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  • b3c87e0206 Bugfix, code to clean out old dataset cache files Kevin Wu 2022-12-07 12:59:28 -08:00
  • 098e01d870 Dynamically set cache filename based on input Kevin Wu 2022-11-29 14:12:07 -08:00
  • 22161d23e3 Generalize dataset to work with more inputs Kevin Wu 2022-11-29 13:48:52 -08:00
  • 3799679b20 Support for computing featurization from gzip pdbs Kevin Wu 2022-11-29 13:48:33 -08:00
  • 0aa1040f7f Fix alphafold script to download v4 Kevin Wu 2022-11-28 14:51:41 -08:00
  • 98e9165531 Misc. cleanup Kevin Wu 2022-11-23 22:36:51 -08:00
  • fb6699d518 README updates Kevin Wu 2022-11-23 22:16:40 -08:00
  • 658de68a49 Fix cath download script cosmetic error Kevin Wu 2022-11-23 21:38:46 -08:00
  • 93f0db0d8a AF stuffs Kevin Wu 2022-11-18 12:59:34 -08:00
  • 23c235c52e Ability to write raw counts of ss Kevin Wu 2022-11-18 11:59:25 -08:00
  • 8d58686a23 Update plot with ProteinMPNN results Kevin Wu 2022-11-17 21:05:30 -08:00
  • 3626b9a8ad Omegafold spread load more evenly across GPUs Kevin Wu 2022-11-17 14:10:41 -08:00
  • d7481e995e Update omegafold wrapper Kevin Wu 2022-11-17 12:22:48 -08:00
  • bc380d5baf Update omegafold on slurm script Kevin Wu 2022-11-17 12:18:04 -08:00
  • a90a1a00b2 More checks Kevin Wu 2022-11-17 11:53:06 -08:00
  • ace4bd906f Fix bug with overglobbing Kevin Wu 2022-11-17 11:44:37 -08:00
  • 80a3457f97 Add a script for running omegafold on slurm Kevin Wu 2022-11-17 11:31:03 -08:00
  • 40ffb3bbe3 Rename script Kevin Wu 2022-11-17 10:58:45 -08:00
  • dd96b1a9a9 Formatting updates Kevin Wu 2022-11-17 10:35:32 -08:00
  • 70542630fe Tweak selftm to be more flexible on inputs Kevin Wu 2022-11-17 10:35:17 -08:00
  • 5609bd3ce2 ProteinMPNN wrapper Kevin Wu 2022-11-16 23:59:14 -08:00
  • 57165f3028 More elegant handling of mp pool Kevin Wu 2022-11-16 14:28:30 -08:00
  • 40b76e6f50 README updates Kevin Wu 2022-11-16 13:50:09 -08:00
  • 7495d49c75 Update example animation Kevin Wu 2022-11-16 13:46:55 -08:00
  • 9fe0d5546c When making gifs, align the images to appear smoother Kevin Wu 2022-11-16 13:45:26 -08:00
  • 5a685a097d Parallelize writing sampled PDB files Kevin Wu 2022-11-16 13:33:44 -08:00
  • 619691295d Misc. updates Kevin Wu 2022-11-14 10:31:19 -08:00
  • 78c0d11ccc Add plot of reconstruction vs. length Kevin Wu 2022-11-12 22:09:05 -08:00
  • 14e8bad7c0 Addtl reporting Kevin Wu 2022-11-11 14:58:02 -08:00
  • d1b1629981 Analysis of test set denoising Kevin Wu 2022-11-11 13:12:34 -08:00
  • 085cc2cdac More utility functions Kevin Wu 2022-11-10 14:52:06 -08:00
  • b49554880f Add docs Kevin Wu 2022-11-10 13:50:54 -08:00
  • 684916124c Merge pull request #8 from microsoft/feature/autoregressive-baseline Kevin Wu 2022-11-10 11:58:25 -08:00
