Datasets:

yashvir
/

seq2state-data

+result_type,comparison_scope,source_name,model_or_feature,scoreboard,evaluation_universe,auprc,ci_low,ci_high,auroc,mrr,recall_at_1,terms_ok_for_training
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results/paper/paper_honest_leaderboard.csv ADDED Viewed

	@@ -0,0 +1,25 @@

+model,scoreboard,n_pairs,prevalence,auprc,auprc_ci_low,auprc_ci_high,auroc,precision_at_1,precision_at_5,precision_at_10,ece
+ensemble_proxy_residual_v1,field_compatible_e2g,16778,0.01734414113720348,0.6265504415205705,0.5661086678015007,0.6865697996597102,0.9798124816449157,0.0,0.4,0.7,0.18599818760260964
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results/paper/paper_incremental_value.csv ADDED Viewed

	@@ -0,0 +1,17 @@

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results/paper/paper_incremental_value.md ADDED Viewed

	@@ -0,0 +1,25 @@

+# Incremental Value Of Sequence Counterfactual Features
+Does adding the sequence counterfactual feature improve AUPRC over the
+strongest trained molecular model, on identical matched rows? `adds_value`
+is True only when the paired region-bootstrap 95% CI of (blend - trained)
+is entirely above zero.
+| panel | trained_model | scoreboard | auprc_trained | auprc_feature | auprc_blend | diff | ci_low | ci_high | adds_value |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| top250 | observed_hic_reabc | strict_all | 0.7278 | 0.6368 | 0.7107 | -0.0171 | -0.0374 | +0.0025 | False |
+| top250 | observed_hic_reabc | high_confidence | 0.9159 | 0.8412 | 0.9015 | -0.0145 | -0.0345 | +0.0035 | False |
+| top250 | observed_hic_reabc | field_compatible_e2g | 0.9380 | 0.8704 | 0.9266 | -0.0114 | -0.0312 | +0.0076 | False |
+| top250 | observed_hic_reabc | very_high_confidence | 0.9264 | 0.8674 | 0.9138 | -0.0126 | -0.0374 | +0.0109 | False |
+| top250 | ensemble_proxy_residual_v1 | strict_all | 0.7314 | 0.6368 | 0.7162 | -0.0152 | -0.0369 | +0.0055 | False |
+| top250 | ensemble_proxy_residual_v1 | high_confidence | 0.9216 | 0.8412 | 0.9069 | -0.0147 | -0.0353 | +0.0037 | False |
+| top250 | ensemble_proxy_residual_v1 | field_compatible_e2g | 0.9396 | 0.8704 | 0.9301 | -0.0095 | -0.0296 | +0.0096 | False |
+| top250 | ensemble_proxy_residual_v1 | very_high_confidence | 0.9398 | 0.8674 | 0.9204 | -0.0194 | -0.0470 | +0.0080 | False |
+| all_positive | observed_hic_reabc | strict_all | 0.6958 | 0.5885 | 0.6754 | -0.0203 | -0.0403 | +0.0011 | False |
+| all_positive | observed_hic_reabc | high_confidence | 0.9044 | 0.8014 | 0.8772 | -0.0272 | -0.0460 | -0.0068 | False |
+| all_positive | observed_hic_reabc | field_compatible_e2g | 0.9229 | 0.8235 | 0.8973 | -0.0256 | -0.0437 | -0.0085 | False |
+| all_positive | observed_hic_reabc | very_high_confidence | 0.8858 | 0.8186 | 0.8770 | -0.0088 | -0.0420 | +0.0203 | False |
+| all_positive | ensemble_proxy_residual_v1 | strict_all | 0.6872 | 0.5885 | 0.6752 | -0.0120 | -0.0325 | +0.0090 | False |
+| all_positive | ensemble_proxy_residual_v1 | high_confidence | 0.9081 | 0.8014 | 0.8807 | -0.0274 | -0.0459 | -0.0081 | False |
+| all_positive | ensemble_proxy_residual_v1 | field_compatible_e2g | 0.9227 | 0.8235 | 0.8995 | -0.0232 | -0.0415 | -0.0059 | False |
+| all_positive | ensemble_proxy_residual_v1 | very_high_confidence | 0.9072 | 0.8186 | 0.8870 | -0.0202 | -0.0551 | +0.0126 | False |

