0.1.0 Submission Release 🧬 🧬 🧬

🚀 What's Changed

Models

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

💾 Data Cleaning

• Clean up DrugBank and TWOSIDES importers by @cthoyt in #57
• Add additional datasets by @cthoyt in #61

🤖 Design

• Provide base class for dataset loaders by @cthoyt in #59
• Move back the BatchGenerator to the data namespace. by @benedekrozemberczki in #80

🏠 House keeping

• Black update conformity by @benedekrozemberczki in #66
• Remove check box that's automated with CI by @cthoyt in #64
• Standardize documentation style with darglint by @cthoyt in #70
• Update citations and add additional testing by @cthoyt in #72
• New release updates, citation modification and correcting paper references by @benedekrozemberczki in #85

New Contributors

• @andrejlamov made their first contribution in #67
• @kajocina made their first contribution in #68
• @mughetto made their first contribution in #71
• @hzcheney made their first contribution in #63
• @andriy-nikolov made their first contribution in #73
• @kkaris made their first contribution in #53
• @YuWVandy made their first contribution in #77
• @sebastiandro made their first contribution in #74

Full Changelog: v0.0.9...v0.1.0

0.0.9. DevOps, Refactoring, New Datasets

What's Changed

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

Full Changelog: v0.0.8...v0.0.9

0.0.8. Data resolver and model releases

What's Changed

• Add Dataset Resolver around Dataset Loader Class by @cthoyt in #24
• DeepSynergy and EPGCN-DS by @benedekrozemberczki in #27

Full Changelog: v0.0.7...v0.0.8

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

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 #18

Full Changelog: v0.0.5...v0.0.6

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 👾 🤖 🎃

0.0.4. - Context feature set and oncology datasets 🧬 💊

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

0.0.3. Unit tests and documentation integration 🎄🎅

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

0.0.2. - Name spaces, documentation.

Created namespaces for:

• Integrated benchmark datasets.

• Main data structures.

• Installation guide.

• Documentation.

0.0.1. - ChemicalX Base Release Test

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