  • e24e434c28 Ability to configure upper frequency for plotting Kevin Wu 2022-11-09 13:20:36 -08:00
  • 8be6f49d0b Progressbar improvements Kevin Wu 2022-11-09 11:09:02 -08:00
  • 734d8c68c5 Flesh out autoregressive sampling script Kevin Wu 2022-11-09 11:05:27 -08:00
  • 9c029f4d74 Device fixes Kevin Wu 2022-11-09 11:05:20 -08:00
  • fde3632c1d Updates to defaults Kevin Wu 2022-11-08 22:03:40 -08:00
  • f044114dae Bugfix for model not learning Kevin Wu 2022-11-08 21:56:18 -08:00
  • 966a3be053 Moar checks Kevin Wu 2022-11-08 21:54:35 -08:00
  • 4be2d89309 Attempted fixes for model not learning Kevin Wu 2022-11-08 21:33:24 -08:00
  • 52a4b48449 More checks and defaults updates Kevin Wu 2022-11-08 21:32:41 -08:00
  • d9773dfb6c Up the default batch size Kevin Wu 2022-11-08 21:04:08 -08:00
  • fdb8b786e2 Initial script for sampling from AR model Kevin Wu 2022-11-08 20:54:19 -08:00
  • beceb29bea Some checks Kevin Wu 2022-11-08 20:54:10 -08:00
  • de6314613b Fix indexing issue with AR sampling Kevin Wu 2022-11-08 20:21:01 -08:00
  • 24590bf817 Format updates Kevin Wu 2022-11-08 14:41:39 -08:00
  • d1ccb7477f Additional tests Kevin Wu 2022-11-07 22:23:01 -08:00
  • 37fa5891d2 Code to sample from AR model Kevin Wu 2022-11-07 19:47:20 -08:00
  • de8941bcb6 sherlock AR baseline script Kevin Wu 2022-11-07 15:08:51 -08:00
  • dd671adbe4 Update some defaults Kevin Wu 2022-11-07 15:06:28 -08:00
  • 355c182257 Add json for pdist loss experiments Kevin Wu 2022-11-07 15:05:10 -08:00
  • fe37588a09 Shape fixes Kevin Wu 2022-11-07 15:03:13 -08:00
  • fc00d30b43 AR model take as input the total seq length Kevin Wu 2022-11-07 14:50:55 -08:00
  • f0c849686d Misc. formatting updates Kevin Wu 2022-11-07 14:41:41 -08:00
  • a29fc8ca2c Additional tests Kevin Wu 2022-11-07 14:41:19 -08:00
  • e13a17384c Provide missing values Kevin Wu 2022-11-07 14:20:44 -08:00
  • 07377b7fb4 Enable LR scheduler for AR model Kevin Wu 2022-11-07 14:13:37 -08:00
  • 4956f42cb8 Update default values for AR training Kevin Wu 2022-11-07 13:55:47 -08:00
  • 4ae35c7c66 Script for training autoregressive model Kevin Wu 2022-11-07 13:46:58 -08:00
  • c0cec8ac6a Fix for position ids and attention mask Kevin Wu 2022-11-07 13:46:47 -08:00
  • ef659c5574 Autoregressive model Kevin Wu 2022-11-07 12:02:37 -08:00
  • 25e8c65806 Update dataset names Kevin Wu 2022-11-07 11:30:15 -08:00
  • f3b57f9d81 Implementation of autoregressive dataset Kevin Wu 2022-11-07 11:02:31 -08:00
  • 3714a328a8 Merge pull request #6 from microsoft/feature/pdist-loss Kevin Wu 2022-11-07 10:31:10 -08:00
  • 89980306ae Compare pairwise dist loss against reconstructed angles (that incorporate error from not having distances, for example) not the original ones feature/pdist-loss Kevin Wu 2022-10-31 15:32:47 -07:00
  • d4646309e5 More tests Kevin Wu 2022-10-31 15:30:35 -07:00