results/paper/paper_matched_panel_comparison.csv ADDED Viewed

	@@ -0,0 +1,129 @@

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+ensemble_proxy_residual_v1,ensemble_proxy_residual_v1,field_compatible_e2g,0.8693197314667904,5.120466290971193,0.9145448654037887,0.6784848484848485,0.194727767857395,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7446111653215407,0.9249626198162256
+observed_hic_reabc,logistic_observed_hic_reabc_c00003,field_compatible_e2g,0.8635892110213016,5.071323309226225,0.9239664340312397,0.6747811447811447,0.194727767857395,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7400424049582041,0.9193389280592186
+re2g_extended_features,logistic_re2g_extended_features_c0003,field_compatible_e2g,0.8568063261389742,4.976749107578518,0.9228230309072781,0.6784848484848485,0.194727767857395,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7463885883249449,0.9182998596179947
+field_leader,logistic_re2g_extended_highconf_c0003,field_compatible_e2g,0.8530401085279381,4.971501844174157,0.9174504818876702,0.6784848484848485,0.194727767857395,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7138880929903099,0.91769324789697
+proxy_v2_rich,logistic_counterfactual_proxy_v2_rich_highconf_c0003,field_compatible_e2g,0.8430651922399172,4.951227917799459,0.9106847789963443,0.6759595959595959,0.194727767857395,0.6623232323232323,0.62,True,top50,oracle_panel_top50,trainable,0.6878188693479794,0.908143259380129
+alphagenome_counterfactual,mask_abs_delta_atac_target_promoter_sum,field_compatible_e2g,0.8208185698696822,4.915917988681295,0.8852900145716696,0.6221717171717172,0.194727767857395,0.5901010101010101,0.62,True,top50,oracle_panel_top50,no_training_oracle,0.6859549080907138,0.8988103632922433
+distance_abc,logistic_distance_abc,field_compatible_e2g,0.802736666348862,4.616580113820362,0.9025021346217758,0.634023569023569,0.194727767857395,0.5767676767676767,0.62,True,top50,oracle_panel_top50,trainable,0.6018439671358028,0.8877193931631341
+residual_gate,residual_deepset_calibrated_gate_v1,high_confidence,0.8708341062614791,5.154720512578149,0.9164703115814227,0.6747811447811447,0.19199891594290844,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7626125866980074,0.9294684685839351
+ensemble_proxy_residual_v1,ensemble_proxy_residual_v1,high_confidence,0.8673089800442743,5.179074047543166,0.9135473251028806,0.6784848484848485,0.19199891594290844,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7435200762612135,0.9245582231734938
+observed_hic_reabc,logistic_observed_hic_reabc_c00003,high_confidence,0.8635892110213016,5.140269957867459,0.9258759553203998,0.6747811447811447,0.19199891594290844,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7400424049582041,0.9193389280592186
+re2g_extended_features,logistic_re2g_extended_features_c0003,high_confidence,0.8565325506668403,5.0429925074123725,0.9237189888301,0.6784848484848485,0.19199891594290844,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.746191076389013,0.9181633091270147
+field_leader,logistic_re2g_extended_highconf_c0003,high_confidence,0.851729339252468,5.0331241136730345,0.9165161669606114,0.6784848484848485,0.19199891594290844,0.6582828282828282,0.62,True,top50,oracle_panel_top50,trainable,0.7132888377821749,0.9171965022589144
+proxy_v2_rich,logistic_counterfactual_proxy_v2_rich_highconf_c0003,high_confidence,0.8405305073063232,5.002058617736717,0.9088853615520283,0.6759595959595959,0.19199891594290844,0.6623232323232323,0.62,True,top50,oracle_panel_top50,trainable,0.687559082003863,0.9077562550449949
+alphagenome_counterfactual,mask_abs_delta_atac_target_promoter_sum,high_confidence,0.8201420465721911,4.982078285360599,0.8856629132184688,0.6221717171717172,0.19199891594290844,0.5901010101010101,0.62,True,top50,oracle_panel_top50,no_training_oracle,0.6859313544771158,0.8987198883922953
+distance_abc,logistic_distance_abc,high_confidence,0.8025475410533536,4.678322109294082,0.903581241803464,0.634023569023569,0.19199891594290844,0.5767676767676767,0.62,True,top50,oracle_panel_top50,trainable,0.6017275038642489,0.8875810240118672
