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  • 75eab28284 Rewrite main sampling logic to be better fit other objects Kevin Wu 2022-08-26 18:14:04 +00:00
  • a2849f0aaf Add loss plots Kevin Wu 2022-08-26 01:55:48 +00:00
  • 048efb8508 Implement loading multiple checkpoints for legacy model loading logic Kevin Wu 2022-08-26 01:02:26 +00:00
  • 82717e7bcc More dimension fixes Kevin Wu 2022-08-26 00:24:44 +00:00
  • fb92f34d46 Autocorrect old loss function names Kevin Wu 2022-08-26 00:12:03 +00:00
  • 33ca23ca85 Notebook sampling all angles Kevin Wu 2022-08-25 23:01:16 +00:00
  • cea3634e75 Fix typing Kevin Wu 2022-08-25 22:50:59 +00:00
  • 4370ad59fe Fix indexing for noise scaling and generation Kevin Wu 2022-08-25 22:39:22 +00:00
  • 116f7fe962 Code to handle either old or new model saving folder structure Kevin Wu 2022-08-25 22:38:57 +00:00
  • a8fed29254 Remove some unused imports Kevin Wu 2022-08-25 21:25:51 +00:00
  • 2abda7c7eb Reorganize some code Kevin Wu 2022-08-25 21:24:54 +00:00
  • 4d38236fda Code cleanup Kevin Wu 2022-08-25 20:10:42 +00:00
  • fdd299360d Remove duplicated code Kevin Wu 2022-08-25 19:00:36 +00:00
  • f7ec932530 Add type annotations Kevin Wu 2022-08-25 18:56:13 +00:00
  • b727a04289 Rename file Kevin Wu 2022-08-25 18:44:41 +00:00
  • 1e5b24f826 Fix distance setting Kevin Wu 2022-08-25 18:42:14 +00:00
  • 873673bf87 Fix bug in given angles not converting between radians and degrees when necessary Kevin Wu 2022-08-25 17:44:24 +00:00
  • 5860096209 Code to sample atomic coordinates from existing pdb files Kevin Wu 2022-08-25 17:25:55 +00:00
  • e64e23591e Code to read in a PDB file, get dihedrals, use dihedrals to create new structure and compare them Kevin Wu 2022-08-25 16:43:45 +00:00
  • def834b07e Kinda working maybe code to use PDB to go from dihedrals to coordinates? Kevin Wu 2022-08-25 00:15:41 +00:00
  • 1881f833c4 Add failing test. Dihedral reversal not really workingz Kevin Wu 2022-08-24 23:39:53 +00:00
  • a287e93c02 Initial reversal of dihedral angle. Seems to work for simple test cases Kevin Wu 2022-08-24 23:21:42 +00:00
  • dec4dae180 Add example pdb file Kevin Wu 2022-08-24 18:36:45 +00:00
  • 73f11617a6 Tweaks Kevin Wu 2022-08-23 22:24:37 -07:00
  • f93d93cd05 More tweaks Kevin Wu 2022-08-23 21:48:54 -07:00
  • fa262f133d More logging cleanup Kevin Wu 2022-08-23 21:41:59 -07:00
  • 9da5ba9acc Streamline some logging Kevin Wu 2022-08-23 21:31:14 -07:00
  • 8fdaf4eea6 Code cleaup Kevin Wu 2022-08-23 18:19:28 -07:00
  • 62631b598a Disable find_ununsed_parameters Kevin Wu 2022-08-23 15:44:15 -07:00
  • 57c8cfef09 Support for giving feature names Kevin Wu 2022-08-23 15:37:22 -07:00
  • c6b5d46d6b Remove some unnecessary sync dist calls Kevin Wu 2022-08-23 15:25:00 -07:00
  • 54a839e9cf Parallelize plotting distributions Kevin Wu 2022-08-23 14:49:48 -07:00
  • fd7e84bedd json file for canonoical angles run Kevin Wu 2022-08-23 21:29:30 +00:00
