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  • e7d26d294a wip: for release ncorley 2025-08-10 09:16:08 -07:00
  • 3df5b3e3d1 Bugfix in AtomAttentionEncoderPairformer (#391) Guangfeng Zhou 2025-07-14 15:51:16 -07:00
  • f6beb2c1b7 Bugfix (#361) Guangfeng Zhou 2025-07-09 10:38:23 -07:00
  • 54cc733a80 chore: apptainer (#352) Nathaniel Corley 2025-07-07 22:40:56 -07:00
  • b1d3bfc11c docs: README and apptainer (#291) Nathaniel Corley 2025-06-23 16:45:43 -07:00
  • a7533a7fe8 fix: sampling set_epoch (#285) Nathaniel Corley 2025-06-19 16:06:56 -07:00
  • 70e8e60cce feat: nvidia kernels (#278) Nathaniel Corley 2025-06-16 23:03:46 -07:00
  • e6a8700659 feat: health and timing callbacks (#277) Nathaniel Corley 2025-06-16 15:38:04 -07:00
  • c7e4e74778 fix: floating point issue with python not returning 1.0 for prob sum (#261) Raktim Mitra 2025-06-11 17:44:42 -07:00
  • 242920dbcd hotfix: ground truth template (#241) Nathaniel Corley 2025-06-03 15:08:21 -07:00
  • 27b25fc606 Update modelhub and cifutils (#231) Frank DiMaio 2025-05-23 17:35:27 -07:00
  • 0ea2573dfe quick fix of confidence_feats and should_early_stop_fn (#229) Odin Zhang 2025-05-23 14:26:53 -07:00
  • bd7b7413ac feat: add runs n' poses val set (#210) Nathaniel Corley 2025-05-16 13:48:49 -07:00
  • 5629dec350 Two bugfixes encountered in inference: (#215) Frank DiMaio 2025-05-16 13:09:50 -07:00
  • eea695a6c0 chore: bump cifutils and datahub submodules (#208) Nathaniel Corley 2025-05-14 13:45:50 -07:00
  • 479318a9e0 fix: force usage of config to set pdb base dir (#209) Rohith Krishna 2025-05-14 13:43:11 -07:00
  • af5e914c3d fix dna sampling default (#205) Rohith Krishna 2025-05-13 17:02:13 -07:00
  • d1305b616b refactor: RF Score (#202) Nathaniel Corley 2025-05-12 16:30:46 -07:00
  • 05bb329452 hotfix: key for loss computation (#201) Nathaniel Corley 2025-05-12 16:19:17 -07:00
  • fa07258b59 refactor: logging and metrics (#200) Nathaniel Corley 2025-05-12 14:41:06 -07:00
  • 26ed40fb07 feat: freeze weights, update resolvers (#199) Nathaniel Corley 2025-05-12 14:15:15 -07:00
  • c31b2fad19 chore: bump libs, apptainer, biotite (#188) Nathaniel Corley 2025-05-02 17:14:41 -07:00
  • e651268958 Chore: Update apptainer to include deepspeed support for H200s (#187) maxkazman 2025-05-02 17:08:21 -07:00
  • 03a6dbb2b0 feat: RFScore arbitrary templating project (#179) Nathaniel Corley 2025-05-01 11:56:57 -07:00
  • 2d38d2554b chore: bump submodules (#182) Nathaniel Corley 2025-05-01 11:46:01 -07:00
  • 5e44eb70b4 fix: properly mask mean_plddt at inference time (#180) Tuscan R Thompson 2025-04-30 12:35:01 -07:00
  • 90fea72272 docs: Update README.md Nathaniel Corley 2025-04-29 14:46:10 -07:00
  • 60810f6c59 chore: switch to the checkpoint symlink (#177) Nathaniel Corley 2025-04-28 22:54:13 -07:00
  • 0996c806ee remove duplicate transform (#175) Rohith Krishna 2025-04-28 22:18:12 -07:00
  • b51791bf0f Soften bfactor re (#176) Rohith Krishna 2025-04-28 22:17:22 -07:00
  • ab0d94af24 fix ckpt path (#174) Rohith Krishna 2025-04-28 22:15:07 -07:00
  • 7d108f7e25 fix: inference (#131) Nathaniel Corley 2025-04-28 19:03:01 -07:00
  • dc83fd4dbf remove chirals from modelhgub as they are in datahub (#171) Rohith Krishna 2025-04-28 13:53:35 -07:00
