├── .gitignore ├── LICENSE ├── README.md ├── closest_string ├── README.md ├── task │ ├── dataset.py │ ├── dataset_generator_genomic.py │ └── dataset_generator_synthetic.py ├── test.py └── triplet │ ├── dataset.py │ ├── models │ ├── cnn │ │ └── train.py │ ├── feedforward │ │ └── train.py │ ├── transformer │ │ └── train.py │ └── triplet_encoder.py │ └── train.py ├── edit_distance ├── README.md ├── baselines │ ├── kmer.py │ └── train.py ├── models │ ├── cnn │ │ ├── model.py │ │ └── train.py │ ├── feedforward │ │ ├── model.py │ │ └── train.py │ ├── hyperbolics.py │ ├── kmer │ │ ├── model.py │ │ └── train.py │ ├── pair_encoder.py │ ├── recurrent │ │ ├── model.py │ │ └── train.py │ └── transformer │ │ ├── model.py │ │ └── train.py ├── task │ ├── dataset.py │ ├── dataset_generator_genomic.py │ └── dataset_generator_synthetic.py └── train.py ├── hierarchical_clustering ├── README.md ├── baselines.py ├── relaxed │ ├── config.py │ ├── data │ │ ├── animals.fasta │ │ └── hc_example.pkl │ ├── datasets │ │ ├── hc_dataset.py │ │ └── triples.py │ ├── models │ │ ├── cnn.py │ │ ├── embeddings.py │ │ ├── linear.py │ │ ├── mlp.py │ │ └── model.py │ ├── mst │ │ ├── mst.pyx │ │ ├── setup.py │ │ └── test_mst.py │ ├── optim │ │ ├── __init__.py │ │ └── radam.py │ ├── train.py │ ├── unionfind │ │ ├── setup.py │ │ ├── test_uf.py │ │ └── unionfind.pyx │ ├── utils │ │ ├── lca.py │ │ ├── linkage.py │ │ ├── metrics.py │ │ ├── training.py │ │ ├── tree.py │ │ └── visualization.py │ └── visualize.py ├── task │ ├── dataset_generator_example.py │ ├── dataset_generator_genomic.py │ └── dataset_generator_synthetic.py └── unsupervised │ └── unsupervised.py ├── multiple_alignment ├── README.md ├── guide_tree │ ├── guide_tree.py │ └── matrix.txt └── steiner_string │ ├── baselines.py │ ├── models │ ├── convolutional │ │ ├── model.py │ │ └── train.py │ ├── loss.py │ ├── mlp │ │ ├── 19.pkl │ │ ├── 74.pkl │ │ ├── model.py │ │ └── train.py │ ├── msa_autoencoder.py │ └── pair_autoencoder.py │ ├── parser.py │ ├── task │ ├── dataset.py │ └── dataset_generator_genome.py │ └── train.py ├── requirements.txt ├── tests ├── __init__.py ├── bioinformatics_algorithms │ ├── __init__.py │ ├── test_edit_distance.py │ └── test_exact_matching.py ├── closest_string_tests │ ├── __init__.py │ ├── test_closest_dataset_generation_genomic.py │ ├── test_closest_dataset_generation_synthetic.py │ └── test_closest_testing.py ├── distance_functions │ ├── __init__.py │ └── test_distance_torch.py ├── edit_distance_tests │ ├── __init__.py │ ├── test_ed_dataset_generation_genomic.py │ ├── test_ed_dataset_generation_synthetic.py │ └── test_ed_training.py ├── hierarchical_clustering_tests │ ├── __init__.py │ ├── test_hc_dataset_generation_genomic.py │ ├── test_hc_dataset_generation_synthetic.py │ └── test_hc_unsupervised_testing.py └── multiple_sequence_alignment_tests │ ├── __init__.py │ ├── test_msa_guide_testing.py │ ├── test_msa_steiner_dataset_generation.py │ └── test_msa_steiner_training.py ├── tutorial ├── NeuroSEED.ipynb ├── closest_diagram.png ├── closest_real.png ├── closest_synthetic.png ├── cover.png ├── edit_diagram.PNG ├── edit_dimension.png ├── edit_real.PNG ├── edit_synthetic.PNG ├── hc_animals.png ├── hc_average.png ├── hyphc_plots.png ├── microbiome_analysis.png ├── msa_guide_table.png ├── msa_steiner_diagram.png └── msa_steiner_table.png └── util ├── bioinformatics_algorithms ├── edit_distance.py ├── exact_matching.py └── inexact_matching.py ├── data_handling ├── data_loader.py └── string_generator.py ├── distance_functions ├── distance_functions.py ├── distance_matrix.py └── geometric_median.py └── ml_and_math ├── layers.py ├── loss_functions.py ├── math.py └── poincare.py /.gitignore: -------------------------------------------------------------------------------- 1 | .idea/* 2 | data/* -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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