  • 00972e31d0 Comments and code simplifications Kevin Wu 2022-08-23 21:26:41 +00:00
  • e75d3cad5c Reduce size of short and sweet model Kevin Wu 2022-08-23 14:21:42 -07:00
  • 66b18c323b Logging and formatting Kevin Wu 2022-08-23 12:08:50 -07:00
  • 62b94d494e Add script to download from CATH Kevin Wu 2022-08-23 18:50:37 +00:00
  • 1cd5222c13 Implement caching of CATH consecutive angle dataset Kevin Wu 2022-08-23 18:47:26 +00:00
  • 34ecc9c363 Tar extract file instead of syncing up Kevin Wu 2022-08-23 03:18:34 +00:00
  • 100794ae3c Avoid nans in cath dataset Kevin Wu 2022-08-23 02:09:56 +00:00
  • 855b2614d1 Add biopython dependency Kevin Wu 2022-08-23 02:09:34 +00:00
  • 4b7ba84ec9 More informative logging Kevin Wu 2022-08-23 02:07:56 +00:00
  • bf49e24901 Hook different CATH datasets into training script Kevin Wu 2022-08-23 01:58:00 +00:00
  • 2a6dcf29ba Feature parity between CATH datasets Kevin Wu 2022-08-23 00:22:03 +00:00
  • c8efe948ba Update training call to build noised datasets Kevin Wu 2022-08-23 00:08:38 +00:00
  • 6dc5e2cabb More flexible definition of variances for angular and nonangular variables for noiser Kevin Wu 2022-08-23 00:01:35 +00:00
  • 00f995e516 Better handling of nan values in wrapped modulo Kevin Wu 2022-08-23 00:00:47 +00:00
  • 92195b819f Class variables defining whether features are angular Kevin Wu 2022-08-22 23:46:38 +00:00
  • c1fe5818b3 Ignore CATH data files Kevin Wu 2022-08-22 23:43:27 +00:00
  • b208f2eec7 Add features definition Kevin Wu 2022-08-22 23:40:59 +00:00
  • 2f43aa75fc Additionally return tau angle for canonical angle set Kevin Wu 2022-08-22 23:37:13 +00:00
  • 325302160d Initial implementation of Cath dataset with canonical angles Kevin Wu 2022-08-22 23:27:08 +00:00
  • ae90a2c761 Add documentatoin Kevin Wu 2022-08-22 21:18:27 +00:00
  • c2ce89a3de File cleanup Kevin Wu 2022-08-22 17:37:39 +00:00
  • 30e8cf427c Update env yml Kevin Wu 2022-08-22 06:06:24 +00:00
  • da7244fa2d Make loss plotting order more consistent Kevin Wu 2022-08-22 05:58:59 +00:00
  • ab22fef1c3 Typo fixes Kevin Wu 2022-08-19 20:36:30 +00:00
  • aad06dd86a Update amlt and config files for full run Kevin Wu 2022-08-19 20:33:07 +00:00
  • b57da0647b Only log args once Kevin Wu 2022-08-19 13:25:31 -07:00
  • 40e8dcc76d Adjust effective batch size accordingly Kevin Wu 2022-08-19 12:01:56 -07:00
  • 4c01ad75c5 Tweak logging Kevin Wu 2022-08-19 11:47:02 -07:00
  • d25c9ca5c9 Create plots for timestep distributions once only Kevin Wu 2022-08-19 11:45:33 -07:00
  • 69b1ee90cf Make print statements zero rank debug statements Kevin Wu 2022-08-19 11:39:49 -07:00
  • d1cdc54fa4 Logging on rank zero only Kevin Wu 2022-08-19 11:25:52 -07:00
  • c30e03e980 Specify accelerator and strategy separately, misc. other training script tweaks Kevin Wu 2022-08-19 11:21:46 -07:00
