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aws-finetuning-code
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504 Commits

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Author SHA1 Message Date
Sachin Kadyan
1b5813df76 Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances. 2023-01-09 20:55:03 -05:00
Gustaf Ahdritz
ec5619fc97 Add AlphaFold-Multimer disclaimer 2022-05-25 16:58:43 -04:00
Gustaf Ahdritz
064cd20db1 Add note on AlphaFold-Gap 2022-05-25 16:28:39 -04:00
Gustaf Ahdritz
a1cf74544a Fix another undefined reference 2022-05-25 16:22:22 -04:00
Gustaf Ahdritz
be87500ac3 Fix undefined reference 2022-05-25 16:03:28 -04:00
Gustaf Ahdritz
197029b1ed Fix config default 2022-05-25 16:00:52 -04:00
Gustaf Ahdritz
f4043e1c73 Add AlphaFold-Gap inference 2022-05-25 16:00:06 -04:00
Gustaf Ahdritz
89f0549704 Merge branch 'main' of github.com:aqlaboratory/openfold into main 2022-05-25 15:53:41 -04:00
Gustaf Ahdritz
a14e8360ad Never checkpoint with grad disabled 2022-05-25 15:53:07 -04:00
Gustaf Ahdritz
67e34d9264 Avoid calling the checkpointing function with grad disabled 2022-05-25 15:50:38 -04:00
Gustaf Ahdritz
24118e8045 Update pretrained script usage notes 2022-05-13 13:59:38 -04:00
Gustaf Ahdritz
c290ff8784 Add LMA writeup 2022-05-12 23:32:01 -04:00
Gustaf Ahdritz
1fc3ca2ef1 Merge branch 'main' of github.com:aqlaboratory/openfold into main 2022-05-12 23:23:16 -04:00
Gustaf Ahdritz
e4b701f004 Update inference script usage example 2022-05-12 23:22:58 -04:00
Gustaf Ahdritz
722a5e0171 Improve ease of use of LMA 2022-05-12 23:21:51 -04:00
Gustaf Ahdritz
a5df96c334 Fix typo 2022-05-10 23:03:42 -04:00
Gustaf Ahdritz
237e26c423 Bullet README 2022-05-10 19:16:45 -04:00
Gustaf Ahdritz
c4a4df22b3 Trim OpenFoldBatchCollator 2022-05-09 19:33:02 -04:00
Gustaf Ahdritz
954ed3d3da Merge pull request #101 from CyrusBiotechnology/fix-docker-keys 
add correct GPG key to dockerfile
 2022-05-09 13:48:09 -04:00
Sam DeLuca
fdec6ef5df add correct GPG key to dockerfile 2022-05-09 11:38:34 -04:00
Gustaf Ahdritz
cd41d73f31 Add shape assertion to rotation code 2022-05-07 19:28:13 -04:00
Gustaf Ahdritz
253aff644e Further simplify rotation multiplication code 2022-05-07 19:26:20 -04:00
Gustaf Ahdritz
4e9f7a9d9a Simplify rotation multiplication code 2022-05-07 19:24:25 -04:00
Gustaf Ahdritz
1eb4fcdd44 Remove redundant condition 2022-05-07 17:03:03 -04:00
Gustaf Ahdritz
576174f08c Fix bug in MSA chunking code 2022-04-28 15:26:45 -04:00
Gustaf Ahdritz
de60b4101c Dockerfile CUDA compilation round 10 2022-04-27 23:47:34 -04:00
Gustaf Ahdritz
3f6b73b33f Dockerfile CUDA compilation round 9 2022-04-27 23:29:11 -04:00
Gustaf Ahdritz
f24096690b Dockerfile CUDA compilation round 8 2022-04-27 23:25:33 -04:00
Gustaf Ahdritz
fa961fa000 Dockerfile CUDA compilation round 7 2022-04-27 23:22:07 -04:00
Gustaf Ahdritz
1077644288 Dockerfile CUDA compilation round 6 2022-04-27 23:17:52 -04:00
Gustaf Ahdritz
165603f101 Dockerfile CUDA compilation round 5 2022-04-27 22:59:00 -04:00
Gustaf Ahdritz
e9b75b2da1 Dockerfile CUDA compilation round 4 2022-04-27 22:55:28 -04:00
Gustaf Ahdritz
9fa79bd013 Dockerfile CUDA compilation round 3 2022-04-27 22:43:05 -04:00
Gustaf Ahdritz
453c90aeae Dockerfile CUDA compilation round 2 2022-04-27 22:22:54 -04:00
Gustaf Ahdritz
23c69cbf1c Test Dockerfile CUDA compilation 2022-04-27 22:07:54 -04:00
Gustaf Ahdritz
78567a864c Fix validation metric bugs 2022-04-27 21:09:35 -04:00
Gustaf Ahdritz
e1796607a1 Update environment.yml 2022-04-26 18:33:15 -04:00
Gustaf Ahdritz
50078a622b Add type check to attention kernel 2022-04-26 16:41:03 -04:00
Gustaf Ahdritz
aada2a46dd Remove stray comment 2022-04-26 14:20:49 -04:00
Gustaf Ahdritz
41c3b0bc4e Add licence notice to kernel files 2022-04-26 14:19:43 -04:00
Gustaf Ahdritz
67b35775d1 Add FastFold link 2022-04-26 13:51:32 -04:00
Gustaf Ahdritz
edb7d341f0 Add memory-efficient attention kernels 2022-04-26 02:11:18 -04:00
Gustaf Ahdritz
816c184396 Merge pull request #97 from CyrusBiotechnology/small-bugfixes 
fixing CUDA versions in dockerfile and a small bug in run_pretrained_openfold.py
 2022-04-21 13:41:48 -04:00
Sam DeLuca
102c446ff2 fixing dockerfile and small bug in run_pretrained_openfold.py 2022-04-21 13:37:38 -04:00
Gustaf Ahdritz
a43848dc16 Correct wording in README 2022-04-20 19:09:58 -04:00
Gustaf Ahdritz
bc35baa0e1 Add LMA arXiv link to README 2022-04-20 19:09:02 -04:00
Gustaf Ahdritz
7e2b311f33 Add features to README 2022-04-20 19:08:06 -04:00
Gustaf Ahdritz
591d10d267 Fix template bugs 2022-04-19 16:48:40 -04:00
Gustaf Ahdritz
8c169fb623 Add missing pLDDT test 2022-04-15 01:10:19 -04:00
Gustaf Ahdritz
857e9b7cc9 Fix evoformer paths in some old tests 2022-04-13 23:18:57 -04:00