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Recent Releases of https://github.com/astrazeneca/chemicalx

https://github.com/astrazeneca/chemicalx - 0.1.0 Submission Release 🧬 🧬 🧬

🚀 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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.9. DevOps, Refactoring, New Datasets

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.8. Data resolver and model releases

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.7 - In memory Torch Vectors 🧬🧬🧬

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.6 - Model Base Class, Batch iterators, Batch 🧬🧬🧬

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.5 Drug Feature Set, Labeled Triples and Data Loaders 👾 🤖 🎃

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.4. - Context feature set and oncology datasets 🧬 💊

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.3. Unit tests and documentation integration 🎄🎅

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

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.2. - Name spaces, documentation.

Created namespaces for:

  • Integrated benchmark datasets.

  • Main data structures.

  • Installation guide.

  • Documentation.

- Python
Published by benedekrozemberczki over 4 years ago

https://github.com/astrazeneca/chemicalx - 0.0.1. - ChemicalX Base Release Test

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

- Python
Published by benedekrozemberczki over 4 years ago