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• ecaa0d99fb initial change for new datahub Rohith Krishna 2024-10-21 18:27:56 -07:00
• ff6609be60 fix: update with latest datahub ncorley 2024-10-21 13:32:12 -07:00
• 7751d981f3 fix deepspeed code Rohith Krishna 2024-10-21 13:09:23 -07:00
• f9bc99b282 commit to be squashed Rohith Krishna 2024-10-17 18:07:43 -07:00
• 24414508b6 adding deepspeed to diffusion transformer Rohith Krishna 2024-10-17 10:40:54 -07:00
• a30a8e4c07 changes to run validation Rohith Krishna 2024-10-16 17:58:52 -07:00
• 0f45fd8594 refactor for speed and deprecating ddp param buffers Rohith Krishna 2024-10-15 17:01:49 -07:00
• c7bbb34398 changes for new datasets Rohith Krishna 2024-10-11 14:00:25 -07:00
• 39a7dd3e12 add new dataset code Rohith Krishna 2024-10-09 10:01:34 -07:00
• 1489afa79d updates for changing diffusion batch size Rohith Krishna 2024-10-08 18:17:55 -07:00
• 33d69b1637 use new dataset with msa module Rohith Krishna 2024-10-08 15:43:04 -07:00
• 2c2afd2303 remove adding extra dependencies in the trainer Rohith Krishna 2024-10-08 15:11:42 -07:00
• 0d1b909993 separated out trainers into experiments folder; added in support for datahub Rohith Krishna 2024-10-08 15:08:45 -07:00
• 5b74e22854 point to af3 pipeline Rohith Krishna 2024-09-25 21:40:17 -07:00
• 0955127674 initial work to get datahub dataloader working Rohith Krishna 2024-09-25 21:18:49 -07:00
• 8bd12c2ab2 use msa extra for msa inputs Rohith Krishna 2024-09-24 11:38:40 -07:00
• 83fb88ad77 added rollout Rohith Krishna 2024-09-20 11:34:55 -07:00
• 3e523bbe7b af3 losses and rollout Rohith Krishna 2024-09-10 12:30:53 -07:00
• d39929a2ac latest code checkin Rohith Krishna 2024-09-10 11:53:04 -07:00
• ecf5af94c8 fix bugs in dataloading, add residual connection Rohith Krishna 2024-09-04 14:53:57 -07:00
• a740648e4c changes for training af3 repro with distogram Rohith Krishna 2024-08-14 12:18:51 -07:00
• 1e7d60772d add changes to transforms Rohith Krishna 2024-08-02 13:28:18 -07:00
• 5907e4375e changes for running af3 repro in trainer-new Rohith Krishna 2024-08-02 13:27:49 -07:00
• 235f892c21 add in logic for running validation cycles during training Rohith Krishna 2024-07-16 15:19:27 -07:00
• 272cbffac8 added in transform file Rohith Krishna 2024-07-16 14:16:30 -07:00
• acb475ebde changes for stable training Rohith Krishna 2024-07-15 11:16:24 -07:00
• a9e3fb9894 stage for training- bugfixes in chemical, add logging of lddts and introduce checkpointing Rohith Krishna 2024-07-08 17:45:52 -07:00
• f5ade30c6f more work Rohith Krishna 2024-06-25 10:28:37 -07:00
• 3fc7585134 spoofing works for complexes Rohith Krishna 2024-06-21 17:12:05 -07:00
• ebba9e2a3e progress on unified loading Rohith Krishna 2024-06-21 14:08:18 -07:00
• e215d630b9 progress towards msa module working Rohith Krishna 2024-06-05 19:45:32 -07:00
• ae95760f1f Add inference tooling. Woody Ahern 2024-06-13 12:34:41 -07:00
• 11101963df Use loggers Woody Ahern 2024-05-14 14:22:43 -07:00
• d33c097ff5 Add af3-style 2track net fdimaio 2024-05-03 18:34:49 -07:00
