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  • 1f0c9a2bf8 Swap command names Daniel E. Schaffer 2025-07-21 10:26:34 -04:00
  • 724c402b79 Update train.py Samuel Sledzieski 2025-07-21 10:24:21 -04:00
  • 44fc7ab723 Remove old file Daniel E. Schaffer 2025-07-21 10:13:16 -04:00
  • 8b0a7b1735 Update autorun-tests.yml Samuel Sledzieski 2025-07-21 09:41:11 -04:00
  • 7f6c368151 Update usage.rst Daniel Schaffer 2025-07-18 15:29:48 -04:00
  • f3e4672e3c tweak help messages Daniel E. Schaffer 2025-07-18 15:29:25 -04:00
  • b4bcfa3664 Update requirements.txt Samuel Sledzieski 2025-07-07 11:25:42 -04:00
  • 3a272cb719 Fix negation bug Daniel E. Schaffer 2025-06-11 13:36:50 -04:00
  • 650f3b5a36 Add bipartite prediction command (with blocking and multi-GPU support); minor tweaks Daniel E. Schaffer 2025-06-09 18:53:58 -04:00
  • 9caca8c672 Remove predict_par as a seperate command Daniel E. Schaffer 2025-06-09 14:41:57 -04:00
  • 881ad4bcc2 Cleanup & tweaks Daniel E. Schaffer 2025-06-09 14:23:45 -04:00
  • 967adda9d4 Rework/expand blocked prediction to support ~all use cases (protein list/dense pair list/sparse pair list) Daniel E. Schaffer 2025-04-30 20:21:12 -04:00
  • 8f2d3286f0 explicitly clear worker-side references to shared tensors Daniel E. Schaffer 2025-04-27 15:41:00 -04:00
  • cc023e5ff0 Enable multi-GPU blocked prediction (also, fix issue in foldseek loading) Daniel E. Schaffer 2025-04-27 15:35:01 -04:00
  • 58495dc437 Re-enable foldseek usage with blocked prediction Daniel E. Schaffer 2025-04-27 14:56:30 -04:00
  • 16bbf70acb Add waiting so only 3 blocks are logically needed at any time Daniel E. Schaffer 2025-04-24 02:58:49 -04:00
  • a21dd6bfeb Add prediction mode with blocked embedding loading Daniel E. Schaffer 2025-04-24 02:07:11 -04:00
  • c1caa49094 Further change loading behavior to default to returning a list Daniel E. Schaffer 2025-04-24 00:16:25 -04:00
  • baaf365454 Make each loader single-threaded Daniel E. Schaffer 2025-04-23 23:15:56 -04:00
  • d3ef9503ee Revise embedding loading to allow the calling process more control Daniel E. Schaffer 2025-04-23 19:39:58 -04:00
  • 58bcf9f7d2 Add parallel multiprocess inference Daniel E. Schaffer 2025-02-23 21:48:12 -05:00
  • bb2ccb0b02 Switch to torch.mp Daniel E. Schaffer 2025-02-20 13:35:19 -05:00
  • 91a90c8d90 IO-efficient loading Daniel E. Schaffer 2025-02-20 13:30:34 -05:00
  • e14c3a27ea Delete .github/workflows/pypi_publish.yml v0.2.8 Samuel Sledzieski 2024-09-16 09:37:54 -04:00
  • 687f5b09a3 Update version, fix model cuda bug Samuel Sledzieski 2024-09-16 09:35:49 -04:00
  • f828adda12 Update predict.py Samuel Sledzieski 2024-09-15 21:46:29 -04:00
  • e4304a85b0 Update pypi_publish.yml Samuel Sledzieski 2024-09-13 12:09:50 -04:00
  • 4a82baaa0c Merge pull request #69 from samsledje/huggingface_models v0.2.7 Samuel Sledzieski 2024-09-13 11:35:31 -04:00
  • 399a39dd14 Update environment.yml Samuel Sledzieski 2024-09-13 11:11:19 -04:00
  • 5c30f2ebb2 Update requirements.txt for autobuild Samuel Sledzieski 2024-09-13 11:10:18 -04:00
  • 2f4c222717 Update documentation to explain hfh Samuel Sledzieski 2024-09-13 11:06:30 -04:00
  • bb4ee75a66 Upload models to huggingface hub, update prediction script to take hf path Samuel Sledzieski 2024-09-13 11:02:23 -04:00
