| { |
| "per_regulator": { |
| "CDK12": { |
| "auroc": 0.6329, |
| "auprc": 0.179, |
| "best_epoch": 0, |
| "regulator": "CDK12", |
| "n_pos": 724, |
| "n_edges": 8459 |
| }, |
| "ATP1A1": { |
| "auroc": 0.5181, |
| "auprc": 0.0816, |
| "best_epoch": 12, |
| "regulator": "ATP1A1", |
| "n_pos": 449, |
| "n_edges": 8263 |
| }, |
| "MED1": { |
| "auroc": 0.6832, |
| "auprc": 0.1065, |
| "best_epoch": 1, |
| "regulator": "MED1", |
| "n_pos": 349, |
| "n_edges": 8389 |
| }, |
| "IFNAR2": { |
| "auroc": 0.3728, |
| "auprc": 0.0181, |
| "best_epoch": 10, |
| "regulator": "IFNAR2", |
| "n_pos": 191, |
| "n_edges": 8435 |
| }, |
| "CSNK2A1": { |
| "auroc": 0.5631, |
| "auprc": 0.0433, |
| "best_epoch": 3, |
| "regulator": "CSNK2A1", |
| "n_pos": 165, |
| "n_edges": 8048 |
| }, |
| "STK40": { |
| "auroc": 0.5734, |
| "auprc": 0.0398, |
| "best_epoch": 1, |
| "regulator": "STK40", |
| "n_pos": 163, |
| "n_edges": 8302 |
| }, |
| "TGFBR2": { |
| "auroc": 0.809, |
| "auprc": 0.1209, |
| "best_epoch": 7, |
| "regulator": "TGFBR2", |
| "n_pos": 162, |
| "n_edges": 8389 |
| }, |
| "MAPK14": { |
| "auroc": 0.531, |
| "auprc": 0.0314, |
| "best_epoch": 30, |
| "regulator": "MAPK14", |
| "n_pos": 138, |
| "n_edges": 8476 |
| }, |
| "CSF2RB": { |
| "auroc": 0.8126, |
| "auprc": 0.115, |
| "best_epoch": 4, |
| "regulator": "CSF2RB", |
| "n_pos": 95, |
| "n_edges": 8278 |
| }, |
| "LSM6": { |
| "auroc": 0.6383, |
| "auprc": 0.0082, |
| "best_epoch": 12, |
| "regulator": "LSM6", |
| "n_pos": 40, |
| "n_edges": 8949 |
| }, |
| "CSF1R": { |
| "auroc": 0.5612, |
| "auprc": 0.0121, |
| "best_epoch": 14, |
| "regulator": "CSF1R", |
| "n_pos": 37, |
| "n_edges": 8255 |
| }, |
| "DDX39B": { |
| "auroc": 0.637, |
| "auprc": 0.0062, |
| "best_epoch": 14, |
| "regulator": "DDX39B", |
| "n_pos": 32, |
| "n_edges": 8449 |
| }, |
| "NDUFS5": { |
| "auroc": 0.8351, |
| "auprc": 0.0253, |
| "best_epoch": 26, |
| "regulator": "NDUFS5", |
| "n_pos": 32, |
| "n_edges": 8446 |
| }, |
| "CSF2RA": { |
| "auroc": 0.3103, |
| "auprc": 0.0026, |
| "best_epoch": 2, |
| "regulator": "CSF2RA", |
| "n_pos": 31, |
| "n_edges": 8299 |
| }, |
| "CDK8": { |
| "auroc": 0.4762, |
| "auprc": 0.004, |
| "best_epoch": 0, |
| "regulator": "CDK8", |
| "n_pos": 22, |
| "n_edges": 8328 |
| }, |
| "NDUFA8": { |
| "auroc": 0.4363, |
| "auprc": 0.0021, |
| "best_epoch": 8, |
| "regulator": "NDUFA8", |
| "n_pos": 18, |
| "n_edges": 8497 |
| }, |
| "PLK1": { |
| "auroc": 0.6423, |
| "auprc": 0.0031, |
| "best_epoch": 20, |
| "regulator": "PLK1", |
| "n_pos": 16, |
| "n_edges": 8507 |
| }, |
| "RIOK2": { |
| "auroc": 0.6557, |
| "auprc": 0.0029, |
| "best_epoch": 10, |
| "regulator": "RIOK2", |
| "n_pos": 14, |
| "n_edges": 8609 |
| }, |
| "AURKB": { |
| "auroc": 0.6521, |
| "auprc": 0.0022, |
| "best_epoch": 18, |
| "regulator": "AURKB", |
| "n_pos": 10, |
| "n_edges": 8791 |
| }, |
| "MAP2K6": { |
| "auroc": 0.3484, |
| "auprc": 0.0011, |
| "best_epoch": 6, |
| "regulator": "MAP2K6", |
| "n_pos": 10, |
| "n_edges": 8423 |
| }, |
| "SPTLC2": { |
| "auroc": 0.9621, |
| "auprc": 0.0189, |
| "best_epoch": 17, |
| "regulator": "SPTLC2", |
| "n_pos": 7, |