+residual_gate,residual_deepset_calibrated_gate_v1,strict_all,0.6591349082385205,3.7768152395940526,0.816565915309706,0.8702356902356903,0.17909427347680834,0.8157575757575758,0.3,True,top50,oracle_panel_top50,trainable,0.540136940721178,0.7356455167435537
+observed_hic_reabc,logistic_observed_hic_reabc_c00003,strict_all,0.6522592075451914,3.7563475726834397,0.8174041391697452,0.8835353535353535,0.17909427347680834,0.8379797979797979,0.3,True,top50,oracle_panel_top50,trainable,0.5433004257957977,0.7339924688173446
+re2g_extended_features,logistic_re2g_extended_features_c0003,strict_all,0.6501403822677215,3.732002247240841,0.8134382211025667,0.880238751147842,0.17909427347680834,0.8379797979797979,0.3,True,top50,oracle_panel_top50,trainable,0.5141987370926926,0.723515950332075
+ensemble_proxy_residual_v1,ensemble_proxy_residual_v1,strict_all,0.6468922528813204,3.717691572454746,0.8116464133443019,0.8645286195286195,0.17909427347680834,0.8157575757575758,0.3,True,top50,oracle_panel_top50,trainable,0.5283794444076875,0.7277216716329672
+alphagenome_counterfactual,mask_abs_delta_atac_target_promoter_sum,strict_all,0.6456789830645786,3.7544259416312684,0.80905433306664,0.9385185185185184,0.17909427347680834,0.8965656565656566,0.3,True,top50,oracle_panel_top50,no_training_oracle,0.5289455678969394,0.6937037673214014
+distance_abc,logistic_distance_abc,strict_all,0.6383380089843127,3.650414779023727,0.8123508116154141,0.8802286501377411,0.17909427347680834,0.8468686868686868,0.3,True,top50,oracle_panel_top50,trainable,0.512670735239954,0.7022397063907455
+field_leader,logistic_re2g_extended_highconf_c0003,strict_all,0.6328762071975002,3.6448034629220514,0.7861918218017477,0.8618686868686869,0.17909427347680834,0.8024242424242424,0.3,True,top50,oracle_panel_top50,trainable,0.49416250497048353,0.7138082723876921
+proxy_v2_rich,logistic_counterfactual_proxy_v2_rich_highconf_c0003,strict_all,0.5973026887573207,3.4294542025272703,0.7802346043948216,0.8542472342472343,0.17909427347680834,0.8024242424242424,0.3,True,top50,oracle_panel_top50,trainable,0.4744801164248929,0.6883532433138133
+residual_gate,residual_deepset_calibrated_gate_v1,very_high_confidence,0.9868131868131869,10.760439560439561,0.9877551020408163,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.926640695719643,1.0
+ensemble_proxy_residual_v1,ensemble_proxy_residual_v1,very_high_confidence,0.9847619047619048,10.754285714285714,0.9836734693877551,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.918313749743655,1.0
+re2g_extended_features,logistic_re2g_extended_features_c0003,very_high_confidence,0.9773809523809524,10.693253968253968,0.9840476190476191,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.9046459345906621,1.0
+proxy_v2_rich,logistic_counterfactual_proxy_v2_rich_highconf_c0003,very_high_confidence,0.9717647058823529,10.715294117647058,0.9714285714285713,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.8693822661442518,1.0
+observed_hic_reabc,logistic_observed_hic_reabc_c00003,very_high_confidence,0.9714285714285713,10.692063492063493,0.9787585034013606,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.871221734690582,1.0
+alphagenome_counterfactual,mask_abs_delta_atac_target_promoter_sum,very_high_confidence,0.9646703296703297,10.69401098901099,0.9734693877551021,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,no_training_oracle,0.8301155272283115,0.995842803030303
+field_leader,logistic_re2g_extended_highconf_c0003,very_high_confidence,0.9638605442176871,10.66935941043084,0.9726360544217687,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.8531414625486242,0.9980731225296441
+distance_abc,logistic_distance_abc,very_high_confidence,0.9589285714285714,10.654563492063494,0.9685544217687075,0.425,0.1803931766174329,0.425,0.7,True,top50,oracle_panel_top50,trainable,0.7979960099862667,0.9812789446442192

