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PROTAC-Degradation-Predictor

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PROTAC-Degradation-Predictor

Commit History

Added LR scheduler + set default sum of embeddings

62ccb16

ribesstefano commited on Apr 28

Added majority voting evaluation

b86d3ec

ribesstefano commited on Apr 26

Improved plotting code

74a86c6

ribesstefano commited on Apr 26

Pushing current results

9692a92

ribesstefano commited on Apr 26

Working loading and predicting with pretrained model + Added scaling in "pure" pytorch during forwarding

15216c3

ribesstefano commited on Apr 25

Improved logging + current optuna studies

0171744

ribesstefano commited on Apr 24

Added model tests + checkpointing of the scaler object

de956c8

ribesstefano commited on Apr 24

Refactored experiments + fixed bug in dataset when applying scaling to val and test sets

6a5a99e

ribesstefano commited on Apr 23

Updated protac dataset to handle missing values in embedding dictionaries

4d17fea

ribesstefano commited on Apr 23

refactored package code and fine running experimental code

165d38a

ribesstefano commited on Apr 23

added rdkit to setup

74be897

ribesstefano commited on Apr 22

started testing package code

ea572f9

ribesstefano commited on Apr 22

Started working on packaging the repository

5e01175

ribesstefano commited on Apr 22

Updated 10% test with fixed Tanimoto-based split

6101de8

ribesstefano commited on Apr 21

Updated reports with ablation studies w/out E3

b496192

ribesstefano commited on Apr 21

Started working on optuna-based sklearn models training

f9a730b

ribesstefano commited on Apr 21

test commit

40d8875

ribesstefano commited on Apr 21

Plotting notebook

c9f60cb

ribesstefano commited on Apr 21

Added notebook on predicting degradation with sklearn models

f258949

ribesstefano commited on Apr 21

Added IaP to IAP conversion in data curation

e7f9851

ribesstefano commited on Apr 21

Added save and restore of Optuna studies

dafeec2

ribesstefano commited on Apr 8

Updated eports

6f31d02

ribesstefano commited on Apr 7

Fixed reporting

9fc7496

ribesstefano commited on Apr 7

Fixed verbose on earlystopping and added results

8cfcefe

ribesstefano commited on Apr 6

Finalized predictor script

ab45a22

ribesstefano commited on Apr 5

Added scaling to the dataset and concatenation at the beginning of the model

acd572a

ribesstefano commited on Mar 28

Added CV hparam train with 512bit fingerprints

00f11cc

ribesstefano commited on Mar 21

Added CV hparam training with dropout included

4154723

ribesstefano commited on Mar 20

Updated CV hparam training report with remaining ablation studies

ecae250

ribesstefano commited on Mar 19

Uploading CV hparam training and ablation study results

03abf18

ribesstefano commited on Mar 18

Polished hparam code and added ablation studies

91692a4

ribesstefano commited on Mar 15

Added report for CV-hparam "Active - AND"

022416b

ribesstefano commited on Mar 13

Changed log names

4761f4d

ribesstefano commited on Mar 13

Fixed typo

aa9bb1b

ribesstefano commited on Mar 13

Added "Active-OR" report and modified report name

0c6f1b3

ribesstefano commited on Mar 13

Added chirality to Morgan FP and improved logging

d6ec1f3

ribesstefano commited on Mar 12

Polished scripted version of Hparam-CV training

d36ec1d

ribesstefano commited on Mar 12

Added report on Hparam-CV for "Active - OR"

87b14e7

ribesstefano commited on Mar 12

Added SMOTE k neighbors to hparam search

7e4c438

ribesstefano commited on Mar 11

Added script file for hparam CV training

b09510c

ribesstefano commited on Mar 11

Introduced CV and ORed activity definition

5c27a23

ribesstefano commited on Mar 8

Initial work on retrieving article information

c3ef58b

ribesstefano commited on Feb 28

Improved CV plotting

dcdef98

ribesstefano commited on Feb 26

Normalized some metrics in CV results

b2864fc

ribesstefano commited on Feb 23

Polished CV traning code and added CV report

1b2eb07

ribesstefano commited on Feb 23

Written CV training code

b276805

ribesstefano commited on Feb 23

Polished CV folds plotting

f595672

ribesstefano commited on Feb 23

Added PCA and improved CV

66f3242

ribesstefano commited on Feb 22

Update README.md

01e1181
unverified

ribesstefano commited on Feb 15

Fixed typo in a path

9e1547d

ribesstefano commited on Feb 15