├── .bumpversion.cfg ├── .devcontainer ├── devcontainer.Dockerfile └── devcontainer.json ├── .gitattributes ├── .github ├── pull_request_template.md └── workflows │ ├── auto-release.yml │ ├── continuous-integration.yml │ └── deploy-docs.yml ├── .gitignore ├── .here ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE ├── Makefile ├── README.md ├── docs ├── advanced.md ├── api.md ├── contributing.md ├── css │ └── custom.css ├── development.md ├── fitting.ipynb ├── getting-started.md ├── improvements.md └── index.md ├── environment.yml ├── examples ├── draft_cli.py ├── enzymes.fa └── evotuning.py ├── install_jaxgpu.sh ├── jax_unirep ├── __init__.py ├── activations.py ├── errors.py ├── evotuning.py ├── evotuning_models.py ├── featurize.py ├── layers.py ├── losses.py ├── optimizers.py ├── sampler.py ├── utils.py ├── version.py └── weights │ └── uniref50 │ ├── 1900_weights │ └── model_weights.pkl │ ├── 256_weights │ └── model_weights.pkl │ └── 64_weights │ └── model_weights.pkl ├── mkdocs.yml ├── paper ├── .gitignore ├── build.sh ├── cabios-template │ ├── OUP_First_SBk_Bot_8401.eps │ ├── algorithm.sty │ ├── algorithm2e.sty │ ├── algorithmic.sty │ ├── algorithmicx.sty │ ├── algpseudocode.sty │ ├── alltt.sty │ ├── array.sty │ ├── bioinfo.cls │ ├── caption.sty │ ├── chngpage.sty │ ├── color.sty │ ├── crop.cfg │ ├── crop.sty │ ├── fig01.jpg │ ├── float.sty │ ├── flushend.sty │ ├── graphicx.sty │ ├── landscap.sty │ ├── main.bbl │ ├── main.blg │ ├── main.dvi │ ├── main.tex │ ├── natbib.bst │ ├── natbib.sty │ ├── plain.bst │ ├── references.bib │ ├── speed-profiling.csv │ ├── stfloats.sty │ └── url.sty ├── data │ └── amino_acid_genotypes_to_brightness.tsv ├── environment-gfp.yml ├── figures │ ├── jax-unirep-profile.png │ ├── rep_trace.png │ ├── rep_trace_lf.png │ ├── speed_barplot.png │ ├── speed_comparison.png │ ├── top_model.png │ └── unirep-profile.png ├── gfp_prediction.ipynb ├── jmlr │ ├── .gitignore │ ├── build.sh │ ├── cover-letter.md │ ├── fig01.jpg │ ├── jmlr2e.sty │ ├── references.bib │ └── sample.tex ├── paper.md ├── references.bib ├── style.css ├── suppinf.md ├── template.html └── template.tex ├── pyproject.toml ├── scripts ├── ci │ ├── build_docs.sh │ ├── build_environment.sh │ └── unpack_environment.sh ├── get_reps_benchmark.py └── testdrive_sampling.py ├── setup.py └── tests ├── __init__.py ├── test_activations.py ├── test_evotuning.py ├── test_evotuning_models.py ├── test_featurize.py ├── test_layers.py ├── test_sampler.py └── test_utils.py /.bumpversion.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ElArkk/jax-unirep/HEAD/.bumpversion.cfg -------------------------------------------------------------------------------- /.devcontainer/devcontainer.Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ElArkk/jax-unirep/HEAD/.devcontainer/devcontainer.Dockerfile 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