results/paper/paper_matched_panel_comparison.md ADDED Viewed

	@@ -0,0 +1,161 @@

+# Matched-Universe Panel Comparison
+Every predictor below is restricted to the **same** AlphaGenome panel
+region-gene pairs before scoring, so oracle and trainable AUPRCs share an
+identical candidate universe and positive prevalence. This replaces the
+earlier headline table, which compared the oracle on a high-prevalence panel
+against trainable models on the low-prevalence full 138k benchmark.
+## Matched scoreboards (balanced chromosome-fold test means)
+| panel | scoreboard | result_type | model_name | prevalence | auprc | ci_low | ci_high | auroc |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| all_positive | field_compatible_e2g | trainable | ensemble_proxy_residual_v1 | 0.1146 | 0.9273 | 0.8982 | 0.9461 | 0.9799 |
+| all_positive | field_compatible_e2g | trainable | logistic_observed_hic_reabc_c00003 | 0.1146 | 0.9262 | 0.8988 | 0.9466 | 0.9785 |
+| all_positive | field_compatible_e2g | trainable | residual_deepset_calibrated_gate_v1 | 0.1146 | 0.9237 | 0.8925 | 0.9441 | 0.9788 |
+| all_positive | field_compatible_e2g | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1146 | 0.9127 | 0.8816 | 0.9364 | 0.9728 |
+| all_positive | field_compatible_e2g | trainable | logistic_re2g_extended_highconf_c0003 | 0.1146 | 0.9124 | 0.8789 | 0.9348 | 0.9729 |
+| all_positive | field_compatible_e2g | trainable | logistic_re2g_extended_features_c0003 | 0.1146 | 0.9081 | 0.8757 | 0.9306 | 0.9756 |
+| all_positive | field_compatible_e2g | trainable | logistic_distance_abc | 0.1146 | 0.8469 | 0.7948 | 0.8858 | 0.9590 |
+| all_positive | field_compatible_e2g | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1146 | 0.8282 | 0.7869 | 0.8606 | 0.9358 |
+| all_positive | high_confidence | trainable | ensemble_proxy_residual_v1 | 0.1136 | 0.9127 | 0.8795 | 0.9354 | 0.9743 |
+| all_positive | high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.1136 | 0.9089 | 0.8754 | 0.9309 | 0.9712 |
+| all_positive | high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.1136 | 0.9083 | 0.8763 | 0.9322 | 0.9735 |
+| all_positive | high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1136 | 0.9011 | 0.8681 | 0.9255 | 0.9682 |
+| all_positive | high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.1136 | 0.8931 | 0.8602 | 0.9197 | 0.9663 |
+| all_positive | high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.1136 | 0.8879 | 0.8515 | 0.9150 | 0.9676 |
+| all_positive | high_confidence | trainable | logistic_distance_abc | 0.1136 | 0.8370 | 0.7887 | 0.8751 | 0.9546 |
+| all_positive | high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1136 | 0.8064 | 0.7619 | 0.8372 | 0.9201 |
+| all_positive | strict_all | trainable | logistic_observed_hic_reabc_c00003 | 0.1137 | 0.6969 | 0.6582 | 0.7346 | 0.8725 |
+| all_positive | strict_all | trainable | residual_deepset_calibrated_gate_v1 | 0.1137 | 0.6906 | 0.6515 | 0.7291 | 0.8864 |
+| all_positive | strict_all | trainable | ensemble_proxy_residual_v1 | 0.1137 | 0.6897 | 0.6520 | 0.7273 | 0.8769 |
+| all_positive | strict_all | trainable | logistic_re2g_extended_features_c0003 | 0.1137 | 0.6710 | 0.6285 | 0.7088 | 0.8665 |
+| all_positive | strict_all | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1137 | 0.6628 | 0.6245 | 0.7028 | 0.8549 |
+| all_positive | strict_all | trainable | logistic_re2g_extended_highconf_c0003 | 0.1137 | 0.6598 | 0.6189 | 0.6981 | 0.8556 |
+| all_positive | strict_all | trainable | logistic_distance_abc | 0.1137 | 0.6423 | 0.5990 | 0.6785 | 0.8578 |
+| all_positive | strict_all | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1137 | 0.5952 | 0.5536 | 0.6225 | 0.8268 |
