Machine Learning in Life Science

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15 repositories

awesome-protein-foundation-models
Public
A curated list of protein foundation models, protein language models (pLMs), and generative models for sequence, structure, and multimodal protein modeling.
machine-learning awesome bioinformatics
machine-learning awesome bioinformatics deep-learning protein-structure transformers computational-biology protein awesome-list representation-learning
MIT License
•0•1•0•0•Updated Mar 6, 2026Mar 6, 2026
inverse_folding_free_energies
Public
Code for the "Zero-shot protein stability prediction by inverse folding models: a free energy interpretation" paper.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Jan 16, 2026Jan 16, 2026
HackathonEBM
Public
Jupyter Notebook
•1•4•0•0•Updated Nov 24, 2025Nov 24, 2025
poli
Public
A library of discrete objectives
Python
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MIT License
•1•27•55•4•Updated Oct 5, 2025Oct 5, 2025
poli-docs
Public
Documentation for poli and poli-baselines
0•6•6•2•Updated Sep 28, 2025Sep 28, 2025
poli-baselines
Public
A collection of objective functions and black box optimization algorithms related to proteins and small molecules
Python
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MIT License
•6•9•16•4•Updated Mar 3, 2025Mar 3, 2025
hdbo_benchmark
Public
Code for "A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences"
Python
•2•16•3•1•Updated Feb 24, 2025Feb 24, 2025
BEND
Public
Benchmarking DNA Language Models on Biologically Meaningful Tasks
Python
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BSD 3-Clause "New" or "Revised" License
•19•1•1•0•Updated Oct 31, 2024Oct 31, 2024
poli-assets
Public
Assets and datasets for `poli` and `poli-baselines`
0•0•0•0•Updated Sep 12, 2024Sep 12, 2024
protein_regression
Public
The codebase to replicate the analysis of "A systematic analysis of regression models for protein engineering" (2024).
benchmark machine-learning computational-biology
benchmark machine-learning computational-biology uncertainty-quantification
Jupyter Notebook
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MIT License
•2•5•0•0•Updated Jun 12, 2024Jun 12, 2024
corel
Public
Python
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MIT License
•1•3•4•0•Updated Apr 12, 2024Apr 12, 2024
stochman
Public
Algorithms for computations on random manifolds made easier
python machine-learning pytorch
python machine-learning pytorch manifold riemannian-geometry
Python
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Apache License 2.0
•10•94•10•0•Updated Dec 4, 2023Dec 4, 2023
.github
Public
0•1•0•0•Updated Aug 18, 2023Aug 18, 2023
meaningful-protein-representations
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•7•110•4•0•Updated Mar 7, 2022Mar 7, 2022
torchplot
Public
Plotting pytorch tensors made easy!
Python
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Apache License 2.0
•1•15•0•0•Updated Jan 28, 2021Jan 28, 2021