• 22dd371a4e early work on flow matching Rohith Krishna 2024-03-21 16:47:22 -07:00
• 71c484d18e added spoofing psturmfels 2024-05-31 09:49:24 -07:00
• fa95b98634 step 1 of refactor - this commit just shuffles a few things around psturmfels 2024-05-14 15:43:47 -07:00
• a290161d00 Loss testing Rohith Krishna 2024-06-11 01:48:14 +00:00
• 4ae8684272 Refactor of main loader to be more compartmentalized Pascal Sturmfels 2024-05-29 21:15:48 +00:00
• b1e08663a8 add device kwarg in test semantics Rohith Krishna 2024-05-27 16:38:28 -07:00
• 6bcdd9ad13 CI automated testing Will Sheffler 2024-05-28 01:36:55 +00:00
• 172d9ee47e Fix broken checkpoint.checkpoint calls Brian Coventry 2024-05-24 20:48:10 +00:00
• 502b9fa616 Make loader_sm_compl_assembly work for NA acids Pascal Sturmfels 2024-05-20 18:07:45 +00:00
• 21f9f21915 Backwards compatibility (tiny) Will Sheffler 2024-05-17 20:27:26 +00:00
• 9a2aec84de featurize_asmb_prot -> featurize_asmb_poly Pascal Sturmfels 2024-05-15 21:48:51 +00:00
• 3a87a46ca4 Step 2: fixing cif prot to work for NA examples Pascal Sturmfels 2024-05-15 20:39:22 +00:00
• 460a152878 fix typo Rohith Krishna 2024-05-15 12:51:36 -07:00
• b0a587bbd9 Dimaio/stability fixes Frank DiMaio 2024-05-15 19:48:17 +00:00
• 71ed452ba5 added configs to benchmark legacy models Rohith Krishna 2024-05-15 18:37:17 +00:00
• 4292572398 Start of refactor to loader_sm_compl_assembly with separate files for protein, small molecule and nucleic acid partners Pascal Sturmfels 2024-05-15 18:32:45 +00:00
• 710aad52f8 Rf2aa nucleic dev v2 Han Raut Altae-Tran 2024-05-09 22:40:15 +00:00
• 12ee6aa236 Refactor configs Rohith Krishna 2024-05-08 20:05:33 +00:00
• 2e961c1483 Add ligands_to_remove and min_metal_contacts as default params bcov77 2024-05-06 14:08:02 -07:00
• 146beb3f0d Dj pseudo cherrypick2 Rohith Krishna 2024-05-02 19:52:49 +00:00
• 72d8c0f45c left in a silly typo in previous branch - fix cast to torch Pascal Sturmfels 2024-05-01 19:08:38 +00:00
• 3e4f673046 fixes to how msas are joined and paired Pascal Sturmfels 2024-04-30 12:56:29 +00:00
• 9b45c3910a Recurate data Pascal Sturmfels 2024-04-27 16:34:10 +00:00
• 41af788865 We actually needed d_t2d not additional_t2d bcov77 2024-04-23 19:15:09 -07:00
• 3c0023197c Adding in additional_dt2d to LegacyRoseTTAFoldModule to allow add_extra_t2d in diffusion. Brian Coventry 2024-04-23 21:31:46 +00:00
• 95abfed2bb Fix LJ parameters for small molecules. Adjust per-atom normalization. Fix... Frank DiMaio 2024-04-19 18:13:14 +00:00
• 46e19f64b0 Small bugfix for validation fdimaio 2024-04-15 13:33:36 -07:00
• e9c9eb84dd add spec file for apptainer Rohith Krishna 2024-04-12 16:31:36 -07:00
• f055a32316 default for chemical Rohith Krishna 2024-04-13 00:14:17 +00:00
• df08c242c0 commit to add in metrics manager Rohith Krishna 2024-04-08 18:08:47 -07:00
• ff064f6f9a Dimaio/remove uncoord metal bugfix Frank DiMaio 2024-04-10 20:36:54 +00:00
• 8c046ff44b update config files fdimaio 2024-04-09 13:19:01 -07:00
• 2ee531e94c Two small changes for validation: a) add a cleaned posebusters set only... Frank DiMaio 2024-04-09 19:43:13 +00:00
