Commits · f96e254e6da73daba42db4d38727f71c2f6fcee5 · ModelZoo / alphafold2_jax

21 Dec, 2022 1 commit
- Add `eval_dropout` option for using dropout in trunk at eval time. · f96e254e
  Josh Abramson authored Dec 21, 2022
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11 Dec, 2022 1 commit
- Release code for v2.3.0 · 9b18d6a9
  Augustin Zidek authored Dec 11, 2022
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  9b18d6a9
13 Oct, 2022 1 commit

[JAX] Import scipy submodules directly in code that uses them. · a31061e8

Peter Hawkins authored Oct 13, 2022

JAX will soon import scipy lazily, so code that relies on JAX having already imported submodules of scipy will fail. Change code to import what it uses.

PiperOrigin-RevId: 480841853
Change-Id: I18a744a561d73da3ccd43c26fcd99d10070c058e

a31061e8

16 Sep, 2022 2 commits
- Fix incorrect length_scale argument · 5352e298
  Hamish Tomlinson authored Sep 16, 2022
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- Update Jax and Haiku versions · 5e702ce1
  Hamish Tomlinson authored Sep 16, 2022
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14 Jun, 2022 2 commits

Migrate from `collections.Iterable` to `collections.abc.Iterable`. · 7b2a4c5a

Tom Ward authored Jun 14, 2022

Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working.

PiperOrigin-RevId: 454823734
Change-Id: Ic1d22c0badd76c41693967f785f8861746657731

7b2a4c5a

Move `disable_v2_behaviour()` to `setUp` to enable running tests in test suites. · 5f4a9cc3
Tom Ward authored Jun 14, 2022
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5f4a9cc3

31 May, 2022 1 commit
- Fix jax.tree_multimap deprecation warning. · d9e5e1d9
  Augustin Zidek authored May 31, 2022
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21 Mar, 2022 1 commit

Silence some pytype errors. · ed0886cb

Rebecca Chen authored Mar 21, 2022

PiperOrigin-RevId: 436161190
Change-Id: Ia10df42f5f3f638a7a5b7b804c593a1e28a4ef44

ed0886cb

07 Mar, 2022 1 commit
- Update open source between_residue_clash_loss to take into account multiple chains. · 481b8be2
  Rich Evans authored Mar 07, 2022
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03 Mar, 2022 1 commit
- Update multimer models to v2. · eba82a65
  Sebastian Bodenstein authored Mar 03, 2022
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02 Mar, 2022 1 commit
- Remove unused function casp_model_names. · 189f7d81
  Sebastian Bodenstein authored Mar 02, 2022
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  189f7d81
21 Feb, 2022 1 commit
- Remove unused bias arg in GlobalAttention. · 16bab4d3
  Tim Green authored Feb 21, 2022
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16 Feb, 2022 1 commit

Improve support for num_recycle=0. · 2cd61ade

Michael Figurnov authored Feb 16, 2022

Previously, setting num_recycle=0 in a pretrained recycling model skipped creating some Linears and LayerNorms. This meant that the the offsets of these modules were not applied leading to a degraded performance in that case.

PiperOrigin-RevId: 429075328
Change-Id: I9257f859521799f45e2deef3803c249311051225

2cd61ade

14 Feb, 2022 1 commit

Add split_rng=False (current default) to sharded_map. · 929b188a

Tom Hennigan authored Feb 13, 2022

Haiku plans to make split_rng a required argument to hk.vmap in an upcoming
release. This change updates AlphaFold to preserve the current behaviour. We
also handle the case where users are using a release of Haiku without the
split_rng option, for these users split_rng=False is implied.

PiperOrigin-RevId: 428429472
Change-Id: I3292396eb330ffabf2f36f5364aa0ae1bc74cf71

929b188a

27 Jan, 2022 1 commit
- Release code for v2.1.2 · 57a2455e
  Augustin Zidek authored Jan 27, 2022
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02 Nov, 2021 1 commit
- Add code for AlphaFold-Multimer. · 0be2b30b
  Augustin-Zidek authored Nov 02, 2021
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31 Aug, 2021 1 commit

Ensure values passed to jax.numpy functions are arrays rather than lists. · 98caef21

Jake VanderPlas authored Aug 31, 2021

Why? This will soon be a requirement in JAX; see https://github.com/google/jax/issues/7737

PiperOrigin-RevId: 394105499
Change-Id: I6f76e3f47b7906616c1f988be58d29c828414060

98caef21

02 Aug, 2021 1 commit

Fix a few typos. · 41232dc7

Augustin Zidek authored Aug 02, 2021

PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab

41232dc7

30 Jul, 2021 1 commit
- Add a comment on the TriangleMultiplication notation. · b88f8dac
  DeepMind authored Jul 30, 2021
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27 Jul, 2021 1 commit

Fix import ordering. · 1e216f93

Tom Ward authored Jul 27, 2021

PiperOrigin-RevId: 387085679
Change-Id: I73287fcd0a29e899543b64c596e306195a2f435e

1e216f93

22 Jul, 2021 1 commit
- Add a Colab notebook, add reduced BFD, and various other fixes and improvements. · 0bab1bf8
  Saran Tunyasuvunakool authored Jul 22, 2021
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15 Jul, 2021 1 commit
- Initial release of AlphaFold. · 1109480e
  Augustin-Zidek authored Jul 15, 2021
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  1109480e