  • fabfb694cc Fix some tests Kevin Wu 2022-10-31 15:10:20 -07:00
  • c382538645 Adjust weighting to not be overly compounded Kevin Wu 2022-10-31 14:55:02 -07:00
  • b4c825ddaf Support for varying lambda for the pairwise dist loss based on timestep Kevin Wu 2022-10-31 12:32:18 -07:00
  • e767a4f49a More tests Kevin Wu 2022-10-31 11:16:49 -07:00
  • 732d6d7787 More tests Kevin Wu 2022-10-31 10:57:50 -07:00
  • 8c98ec548c Tweak pairwise dist to have a coefficient Kevin Wu 2022-10-31 00:16:05 -07:00
  • 39dc0fa2c6 Experimental usage of a pairwise ca distance loss Kevin Wu 2022-10-31 00:04:26 -07:00
  • f152f6e464 Fixes for device placement Kevin Wu 2022-10-30 23:57:27 -07:00
  • 985b51d13c Clean up some imports Kevin Wu 2022-10-30 19:57:33 -07:00
  • 5e8b215c8d Tests for pairwise distance loss Kevin Wu 2022-10-30 19:41:55 -07:00
  • 6b98e00ddc Loss on pairwise distances given 3D coordinates are starting inputs Kevin Wu 2022-10-30 15:51:33 -07:00
  • 766d51f3ad Doc updates Kevin Wu 2022-10-30 13:02:40 -07:00
  • 821488454e Test that backbone building works with nan padding Kevin Wu 2022-10-30 12:57:02 -07:00
  • 3e4380cc50 More thorough tests Kevin Wu 2022-10-30 12:26:16 -07:00
  • 945a1831c4 Update plot colors Kevin Wu 2022-10-25 17:45:55 -07:00
  • e1cd243be6 Batched nerf building Kevin Wu 2022-10-21 15:08:17 -07:00
  • 57f403ccc6 Split apart some functions Kevin Wu 2022-10-21 14:28:32 -07:00
  • f62efd40f9 Additional testing for vectorized dihedral placement Kevin Wu 2022-10-21 13:29:06 -07:00
  • 9a994514c3 Vectorize calculation of NERF Kevin Wu 2022-10-21 11:52:59 -07:00
  • 47b46893db More refactoring of NERF code Kevin Wu 2022-10-19 11:33:48 -07:00
  • 1d751376d6 Simplify NERF pytorch code Kevin Wu 2022-10-19 11:12:09 -07:00
  • b408458ede Misc fixes for torcy nerf Kevin Wu 2022-10-18 23:11:23 -07:00
  • 739df32fb8 Remove unused imports Kevin Wu 2022-10-18 16:39:33 -07:00
  • 0be75b5bc4 Implement NERF reconstruction with pytorch Kevin Wu 2022-10-18 15:07:44 -07:00
  • 15451bf6ae Remove some unused code Kevin Wu 2022-10-18 14:29:11 -07:00
  • 0966b58910 Code to compute clustering between natural structures Kevin Wu 2022-10-13 10:59:41 -07:00
  • fe7418e7e3 Make sure repeated running sampling code is reproducible Kevin Wu 2022-10-13 10:22:22 -07:00
  • 32bfa9416d Misc. Kevin Wu 2022-10-11 21:33:47 -07:00
  • 272f32c0a6 scTM of natural structures Kevin Wu 2022-10-11 20:46:51 -07:00
  • e1ee114d44 Minor cosmetic updates Kevin Wu 2022-10-11 20:46:41 -07:00
  • 0bd8b2d4bd Ensure that baseline scTM strucures are short Kevin Wu 2022-10-11 16:20:53 -07:00
  • c113c9e1d7 Cache calculated lengths of PDB files Kevin Wu 2022-10-11 16:15:36 -07:00
  • 576b4ad5df Tweak baseline sctm score setup script to also include angle conversion Kevin Wu 2022-10-11 12:06:42 -07:00