Commits · 1606ac083425e948f13bead42c664300c3588db4 · OpenDAS / OpenFold

"examples/llm/benchmarks/disagg.py" did not exist on "03b0101e4d4013874e33f8144c9793567e762c9f"

11 Dec, 2023 1 commit
- Merge branch 'main' into multimer · 1606ac08
  Christina Floristean authored Dec 11, 2023
  
  1606ac08
08 Dec, 2023 4 commits
- Remove env restart from setup script · 67a00a6c
  Christina Floristean authored Dec 08, 2023
  
  67a00a6c
- Merge pull request #378 from aqlaboratory/deepspeed-evo-attention · a13c0ce5
  Christina Floristean authored Dec 08, 2023
```
Deepspeed evoformer attention
```
  a13c0ce5
- Minor change to tests · 40d76358
  Christina Floristean authored Dec 08, 2023
  
  40d76358
- Minor test and README changes · 336c899a
  Christina Floristean authored Dec 08, 2023
  
  336c899a
06 Dec, 2023 1 commit
- Updated DeepSpeed version, added inplace_safe for template offloading · cdd97841
  Christina Floristean authored Dec 06, 2023
  
  cdd97841
05 Dec, 2023 3 commits
- Exclude uniprot hits from regular msa feature processing · 58d65692
  Christina Floristean authored Dec 05, 2023
  
  58d65692
- Merge pull request #375 from aqlaboratory/jackhmmer_query_update · 96f46b08
  Jennifer Wei authored Dec 05, 2023
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Adds query_multiple to jackhammer.py
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  96f46b08
- Merge branch 'main' into deepspeed-evo-attention · 9236c1e3
  Christina Floristean authored Dec 05, 2023
  
  9236c1e3
04 Dec, 2023 4 commits
- Adds query_multiple to jackhammer.py · 4958683b
  Jennifer authored Dec 04, 2023
  
  4958683b
- Merge pull request #374 from aqlaboratory/msa-block-deletion · 2dc080ce
  Christina Floristean authored Dec 04, 2023
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Fix for MSA block deletion
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  2dc080ce
- Fix bugs in block deletion, disable for soloseq · b935639b
  Christina Floristean authored Dec 04, 2023
  
  b935639b
- Fix for MSA block deletion · 616de3df
  Christina Floristean authored Dec 04, 2023
  
  616de3df
30 Nov, 2023 1 commit
- Merge pull request #373 from aqlaboratory/soloseq-params · a64f1a29
  Jennifer Wei authored Nov 30, 2023
```
Adds Soloseq parameter download script.
```
  a64f1a29
29 Nov, 2023 2 commits
- Adds Soloseq parameter download script. · 4a50c9c4
  jnwei authored Nov 29, 2023
  
  4a50c9c4
- Fix for issue #367 · 2c36cb8b
  Christina Floristean authored Nov 29, 2023
  
  2c36cb8b
21 Nov, 2023 6 commits
- Merge pull request #372 from aqlaboratory/fix-colab-imports · bc20f02f
  Jennifer Wei authored Nov 21, 2023
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Fixes imports to colab notebook.
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  bc20f02f
- Update OpenFold.ipynb · 4384ac08
  Jennifer Wei authored Nov 21, 2023
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fix small typo on button.
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  4384ac08
- Update OpenFold.ipynb · 59be42ca
  Jennifer Wei authored Nov 21, 2023
```
Adds cell to add a button to launch colab from github.
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  59be42ca
- Includes button for colab link and specifies GPU type · 6f10686b
  Jennifer Wei authored Nov 21, 2023
```
Edits colab metadata
```
  6f10686b
- Fixes imports to colab notebook. · e09dd313
  jnwei authored Nov 21, 2023
  
  e09dd313
- Fix for issue ##369: Bug in multimer deterministic train filter · cdeb8d1b
  Christina Floristean authored Nov 21, 2023
  
  cdeb8d1b
16 Nov, 2023 1 commit
- Use ds kernel for default long seq inference · 1271a03f
  Christina Floristean authored Nov 16, 2023
  
  1271a03f
13 Nov, 2023 4 commits
- Config file fix · 71526dff
  Christina Floristean authored Nov 13, 2023
  
  71526dff
- Config fixes for when using ds kernel · aebda3d8
  Christina Floristean authored Nov 13, 2023
  
  aebda3d8
- Minor test fix · f1563999
  Christina Floristean authored Nov 13, 2023
  
  f1563999
- Update setup script and refactor qkv prep · 7fb12cf5
  Christina Floristean authored Nov 13, 2023
  
  7fb12cf5
10 Nov, 2023 2 commits
- Fix naming error in alignment runner, add error message for missing uniprot files. · d8c2a979
  Christina Floristean authored Nov 10, 2023
  
  d8c2a979
- Return to regular kernel usage · 54d414e4
  Christina Floristean authored Nov 10, 2023
  
  54d414e4
08 Nov, 2023 2 commits
- Use EvoformerFusedAttention directly to avoid all-zero bias term in column attention · b7f35dce
  Christina Floristean authored Nov 08, 2023
  
  b7f35dce
- Merge branch 'main' into deepspeed-evo-attention · 5aa54958
  Christina Floristean authored Nov 08, 2023
  
  5aa54958
06 Nov, 2023 5 commits
- Fix for feature indexing when creating output protein object · 7e2b36e0
  Christina Floristean authored Nov 06, 2023
  
  7e2b36e0
- Add description to dummy msa feats · c05b4674
  Christina Floristean authored Nov 06, 2023
  
  c05b4674
- Another fix for dummy msa feature creation · d0f5531b
  Christina Floristean authored Nov 06, 2023
  
  d0f5531b
- Fix for creating msa dummy features · e67d0417
  Christina Floristean authored Nov 06, 2023
  
  e67d0417
- Hotfix to correct seed type in inference · 099769d2
  Christina Floristean authored Nov 06, 2023
  
  099769d2
03 Nov, 2023 1 commit
- Fix for loading old OF weights into refactored model · f65b75fe
  Christina Floristean authored Nov 03, 2023
  
  f65b75fe
02 Nov, 2023 3 commits
- Unit test fixes for when AF2 is not installed · 5fcd6ed2
  Christina Floristean authored Nov 02, 2023
  
  5fcd6ed2
- Change order of numpy and pandas dependencies to keep numpy version. · f95d9a57
  jnwei authored Nov 02, 2023
  
  f95d9a57
- Fixes for inference alignment generation · f94ee668
  Christina Floristean authored Nov 02, 2023
  
  f94ee668