  • ec696acbed run make format on trunk and add CI for make format checks (#162) Simon Mathis 2025-04-24 19:13:18 +01:00
  • b8082fa5fc FF datahub to main Rohith Krishna 2025-04-21 14:17:48 -07:00
  • f064287b27 add run name to wandb (#147) Fanglei Xue 2025-04-21 14:14:31 -07:00
  • e82e1718c2 move arguments to init Rohith Krishna 2025-04-16 21:29:35 -07:00
  • 46616dd5fb fix docstring Rohith Krishna 2025-04-16 21:23:04 -07:00
  • 945e148f31 format Rohith Krishna 2025-04-16 21:21:52 -07:00
  • e661b96b42 add rasa.py Rohith Krishna 2025-04-16 21:19:57 -07:00
  • f6e7851187 add datahub main commit Rohith Krishna 2025-04-16 21:16:57 -07:00
  • b496b51667 commit the datahub commit Rohith Krishna 2025-04-16 13:38:41 -07:00
  • 7fca005a26 Change params so input as separate min and max fdimaio 2025-04-17 16:26:54 -07:00
  • 973ff23c7d Update filenames. Remove unnecessary includes fdimaio 2025-04-17 16:01:11 -07:00
  • 78ffe6f550 Add missing file fdimaio 2025-04-17 15:53:02 -07:00
  • 8e46855ef7 Add Bfactor trimming of models. Use for removing low-confidence regions in af2 distill set fdimaio 2025-04-17 15:50:05 -07:00
  • e07940fdc3 Add dna distill data. Update gitmodules. (#127) Frank DiMaio 2025-04-16 15:43:36 -07:00
  • d801e186f3 ruff: format (#119) Nathaniel Corley 2025-04-11 13:56:14 -07:00
  • 5eb870cac2 feat: submodules (#117) Nathaniel Corley 2025-04-11 13:48:48 -07:00
  • 8fc545c59b feat: distogram metrics, chiral metrics, path updates (#115) Nathaniel Corley 2025-04-11 13:13:20 -07:00
  • 9a8307f105 feat: Allow dataset filtering by ChainType (#116) Rafael Brent 2025-04-09 12:12:23 -07:00
  • 1533ed8e1f feat: updates paths to be platform agnostic (#114) Nathaniel Corley 2025-04-08 21:54:10 -07:00
  • 51308df97f Revert "Merge main onto aa_design" ncorley 2025-04-08 21:50:41 -07:00
  • 3d3192ee5e Merge main onto aa_design jbutch 2025-04-08 19:00:26 -07:00
  • 8c810c9167 feat: projects (#113) Nathaniel Corley 2025-04-08 15:26:03 -07:00
  • 22e251716f refactor/remove old files (#110) Nathaniel Corley 2025-04-08 15:09:38 -07:00
  • 5a492032d5 refactor: new modelhub (#109) Nathaniel Corley 2025-04-08 13:33:17 -07:00
  • 1fd848a861 feat: expose p_skip of PadDNA to the pipeline so it can be changed in config (#95) Ryan McHugh 2025-03-27 11:28:17 -07:00
  • 15d4051d28 Fix datahub path fdimaio 2025-03-20 18:31:50 -07:00
  • 1731cff60a feat: add PadDNA to data pipeline Ryan McHugh 2025-03-20 14:06:44 -07:00
  • 9cbefbb183 Merge pull request #84 from baker-laboratory/feat/inference_config_override Ryan McHugh 2025-03-20 14:37:12 -07:00
  • 2de49867ff Merge pull request #90 from baker-laboratory/trunk Ryan McHugh 2025-03-20 14:16:38 -07:00
  • 51351830fc fix initialization for chirals Rohith Krishna 2025-03-17 12:44:28 -07:00
  • 74081c9518 use default pytorch reset parameters Rohith Krishna 2025-03-17 12:40:57 -07:00
  • ce2238ea94 Move initialization to new func fdimaio 2025-03-17 12:12:46 -07:00
  • 2815741df4 Update the way chiral features are incorporated into the model Frank DiMaio 2025-03-17 11:49:07 -07:00
  • 6036331fc6 rename argument of confidence head HaotianZhangAI4Science 2025-03-12 21:28:23 -07:00
  • 4ccd641321 config HaotianZhangAI4Science 2025-03-12 10:19:20 -07:00
