En transformer
1.6.6
E(n)-Equivariant Transformer 的實現，它透過注意力機制和 Transformer 架構的想法擴展了 Welling 的 E(n)-Equivariant 圖神經網路的想法。
更新：用於設計抗體中的 CDR 環！
$ 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)讓網路同時處理原子和鍵類型嵌入
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)如果您只想專注於由鄰接矩陣（例如原子）定義的稀疏鄰居，則必須再設定一個標誌，然後傳入N x N鄰接矩陣。
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) 如果需要傳入連續的邊
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 )要執行蛋白質骨幹座標去噪玩具任務，首先安裝sidechainnet
$ pip install sidechainnet然後
$ 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 }
}
