├── .gitignore ├── 1_ADNI_GNNs_networks.ipynb ├── 2_ADNI_GNNs_vs_nonGNNs.ipynb ├── 3_ADNI_GNNs_random_networks.ipynb ├── 4_LOAD_GNNs.ipynb ├── LICENSE ├── README.md ├── create_datasets ├── create_nx_datasets.py ├── create_splits.py └── create_table_datasets.py ├── data ├── AD_GDAs.tsv ├── AD_GDAs.txt ├── BED_files │ └── AD_PPI │ │ ├── AD_PPI.genes.bed │ │ ├── chr1.genes.bed │ │ ├── chr10.genes.bed │ │ ├── chr11.genes.bed │ │ ├── chr12.genes.bed │ │ ├── chr14.genes.bed │ │ ├── chr15.genes.bed │ │ ├── chr16.genes.bed │ │ ├── chr17.genes.bed │ │ ├── chr18.genes.bed │ │ ├── chr19.genes.bed │ │ ├── chr2.genes.bed │ │ ├── chr21.genes.bed │ │ ├── chr22.genes.bed │ │ ├── chr3.genes.bed │ │ ├── chr4.genes.bed │ │ ├── chr6.genes.bed │ │ ├── chr7.genes.bed │ │ ├── chr8.genes.bed │ │ ├── chrHG344_PATCH.genes.bed │ │ ├── chrHSCHR6_MHC_APD.genes.bed │ │ ├── chrHSCHR6_MHC_COX.genes.bed │ │ ├── chrHSCHR6_MHC_DBB.genes.bed │ │ ├── chrHSCHR6_MHC_MANN.genes.bed │ │ ├── chrHSCHR6_MHC_MCF.genes.bed │ │ ├── chrHSCHR6_MHC_QBL.genes.bed │ │ ├── chrHSCHR6_MHC_SSTO.genes.bed │ │ └── chrX.genes.bed ├── bio_networks │ ├── AD_BioGrid_PPI.edgelist │ ├── AD_GIANT_brain.edgelist │ ├── AD_HuRI_PPI.edgelist │ ├── AD_SNAP_PPI_brain.edgelist │ ├── AD_SNAP_PPI_brain_noAPOE.edgelist │ ├── AD_STRING_PPI.edgelist │ ├── HuRI_download_interactions_dec_16_2021_11_54_03.csv │ ├── PPT-Ohmnet_tissues-brain.edgelist │ ├── PPT-Ohmnet_tissues-combined.edgelist │ └── brain_C1.dat ├── random_networks │ ├── AD_PPI_rewired100_edgelist.txt │ ├── AD_PPI_rewired10_edgelist.txt │ ├── AD_PPI_rewired11_edgelist.txt │ ├── AD_PPI_rewired12_edgelist.txt │ ├── AD_PPI_rewired13_edgelist.txt │ ├── AD_PPI_rewired14_edgelist.txt │ ├── AD_PPI_rewired15_edgelist.txt │ ├── AD_PPI_rewired16_edgelist.txt │ ├── AD_PPI_rewired17_edgelist.txt │ ├── AD_PPI_rewired18_edgelist.txt │ ├── AD_PPI_rewired19_edgelist.txt │ ├── AD_PPI_rewired1_edgelist.txt │ ├── AD_PPI_rewired20_edgelist.txt │ ├── AD_PPI_rewired21_edgelist.txt │ ├── AD_PPI_rewired22_edgelist.txt │ ├── AD_PPI_rewired23_edgelist.txt │ ├── AD_PPI_rewired24_edgelist.txt │ ├── AD_PPI_rewired25_edgelist.txt │ ├── AD_PPI_rewired26_edgelist.txt │ ├── AD_PPI_rewired27_edgelist.txt │ ├── AD_PPI_rewired28_edgelist.txt │ ├── AD_PPI_rewired29_edgelist.txt │ ├── AD_PPI_rewired2_edgelist.txt │ ├── AD_PPI_rewired30_edgelist.txt │ ├── AD_PPI_rewired31_edgelist.txt │ ├── AD_PPI_rewired32_edgelist.txt │ ├── AD_PPI_rewired33_edgelist.txt │ ├── AD_PPI_rewired34_edgelist.txt │ ├── AD_PPI_rewired35_edgelist.txt │ ├── AD_PPI_rewired36_edgelist.txt │ ├── AD_PPI_rewired37_edgelist.txt │ ├── AD_PPI_rewired38_edgelist.txt │ ├── AD_PPI_rewired39_edgelist.txt │ ├── AD_PPI_rewired3_edgelist.txt │ ├── AD_PPI_rewired40_edgelist.txt │ ├── AD_PPI_rewired41_edgelist.txt │ ├── AD_PPI_rewired42_edgelist.txt │ ├── AD_PPI_rewired43_edgelist.txt │ ├── AD_PPI_rewired44_edgelist.txt │ ├── AD_PPI_rewired45_edgelist.txt │ ├── AD_PPI_rewired46_edgelist.txt │ ├── AD_PPI_rewired47_edgelist.txt │ ├── AD_PPI_rewired48_edgelist.txt │ ├── AD_PPI_rewired49_edgelist.txt │ ├── AD_PPI_rewired4_edgelist.txt │ ├── AD_PPI_rewired50_edgelist.txt │ ├── AD_PPI_rewired51_edgelist.txt │ ├── AD_PPI_rewired52_edgelist.txt │ ├── AD_PPI_rewired53_edgelist.txt │ ├── AD_PPI_rewired54_edgelist.txt │ ├── AD_PPI_rewired55_edgelist.txt │ ├── AD_PPI_rewired56_edgelist.txt │ ├── AD_PPI_rewired57_edgelist.txt │ ├── AD_PPI_rewired58_edgelist.txt │ ├── AD_PPI_rewired59_edgelist.txt │ ├── AD_PPI_rewired5_edgelist.txt │ ├── AD_PPI_rewired60_edgelist.txt │ ├── AD_PPI_rewired61_edgelist.txt │ ├── AD_PPI_rewired62_edgelist.txt │ ├── AD_PPI_rewired63_edgelist.txt │ ├── AD_PPI_rewired64_edgelist.txt │ ├── AD_PPI_rewired65_edgelist.txt │ ├── AD_PPI_rewired66_edgelist.txt │ ├── AD_PPI_rewired67_edgelist.txt │ ├── AD_PPI_rewired68_edgelist.txt │ ├── AD_PPI_rewired69_edgelist.txt │ ├── AD_PPI_rewired6_edgelist.txt │ ├── AD_PPI_rewired70_edgelist.txt │ ├── AD_PPI_rewired71_edgelist.txt │ ├── AD_PPI_rewired72_edgelist.txt │ ├── AD_PPI_rewired73_edgelist.txt │ ├── AD_PPI_rewired74_edgelist.txt │ ├── AD_PPI_rewired75_edgelist.txt │ ├── AD_PPI_rewired76_edgelist.txt │ ├── AD_PPI_rewired77_edgelist.txt │ ├── AD_PPI_rewired78_edgelist.txt │ ├── AD_PPI_rewired79_edgelist.txt │ ├── AD_PPI_rewired7_edgelist.txt │ ├── AD_PPI_rewired80_edgelist.txt │ ├── AD_PPI_rewired81_edgelist.txt │ ├── AD_PPI_rewired82_edgelist.txt │ ├── AD_PPI_rewired83_edgelist.txt │ ├── AD_PPI_rewired84_edgelist.txt │ ├── AD_PPI_rewired85_edgelist.txt │ ├── AD_PPI_rewired86_edgelist.txt │ ├── AD_PPI_rewired87_edgelist.txt │ ├── AD_PPI_rewired88_edgelist.txt │ ├── AD_PPI_rewired89_edgelist.txt │ ├── AD_PPI_rewired8_edgelist.txt │ ├── AD_PPI_rewired90_edgelist.txt │ ├── AD_PPI_rewired91_edgelist.txt │ ├── AD_PPI_rewired92_edgelist.txt │ ├── AD_PPI_rewired93_edgelist.txt │ ├── AD_PPI_rewired94_edgelist.txt │ ├── AD_PPI_rewired95_edgelist.txt │ ├── AD_PPI_rewired96_edgelist.txt │ ├── AD_PPI_rewired97_edgelist.txt │ ├── AD_PPI_rewired98_edgelist.txt │ ├── AD_PPI_rewired99_edgelist.txt │ ├── AD_PPI_rewired9_edgelist.txt │ ├── AD_PPI_shuffled100_edgelist.txt │ ├── AD_PPI_shuffled10_edgelist.txt │ ├── AD_PPI_shuffled11_edgelist.txt │ ├── AD_PPI_shuffled12_edgelist.txt │ ├── AD_PPI_shuffled13_edgelist.txt │ ├── AD_PPI_shuffled14_edgelist.txt │ ├── AD_PPI_shuffled15_edgelist.txt │ ├── AD_PPI_shuffled16_edgelist.txt │ ├── AD_PPI_shuffled17_edgelist.txt │ ├── AD_PPI_shuffled18_edgelist.txt │ ├── AD_PPI_shuffled19_edgelist.txt │ ├── AD_PPI_shuffled1_edgelist.txt │ ├── AD_PPI_shuffled20_edgelist.txt │ ├── AD_PPI_shuffled21_edgelist.txt │ ├── AD_PPI_shuffled22_edgelist.txt │ ├── AD_PPI_shuffled23_edgelist.txt │ ├── AD_PPI_shuffled24_edgelist.txt │ ├── AD_PPI_shuffled25_edgelist.txt │ ├── AD_PPI_shuffled26_edgelist.txt │ ├── AD_PPI_shuffled27_edgelist.txt │ ├── AD_PPI_shuffled28_edgelist.txt │ ├── AD_PPI_shuffled29_edgelist.txt │ ├── AD_PPI_shuffled2_edgelist.txt │ ├── AD_PPI_shuffled30_edgelist.txt │ ├── AD_PPI_shuffled31_edgelist.txt │ ├── AD_PPI_shuffled32_edgelist.txt │ ├── AD_PPI_shuffled33_edgelist.txt │ ├── AD_PPI_shuffled34_edgelist.txt │ ├── AD_PPI_shuffled35_edgelist.txt │ ├── AD_PPI_shuffled36_edgelist.txt │ ├── AD_PPI_shuffled37_edgelist.txt │ ├── AD_PPI_shuffled38_edgelist.txt │ ├── AD_PPI_shuffled39_edgelist.txt │ ├── AD_PPI_shuffled3_edgelist.txt │ ├── AD_PPI_shuffled40_edgelist.txt │ ├── AD_PPI_shuffled41_edgelist.txt │ ├── AD_PPI_shuffled42_edgelist.txt │ ├── AD_PPI_shuffled43_edgelist.txt │ ├── AD_PPI_shuffled44_edgelist.txt │ ├── AD_PPI_shuffled45_edgelist.txt │ ├── AD_PPI_shuffled46_edgelist.txt │ ├── AD_PPI_shuffled47_edgelist.txt │ ├── AD_PPI_shuffled48_edgelist.txt │ ├── AD_PPI_shuffled49_edgelist.txt │ ├── AD_PPI_shuffled4_edgelist.txt │ ├── AD_PPI_shuffled50_edgelist.txt │ ├── AD_PPI_shuffled51_edgelist.txt │ ├── AD_PPI_shuffled52_edgelist.txt │ ├── AD_PPI_shuffled53_edgelist.txt │ ├── AD_PPI_shuffled54_edgelist.txt │ ├── AD_PPI_shuffled55_edgelist.txt │ ├── AD_PPI_shuffled56_edgelist.txt │ ├── AD_PPI_shuffled57_edgelist.txt │ ├── AD_PPI_shuffled58_edgelist.txt │ ├── AD_PPI_shuffled59_edgelist.txt │ ├── AD_PPI_shuffled5_edgelist.txt │ ├── AD_PPI_shuffled60_edgelist.txt │ ├── AD_PPI_shuffled61_edgelist.txt │ ├── AD_PPI_shuffled62_edgelist.txt │ ├── AD_PPI_shuffled63_edgelist.txt │ ├── AD_PPI_shuffled64_edgelist.txt │ ├── AD_PPI_shuffled65_edgelist.txt │ ├── AD_PPI_shuffled66_edgelist.txt │ ├── AD_PPI_shuffled67_edgelist.txt │ ├── AD_PPI_shuffled68_edgelist.txt │ ├── AD_PPI_shuffled69_edgelist.txt │ ├── AD_PPI_shuffled6_edgelist.txt │ ├── AD_PPI_shuffled70_edgelist.txt │ ├── AD_PPI_shuffled71_edgelist.txt │ ├── AD_PPI_shuffled72_edgelist.txt │ ├── AD_PPI_shuffled73_edgelist.txt │ ├── AD_PPI_shuffled74_edgelist.txt │ ├── AD_PPI_shuffled75_edgelist.txt │ ├── AD_PPI_shuffled76_edgelist.txt │ ├── AD_PPI_shuffled77_edgelist.txt │ ├── AD_PPI_shuffled78_edgelist.txt │ ├── AD_PPI_shuffled79_edgelist.txt │ ├── AD_PPI_shuffled7_edgelist.txt │ ├── AD_PPI_shuffled80_edgelist.txt │ ├── AD_PPI_shuffled81_edgelist.txt │ ├── AD_PPI_shuffled82_edgelist.txt │ ├── AD_PPI_shuffled83_edgelist.txt │ ├── AD_PPI_shuffled84_edgelist.txt │ ├── AD_PPI_shuffled85_edgelist.txt │ ├── AD_PPI_shuffled86_edgelist.txt │ ├── AD_PPI_shuffled87_edgelist.txt │ ├── AD_PPI_shuffled88_edgelist.txt │ ├── AD_PPI_shuffled89_edgelist.txt │ ├── AD_PPI_shuffled8_edgelist.txt │ ├── AD_PPI_shuffled90_edgelist.txt │ ├── AD_PPI_shuffled91_edgelist.txt │ ├── AD_PPI_shuffled92_edgelist.txt │ ├── AD_PPI_shuffled93_edgelist.txt │ ├── AD_PPI_shuffled94_edgelist.txt │ ├── AD_PPI_shuffled95_edgelist.txt │ ├── AD_PPI_shuffled96_edgelist.txt │ ├── AD_PPI_shuffled97_edgelist.txt │ ├── AD_PPI_shuffled98_edgelist.txt │ ├── AD_PPI_shuffled99_edgelist.txt │ └── AD_PPI_shuffled9_edgelist.txt └── splits │ ├── 10Fold_CV_LOAD │ ├── k10_LOAD.pkl │ ├── k1_LOAD.pkl │ ├── k2_LOAD.pkl │ ├── k3_LOAD.pkl │ ├── k4_LOAD.pkl │ ├── k5_LOAD.pkl │ ├── k6_LOAD.pkl │ ├── k7_LOAD.pkl │ ├── k8_LOAD.pkl │ └── k9_LOAD.pkl │ ├── 10Fold_CV_PET │ ├── fold10_val_samples.csv │ ├── fold1_val_samples.csv │ ├── fold2_val_samples.csv │ ├── fold3_val_samples.csv │ ├── fold4_val_samples.csv │ ├── fold5_val_samples.csv │ ├── fold6_val_samples.csv │ ├── fold7_val_samples.csv │ ├── fold8_val_samples.csv │ ├── fold9_val_samples.csv │ ├── k10_PET.pkl │ ├── k1_PET.pkl │ ├── k2_PET.pkl │ ├── k3_PET.pkl │ ├── k4_PET.pkl │ ├── k5_PET.pkl │ ├── k6_PET.pkl │ ├── k7_PET.pkl │ ├── k8_PET.pkl │ └── k9_PET.pkl │ └── 10Fold_CV_PETandDX │ ├── fold10_val_samples.csv │ ├── fold1_val_samples.csv │ ├── fold2_val_samples.csv │ ├── fold3_val_samples.csv │ ├── fold4_val_samples.csv │ ├── fold5_val_samples.csv │ ├── fold6_val_samples.csv │ ├── fold7_val_samples.csv │ ├── fold8_val_samples.csv │ ├── fold9_val_samples.csv │ ├── k10_PETandDX.pkl │ ├── k1_PETandDX.pkl │ ├── k2_PETandDX.pkl │ ├── k3_PETandDX.pkl │ ├── k4_PETandDX.pkl │ ├── k5_PETandDX.pkl │ ├── k6_PETandDX.pkl │ ├── k7_PETandDX.pkl │ ├── k8_PETandDX.pkl │ └── k9_PETandDX.pkl ├── data_preprocessing ├── ADNIMERGE_processing.py ├── extract_and_annotate_missense_ADNI.sh ├── extract_and_annotate_missense_LOAD.sh ├── get_GDAs.R └── make_BED_files.R ├── figures ├── figure1.png ├── figure2.eps ├── figure2.png ├── figure3.eps ├── figure3.png ├── figure4.eps ├── figure4.png ├── figure5.eps ├── figure5.png └── supp_fig1.png ├── graphgenetics.yml ├── graphgym_files └── run │ ├── configs │ ├── LOAD.yaml │ ├── PET.yaml │ ├── PET_noAPOE.yaml │ ├── PET_random.yaml │ ├── PETandDX.yaml │ ├── PETandDX_noAPOE.yaml │ └── PETandDX_random.yaml │ ├── grids │ ├── missense_2MP.txt │ ├── missense_2MP_LOAD.txt │ ├── missense_PET_noAPOE.txt │ ├── missense_PET_random.txt │ ├── missense_PETandDX_noAPOE.txt │ └── missense_PETandDX_random.txt │ ├── run_batch_LOAD_missense_2MP.sh │ ├── run_batch_PET_missense_2MP.sh │ ├── run_batch_PET_missense_noAPOE.sh │ ├── run_batch_PET_missense_random.sh │ ├── run_batch_PETandDX_missense_2MP.sh │ ├── run_batch_PETandDX_missense_noAPOE.sh │ └── run_batch_PETandDX_missense_random.sh ├── ml_models ├── create_labels.py └── models_stats.py ├── networks ├── bio_networks.py ├── networks_stats.py └── randomize_network.py └── results ├── 2022_03_baseline_models_LOAD.csv ├── 2022_03_baseline_models_PET.csv ├── 2022_03_baseline_models_PETandDX.csv ├── 2022_03_networks_PET.csv ├── 2022_03_networks_PETandDX.csv ├── 2022_03_nonGNN_models_LOAD.csv ├── 2022_03_nonGNN_models_PET.csv ├── 2022_03_nonGNN_models_PETandDX.csv ├── 2022_04_networks_LOAD.csv ├── 2022_04_networks_PET_noAPOE.csv ├── 2022_04_networks_PET_random_rewired.csv ├── 2022_04_networks_PET_random_shuffled.csv ├── 2022_04_networks_PETandDX_noAPOE.csv ├── 2022_04_networks_PETandDX_random_rewired.csv ├── 2022_04_networks_PETandDX_random_shuffled.csv ├── 2022_04_nonGNN_models_PET_noAPOE.csv ├── 2022_04_nonGNN_models_PETandDX_noAPOE.csv ├── 2022_05_sensitivity_analysis_edges_PET.csv ├── 2022_05_sensitivity_analysis_edges_PETandDX.csv ├── 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