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OpenDAS
OpenFold
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c290ff87
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c290ff87
authored
May 12, 2022
by
Gustaf Ahdritz
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Add LMA writeup
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1fc3ca2e
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@@ -141,6 +141,14 @@ Note that chunking (as defined in section 1.11.8 of the AlphaFold 2 supplement)
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@@ -141,6 +141,14 @@ Note that chunking (as defined in section 1.11.8 of the AlphaFold 2 supplement)
is enabled by default in inference mode. To disable it, set
`globals.chunk_size`
is enabled by default in inference mode. To disable it, set
`globals.chunk_size`
to
`None`
in the config.
to
`None`
in the config.
Inference-time low-memory attention (LMA) can be enabled in the model config.
This setting trades off speed for vastly improved memory usage. By default,
LMA is run with query and key chunk sizes of 1024 and 4096, respectively.
These represent a favorable tradeoff in most memory-constrained cases.
Powerusers can choose to tweak these settings in
`openfold/model/primitives.py`
. For more information on the LMA algorithm,
see the aforementioned Staats & Rabe preprint.
### Training
### Training
To train the model, you will first need to precompute protein alignments.
To train the model, you will first need to precompute protein alignments.
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