├── .gitignore ├── .ipynb_checkpoints ├── Untitled-checkpoint.ipynb └── batch_effect_normalization-Copy1-checkpoint.ipynb ├── LICENSE ├── Paper_Analyses ├── .ipynb_checkpoints │ ├── CV_Prediction_Performance-checkpoint.ipynb │ ├── Evaluate_Embedding_Correlations-checkpoint.ipynb │ ├── External_validation_predictions-checkpoint.ipynb │ ├── Final_genes_color_by_genesets-checkpoint.ipynb │ ├── Final_genes_interaction_analyses-checkpoint.ipynb │ ├── Final_genes_rank_comparisons-checkpoint.ipynb │ ├── Subsets_CV_ROSMAP_Plots-checkpoint.ipynb │ ├── t-SNE_plots_external-checkpoint.ipynb │ └── t-SNE_plots_internal-checkpoint.ipynb ├── CV_Prediction_Performance-SuppFig11c.ipynb ├── CV_Prediction_Performance.ipynb ├── Evaluate_Embedding_Correlations.ipynb ├── External_validation_predictions.ipynb ├── Final_genes_color_by_genesets.ipynb ├── Final_genes_interaction_analyses.ipynb ├── Final_genes_rank_comparisons.ipynb ├── Generate_data_summary_tables.ipynb ├── Subsets_CV_ROSMAP_Plots.ipynb ├── __pycache__ │ ├── geneset_plotting_functions.cpython-36.pyc │ ├── geneset_plotting_functions.cpython-37.pyc │ ├── plotting_functions.cpython-36.pyc │ ├── plotting_functions.cpython-37.pyc │ ├── tsne_plotting_functions.cpython-36.pyc │ └── tsne_plotting_functions.cpython-37.pyc ├── alternate_architectures_experiments.ipynb ├── final_selected_hyperparameters.csv ├── geneset_plotting_functions.py ├── plotting_functions.py ├── selected_hyperparameters.csv ├── selected_hyperparameters_supfig11c.csv ├── t-SNE_plots_external.ipynb ├── t-SNE_plots_internal.ipynb ├── test_set_variances.csv └── tsne_plotting_functions.py ├── Pipeline_Code ├── .ipynb_checkpoints │ └── Get_MDAD_IG_weights-checkpoint.ipynb ├── External_Validation │ ├── .ipynb_checkpoints │ │ ├── Save_intersecting_model_predictions_runs-checkpoint.ipynb │ │ ├── Save_transfer_predictions_runs-checkpoint.ipynb │ │ ├── compute_final_model_predictions-checkpoint.ipynb │ │ ├── linear_model_ext_val-checkpoint.ipynb │ │ ├── save_MDAD_embeddings_ext_val-checkpoint.ipynb │ │ └── save_cleaned_results_for_plots-checkpoint.ipynb │ ├── Save_intersecting_model_predictions_runs.ipynb │ ├── Save_transfer_predictions_runs.ipynb │ ├── Train_intersecting_MLP_models.py │ ├── Train_intersecting_MTL_models.py │ ├── compute_final_model_predictions.ipynb │ ├── linear_model_ext_val.ipynb │ ├── model_transformations │ │ └── all_human │ │ │ ├── HBTRC_GEO_CER.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── HBTRC_GEO_PFC.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── HBTRC_GEO_VC.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── HBTRC_synapse.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── MTL │ │ │ └── 1 │ │ │ │ └── train │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 10.txt │ │ │ │ ├── 11.txt │ │ │ │ ├── 12.txt │ │ │ │ ├── 13.txt │ │ │ │ ├── 14.txt │ │ │ │ ├── 15.txt │ │ │ │ ├── 16.txt │ │ │ │ ├── 17.txt │ │ │ │ ├── 18.txt │ │ │ │ ├── 19.