deepchem
pytorch_tempest
| deepchem | pytorch_tempest | |
|---|---|---|
| 4 | 3 | |
| 5,124 | 201 | |
| 1.8% | - | |
| 9.9 | 5.0 | |
| 5 days ago | 6 months ago | |
| Python | Python | |
| MIT License | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
deepchem
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Query
You can see a number of splitter implementations from the DeepChem package here. The code is quite elaborate but for your case it may not need to be. Still, if you can use their package for splitting that would be easiest.
- Deepchem – Democratizing Deep-Learning for Drug Discovery
- Deepchem dataset load_tox21()
- How do I transition into bioinformatics from a senior software engineer (14 years of experience)?
pytorch_tempest
- For what reason do you, or don't you, use PyTorch Lightning?
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If you're using Python, you should probably use a code formatter. (e.g. black)
Here you can see an example of ci in my training pipeline: https://github.com/Erlemar/pytorch_tempest/blob/master/.github/workflows/ci.yml
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Nicest and cleanest Deep Learning codebases out there
DL is all experimentation. You need a framework that makes modification easy, trackable and reproducible. The closest to achieving that these days is based on pytorch lightning with hydra. Check out this video and repo: https://www.youtube.com/watch?v=w10WrRA-6uI https://github.com/Erlemar/pytorch_tempest
What are some alternatives?
torchdrug - A powerful and flexible machine learning platform for drug discovery
lightning-hydra-template - PyTorch Lightning + Hydra. A very user-friendly template for ML experimentation. ⚡🔥⚡
deepqmc - Deep learning quantum Monte Carlo for electrons in real space
omegaconf - Flexible Python configuration system. The last one you will ever need.
bidd-molmap - MolMapNet: An Efficient ConvNet with Knowledge-based Molecular Represenations for Molecular Deep Learning
nn-template - Generic template to bootstrap your PyTorch project.
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
pytorch-lightning - Build high-performance AI models with PyTorch Lightning (organized PyTorch). Deploy models with Lightning Apps (organized Python to build end-to-end ML systems). [Moved to: https://github.com/Lightning-AI/lightning]
chemicalx - A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
black - The uncompromising Python code formatter
caer - High-performance Vision library in Python. Scale your research, not boilerplate.
Wham - Structural variant detection and association testing