| "n_edges": 8444 |
| }, |
| "NDUFV2": { |
| "auroc": 0.8902, |
| "auprc": 0.0093, |
| "best_epoch": 9, |
| "regulator": "NDUFV2", |
| "n_pos": 5, |
| "n_edges": 8319 |
| } |
| }, |
| "aggregate": { |
| "n_regulators": 22, |
| "auroc_median": 0.635, |
| "auroc_mean": 0.6155, |
| "auroc_std": 0.169, |
| "auroc_iqr": [ |
| 0.5213, |
| 0.6763 |
| ], |
| "frac_above_0.5": 0.7727, |
| "frac_above_0.7": 0.2273, |
| "auprc_median": 0.0151, |
| "auroc_vs_log_npos_spearman": -0.2113, |
| "auroc_vs_log_npos_pvalue": 0.345196, |
| "predictor_model_r_squared": 0.066914, |
| "predictor_model_adj_r_squared": -0.088601, |
| "predictor_model_f_pvalue": 0.73382, |
| "predictor_model_significant_predictors": [] |
| }, |
| "predictor_analysis": { |
| "n_regulators": 22, |
| "family_summary": [ |
| { |
| "family": "Non-TF", |
| "n_regulators": 22, |
| "auroc_median": 0.635, |
| "auroc_mean": 0.6155, |
| "auroc_iqr": [ |
| 0.5213, |
| 0.6763 |
| ] |
| } |
| ], |
| "regression": { |
| "status": "ok", |
| "formula": "auroc ~ log_n_pos + expr_level + string_degree", |
| "n_samples": 22, |
| "r_squared": 0.066914, |
| "adj_r_squared": -0.088601, |
| "f_statistic": 0.430273, |
| "f_pvalue": 0.73382, |
| "coefficients": { |
| "Intercept": { |
| "coef": 0.634884, |
| "std_err": 0.13455, |
| "t": 4.71858, |
| "p_value": 0.000171, |
| "ci95": [ |
| 0.352205, |
| 0.917562 |
| ] |
| }, |
| "log_n_pos": { |
| "coef": -0.022024, |
| "std_err": 0.027726, |
| "t": -0.794358, |
| "p_value": 0.437335, |
| "ci95": [ |
| -0.080274, |
| 0.036225 |
| ] |
| }, |
| "expr_level": { |
| "coef": 0.058614, |
| "std_err": 0.142971, |
| "t": 0.40997, |
| "p_value": 0.686666, |
| "ci95": [ |
| -0.241757, |
| 0.358984 |
| ] |
| }, |
| "string_degree": { |
| "coef": 0.000176, |
| "std_err": 0.000217, |
| "t": 0.811344, |
| "p_value": 0.427767, |
| "ci95": [ |
| -0.00028, |
| 0.000632 |
| ] |
| } |
| }, |
| "significant_predictors": [], |
| "family_effect_lrt": null, |
| "family_levels": [ |
| "Non-TF" |
| ] |
| }, |
| "per_regulator": [ |
| { |
| "regulator": "ATP1A1", |
| "auroc": 0.5181, |
| "n_pos": 449, |
| "expr_level": 0.298494, |
| "string_degree": 105.000019, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "AURKB", |
| "auroc": 0.6521, |
| "n_pos": 10, |
| "expr_level": 0.012576, |
| "string_degree": 496.000002, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "CDK12", |
| "auroc": 0.6329, |
| "n_pos": 724, |
| "expr_level": 0.398531, |
| "string_degree": 181.999973, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "CDK8", |
| "auroc": 0.4762, |
| "n_pos": 22, |
| "expr_level": 0.431748, |
| "string_degree": 159.999975, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "CSF1R", |
| "auroc": 0.5612, |
| "n_pos": 37, |
| "expr_level": 0.761295, |
| "string_degree": 462.000096, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "CSF2RA", |
| "auroc": 0.3103, |
| "n_pos": 31, |
| "expr_level": 0.811523, |
| "string_degree": 89.000006, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "CSF2RB", |
| "auroc": 0.8126, |
| "n_pos": 95, |
| "expr_level": 0.074185, |
| "string_degree": 175.000012, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "CSNK2A1", |
