├── .gitignore ├── LICENSE ├── README.md ├── analysis ├── figures │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_stacked_binomial.pdf │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_stacked_binomial.pdf │ ├── CNN-prediction-with-REGN-pilot-version-2_full_all_multinomial.pdf │ ├── CNN-prediction-with-REGN-pilot-version-2_full_stacked_binomial.pdf │ ├── fitted_gene_v_full_logx_err.pdf │ ├── gene_plots │ │ ├── GILGFVFTL_cluster0.pdf │ │ ├── GILGFVFTL_cluster1.pdf │ │ ├── GLCTLVAML_cluster0.pdf │ │ ├── GLCTLVAML_cluster1.pdf │ │ ├── GLCTLVAML_cluster2.pdf │ │ ├── GLCTLVAML_cluster3.pdf │ │ └── GLCTLVAML_cluster4.pdf │ ├── inference │ │ ├── ELAGIGILTV │ │ │ └── from_public_TCRs_using_CNN-prediction-with-REGN-pilot-version-2 │ │ │ │ └── cluster_ELAGIGILTV_frompublic_TCRs_using_CNN-prediction-with-REGN-pilot-version-2_all_full.pdf │ │ ├── GILGFVFTL │ │ │ └── from_public_TCRs_using_CNN-prediction-with-REGN-pilot-version-2 │ │ │ │ └── cluster_GILGFVFTL_frompublic_TCRs_using_CNN-prediction-with-REGN-pilot-version-2_all_full.pdf │ │ ├── GLCTLVAML │ │ │ └── from_public_TCRs_using_CNN-prediction-with-REGN-pilot-version-2 │ │ │ │ └── cluster_GLCTLVAML_frompublic_TCRs_using_CNN-prediction-with-REGN-pilot-version-2_all_full.pdf │ │ └── NLVPMVATV │ │ │ ├── fromCNN-prediction-with-REGN-pilot-version-2_using_public_TCRs_all_full │ │ │ └── cluster_NLVPMVATV_fromCNN-prediction-with-REGN-pilot-version-2_using_public_TCRs_all_full.pdf │ │ │ └── from_public_TCRs_using_CNN-prediction-with-REGN-pilot-version-2 │ │ │ └── cluster_NLVPMVATV_frompublic_TCRs_using_CNN-prediction-with-REGN-pilot-version-2_all_full.pdf │ ├── pbmc │ │ └── full_model_umap.pdf │ ├── public_TCRs_alpha_stacked_binomial.pdf │ ├── public_TCRs_beta_stacked_binomial.pdf │ ├── public_TCRs_full_public-key_multinomial.pdf │ ├── public_TCRs_full_stacked_binomial.pdf │ └── roc_inferred_with_public_TCRs_using_CNN-prediction-with-REGN-pilot-version-2_full.pdf ├── motif │ └── CNN-prediction-with-REGN-pilot-version-2 │ │ ├── GILGFVFTL │ │ ├── cluster_0 │ │ │ ├── GILGFVFTL_cluster0_TRA_cdr3_topbinders.fasta │ │ │ ├── GILGFVFTL_cluster0_TRA_cdr3_topbinders_logo.pdf │ │ │ ├── GILGFVFTL_cluster0_TRB_cdr3_topbinders.fasta │ │ │ ├── GILGFVFTL_cluster0_TRB_cdr3_topbinders_logo.pdf │ │ │ ├── GILGFVFTL_cluster0_pie_TRA_j_gene.pdf │ │ │ ├── GILGFVFTL_cluster0_pie_TRA_j_gene_table.csv │ │ │ ├── GILGFVFTL_cluster0_pie_TRA_v_gene.pdf │ │ │ ├── GILGFVFTL_cluster0_pie_TRA_v_gene_table.csv │ │ │ ├── GILGFVFTL_cluster0_pie_TRB_j_gene.pdf │ │ │ ├── GILGFVFTL_cluster0_pie_TRB_j_gene_table.csv │ │ │ ├── GILGFVFTL_cluster0_pie_TRB_v_gene.pdf │ │ │ ├── GILGFVFTL_cluster0_pie_TRB_v_gene_table.csv │ │ │ └── GILGFVFTL_df_cluster0.csv │ │ ├── cluster_1 │ │ │ ├── GILGFVFTL_cluster1_TRA_cdr3_topbinders.fasta │ │ │ ├── GILGFVFTL_cluster1_TRA_cdr3_topbinders_logo.pdf │ │ │ ├── GILGFVFTL_cluster1_TRB_cdr3_topbinders.fasta │ │ │ ├── GILGFVFTL_cluster1_TRB_cdr3_topbinders_logo.pdf │ │ │ ├── GILGFVFTL_cluster1_pie_TRA_j_gene.pdf │ │ │ ├── GILGFVFTL_cluster1_pie_TRA_j_gene_table.csv │ │ │ ├── GILGFVFTL_cluster1_pie_TRA_v_gene.pdf │ │ │ ├── GILGFVFTL_cluster1_pie_TRA_v_gene_table.csv │ │ │ ├── GILGFVFTL_cluster1_pie_TRB_j_gene.pdf │ │ │ ├── GILGFVFTL_cluster1_pie_TRB_j_gene_table.csv │ │ │ ├── GILGFVFTL_cluster1_pie_TRB_v_gene.pdf │ │ │ ├── GILGFVFTL_cluster1_pie_TRB_v_gene_table.csv │ │ │ └── GILGFVFTL_df_cluster1.csv │ │ ├── cluster_kmeans_self_GILGFVFTL_all_full.pdf │ │ └── cluster_kmeans_self_GILGFVFTL_all_full_nolegend.pdf │ │ └── GLCTLVAML │ │ ├── cluster_0 │ │ ├── GLCTLVAML_cluster0_TRA_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster0_TRA_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster0_TRB_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster0_TRB_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster0_pie_TRA_j_gene.pdf │ │ ├── GLCTLVAML_cluster0_pie_TRA_j_gene_table.csv │ │ ├── GLCTLVAML_cluster0_pie_TRA_v_gene.pdf │ │ ├── GLCTLVAML_cluster0_pie_TRA_v_gene_table.csv │ │ ├── GLCTLVAML_cluster0_pie_TRB_j_gene.pdf │ │ ├── GLCTLVAML_cluster0_pie_TRB_j_gene_table.csv │ │ ├── GLCTLVAML_cluster0_pie_TRB_v_gene.pdf │ │ ├── GLCTLVAML_cluster0_pie_TRB_v_gene_table.csv │ │ └── GLCTLVAML_df_cluster0.csv │ │ ├── cluster_1 │ │ ├── GLCTLVAML_cluster1_TRA_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster1_TRA_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster1_TRB_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster1_TRB_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster1_pie_TRA_j_gene.pdf │ │ ├── GLCTLVAML_cluster1_pie_TRA_j_gene_table.csv │ │ ├── GLCTLVAML_cluster1_pie_TRA_v_gene.pdf │ │ ├── GLCTLVAML_cluster1_pie_TRA_v_gene_table.csv │ │ ├── GLCTLVAML_cluster1_pie_TRB_j_gene.pdf │ │ ├── GLCTLVAML_cluster1_pie_TRB_j_gene_table.csv │ │ ├── GLCTLVAML_cluster1_pie_TRB_v_gene.pdf │ │ ├── GLCTLVAML_cluster1_pie_TRB_v_gene_table.csv │ │ └── GLCTLVAML_df_cluster1.csv │ │ ├── cluster_2 │ │ ├── GLCTLVAML_cluster2_TRA_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster2_TRA_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster2_TRB_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster2_TRB_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster2_pie_TRA_j_gene.pdf │ │ ├── GLCTLVAML_cluster2_pie_TRA_j_gene_table.csv │ │ ├── GLCTLVAML_cluster2_pie_TRA_v_gene.pdf │ │ ├── GLCTLVAML_cluster2_pie_TRA_v_gene_table.csv │ │ ├── GLCTLVAML_cluster2_pie_TRB_j_gene.pdf │ │ ├── GLCTLVAML_cluster2_pie_TRB_j_gene_table.csv │ │ ├── GLCTLVAML_cluster2_pie_TRB_v_gene.pdf │ │ ├── GLCTLVAML_cluster2_pie_TRB_v_gene_table.csv │ │ └── GLCTLVAML_df_cluster2.csv │ │ ├── cluster_3 │ │ ├── GLCTLVAML_cluster3_TRA_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster3_TRA_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster3_TRB_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster3_TRB_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster3_pie_TRA_j_gene.pdf │ │ ├── GLCTLVAML_cluster3_pie_TRA_j_gene_table.csv │ │ ├── GLCTLVAML_cluster3_pie_TRA_v_gene.pdf │ │ ├── GLCTLVAML_cluster3_pie_TRA_v_gene_table.csv │ │ ├── GLCTLVAML_cluster3_pie_TRB_j_gene.pdf │ │ ├── GLCTLVAML_cluster3_pie_TRB_j_gene_table.csv │ │ ├── GLCTLVAML_cluster3_pie_TRB_v_gene.pdf │ │ ├── GLCTLVAML_cluster3_pie_TRB_v_gene_table.csv │ │ └── GLCTLVAML_df_cluster3.csv │ │ ├── cluster_4 │ │ ├── GLCTLVAML_cluster4_TRA_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster4_TRA_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster4_TRB_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster4_TRB_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster4_pie_TRA_j_gene.pdf │ │ ├── GLCTLVAML_cluster4_pie_TRA_j_gene_table.csv │ │ ├── GLCTLVAML_cluster4_pie_TRA_v_gene.pdf │ │ ├── GLCTLVAML_cluster4_pie_TRA_v_gene_table.csv │ │ ├── GLCTLVAML_cluster4_pie_TRB_j_gene.pdf │ │ ├── GLCTLVAML_cluster4_pie_TRB_j_gene_table.csv │ │ ├── GLCTLVAML_cluster4_pie_TRB_v_gene.pdf │ │ ├── GLCTLVAML_cluster4_pie_TRB_v_gene_table.csv │ │ └── GLCTLVAML_df_cluster4.csv │ │ ├── cluster_5 │ │ ├── GLCTLVAML_cluster5_TRA_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster5_TRA_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster5_TRB_cdr3_topbinders.fasta │ │ ├── GLCTLVAML_cluster5_TRB_cdr3_topbinders_logo.pdf │ │ ├── GLCTLVAML_cluster5_pie_TRA_j_gene.pdf │ │ ├── GLCTLVAML_cluster5_pie_TRA_j_gene_table.csv │ │ ├── GLCTLVAML_cluster5_pie_TRA_v_gene.pdf │ │ ├── GLCTLVAML_cluster5_pie_TRA_v_gene_table.csv │ │ ├── GLCTLVAML_cluster5_pie_TRB_j_gene.pdf │ │ ├── GLCTLVAML_cluster5_pie_TRB_j_gene_table.csv │ │ ├── GLCTLVAML_cluster5_pie_TRB_v_gene.pdf │ │ ├── GLCTLVAML_cluster5_pie_TRB_v_gene_table.csv │ │ └── GLCTLVAML_df_cluster5.csv │ │ ├── cluster_kmeans_self_GLCTLVAML_all_full.pdf │ │ └── cluster_kmeans_self_GLCTLVAML_all_full_nolegend.pdf └── tables │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_binomial_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_multinomial_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_binomial_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_multinomial_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_binomial_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_multinomial_table.csv │ ├── inferred_on_public_TCRs_with_CNN-prediction-with-REGN-pilot-version-2_full.csv │ ├── public_TCRs_alpha_binomial_table.csv │ ├── public_TCRs_alpha_multinomial_table.csv │ ├── public_TCRs_beta_binomial_table.csv │ ├── public_TCRs_beta_multinomial_table.csv │ ├── public_TCRs_full_binomial_table.csv │ ├── public_TCRs_full_multinomial_table.csv │ ├── public_TCRs_gene_binomial_table.csv │ ├── public_TCRs_gene_multinomial_table.csv │ └── roc_data │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_AVFDRKSDAK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_ELAGIGILTV_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_GILGFVFTL_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_GLCTLVAML_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_IPSINVHHY_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_IVTDFSVIK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_KLGGALQAK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_NLVPMVATV_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_alpha_RAKFKQLL_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_AVFDRKSDAK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_ELAGIGILTV_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_GILGFVFTL_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_GLCTLVAML_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_IPSINVHHY_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_IVTDFSVIK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_KLGGALQAK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_NLVPMVATV_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_beta_RAKFKQLL_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_AVFDRKSDAK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_ELAGIGILTV_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_GILGFVFTL_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_GLCTLVAML_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_IPSINVHHY_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_IVTDFSVIK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_KLGGALQAK_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_NLVPMVATV_roc_table.csv │ ├── CNN-prediction-with-REGN-pilot-version-2_full_RAKFKQLL_roc_table.csv │ ├── public_TCRs_alpha_CINGVCWTV_roc_table.csv │ ├── public_TCRs_alpha_ELAGIGILTV_roc_table.csv │ ├── public_TCRs_alpha_GILGFVFTL_roc_table.csv │ ├── public_TCRs_alpha_GLCTLVAML_roc_table.csv │ ├── public_TCRs_alpha_IVTDFSVIK_roc_table.csv │ ├── public_TCRs_alpha_KAFSPEVIPMF_roc_table.csv │ ├── public_TCRs_alpha_KLVALGINAV_roc_table.csv │ ├── public_TCRs_alpha_LLWNGPMAV_roc_table.csv │ ├── public_TCRs_alpha_NLVPMVATV_roc_table.csv │ ├── public_TCRs_alpha_PKYVKQNTLKLAT_roc_table.csv │ ├── public_TCRs_alpha_RPRGEVRFL_roc_table.csv │ ├── public_TCRs_alpha_RYPLTFGWCF_roc_table.csv │ ├── public_TCRs_beta_AVFDRKSDAK_roc_table.csv │ ├── public_TCRs_beta_CINGVCWTV_roc_table.csv │ ├── public_TCRs_beta_ELAGIGILTV_roc_table.csv │ ├── public_TCRs_beta_GILGFVFTL_roc_table.csv │ ├── public_TCRs_beta_GLCTLVAML_roc_table.csv │ ├── public_TCRs_beta_IVTDFSVIK_roc_table.csv │ ├── public_TCRs_beta_KAFSPEVIPMF_roc_table.csv │ ├── public_TCRs_beta_KLVALGINAV_roc_table.csv │ ├── public_TCRs_beta_LLWNGPMAV_roc_table.csv │ ├── public_TCRs_beta_NLVPMVATV_roc_table.csv │ ├── public_TCRs_beta_PKYVKQNTLKLAT_roc_table.csv │ ├── public_TCRs_beta_RPRGEVRFL_roc_table.csv │ ├── public_TCRs_beta_RYPLTFGWCF_roc_table.csv │ ├── public_TCRs_full_AVFDRKSDAK_roc_table.csv │ ├── public_TCRs_full_CINGVCWTV_roc_table.csv │ ├── public_TCRs_full_ELAGIGILTV_roc_table.csv │ ├── public_TCRs_full_GILGFVFTL_roc_table.csv │ ├── public_TCRs_full_GLCTLVAML_roc_table.csv │ ├── public_TCRs_full_IVTDFSVIK_roc_table.csv │ ├── public_TCRs_full_KAFSPEVIPMF_roc_table.csv │ ├── public_TCRs_full_KLVALGINAV_roc_table.csv │ ├── public_TCRs_full_LLWNGPMAV_roc_table.csv │ ├── public_TCRs_full_NLVPMVATV_roc_table.csv │ ├── public_TCRs_full_PKYVKQNTLKLAT_roc_table.csv │ ├── public_TCRs_full_RPRGEVRFL_roc_table.csv │ ├── public_TCRs_full_RYPLTFGWCF_roc_table.csv │ ├── public_TCRs_gene_CINGVCWTV_roc_table.csv │ ├── public_TCRs_gene_ELAGIGILTV_roc_table.csv │ ├── public_TCRs_gene_GILGFVFTL_roc_table.csv │ ├── public_TCRs_gene_GLCTLVAML_roc_table.csv │ ├── public_TCRs_gene_IVTDFSVIK_roc_table.csv │ ├── public_TCRs_gene_KAFSPEVIPMF_roc_table.csv │ ├── public_TCRs_gene_KLVALGINAV_roc_table.csv │ ├── public_TCRs_gene_LLWNGPMAV_roc_table.csv │ ├── public_TCRs_gene_NLVPMVATV_roc_table.csv │ ├── public_TCRs_gene_PKYVKQNTLKLAT_roc_table.csv │ ├── public_TCRs_gene_RPRGEVRFL_roc_table.csv │ └── public_TCRs_gene_RYPLTFGWCF_roc_table.csv ├── data ├── CNN-prediction-with-REGN-pilot-version-2.csv ├── CNN-prediction-with-REGN-pilot-version-2_id_df.csv ├── public_TCRs.csv └── public_TCRs_id_df.csv ├── notebooks ├── gene_usage.ipynb └── simple_example_binomial.ipynb ├── results ├── cdr3_results │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_AVFDRKSDAK_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_AVFDRKSDAK_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_AVFDRKSDAK_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_ELAGIGILTV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_ELAGIGILTV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_ELAGIGILTV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_GILGFVFTL_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_GILGFVFTL_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_GILGFVFTL_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_GLCTLVAML_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_GLCTLVAML_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_GLCTLVAML_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_IPSINVHHY_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_IPSINVHHY_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_IPSINVHHY_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_IVTDFSVIK_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_IVTDFSVIK_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_IVTDFSVIK_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_KLGGALQAK_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_KLGGALQAK_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_KLGGALQAK_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_NLVPMVATV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_NLVPMVATV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_NLVPMVATV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_RAKFKQLL_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_RAKFKQLL_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_CNN-prediction-with-REGN-pilot-version-2_RAKFKQLL_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_AVFDRKSDAK_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_AVFDRKSDAK_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_CINGVCWTV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_CINGVCWTV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_CINGVCWTV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_ELAGIGILTV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_ELAGIGILTV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_ELAGIGILTV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_GILGFVFTL_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_GILGFVFTL_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_GILGFVFTL_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_GLCTLVAML_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_GLCTLVAML_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_GLCTLVAML_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_IVTDFSVIK_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_IVTDFSVIK_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_IVTDFSVIK_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_KAFSPEVIPMF_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_KAFSPEVIPMF_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_KAFSPEVIPMF_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_KLVALGINAV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_KLVALGINAV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_KLVALGINAV