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ ├── 4.txt │ │ │ │ ├── 5.txt │ │ │ │ ├── 6.txt │ │ │ │ ├── 7.txt │ │ │ │ ├── 8.txt │ │ │ │ └── 9.txt │ │ │ ├── MayoRNASeq.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── Mayo_CER.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── Mayo_TCX.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── ROSMAP_GE2.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_anterior cingulate_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_caudate nucleus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_dorsolateral prefrontal cortex_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_frontal pole_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_hippocampus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_inferior frontal gyrus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_inferior temporal gyrus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_middle temporal gyrus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_occipital visual cortex_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_parahippocampal gyrus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ ├── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ │ └── train │ │ │ │ ├── 0.txt │ │ │ │ └── 1.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_posterior cingulate cortex_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_precentral gyrus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_prefrontal cortex_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_putamen_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_superior parietal lobule_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_superior temporal gyrus_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133ab_temporal pole_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ ├── amp-ad_msbb_mssm_affymetrixu133plus2_amygdala_rspp-adj.tsv │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ └── test │ │ │ │ ├── 0.txt │ │ │ │ ├── 1.txt │ │ │ │ ├── 2.txt │ │ │ │ ├── 3.txt │ │ │ │ └── 4.txt │ │ │ └── amp-ad_msbb_mssm_affymetrixu133plus2_nucleus accumbens_rspp-adj.tsv │ │ │ └── MTL │ │ │ └── 1 │ │ │ └── test │ │ │ ├── 0.txt │ │ │ ├── 1.txt │ │ │ ├── 2.txt │ │ │ ├── 3.txt │ │ │ └── 4.txt │ ├── model_transformations_intersection │ │ ├── Blood_GSE63060 │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ ├── test │ │ │ │ └── 0.txt │ │ │ │ └── train │ │ │ │ └── 0.txt │ │ ├── Blood_GSE63061 │ │ │ └── MTL │ │ │ │ └── 1 │ │ │ │ ├── test │ │ │ │ └── 0.txt │ │ │ │ └── train │ │ │ │ └── 0.txt │ │ └── Mouse │ │ │ └── MTL │ │ │ └── 1 │ │ │ ├── test │ │ │ └── 0.txt │ │ │ └── train │ │ │ └── 0.txt │ ├── predictions │ │ └── amp-ad_msbb_mssm_affymetrixu133ab_parahippocampal gyrus_rspp-adj.tsv │ │ │ ├── MLP_baselines │ │ │ ├── 0.csv │ │ │ ├── 1.csv │ │ │ ├── 2.csv │ │ │ ├── 3.csv │ │ │ ├── 4.csv │ │ │ ├── 5.csv │ │ │ └── 6.csv │ │ │ └── MTL │ │ │ └── 200_relu_[500, 100]_[50, 10]_0.100000_0.001000_0.001000_[1, 1]_0.100000_20 │ │ │ ├── 0.csv │ │ │ ├── 1.csv │ │ │ ├── 10.csv │ │ │ ├── 11.csv │ │ │ ├── 12.csv │ │ │ ├── 