| "auroc": 0.5631, |
| "n_pos": 165, |
| "expr_level": 0.369979, |
| "string_degree": 371.999995, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "DDX39B", |
| "auroc": 0.637, |
| "n_pos": 32, |
| "expr_level": 0.0, |
| "string_degree": 407.000004, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "IFNAR2", |
| "auroc": 0.3728, |
| "n_pos": 191, |
| "expr_level": 0.0, |
| "string_degree": 159.999975, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "LSM6", |
| "auroc": 0.6383, |
| "n_pos": 40, |
| "expr_level": 0.068675, |
| "string_degree": 179.999961, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "MAP2K6", |
| "auroc": 0.3484, |
| "n_pos": 10, |
| "expr_level": 0.136931, |
| "string_degree": 112.999997, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "MAPK14", |
| "auroc": 0.531, |
| "n_pos": 138, |
| "expr_level": 0.474831, |
| "string_degree": 447.999944, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "MED1", |
| "auroc": 0.6832, |
| "n_pos": 349, |
| "expr_level": 0.151198, |
| "string_degree": 732.999858, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "NDUFA8", |
| "auroc": 0.4363, |
| "n_pos": 18, |
| "expr_level": 0.052815, |
| "string_degree": 273.000022, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "NDUFS5", |
| "auroc": 0.8351, |
| "n_pos": 32, |
| "expr_level": 0.104842, |
| "string_degree": 210.000001, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "NDUFV2", |
| "auroc": 0.8902, |
| "n_pos": 5, |
| "expr_level": 0.218877, |
| "string_degree": 319.999955, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "PLK1", |
| "auroc": 0.6423, |
| "n_pos": 16, |
| "expr_level": 0.01505, |
| "string_degree": 609.999878, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "RIOK2", |
| "auroc": 0.6557, |
| "n_pos": 14, |
| "expr_level": 0.074441, |
| "string_degree": 267.99998, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "SPTLC2", |
| "auroc": 0.9621, |
| "n_pos": 7, |
| "expr_level": 0.751476, |
| "string_degree": 84.999986, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "STK40", |
| "auroc": 0.5734, |
| "n_pos": 163, |
| "expr_level": 0.258644, |
| "string_degree": 27.999997, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| }, |
| { |
| "regulator": "TGFBR2", |
| "auroc": 0.809, |
| "n_pos": 162, |
| "expr_level": 0.820096, |
| "string_degree": 340.999999, |
| "tf_family": "Non-TF", |
| "tf_family_grouped": "Non-TF" |
| } |
| ], |
| "metadata": { |
| "n_input_regulators": 22, |
| "n_mapped_regulators": 22, |
| "n_tf_regulators": 0, |
| "n_non_tf_regulators": 22, |
| "expression_proxy": "log1p(mean expression in TAM atlas cells)", |
| "string_degree_source": "H-GFB raw network feature 0 (STRING v12 score>=400, expm1)", |
| "tf_family_source": "HumanTFs_DatabaseExtract_v_1.01.txt (DBD column)", |
| "min_family_size_for_grouping": 2 |
| } |
| }, |
| "embedding_source": "geneformer", |
| "min_pos_edges": 5, |
| "hyperparameters": { |
| "rank": 16, |
| "dim": 256, |
| "batch_size": 2048, |
| "lr": 0.003, |
| "wd": 1e-05, |
| "max_epochs": 200, |
| "patience": 15, |
| "seed": 42 |
| } |
| } |