77 Commits

Author	SHA1	Message	Date
Samuel Sledzieski	01125ef013	Update predict.py	2025-07-21 10:39:38 -04:00
Samuel Sledzieski	c1b88c909f	Update evaluate.py	2025-07-21 10:38:35 -04:00
Samuel Sledzieski	724c402b79	Update train.py	2025-07-21 10:24:21 -04:00
Samuel Sledzieski	f828adda12	Update predict.py	2024-09-15 21:46:29 -04:00
Samuel Sledzieski	2f4c222717	Update documentation to explain hfh	2024-09-13 11:06:30 -04:00
Samuel Sledzieski	bb4ee75a66	Upload models to huggingface hub, update prediction script to take hf path	2024-09-13 11:02:23 -04:00
Samuel Sledzieski	b4fd8b4244	Predict script now doesn't store contact maps by default	2024-09-13 09:46:49 -04:00
samsledje	4e6c0d9b21	debugging foldseek predict	2023-07-24 11:27:08 -04:00
samsledje	521ade48de	update logging and error raising	2023-07-24 08:42:08 -04:00
samsledje	ce46ba69b1	added foldseek prediction, untested	2023-07-24 08:34:48 -04:00
samsledje	cd1fed9887	fix bad linting	2023-05-26 15:13:59 -04:00
Samuel Sledzieski	e70ee3d7dc	Resolve merge conflict	2023-05-26 08:47:11 -07:00
Kapil Devkota	84ceab3843	Removed train_fseek.py for this branch	2023-05-25 12:13:05 -04:00
Kapil Devkota	e2700ce39f	Minor housekeeping/refactoring	2023-05-25 12:11:14 -04:00
Kapil Devkota	dfa984ac90	Minor housekeeping and refactoring	2023-05-25 12:01:13 -04:00
Kapil Devkota	5b3636246c	Removed the train_fseek_embed.py file for this branch	2023-05-25 11:40:44 -04:00
Kapil Devkota	34497c0917	Cleaning train.py	2023-05-09 13:46:22 -04:00
samsledje	620bd1f1e1	add extract 3di command	2023-05-09 10:14:43 -04:00
Kapil Devkota	3afad84144	Added fseek changes	2023-05-08 00:43:40 -04:00
Samuel Sledzieski	6016965b51	Update train.py	2023-04-18 11:36:15 -04:00
Samuel Sledzieski	b0c4677709	Update train.py	2023-04-18 11:32:33 -04:00
Samuel Sledzieski	9a85e3c8da	Update train.py	2023-04-18 11:29:34 -04:00
Samuel Sledzieski	18b0d9a156	Minor output fixes	2022-12-15 10:59:05 -05:00
Samuel Sledzieski	cda1518f16	Update bad label	2022-12-15 10:41:58 -05:00
Samuel Sledzieski	958bcb6f8d	Print out metrics on evaluate	2022-12-15 10:38:24 -05:00
Samuel Sledzieski	952447d34e	Merge branch 'ismb22-contacts' into kapil_foldseek_branch	2022-11-23 09:11:40 -05:00
samsledje	324be05f22	added ability to set random seed for training	2022-11-16 13:39:29 -05:00
Kapil Devkota	919349dace	Added foldseek branch	2022-11-12 00:50:00 -05:00
Mert Erden	e4adc459a3	enhancement: added typing documentation & automatic retrying for corrupted models	2022-06-29 14:09:44 -04:00
Samuel Sledzieski	1b598e4762	Update glider-thresh argument help string ... "threshold beyond which GLIDER scores treated as positive edges (0 < gt < 1) (default: 0.925)"	2022-06-24 19:33:56 -04:00
samsledje	e148390f7f	load embeddings in parallel	2022-06-23 16:06:22 -04:00
samsledje	dfbc81829f	use biopython for fasta io	2022-06-23 13:36:06 -04:00
samsledje	6000faccfb	fix training script	2022-06-23 12:03:39 -04:00
samsledje	1b63b008fd	testing embed, evaluate, predict	2022-06-23 11:58:23 -04:00
samsledje	ea41becbb6	update gitignore, logging, and docs	2022-06-23 11:38:08 -04:00
samsledje	78ca8aad61	clean up docs	2022-04-29 10:44:20 -04:00
samsledje	ceca25a2c2	update documentation	2022-04-29 10:15:04 -04:00
samsledje	aa855550b8	Merge master into topsy turvy	2022-04-29 09:58:13 -04:00
Samuel Sledzieski	970e909f3a	Update evaluate.py	2022-04-12 18:06:22 -04:00
samsledje	431946f19f	Merge remote-tracking branch 'origin/main' into topsyturvy	2022-03-07 17:44:14 -05:00
samsledje	57bc2fa4d4	fixed how cpu mapping works	2022-03-07 15:17:35 -05:00
samsledje	2caf7712f5	tt cleaning	2022-03-07 14:51:44 -05:00
samsledje	f2429adeaa	initial topsy turvy port	2022-03-07 13:42:10 -05:00
samsledje	b052dbe30e	fix issue relating to pretrained models and updated model arguments/parameters	2022-02-11 11:55:55 -05:00
samsledje	a82dd7d6b8	code style updated with black	2022-02-08 12:00:11 -05:00
samsledje	65ebd2381e	training seems to be fixed, require a few more cleaning passes and tests before publishing	2022-02-07 12:56:32 -05:00
samsledje	45d693bc2d	updated docstrings from legacy code	2021-12-07 12:18:38 -05:00
samsledje	df4e1bf729	0.1.7-dev7 -- training fixed but code extremely messy	2021-12-07 11:46:13 -05:00
samsledje	3fa7ea685f	v0.1.6 Fixed bug in data augmentation	2021-09-06 13:18:27 -04:00
Samuel Sledzieski	8a55490180	Use sensible defaults for epoch and epoch scale ... epoch: 100 -> 10 epoch_scale: 5 -> 1	2021-06-24 13:49:33 -04:00