lucidrains alphafold2 issues

lucidrains / alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

MIT License

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issues

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How to adjust the recycling times in model?

#109 Syaoran036 opened 1 year ago
0
CVE-2007-4559 Patch

#106 TrellixVulnTeam opened 1 year ago
0
read me dimensions are off. Example to run alpha fold 2 msa, and seq lengths should be the same. One is 128, the other is 120.

#104 ofTarradiddle opened 2 years ago
0
How can I get the coordinates of all the atoms?

#103 RayTang88 opened 2 years ago
0
outerMean module question

#102 ifromeast opened 2 years ago
1
__init__() got an unexpected keyword argument 'structure_module_type'

#101 ifromeast opened 2 years ago
4
Can AlphaFold2 predict the structure of cyclic peptides?

#98 JustinDoIt opened 3 years ago
1
[todo] ensembling

#97 lucidrains opened 3 years ago
0
Make sure random_tokens is on correct device

#96 aced125 closed 3 years ago
0
Typo?

#95 CiaoHe closed 3 years ago
3
Example script of an end-to-end prediction from FASTA sequence to 3D pdb

#94 h-midlothian closed 3 years ago
2
[todo] structure module

#93 lucidrains opened 3 years ago
3
Missing adding the `relpos` to pairwise-repr `x`

#92 CiaoHe closed 3 years ago
1
Maybe duplicate residual addition

#91 CiaoHe closed 3 years ago
1
Should be first MSA-attention then Pairwise-Attention

#90 CiaoHe closed 3 years ago
1
pairwise_repr should be used in rowAttention

#89 CiaoHe closed 3 years ago
1
Maybe Inverse of the outgoing-attention and ingoing-attention here

#88 CiaoHe closed 3 years ago
1
TypeError: __init__() got an unexpected keyword argument 'num_backbone_atoms'

#87 jackli777 opened 3 years ago
3
OuterMean block's typo

#86 CiaoHe closed 3 years ago
4
The definition of row-wise attention and col-wise attention

#85 CiaoHe closed 3 years ago
1
MSA attention gated problem

#84 CiaoHe closed 3 years ago
1
ModuleNotFoundError: No module named 'invariant_point_attention'

#83 jackli777 closed 3 years ago
2
[todo] positional encoding

#82 lucidrains closed 3 years ago
1
[todo] checkpointing

#81 lucidrains opened 3 years ago
3
[todo] BERT loss on MSA

#80 lucidrains opened 3 years ago
4
[todo] FAPE loss

#79 lucidrains closed 3 years ago
2
[todo] recycling

#78 lucidrains closed 3 years ago
1
[todo] embeddings

#77 lucidrains closed 3 years ago
1
problem with alphafold2/train_pre.py

#76 jackli777 opened 3 years ago
0
Dev

#75 CiaoHe closed 3 years ago
0
Add simple training script

#74 superantichrist opened 3 years ago
2
no coords_3d in train_end2end.py

#73 moonblue333 closed 3 years ago
2
Integrate newest changes

#72 hypnopump closed 3 years ago
1
the dimensions of coordinates in CASP12

#71 zhangyi-taotao closed 3 years ago
3
demonstrate sidechain

#70 hypnopump closed 3 years ago
1
Fix utils for better training

#69 hypnopump closed 3 years ago
2
solve mds problems?

#68 hypnopump closed 3 years ago
5
MDScaling isn't working right!

#67 xiongzhp closed 3 years ago
3
add new results from @lhatsk

#66 lucidrains closed 3 years ago
0
fix tests

#65 lucidrains closed 3 years ago
0
solving adjmat and a couple issues in utils

#64 hypnopump closed 3 years ago
0
fix row scaling dtype

#63 lucidrains closed 3 years ago
0
allow for tied row attention with uneven number of MSAs per sequence …

#62 lucidrains closed 3 years ago
2
Basic pretrained models + quickstart instructions?

#61 TylerBalsam opened 3 years ago
1
fix mds tensors not in same device

#60 hypnopump closed 3 years ago
1
Add PL Lightning to Enable Distributed Training and Deep Speed

#59 aribornstein opened 3 years ago
3
Add trrosetta dataset

#58 blazingsiyan closed 3 years ago
4
test error in utils

#57 lucidrains closed 3 years ago
1
MSA tensor format

#56 panganqi opened 3 years ago
5
fix embeddings with esm + msa mask

#55 hypnopump closed 3 years ago
0