Chemicalx Versions Save

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

v0.1.0

2 years ago

🚀 What's Changed

Models

Implement MatchMaker by @andrejlamov in https://github.com/AstraZeneca/chemicalx/pull/67
Implement GCN-BMP by @mughetto in https://github.com/AstraZeneca/chemicalx/pull/71
Implement DeepDrug by @kajocina in https://github.com/AstraZeneca/chemicalx/pull/68
Implement DeepDDI by @hzcheney in https://github.com/AstraZeneca/chemicalx/pull/63
Implement CASTER by @andriy-nikolov in https://github.com/AstraZeneca/chemicalx/pull/73
Implement MHCADDI by @sebastiandro in https://github.com/AstraZeneca/chemicalx/pull/74
Implement DeepDDS by @kkaris in https://github.com/AstraZeneca/chemicalx/pull/53
Implement SSIDDI by @YuWVandy in https://github.com/AstraZeneca/chemicalx/pull/77
Implement DeepDDS and CASTER defaults and remove DeepDDS Softmax bug by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/81
Implement MRGNN by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/82
Simplify existing models by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/69
Clean up models and provide abstractions by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/83

💾 Data Cleaning

Clean up DrugBank and TWOSIDES importers by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/57
Add additional datasets by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/61

🤖 Design

Provide base class for dataset loaders by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/59
Move back the BatchGenerator to the data namespace. by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/80

🏠 House keeping

Black update conformity by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/66
Remove check box that's automated with CI by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/64
Standardize documentation style with darglint by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/70
Update citations and add additional testing by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/72
New release updates, citation modification and correcting paper references by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/85

New Contributors

@andrejlamov made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/67
@kajocina made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/68
@mughetto made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/71
@hzcheney made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/63
@andriy-nikolov made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/73
@kkaris made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/53
@YuWVandy made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/77
@sebastiandro made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/74

Full Changelog: https://github.com/AstraZeneca/chemicalx/compare/v0.0.9...v0.1.0

v0.0.9

2 years ago

What's Changed

Re-enable flake8 check by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/26
Remove circular imports by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/31
Cleanup testing configuration by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/33
Add more flake8 checks by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/35
Remove DPDDI and AUDNNSynergy by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/36
Update documentation build by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/38
Add unified training and evaluation pipeline by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/32
Read the docs deployment fix. by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/39
Adding Default Read The Docs Path by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/40
Adding the autodoc hinting by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/41
DeepCCI removal and out channel parameters by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/43
Update CI by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/44
Update README python code comments and remove DeepCCI by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/45
Add additional model tests by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/46
Adding DrugBank DDI and Two Sides. by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/48
Fix unit tests for DDI and TwoSides by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/51
Expose dataset properties by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/52
Reorganize batching by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/54
Clean up feature sets and labels flag by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/55
ChemicalX 0.0.9 Release by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/56

Full Changelog: https://github.com/AstraZeneca/chemicalx/compare/v0.0.8...v0.0.9

v0.0.8

2 years ago

What's Changed

Add Dataset Resolver around Dataset Loader Class by @cthoyt in https://github.com/AstraZeneca/chemicalx/pull/24
DeepSynergy and EPGCN-DS by @benedekrozemberczki in https://github.com/AstraZeneca/chemicalx/pull/27

Full Changelog: https://github.com/AstraZeneca/chemicalx/compare/v0.0.7...v0.0.8

v0.0.7

2 years ago

Context feature sets store feature vectors as torch.FloatTensors
Drug feature sets store feature vectors as torch.FloatTensors

v0.0.6

2 years ago

What's Changed

Add base model and implement model class resolution by @cthoyt
Batch generators
Batch class

New Contributors

@cthoyt made their first contribution in https://github.com/AstraZeneca/chemicalx/pull/18

Full Changelog: https://github.com/AstraZeneca/chemicalx/compare/v0.0.5...v0.0.6

v0.0.5

2 years ago

Adds Data Loaders for DrugComb and DrugCombDB 👾 🤖 🎃
Drug Feature Set for feature storage 👾 🤖 🎃
Labeled Triples 👾 🤖 🎃

v0.0.4

2 years ago

Integrates DrugCombDB 🧬 💊
Integrated DrugComb 🧬 💊
Defines ContextFeatureSets with the class methods 🧬 💊
Add tests for ContextFeatureSets 🧬 💊

v_00003

2 years ago

Adds unit tests to data structures and datasets 🎄🎅
Adds documentation of data structures and datasets 🎄🎅

v_00002

2 years ago

Created namespaces for:

Integrated benchmark datasets.
Main data structures.
Installation guide.
Documentation.

v_00001

2 years ago

A PyTorch-based deep learning library for drug-drug interaction, polypharmacy side effect and synergy prediction.