  • f2032b3669 Update af3_auxiliary_heads.py Odin Zhang 2025-03-12 10:08:01 -07:00
  • a0d46bae55 layer norm should only operate on the feature dim HaotianZhangAI4Science 2025-03-11 16:57:39 -07:00
  • 357b381e58 feat: config to control overwriting existing outputs for backfill compatibility Ryan McHugh 2025-03-20 11:16:19 -07:00
  • 82510cf1f7 fix initialization for chirals Rohith Krishna 2025-03-17 12:44:28 -07:00
  • 44564ef0be use default pytorch reset parameters Rohith Krishna 2025-03-17 12:40:57 -07:00
  • 523b7d16ea Move initialization to new func fdimaio 2025-03-17 12:12:46 -07:00
  • 10b620816b Update the way chiral features are incorporated into the model Frank DiMaio 2025-03-17 11:49:07 -07:00
  • afb7f4d148 fix: proper handling of yaml config Ryan McHugh 2025-03-13 14:11:59 -07:00
  • 2860599224 Merge pull request #83 from baker-laboratory/layer_norm_fix Odin Zhang 2025-03-12 21:29:06 -07:00
  • f26fc5c3a4 rename argument of confidence head HaotianZhangAI4Science 2025-03-12 21:28:23 -07:00
  • 875b991058 feat: option to supply override configs in inference Ryan McHugh 2025-03-12 18:21:17 -07:00
  • d1268a6940 config HaotianZhangAI4Science 2025-03-12 10:19:20 -07:00
  • 2bf31781c2 Update af3_auxiliary_heads.py Odin Zhang 2025-03-12 10:08:01 -07:00
  • 85f620151c layer norm should only operate on the feature dim HaotianZhangAI4Science 2025-03-11 16:57:39 -07:00
  • c17cdc94fd Missed one line in previous commit fdimaio 2025-03-07 14:29:51 -08:00
  • 85193e07eb Restoring flag fdimaio 2025-03-07 14:28:49 -08:00
  • 3eb039ce40 Remove option for double residual connection. Add kq_norm oiptions to base (20250125) config. fdimaio 2025-03-07 14:17:07 -08:00
  • f5abaf28d6 Add chiral metric fdimaio 2025-03-04 15:58:02 -08:00
  • 24a156f365 Initial checkin of chiral feature code fdimaio 2025-03-04 14:15:29 -08:00
  • c9f0d58460 Initial commit of chiral changes fdimaio 2025-02-14 17:14:22 -08:00
  • 449b6c0652 fix minor change in rollout yaml Tuscan Thompson 2025-02-26 16:39:05 -08:00
  • 80fbf29175 Raise a ValueError if using the weights with the bugged plddt Tuscan Thompson 2025-02-26 15:54:26 -08:00
  • a13984aa67 fix: fix reshape in exp_resolved_logits Tuscan Thompson 2025-02-18 13:26:39 -08:00
  • f93790e289 cleanup for merge Tuscan Thompson 2025-02-18 13:12:13 -08:00
  • 44324493fd fix: update plddt reshaping and permute Tuscan Thompson 2025-02-18 13:05:54 -08:00
  • 022df83dad WIP: implemented outline of atomic deviation prediction loss Tuscan Thompson 2025-02-12 15:00:31 -08:00
  • 88dc1cfba8 Merge pull request #59 from baker-laboratory/fix/update_pipeline_w_datahub_changes Frank DiMaio 2025-02-26 11:54:59 -08:00
  • c0a7aac235 Update pipeline to work with latest datahub fdimaio 2025-02-26 11:51:15 -08:00
  • 6be9cea52b Fix a bug (thanks Tuscan) where a permute was missing before calling CCE loss in the pLDDT confidence head. fdimaio 2025-02-14 15:29:49 -08:00
  • c506b69fa7 clean up configs Rohith Krishna 2025-02-13 17:55:28 -08:00
  • 156c6259d3 updates for training with new residual connection: Rohith Krishna 2025-02-13 17:35:42 -08:00
  • 679451b1b7 add flag for af3 diffusion encoder bug Rohith Krishna 2025-02-13 16:22:07 -08:00