+| all_positive | very_high_confidence | trainable | ensemble_proxy_residual_v1 | 0.0791 | 0.9203 | 0.8571 | 0.9475 | 0.9792 |
+| all_positive | very_high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.0791 | 0.9184 | 0.8594 | 0.9456 | 0.9813 |
+| all_positive | very_high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.0791 | 0.9139 | 0.8516 | 0.9396 | 0.9790 |
+| all_positive | very_high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.0791 | 0.9004 | 0.8342 | 0.9311 | 0.9704 |
+| all_positive | very_high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.0791 | 0.8973 | 0.8271 | 0.9295 | 0.9779 |
+| all_positive | very_high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.0791 | 0.8862 | 0.8182 | 0.9215 | 0.9684 |
+| all_positive | very_high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.0791 | 0.8396 | 0.7519 | 0.8793 | 0.9296 |
+| all_positive | very_high_confidence | trainable | logistic_distance_abc | 0.0791 | 0.8266 | 0.7399 | 0.8897 | 0.9659 |
+| top100 | field_compatible_e2g | trainable | ensemble_proxy_residual_v1 | 0.1831 | 0.8970 | 0.8333 | 0.9472 | 0.9479 |
+| top100 | field_compatible_e2g | trainable | residual_deepset_calibrated_gate_v1 | 0.1831 | 0.8947 | 0.8370 | 0.9467 | 0.9453 |
+| top100 | field_compatible_e2g | trainable | logistic_re2g_extended_highconf_c0003 | 0.1831 | 0.8909 | 0.8201 | 0.9425 | 0.9486 |
+| top100 | field_compatible_e2g | trainable | logistic_observed_hic_reabc_c00003 | 0.1831 | 0.8879 | 0.8161 | 0.9404 | 0.9497 |
+| top100 | field_compatible_e2g | trainable | logistic_re2g_extended_features_c0003 | 0.1831 | 0.8861 | 0.8189 | 0.9372 | 0.9486 |
+| top100 | field_compatible_e2g | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1831 | 0.8816 | 0.8049 | 0.9349 | 0.9438 |
+| top100 | field_compatible_e2g | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1831 | 0.8477 | 0.7553 | 0.8976 | 0.9211 |
+| top100 | field_compatible_e2g | trainable | logistic_distance_abc | 0.1831 | 0.7901 | 0.6619 | 0.8800 | 0.9162 |
+| top100 | high_confidence | trainable | ensemble_proxy_residual_v1 | 0.1864 | 0.8903 | 0.8268 | 0.9392 | 0.9455 |
+| top100 | high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.1864 | 0.8895 | 0.8303 | 0.9399 | 0.9442 |
+| top100 | high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.1864 | 0.8791 | 0.8054 | 0.9320 | 0.9425 |
+| top100 | high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.1864 | 0.8754 | 0.8031 | 0.9279 | 0.9436 |
+| top100 | high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.1864 | 0.8743 | 0.8023 | 0.9259 | 0.9427 |
+| top100 | high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1864 | 0.8743 | 0.7941 | 0.9244 | 0.9404 |
+| top100 | high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1864 | 0.8291 | 0.7298 | 0.8819 | 0.9030 |
+| top100 | high_confidence | trainable | logistic_distance_abc | 0.1864 | 0.7878 | 0.6741 | 0.8800 | 0.9161 |
+| top100 | strict_all | trainable | residual_deepset_calibrated_gate_v1 | 0.1638 | 0.6719 | 0.5950 | 0.7370 | 0.8365 |
+| top100 | strict_all | trainable | ensemble_proxy_residual_v1 | 0.1638 | 0.6671 | 0.5940 | 0.7353 | 0.8329 |
+| top100 | strict_all | trainable | logistic_observed_hic_reabc_c00003 | 0.1638 | 0.6557 | 0.5842 | 0.7263 | 0.8229 |
+| top100 | strict_all | trainable | logistic_re2g_extended_features_c0003 | 0.1638 | 0.6517 | 0.5684 | 0.7205 | 0.8234 |
+| top100 | strict_all | trainable | logistic_re2g_extended_highconf_c0003 | 0.1638 | 0.6426 | 0.5640 | 0.7150 | 0.8106 |
+| top100 | strict_all | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1638 | 0.6411 | 0.5605 | 0.7133 | 0.8138 |