  • b4fd8b4244 Predict script now doesn't store contact maps by default Samuel Sledzieski 2024-09-13 09:46:49 -04:00
  • 69eba5e745 Remove symlinks and start huggingface file Samuel Sledzieski 2024-09-13 09:38:59 -04:00
  • 628917f6d3 Delete data/human_v1.sav Samuel Sledzieski 2024-08-10 10:24:39 +02:00
  • f586eb2a15 Add files via upload Samuel Sledzieski 2024-08-10 10:20:10 +02:00
  • 0955991a27 Update pypi_publish.yml Samuel Sledzieski 2023-10-24 11:19:43 -04:00
  • 6e28eac2ef add train file with updated 3di file v0.2.6b samsledje 2023-10-24 11:01:56 -04:00
  • a56b83c78b add tt3d structure homology notebooks and update test.sh with new 3di file samsledje 2023-10-24 10:04:11 -04:00
  • eae3112b25 Merge pull request #59 from samsledje/kapil-Oct24-update Samuel Sledzieski 2023-10-24 09:34:45 -04:00
  • 504eb53083 R notebooks added for baseline sequence-based analysis kapil-Oct24-update Kapil Devkota 2023-10-24 01:24:22 -04:00
  • 6772e2e26a Merge branch 'main' of github.com:samsledje/D-SCRIPT v0.2.6 Samuel Sledzieski 2023-09-28 16:00:35 -04:00
  • b0ca7aeb33 add tt3d to pretrained Samuel Sledzieski 2023-09-28 16:00:07 -04:00
  • 6529f1b574 Update .readthedocs.yml Samuel Sledzieski 2023-08-28 10:53:03 -07:00
  • 64ba521374 Update .readthedocs.yml Samuel Sledzieski 2023-08-28 10:37:40 -07:00
  • 3c80995021 Update requirements.txt Samuel Sledzieski 2023-08-28 10:30:04 -07:00
  • 5cefd93122 Add tt3d pretrained model samsledje 2023-07-31 12:44:48 -04:00
  • 3ea021d0bf Merge pull request #51 from samsledje/tt3d-predict v0.2.5 Samuel Sledzieski 2023-07-24 17:35:18 +02:00
  • 4e6c0d9b21 debugging foldseek predict tt3d-predict samsledje 2023-07-24 11:27:08 -04:00
  • 8b0b7f5a61 issue #44 update predict and forward signature for foldseek samsledje 2023-07-24 09:20:13 -04:00
  • 521ade48de update logging and error raising samsledje 2023-07-24 08:42:08 -04:00
  • ce46ba69b1 added foldseek prediction, untested samsledje 2023-07-24 08:34:48 -04:00
  • a039e730e0 Merge pull request #50 from samsledje/samsledje-patch-1 Samuel Sledzieski 2023-05-26 13:09:38 -07:00
  • e9fb5b86dc Update requirements.txt samsledje-patch-1 Samuel Sledzieski 2023-05-26 13:09:16 -07:00
  • cd1fed9887 fix bad linting v0.2.4 samsledje 2023-05-26 15:13:59 -04:00
  • 6668adefa0 Merge pull request #47 from samsledje/kapil-fseek+opt Samuel Sledzieski 2023-05-26 08:47:28 -07:00
  • e70ee3d7dc Resolve merge conflict kapil-fseek+opt Samuel Sledzieski 2023-05-26 08:47:11 -07:00
  • ca04e122a8 Added usage to test.sh Kapil Devkota 2023-05-25 12:15:39 -04:00
  • 84ceab3843 Removed train_fseek.py for this branch Kapil Devkota 2023-05-25 12:13:05 -04:00
  • e2700ce39f Minor housekeeping/refactoring Kapil Devkota 2023-05-25 12:11:14 -04:00
  • 0d02081ae0 Minor housekeeping/refactoring Kapil Devkota 2023-05-25 12:04:53 -04:00
  • dfa984ac90 Minor housekeeping and refactoring Kapil Devkota 2023-05-25 12:01:13 -04:00
  • 5b3636246c Removed the train_fseek_embed.py file for this branch Kapil Devkota 2023-05-25 11:40:44 -04:00
  • 34497c0917 Cleaning train.py Kapil Devkota 2023-05-09 13:46:22 -04:00
  • 620bd1f1e1 add extract 3di command samsledje 2023-05-09 10:14:43 -04:00
