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PROTAC-Degradation-Predictor / notebooks

Commit History

Added updated version of PROTAC-DB and starting applying data curation to it
2ca0a98

ribesstefano commited on

Added experimental results on simple embeddings (one-hot cells and amino acid counts)
14c7b13

ribesstefano commited on

Double checking E3 ligase knockouts
1ee75b1

ribesstefano commited on

Fixed typo in link
e874ff5

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Files and READMEs cleanup
9bae2da

ribesstefano commited on

Added DNN and XGB comparisons on standand split test set
4d221f4

ribesstefano commited on

Moved notebook placed in wrong folder
f194550

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Started renaming splits. Added datasets in paper as separate CSV.
ed339ed

ribesstefano commited on

Created using Colab
f34a470

ribesstefano commited on

Added tutorial to be run in Colab
db62a2a

ribesstefano commited on

Fixed bug on loading cell embeddings in package code
e21cad4

ribesstefano commited on

Added notebook for plotting results
d362c4b

ribesstefano commited on

Added notebook on cell embeddings generation + Added XGBoost reports
8315295

ribesstefano commited on

Added results with FP normalization removed
d8a186f

ribesstefano commited on

Added FP search + Added train metrics to logs
fda7af7

ribesstefano commited on

Started working on packaging the repository
5e01175

ribesstefano commited on

Started working on optuna-based sklearn models training
f9a730b

ribesstefano commited on

Added notebook on predicting degradation with sklearn models
f258949

ribesstefano commited on

Added IaP to IAP conversion in data curation
e7f9851

ribesstefano commited on

Added save and restore of Optuna studies
dafeec2

ribesstefano commited on

Fixed verbose on earlystopping and added results
8cfcefe

ribesstefano commited on

Finalized predictor script
ab45a22

ribesstefano commited on

Added scaling to the dataset and concatenation at the beginning of the model
acd572a

ribesstefano commited on

Polished hparam code and added ablation studies
91692a4

ribesstefano commited on

Added "Active-OR" report and modified report name
0c6f1b3

ribesstefano commited on

Added chirality to Morgan FP and improved logging
d6ec1f3

ribesstefano commited on

Polished scripted version of Hparam-CV training
d36ec1d

ribesstefano commited on

Added SMOTE k neighbors to hparam search
7e4c438

ribesstefano commited on

Added script file for hparam CV training
b09510c

ribesstefano commited on

Introduced CV and ORed activity definition
5c27a23

ribesstefano commited on

Initial work on retrieving article information
c3ef58b

ribesstefano commited on

Improved CV plotting
dcdef98

ribesstefano commited on

Normalized some metrics in CV results
b2864fc

ribesstefano commited on

Polished CV traning code and added CV report
1b2eb07

ribesstefano commited on

Written CV training code
b276805

ribesstefano commited on

Polished CV folds plotting
f595672

ribesstefano commited on

Added PCA and improved CV
66f3242

ribesstefano commited on

Fixed typo in a path
9e1547d

ribesstefano commited on

Renamed data files and notebooks accordingly
cfa31cd

ribesstefano commited on

Add files via upload
63b87d8
unverified

ribesstefano commited on

Created README.md in notebooks
358120f
unverified

ribesstefano commited on