+| top100 | strict_all | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1638 | 0.6058 | 0.5235 | 0.6625 | 0.7839 |
+| top100 | strict_all | trainable | logistic_distance_abc | 0.1638 | 0.5931 | 0.5015 | 0.6601 | 0.7979 |
+| top100 | very_high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.2296 | 0.9742 | 0.9361 | 0.9935 | 0.9890 |
+| top100 | very_high_confidence | trainable | ensemble_proxy_residual_v1 | 0.2296 | 0.9724 | 0.9351 | 0.9942 | 0.9876 |
+| top100 | very_high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.2296 | 0.9648 | 0.9169 | 0.9896 | 0.9821 |
+| top100 | very_high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.2296 | 0.9607 | 0.8942 | 0.9893 | 0.9803 |
+| top100 | very_high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.2296 | 0.9550 | 0.8900 | 0.9844 | 0.9756 |
+| top100 | very_high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.2296 | 0.9539 | 0.8905 | 0.9828 | 0.9782 |
+| top100 | very_high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.2296 | 0.9204 | 0.7996 | 0.9482 | 0.9436 |
+| top100 | very_high_confidence | trainable | logistic_distance_abc | 0.2296 | 0.8917 | 0.8356 | 0.9682 | 0.9701 |
+| top250 | field_compatible_e2g | trainable | ensemble_proxy_residual_v1 | 0.1818 | 0.9457 | 0.9100 | 0.9666 | 0.9791 |
+| top250 | field_compatible_e2g | trainable | residual_deepset_calibrated_gate_v1 | 0.1818 | 0.9440 | 0.9070 | 0.9646 | 0.9779 |
+| top250 | field_compatible_e2g | trainable | logistic_observed_hic_reabc_c00003 | 0.1818 | 0.9404 | 0.9089 | 0.9654 | 0.9778 |
+| top250 | field_compatible_e2g | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1818 | 0.9361 | 0.9009 | 0.9594 | 0.9763 |
+| top250 | field_compatible_e2g | trainable | logistic_re2g_extended_features_c0003 | 0.1818 | 0.9357 | 0.8970 | 0.9580 | 0.9765 |
+| top250 | field_compatible_e2g | trainable | logistic_re2g_extended_highconf_c0003 | 0.1818 | 0.9344 | 0.8936 | 0.9604 | 0.9765 |
+| top250 | field_compatible_e2g | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1818 | 0.8724 | 0.8295 | 0.9083 | 0.9405 |
+| top250 | field_compatible_e2g | trainable | logistic_distance_abc | 0.1818 | 0.8661 | 0.8012 | 0.9146 | 0.9567 |
+| top250 | high_confidence | trainable | ensemble_proxy_residual_v1 | 0.1856 | 0.9276 | 0.8896 | 0.9518 | 0.9688 |
+| top250 | high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.1856 | 0.9261 | 0.8894 | 0.9492 | 0.9690 |
+| top250 | high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1856 | 0.9211 | 0.8822 | 0.9473 | 0.9671 |
+| top250 | high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.1856 | 0.9191 | 0.8822 | 0.9473 | 0.9639 |
+| top250 | high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.1856 | 0.9099 | 0.8668 | 0.9404 | 0.9636 |
+| top250 | high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.1856 | 0.9097 | 0.8667 | 0.9374 | 0.9613 |
+| top250 | high_confidence | trainable | logistic_distance_abc | 0.1856 | 0.8607 | 0.8004 | 0.9045 | 0.9513 |
+| top250 | high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1856 | 0.8443 | 0.7953 | 0.8816 | 0.9156 |
+| top250 | strict_all | trainable | residual_deepset_calibrated_gate_v1 | 0.1401 | 0.7370 | 0.6836 | 0.7807 | 0.8859 |
+| top250 | strict_all | trainable | ensemble_proxy_residual_v1 | 0.1401 | 0.7348 | 0.6833 | 0.7765 | 0.8793 |
+| top250 | strict_all | trainable | logistic_observed_hic_reabc_c00003 | 0.1401 | 0.7294 | 0.6779 | 0.7743 | 0.8676 |
+| top250 | strict_all | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1401 | 0.7154 | 0.6603 | 0.7610 | 0.8662 |
