Commit History

Updated studies datasets
cf7560f

ribesstefano commited on

Updated plotting script (but still broken, use notebook instead)
aa57971

ribesstefano commited on

Fixed issue with duplicates + Experiments now rely on predefined datasets + Added experiments on simple embeddings
251060c

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Fixed bug in hparam tuning for XGBoost + added additional metrics to XGBoost reports
1e811f2

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

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Implemented cell lines one-hot and amino acid sequence count experiments
ccc40da

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Fixed bug on shuffle_embedding_prob in PROTAC_Dataset class
e1370eb

ribesstefano commited on

Started working on cell line one-hot encoding experiments
8aec0bb

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Double checking E3 ligase knockouts
1ee75b1

ribesstefano commited on

Files and READMEs cleanup
9bae2da

ribesstefano commited on

Updated README.md with pointer to the guide for training on custom dataset
5452b6b
unverified

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

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Moved notebook placed in wrong folder
f194550

ribesstefano commited on

Fixed XGBoost prediction and added initial comparison of DNN and XGBoost distributions
7839344

ribesstefano commited on

Fixed some tests and added XGBoost to the API
1171189

ribesstefano commited on

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

ribesstefano commited on

Updated setup.py with XGBoost
394ed39
unverified

ribesstefano commited on

Updated README.md with Hugging Face Spaces link to Gradio app
c630634
unverified

ribesstefano commited on

Created requirements.txt for Gradio app
d95e0fe
unverified

ribesstefano commited on

Created initial version of a Gradio app.
f979fd7
unverified

ribesstefano commited on

Fixed tutorial link (path) in README.md
5c5788c
unverified

ribesstefano commited on

Updated README and Conda environment configuration file
d4cd645

ribesstefano commited on

Added tutorial to be run in Colab
db62a2a

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Fixed minor bug when returning predictions
dcdef4a

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Added support for listing available dataset data
42d3d55

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Fixed bug on averaging predictions in package code
367cf2c

ribesstefano commited on

Fixed predictions moving to CPU from GPU in package code
8d92d67

ribesstefano commited on

Fixed rdkit requirements in setup.py
8489d4a

ribesstefano commited on

Added version requirement on rdkit setup.py
dac3be7

ribesstefano commited on

Fixed code on loading cell embeddings for package
c06df22

ribesstefano commited on

Fixed bug on loading cell embeddings in package code
e21cad4

ribesstefano commited on

Fixed loading cell embeddings in package code
229284f

ribesstefano commited on

Fixed bug when loading cell2embeddings from wrong directory
9bd496b

ribesstefano commited on

Added XGBoost majority vote performances
a8d1800

ribesstefano commited on

Added notebook for plotting results
d362c4b

ribesstefano commited on

Added notebook on cell embeddings generation + Added XGBoost reports
8315295

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Added XGBoost Optuna training + Added Ablation studies with zeroed input vectors
33f1644

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Changed ablation to input zero-valued vactors
4bf0ec2

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Added results with FP normalization removed
d8a186f

ribesstefano commited on

Added Maturity level badge
9e3ebaa

ribesstefano commited on

Added ablation study and performance plots
c8d51e3

ribesstefano commited on

Added ablation study with randomly sampled vectors + Started working on LightningDataModule wrapper
4e1d3f6

ribesstefano commited on

Added convincing results (really, before it was a fast_dev_run)
48aea13

ribesstefano commited on

Added convincing results
b7582e0

ribesstefano commited on