rot
model = EnTransformer (
dim = 512 ,
depth = 1 ,
heads = 4 ,
dim_head = 32 ,
edge_dim = 4 ,
num_nearest_neighbors = 0 ,
only_sparse_neighbors = True
)
feats = torch . randn ( 1 , 16 , 512 )
coors = torch . randn ( 1 , 16 , 3 )
edges = torch . randn ( 1 , 16 , 16 , 4 )
i = torch . arange ( feats . shape [ 1 ])
adj_mat = ( i [:, None ] <= ( i [ None , :] + 1 )) & ( i [:, None ] >= ( i [ None , :] - 1 ))
feats1 , coors1 = model ( feats , coors , adj_mat = adj_mat , edges = edges )要运行蛋白质骨干坐标去噪玩具任务，首先安装sidechainnet
$ pip install sidechainnet然后
$ python denoise.py @misc { satorras2021en ,
title = { E(n) Equivariant Graph Neural Networks } ,
author = { Victor Garcia Satorras and Emiel Hoogeboom and Max Welling } ,
year = { 2021 } ,
eprint = { 2102.09844 } ,
archivePrefix = { arXiv } ,
primaryClass = { cs.LG }
} @misc { shazeer2020talkingheads ,
title = { Talking-Heads Attention } ,
author = { Noam Shazeer and Zhenzhong Lan and Youlong Cheng and Nan Ding and Le Hou } ,
year = { 2020 } ,
eprint = { 2003.02436 } ,
archivePrefix = { arXiv } ,
primaryClass = { cs.LG }
} @misc { liu2021swin ,
title = { Swin Transformer V2: Scaling Up Capacity and Resolution } ,
author = { Ze Liu and Han Hu and Yutong Lin and Zhuliang Yao and Zhenda Xie and Yixuan Wei and Jia Ning and Yue Cao and Zheng Zhang and Li Dong and Furu Wei and Baining Guo } ,
year = { 2021 } ,
eprint = { 2111.09883 } ,
archivePrefix = { arXiv } ,
primaryClass = { cs.CV }
} @inproceedings { Kim2020TheLC ,
title = { The Lipschitz Constant of Self-Attention } ,
author = { Hyunjik Kim and George Papamakarios and Andriy Mnih } ,
booktitle = { International Conference on Machine Learning } ,
year = { 2020 } ,
url = { https://api.semanticscholar.org/CorpusID:219530837 }
} @article { Mahajan2023.07.15.549154 ,
author = { Sai Pooja Mahajan and Jeffrey A. Ruffolo and Jeffrey J. Gray } ,
title = { Contextual protein and antibody encodings from equivariant graph transformers } ,
elocation-id = { 2023.07.15.549154 } ,
year = { 2023 } ,
doi = { 10.1101/2023.07.15.549154 } ,
publisher = { Cold Spring Harbor Laboratory } ,
URL = { https://www.biorxiv.org/content/early/2023/07/29/2023.07.15.549154 } ,
eprint = { https://www.biorxiv.org/content/early/2023/07/29/2023.07.15.549154.full.pdf } ,
journal = { bioRxiv }
} @article { Bondarenko2023QuantizableTR ,
title = { Quantizable Transformers: Removing Outliers by Helping Attention Heads Do Nothing } ,
author = { Yelysei Bondarenko and Markus Nagel and Tijmen Blankevoort } ,
journal = { ArXiv } ,
year = { 2023 } ,
volume = { abs/2306.12929 } ,
url = { https://api.semanticscholar.org/CorpusID:259224568 }
} @inproceedings { Arora2023ZoologyMA ,
title = { Zoology: Measuring and Improving Recall in Efficient Language Models } ,
author = { Simran Arora and Sabri Eyuboglu and Aman Timalsina and Isys Johnson and Michael Poli and James Zou and Atri Rudra and Christopher R'e } ,
year = { 2023 } ,
url = { https://api.semanticscholar.org/CorpusID:266149332 }
}
