├── .github └── workflows │ └── CI_build.yml ├── CITATION.cff ├── LICENSE ├── README.md ├── __version__.py ├── custom_functions ├── library_search.py ├── networking.py ├── plotting_functions.py ├── pubchem_lookup.py └── similarity_matrix.py ├── notebooks ├── iomega-1-mgf_to_cleaned_data.ipynb ├── iomega-10-spectra-networking.ipynb ├── iomega-2-split_data_into_subsets.ipynb ├── iomega-3-classical-spectra-similarities.ipynb ├── iomega-4-fingerprint-based-similarities.ipynb ├── iomega-5-train-spec2vec-model.ipynb ├── iomega-5b-compare_model_iterations.ipynb ├── iomega-5b-train-spec2vec-model-all-gnps.ipynb ├── iomega-6-compute-spec2vec-similarities.ipynb ├── iomega-7-compare-the-different-scores-alternatives.ipynb ├── iomega-7-compare-the-different-scores.ipynb ├── iomega-7-compare_different_classical_score_parameters.ipynb ├── iomega-8-library-matching-pre_revision.ipynb ├── iomega-8-library-matching-scenario1.ipynb ├── iomega-8-library-matching-scenario2.ipynb ├── iomega-8-library-matching-scenario3-known-query-compounds_ge5.ipynb ├── iomega-9-unknown-compound-search-mod-cos.ipynb ├── iomega-9-unknown-compound-search-only-annotated-spectra.ipynb ├── iomega-9-unknown-compound-search.ipynb ├── iomega-extra-classical-spectra-similarities-performance-analysis-synthetic-data.ipynb ├── iomega-extra-evaluate-retraining-effect-5000subset.ipynb ├── iomega-extra-get-spec2vec-embeddings.ipynb ├── iomega-in-depths-spectrum-comparions.ipynb └── iomega-inspect_model_variability.ipynb ├── setup.py └── tests └── test_library_matching.py /.github/workflows/CI_build.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iomega/spec2vec_gnps_data_analysis/HEAD/.github/workflows/CI_build.yml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 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