  • c9e5fdc686 Remove all gather commands for now to debug hang Kevin Wu 2022-08-19 10:45:50 -07:00
  • 72466b1498 Don't obther computing a head mask - we don't use this anyway Kevin Wu 2022-08-19 10:33:19 -07:00
  • 1c910d0d3b Better logging errors Kevin Wu 2022-08-18 22:11:35 -07:00
  • eae636ecd1 Merge branch 'main' of https://github.com/microsoft/protdiff into main Kevin Wu 2022-08-18 21:43:20 +00:00
  • a8cffe4703 Efforts to fix multiGPU Kevin Wu 2022-08-18 21:43:12 +00:00
  • 82d0a4ee6e env updates Kevin Wu 2022-08-18 14:08:03 -07:00
  • 73b0c43ce2 Update cath download script Kevin Wu 2022-08-18 14:01:29 -07:00
  • b8ee432b8c Drastically simplify env Kevin Wu 2022-08-18 13:54:57 -07:00
  • 11c572565a multi GPU fixes Kevin Wu 2022-08-17 22:23:12 +00:00
  • 2405d0147b Update toy tests for dual GPU Kevin Wu 2022-08-17 20:29:43 +00:00
  • acb88c7763 Make sure we save best loss Kevin Wu 2022-08-17 20:26:16 +00:00
  • f962e13fe3 Separate model checkpointing for both validtion and train losses Kevin Wu 2022-08-17 20:24:52 +00:00
  • 6b4f240e93 toggle-able writing of validatoin preds Kevin Wu 2022-08-17 20:15:40 +00:00
  • 2bb17a5e81 Disable training progressbar, use logging instead Kevin Wu 2022-08-17 20:09:01 +00:00
  • 1795d4c7ce Plotting code to compare consecutive angles Kevin Wu 2022-08-17 18:57:44 +00:00
  • 04d6f83e9d Add astropy dependency Kevin Wu 2022-08-17 18:49:54 +00:00
  • eb4c008789 Add mpl scatter density dependency Kevin Wu 2022-08-17 18:41:58 +00:00
  • edc31c65ab Gracefully handle case where git cannot be determined (i.e. on amulet) Kevin Wu 2022-08-17 18:26:50 +00:00
  • aa0f5db2be Bugfix on amulet + misc. code cleanup Kevin Wu 2022-08-17 18:17:46 +00:00
  • 1bc83b704c Reduce batch to fit into memory Kevin Wu 2022-08-17 17:16:41 +00:00
  • ee5cf029cf Amulet yaml without conda Kevin Wu 2022-08-17 17:15:51 +00:00
  • f432dbaa66 Clean up env Kevin Wu 2022-08-17 17:04:49 +00:00
  • 0869f7cea5 Notebook sampling single angle Kevin Wu 2022-08-17 06:35:52 +00:00
  • de18875bde Update docs and type annotations Kevin Wu 2022-08-17 00:26:45 +00:00
  • 845026926b Reimplement sampling Kevin Wu 2022-08-17 00:08:29 +00:00
  • aaeb0c5230 Auto generate position_ids if not given Kevin Wu 2022-08-16 23:33:58 +00:00
  • 0508009c87 Make noise sampling less strict Kevin Wu 2022-08-16 23:01:51 +00:00
  • e921fe7616 More flexible length sampling Kevin Wu 2022-08-16 22:52:29 +00:00
  • fd96ef6b8f Calculate posterior variance Kevin Wu 2022-08-16 22:40:24 +00:00
  • f80b07dd07 Code to automatically load from directory Kevin Wu 2022-08-16 21:45:27 +00:00
  • 77fb858a1f Json config for toy run Kevin Wu 2022-08-16 21:04:41 +00:00
  • 2bf70a5a93 Amulet script for toy run Kevin Wu 2022-08-16 21:04:28 +00:00
  • 33bd83dcfe More amulet Kevin Wu 2022-08-16 18:15:05 +00:00
  • 251ae9f5d3 Amulet update Kevin Wu 2022-08-16 18:14:16 +00:00
  • 4a06cde95c Update loss plotting code Kevin Wu 2022-08-16 18:12:36 +00:00