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Author SHA1 Message Date
Lynn Tao
285dea5e6d adding processing files 2023-02-09 19:47:44 -05:00
Lynn Tao
67b9efd424 revised processing interaction filter limit 2022-12-09 12:24:21 -05:00
Lynn Tao
5dc966adf2 revised processing interaction filter limit 2022-12-09 12:22:53 -05:00
Lynn Tao
7e4726b0a9 debugging process for cmap embedding 2022-11-20 11:57:48 -05:00
Lynn Tao
25086c64fc fixing processing bugs to integrate contact maps 2022-11-18 15:08:58 -05:00
Lynn Tao
16c45acf7c fixing bugs in process.py, preparing integration of cmaps into train.py 2022-11-18 12:22:00 -05:00
Lynn Tao
07a1d7386f setting seed for training validation 2022-11-15 12:33:57 -05:00
Lynn Tao
a3ad39c6b3 debugging train.py, added t/f flag for cmaps, fixing Relu/Sigmoid mismatch 2022-11-06 18:31:46 -05:00
Lynn Tao
1ab8ea8d2d Merge branch 'dev-contacts' of https://github.com/samsledje/D-SCRIPT into dev-contacts 2022-11-06 11:51:41 -05:00
Lynn Tao
fc98d041e3 updated README, made some arg name changes in process.py 2022-11-06 11:51:25 -05:00
samsledje
3b8548801a Merge branch 'dev-contacts' of github.com:samsledje/D-SCRIPT into dev-contacts 2022-11-02 10:43:43 -04:00
samsledje
9bf409fa2f Merge branch 'main' into dev-contacts 2022-11-02 10:43:30 -04:00
Lynn Tao
3364c48e36 updating docstrings, etc. revisions 2022-11-02 07:39:48 -04:00
Lynn Tao
7753bf8c72 added new args, debugging fixes 2022-10-28 16:51:32 -04:00
Lynn Tao
7dd095b582 debugging, fixing errors detected 2022-10-27 20:08:14 -04:00
Lynn Tao
54b3c6a989 final changes, adding new args, more filtering 2022-10-26 10:57:08 -04:00
Lynn Tao
224e80289d made several revisions: added argument for # of chains, all possible combinations of chains, altered filtering requirements, updated fasta and tsv writing 2022-10-16 20:16:03 -04:00
Lynn Tao
51e430730a made processing a module 2022-10-11 10:58:50 -04:00
Lynn Tao
62877bb556 fixing mod res substitutions, checking chain pairs, etc. 2022-10-08 08:44:42 -04:00
Lynn Tao
9f6f45b590 fixing stopiterations and all resulting issues. 2022-10-01 11:25:34 -04:00
Lynn Tao
d54190fcb4 fixing code modifications after testing on dataset 2022-09-20 11:57:56 -04:00
Lynn Tao
ade8f3bf15 fixing code modifications after testing on dataset 2022-09-20 11:57:21 -04:00
Lynn Tao
fff17416de made some changes to input and processing details 2022-09-16 16:37:30 -04:00
Lynn Tao
3ee1a437c0 made some changes to input and processing details 2022-09-16 11:44:05 -04:00
Lynn Tao
bddb63edeb more changes to input, logging, incorporation 2022-09-16 11:40:55 -04:00
Lynn Tao
3d7b954908 made some changes to input and processing details 2022-09-16 09:39:22 -04:00
Lynn Tao
8954c308ff made some changes to input and processing details discussed in meeting 2022-09-16 08:59:40 -04:00
Lynn Tao
0c8c6eaf36 resolving filtering methods and checking for errors 2022-09-08 10:02:40 -04:00
Lynn Tao
ea9eb6b504 edited processing.py to take in inputs, changed __main__ to include processing 2022-09-07 15:40:33 -04:00
Lynn Tao
bce623ceb3 updating docstring 2022-09-06 12:40:21 -04:00
Lynn Tao
a57810424a added helper methods into data processing, wrote more docstrings 2022-09-06 11:48:38 -04:00
Lynn Tao
8acd513789 added docstrings to processing file 2022-09-06 06:53:27 -04:00
Lynn Tao
bde88ced0c made updates to processing.py, incorporating/debugging filtering and sequence alginment code 2022-09-05 06:45:33 -04:00
Lynn Tao
091a8936c7 committing data processing changes and resolved merge conflicts 2022-08-31 10:04:43 -04:00
Samuel Sledzieski
a76d9dd99e Merge pull request #41 from samsledje/fix/update_pretrained 
Fix/update pretrained & Issue #35
 2022-08-26 15:02:49 -04:00
samsledje
5b95875b98 change language_model.py to use with h5py context 2022-08-26 14:56:34 -04:00
samsledje
d858bd6851 rename scripts and update train 2022-08-22 17:26:11 -04:00
samsledje
8ceaa8f7c0 Finishing merge 2022-08-22 16:37:09 -04:00
samsledje
988c1b35ff update language model to fix issue #35 2022-08-18 12:10:32 -04:00
samsledje
b7834b6caa update version number 2022-08-18 11:40:29 -04:00
samsledje
2dcf240101 add topsy turvy pretrained model to api and docs 2022-08-18 11:32:07 -04:00
Lynn Tao
d90069646a fixing training for cuda 2022-07-26 22:22:05 -04:00
Lynn Tao
2a0e656fb5 training fixing cuda errors 2022-07-26 22:09:36 -04:00
Lynn Tao
6907a009ec pushing new train and val cmap dataset and edited training code 2022-07-26 15:57:21 -04:00
Lynn Tao
178b70ec65 committing b4 debugging 2022-07-26 11:12:39 -04:00
Lynn Tao
daf9899a2f training cmap edits 2022-07-26 10:32:38 -04:00
Lynn Tao
d10d725b00 adding data processing files 2022-07-25 16:15:37 -04:00
Lynn Tao
27d5d89524 making train.py more readable, more data processing 2022-07-19 14:31:46 -04:00
Lynn Tao
0f62ae017f dataset fixing 2022-07-19 07:37:38 -04:00
Lynn Tao
d9d33f1346 last of pdb files 2022-07-18 23:23:51 -04:00