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_LLWNGPMAV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_LLWNGPMAV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_LLWNGPMAV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_NLVPMVATV_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_NLVPMVATV_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_NLVPMVATV_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_PKYVKQNTLKLAT_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_PKYVKQNTLKLAT_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_PKYVKQNTLKLAT_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_RPRGEVRFL_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_RPRGEVRFL_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_RPRGEVRFL_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_RYPLTFGWCF_alpha │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_RYPLTFGWCF_beta │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── binomial_public_TCRs_RYPLTFGWCF_full │ │ ├── cross_val_table.csv │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_all_alpha │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_all_beta │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_all_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_shared-by-all_alpha │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_shared-by-all_beta │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_shared-by-all_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_shared-by-final_alpha │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_shared-by-final_beta │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_CNN-prediction-with-REGN-pilot-version-2_shared-by-final_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_all_beta │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_all_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_public-key_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_shared-by-all_alpha │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_shared-by-all_beta │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_shared-by-all_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_shared-by-final_alpha │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ ├── multinomial_public_TCRs_shared-by-final_beta │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv │ └── multinomial_public_TCRs_shared-by-final_full │ │ ├── cross_val_table.csv │ │ ├── int_pmhc_map.pickle │ │ ├── pmhc_int_map.pickle │ │ ├── test_evals.json │ │ ├── test_results.csv │ │ ├── train_results.csv │ │ └── validation_results.csv └── gene_results │ ├── binomial_public_TCRs_CINGVCWTV_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_ELAGIGILTV_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_GILGFVFTL_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_GLCTLVAML_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_IVTDFSVIK_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_KAFSPEVIPMF_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_KLVALGINAV_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_LLWNGPMAV_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_NLVPMVATV_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_PKYVKQNTLKLAT_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ ├── binomial_public_TCRs_RPRGEVRFL_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv │ └── binomial_public_TCRs_RYPLTFGWCF_gene │ ├── cross_val_table.csv │ ├── test_evals.json │ ├── test_results.csv │ ├── train_results.csv │ └── validation_results.csv ├── scripts ├── cluster_inference.py ├── fingerprint_plot.py ├── full_gene_compare.py ├── help.txt ├── motif_kmeans.py ├── multinomial_plot.py ├── results_to_table.py ├── stacked_binomial_plot.py ├── train_tcr_binomial_multinomial_loop.py └── train_tcr_case.py ├── setup.py └── tcrai ├── __init__.py ├── modelling ├── __init__.py ├── base_models.py ├── classification.py ├── closers.py ├── cross_validation.py ├── extractors.py └── processing.py ├── motif ├── __init__.py ├── dim_reduction.py ├── 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