├── .github └── workflows │ ├── publish-to-pypi.yml │ └── release.yml ├── .gitignore ├── .idea ├── .gitignore ├── aws.xml ├── genomap.iml ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── LICENSE.txt ├── MANIFEST.in ├── MATLAB ├── TMdata.mat ├── construct_genomap.m ├── createInteractionMatrix.m ├── createMeshDistanceMatrix.m ├── demo_genomap.asv ├── demo_genomap.m ├── even_or_odd.m ├── freezeWeights.m ├── gromov-wassersteinOT │ ├── README.md │ ├── code │ │ ├── batch_barycenter_distances.m │ │ ├── compute_gw_barycenters.m │ │ ├── groundTruth.mat │ │ ├── mexEMD │ │ │ ├── core.h │ │ │ ├── full_bipartitegraph.h │ │ │ ├── mexEMD.cpp │ │ │ ├── mexEMD.mexa64 │ │ │ ├── mexEMD.mexmaci64 │ │ │ ├── mexEMD.mexw64 │ │ │ └── network_simplex_simple.h │ │ ├── perform_gw_sinkhorn.m │ │ ├── perform_sinkhorn.m │ │ ├── perform_sinkhorn_log.m │ │ ├── plotG.m │ │ ├── preprocess_data.m │ │ ├── reducedData.mat │ │ ├── test_distmat_interpol.m │ │ ├── test_distmat_interpol_T.m │ │ └── toolbox │ │ │ ├── VectorizeCallback.m │ │ │ ├── distmat.m │ │ │ ├── getoptions.m │ │ │ ├── progressbar.m │ │ │ ├── rescale.m │ │ │ └── s2v.m │ └── setparams.m ├── index_TM.mat └── label_TMData.mat ├── README.md ├── data ├── TM_data.csv └── readme.txt ├── genomap ├── __init__.py ├── bregman_genomap │ ├── __init__.py │ └── bregman_genomap.py ├── genoAnnotate │ ├── __init__.py │ └── genoAnnotate.py ├── genoClassification │ ├── __init__.py │ └── genoClassification.py ├── genoDR │ ├── __init__.py │ └── genoDimReduction.py ├── genoMOI │ ├── __init__.py │ └── genoMOI.py ├── genoNet │ ├── __init__.py │ └── genoNet.py ├── genoNetRegression │ ├── __init__.py │ └── genoNet_regression.py ├── genoNetus │ ├── __init__.py │ └── genoNetus.py ├── genoRegression │ ├── __init__.py │ └── genoRegression.py ├── genoSig │ ├── __init__.py │ └── genoSig.py ├── genoTraj │ ├── __init__.py │ └── genoTraj.py ├── genoVis │ ├── __init__.py │ └── genoVis.py ├── genomap.py ├── 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