• 98bb036a3c patch small bugs in sm_compl_assembly from removal of negatives Rohith Krishna 2024-04-06 07:29:59 -07:00
• 99364f892c Resume train Rohith Krishna 2024-04-06 00:49:34 +00:00
• cbb2bee1f8 small fix to cif_prot_to_xyz psturmfels 2024-04-05 14:38:39 -07:00
• fc076678ec fix for automorph failure Rohith Krishna 2024-04-05 20:44:37 +00:00
• fe5e823713 Allow using old-style dataset pickles Woody Ahern 2024-04-04 18:37:38 -07:00
• 0d01a2678b added ligand clustering to training sets Pascal Sturmfels 2024-04-05 20:42:29 +00:00
• c3f1ad50ab fix to ligand cluster weighting Pascal Sturmfels 2024-04-03 00:12:36 +00:00
• f3f3887d1c Remove negative sets Pascal Sturmfels 2024-04-03 00:05:24 +00:00
• db736ce565 New distributed custom sampler Pascal Sturmfels 2024-04-02 22:06:19 +00:00
• 8bd0c8b9c3 Add documentation. Woody Ahern 2024-04-02 13:03:42 -07:00
• dc5e4ed088 Allow legacy model to pass through gradients Woody Ahern 2024-04-01 13:41:20 -07:00
• aa4c0eb162 Add ability to freeze a motif from SE3Transformer updates Woody Ahern 2024-03-30 12:48:07 -07:00
• fada82621b Add new rotation-gradient passthrough block Woody Ahern 2024-04-02 12:20:01 -07:00
• 45d023c2bd Allow running models without flash attention. Woody Ahern 2024-04-01 13:52:09 -07:00
• 39b6b437e7 Revert "RF2AA changes to un-break RFDiffusionAA and enable gradient passthrough" Rohith Krishna 2024-04-02 20:06:20 +00:00
• b23a45979f RF2AA changes to un-break RFDiffusionAA and enable gradient passthrough Woody Ahern 2024-04-02 20:04:55 +00:00
• 964a927718 debug debug_item.py + move into tools/ David Juergens 2024-03-28 20:49:35 +00:00
• 2ecaf087dd A handful of very small updates Frank DiMaio 2024-03-28 18:13:49 +00:00
• 98f7ecb215 Fix to crop chirals Pascal Sturmfels 2024-03-28 17:48:37 +00:00
• 620bd10252 Update validate.py Frank DiMaio 2024-03-27 18:09:38 +00:00
• cf094002d2 fix bug causing determinism in cropping Rohith Krishna 2024-03-27 18:09:14 +00:00
• bb06653ab5 Fix missing random module; Implement logging to W&B with... Nate Corley 2024-03-26 22:16:05 +00:00
• 666559cd2a Update LJ to use RF2 implementation Frank DiMaio 2024-03-26 21:38:30 +00:00
• 54e4845786 add option for ddp backend and set to nccl by default Rohith Krishna 2024-03-26 13:11:35 -07:00
• 4c087448d2 Untie p2p Rohith Krishna 2024-03-26 01:24:14 +00:00
• f648de2705 Dimaio/ligand pruning options Frank DiMaio 2024-03-22 23:12:50 +00:00
• 896cf6ffd0 With grad Rohith Krishna 2024-03-22 01:21:54 +00:00
• 9943a9ba7c Make some tensors buffers so that when the model is moved to a device these tensors are also moved to that device. Woody Ahern 2024-03-16 13:28:45 -07:00
• 8fe918c00c Faster MSA featurize, also slightly broken up into functions Pascal Sturmfels 2024-03-20 17:52:27 +00:00
• 4333122eaa add tolerance for dataset tests Rohith Krishna 2024-03-19 21:09:17 -07:00
• 711b3abc25 Dataloader bugs Rohith Krishna 2024-03-18 18:52:54 +00:00
• 72a5a55cde revert hack with more elegant solution Rohith Krishna 2024-03-15 19:58:00 -07:00
• 7dcc18e760 updated model tests to use random initializations Rohith Krishna 2024-03-15 17:04:31 -07:00