  • 0e9403eab7 Added optimized interaction.py Kapil Devkota 2023-05-08 01:32:04 -04:00
  • 3afad84144 Added fseek changes kapil_foldseek_branch Kapil Devkota 2023-05-08 00:43:40 -04:00
  • 2b673b6dc4 Update .readthedocs.yml Samuel Sledzieski 2023-04-26 15:21:50 -04:00
  • 6016965b51 Update train.py Samuel Sledzieski 2023-04-18 11:36:15 -04:00
  • b0c4677709 Update train.py Samuel Sledzieski 2023-04-18 11:32:33 -04:00
  • 9a85e3c8da Update train.py Samuel Sledzieski 2023-04-18 11:29:34 -04:00
  • 341dc0a219 Changed versioning Kapil Devkota 2023-03-30 11:07:12 -04:00
  • d42decb04f update gitignore ismb23-contacts-alphafold samsledje 2023-03-29 15:30:32 -04:00
  • bc50115a0e add data samsledje 2023-03-29 14:53:32 -04:00
  • 285dea5e6d adding processing files dev-contacts Lynn Tao 2023-02-09 19:47:44 -05:00
  • 34584b62f9 Alphafold style contact map prediction Kapil Devkota 2023-01-13 09:29:45 -05:00
  • 70d2fbea0c Changed evaluate and train foldseek embeddings for unknown proteins ismb22-contacts-dev Kapil Devkota 2023-01-05 15:25:07 -05:00
  • 1afe04c4bc log issues Kapil Devkota 2023-01-04 15:06:14 -05:00
  • dde6cd25cb updated train.py to allow single processor hdfs computation Kapil Devkota 2023-01-04 14:24:42 -05:00
  • 5fd07bc9fa fixed the issue related to the cmap-mode type kapil_foldseek_cmap_branch Kapil Devkota 2023-01-04 03:45:19 -05:00
  • 4fad54d4da merge ismb22-contacts samsledje 2023-01-03 11:17:18 -05:00
  • 0d945c222a formatting fixes samsledje 2023-01-03 11:13:49 -05:00
  • a8c4e471c5 additional changes to bash Kapil Devkota 2023-01-02 11:35:07 -05:00
  • 1f6b7c482e added cmap+foldseek support Kapil Devkota 2022-12-26 12:53:22 -05:00
  • fc8ea9a01d reverted multiprocess loading into interator loading lynntao04 2022-12-16 18:14:14 -05:00
  • 32caf3f628 Add debugging statement Samuel Sledzieski 2022-12-16 12:48:35 -05:00
  • 142cebee1a Don't use all available CPUs to load embeddings Samuel Sledzieski 2022-12-16 12:40:48 -05:00
  • 18b0d9a156 Minor output fixes v0.2.2 Samuel Sledzieski 2022-12-15 10:59:05 -05:00
  • 16c1f5aec8 Merge branch 'ismb22-contacts' of github.com:samsledje/D-SCRIPT into ismb22-contacts samsledje 2022-12-15 10:43:32 -05:00
  • cda1518f16 Update bad label Samuel Sledzieski 2022-12-15 10:41:58 -05:00
  • d6d2fdbebd remove results file samsledje 2022-12-15 10:41:22 -05:00
  • 47c4d0c7cb Update changelog Samuel Sledzieski 2022-12-15 10:39:19 -05:00
  • 958bcb6f8d Print out metrics on evaluate Samuel Sledzieski 2022-12-15 10:38:24 -05:00
  • 67b9efd424 revised processing interaction filter limit Lynn Tao 2022-12-09 12:24:21 -05:00
  • 5dc966adf2 revised processing interaction filter limit Lynn Tao 2022-12-09 12:22:53 -05:00
  • e8d10abe58 added colormap and vmax/vmin in utils lynntao04 2022-12-09 12:11:40 -05:00
  • 81d4fdca0e made torch --> numpy in save_cmap_img cuda compatible lynntao04 2022-12-07 16:50:34 -05:00
  • 036228d6da train - added eval method for cmaps + debug fixes, utils - added cmap display method lynntao04 2022-12-07 10:54:12 -05:00
  • 34ae136448 added if/else torch.stack for cmaps in predict_interaction_cmap(), fixed cmap_loss_fn bug lynntao04 2022-12-02 08:07:27 -05:00
  • 8fd4e1c25f fixed cmap training loop to evaluate with cmap_embeddings lynntao04 2022-12-01 17:49:06 -05:00