13.csv │ │ │ ├── 14.csv │ │ │ ├── 15.csv │ │ │ ├── 16.csv │ │ │ ├── 17.csv │ │ │ ├── 18.csv │ │ │ ├── 19.csv │ │ │ ├── 2.csv │ │ │ ├── 20.csv │ │ │ ├── 21.csv │ │ │ ├── 22.csv │ │ │ ├── 23.csv │ │ │ ├── 24.csv │ │ │ ├── 25.csv │ │ │ ├── 26.csv │ │ │ ├── 27.csv │ │ │ ├── 28.csv │ │ │ ├── 29.csv │ │ │ ├── 3.csv │ │ │ ├── 30.csv │ │ │ ├── 31.csv │ │ │ ├── 32.csv │ │ │ ├── 33.csv │ │ │ ├── 34.csv │ │ │ ├── 35.csv │ │ │ ├── 36.csv │ │ │ ├── 37.csv │ │ │ ├── 38.csv │ │ │ ├── 39.csv │ │ │ ├── 4.csv │ │ │ ├── 40.csv │ │ │ ├── 41.csv │ │ │ ├── 42.csv │ │ │ ├── 43.csv │ │ │ ├── 44.csv │ │ │ ├── 45.csv │ │ │ ├── 46.csv │ │ │ ├── 47.csv │ │ │ ├── 48.csv │ │ │ ├── 49.csv │ │ │ ├── 5.csv │ │ │ ├── 50.csv │ │ │ ├── 51.csv │ │ │ ├── 52.csv │ │ │ ├── 53.csv │ │ │ ├── 54.csv │ │ │ ├── 55.csv │ │ │ ├── 56.csv │ │ │ ├── 57.csv │ │ │ ├── 58.csv │ │ │ ├── 59.csv │ │ │ ├── 6.csv │ │ │ ├── 60.csv │ │ │ ├── 61.csv │ │ │ ├── 62.csv │ │ │ ├── 63.csv │ │ │ ├── 64.csv │ │ │ ├── 65.csv │ │ │ ├── 66.csv │ │ │ ├── 67.csv │ │ │ ├── 68.csv │ │ │ ├── 69.csv │ │ │ ├── 7.csv │ │ │ ├── 70.csv │ │ │ ├── 71.csv │ │ │ ├── 72.csv │ │ │ ├── 73.csv │ │ │ ├── 74.csv │ │ │ ├── 75.csv │ │ │ ├── 76.csv │ │ │ ├── 77.csv │ │ │ ├── 78.csv │ │ │ ├── 79.csv │ │ │ ├── 8.csv │ │ │ ├── 80.csv │ │ │ ├── 81.csv │ │ │ ├── 82.csv │ │ │ ├── 83.csv │ │ │ ├── 84.csv │ │ │ ├── 85.csv │ │ │ ├── 86.csv │ │ │ ├── 87.csv │ │ │ ├── 88.csv │ │ │ └── 9.csv │ ├── predictions_intersection │ │ ├── Blood_GSE63060 │ │ │ └── Linear │ │ │ │ └── final.csv │ │ ├── Blood_GSE63061 │ │ │ └── Linear │ │ │ │ └── final.csv │ │ └── Mouse │ │ │ └── Linear │ │ │ └── final.csv │ ├── save_MDAD_embeddings_ext_val.ipynb │ └── save_cleaned_results_for_plots.ipynb ├── Model_Interpretation │ ├── .ipynb_checkpoints │ │ ├── Get_MDAD_IG_weights-checkpoint.ipynb │ │ ├── Get_ranked_MDAD_genes-checkpoint.ipynb │ │ ├── Get_ranked_correlation_based_genes-checkpoint.ipynb │ │ ├── IG_weights_averaging-checkpoint.ipynb │ │ └── Run_GSEA-checkpoint.ipynb │ ├── Get_MDAD_IG_weights.ipynb │ ├── Get_ranked_MDAD_genes.ipynb │ ├── Get_ranked_correlation_based_genes.ipynb │ ├── IG_weights_averaging.ipynb │ └── Run_GSEA.ipynb ├── ROSMAP_data_validation_experiments.py ├── ROSMAP_data_validation_experiments_helpers.py ├── Train_CV_Models-Baselines.py ├── Train_CV_Models-MDAD.py ├── Train_Final_Model_MDAD.py ├── Train_Final_Model_MLP_baseline.py ├── __pycache__ │ ├── configs.cpython-36.pyc │ ├── configs.cpython-37.pyc │ ├── experiment_helpers.cpython-36.pyc │ └── models.cpython-36.pyc ├── calculate_consensus_MD-AD_embedding.py ├── configs.py ├── experiment_helpers.py ├── models.py ├── save_CV_model_embeddings.py ├── save_MDAD_final_predictions.py ├── save_final_model_embeddings_runs.py ├── select_final_models_from_CV-SuppFig11cd.py └── select_final_models_from_CV.py ├── README.md └── packages └── combat ├── .gitignore ├── .travis.yml ├── LICENSE ├── R-combat.R ├── README.md ├── bladder-expr.txt ├── bladder-pheno.txt ├── 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