+| top250 | strict_all | trainable | logistic_re2g_extended_features_c0003 | 0.1401 | 0.7147 | 0.6558 | 0.7576 | 0.8668 |
+| top250 | strict_all | trainable | logistic_re2g_extended_highconf_c0003 | 0.1401 | 0.7033 | 0.6495 | 0.7493 | 0.8629 |
+| top250 | strict_all | trainable | logistic_distance_abc | 0.1401 | 0.6626 | 0.6043 | 0.7123 | 0.8524 |
+| top250 | strict_all | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1401 | 0.6438 | 0.5857 | 0.6868 | 0.8155 |
+| top250 | very_high_confidence | trainable | ensemble_proxy_residual_v1 | 0.2010 | 0.9501 | 0.9044 | 0.9701 | 0.9761 |
+| top250 | very_high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.2010 | 0.9498 | 0.9043 | 0.9676 | 0.9775 |
+| top250 | very_high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.2010 | 0.9463 | 0.9102 | 0.9719 | 0.9763 |
+| top250 | very_high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.2010 | 0.9320 | 0.8886 | 0.9597 | 0.9646 |
+| top250 | very_high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.2010 | 0.9266 | 0.8732 | 0.9542 | 0.9704 |
+| top250 | very_high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.2010 | 0.9211 | 0.8696 | 0.9499 | 0.9617 |
+| top250 | very_high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.2010 | 0.8881 | 0.8131 | 0.9181 | 0.9222 |
+| top250 | very_high_confidence | trainable | logistic_distance_abc | 0.2010 | 0.8842 | 0.8119 | 0.9377 | 0.9629 |
+| top50 | field_compatible_e2g | trainable | residual_deepset_calibrated_gate_v1 | 0.1947 | 0.8713 | 0.7627 | 0.9296 | 0.9160 |
+| top50 | field_compatible_e2g | trainable | ensemble_proxy_residual_v1 | 0.1947 | 0.8693 | 0.7446 | 0.9250 | 0.9145 |
+| top50 | field_compatible_e2g | trainable | logistic_observed_hic_reabc_c00003 | 0.1947 | 0.8636 | 0.7400 | 0.9193 | 0.9240 |
+| top50 | field_compatible_e2g | trainable | logistic_re2g_extended_features_c0003 | 0.1947 | 0.8568 | 0.7464 | 0.9183 | 0.9228 |
+| top50 | field_compatible_e2g | trainable | logistic_re2g_extended_highconf_c0003 | 0.1947 | 0.8530 | 0.7139 | 0.9177 | 0.9175 |
+| top50 | field_compatible_e2g | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1947 | 0.8431 | 0.6878 | 0.9081 | 0.9107 |
+| top50 | field_compatible_e2g | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1947 | 0.8208 | 0.6860 | 0.8988 | 0.8853 |
+| top50 | field_compatible_e2g | trainable | logistic_distance_abc | 0.1947 | 0.8027 | 0.6018 | 0.8877 | 0.9025 |
+| top50 | high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.1920 | 0.8708 | 0.7626 | 0.9295 | 0.9165 |
+| top50 | high_confidence | trainable | ensemble_proxy_residual_v1 | 0.1920 | 0.8673 | 0.7435 | 0.9246 | 0.9135 |
+| top50 | high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.1920 | 0.8636 | 0.7400 | 0.9193 | 0.9259 |
+| top50 | high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.1920 | 0.8565 | 0.7462 | 0.9182 | 0.9237 |
+| top50 | high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.1920 | 0.8517 | 0.7133 | 0.9172 | 0.9165 |
+| top50 | high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1920 | 0.8405 | 0.6876 | 0.9078 | 0.9089 |
+| top50 | high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1920 | 0.8201 | 0.6859 | 0.8987 | 0.8857 |
+| top50 | high_confidence | trainable | logistic_distance_abc | 0.1920 | 0.8025 | 0.6017 | 0.8876 | 0.9036 |
+| top50 | strict_all | trainable | residual_deepset_calibrated_gate_v1 | 0.1791 | 0.6591 | 0.5401 | 0.7356 | 0.8166 |
+| top50 | strict_all | trainable | logistic_observed_hic_reabc_c00003 | 0.1791 | 0.6523 | 0.5433 | 0.7340 | 0.8174 |
+| top50 | strict_all | trainable | logistic_re2g_extended_features_c0003 | 0.1791 | 0.6501 | 0.5142 | 0.7235 | 0.8134 |
+| top50 | strict_all | trainable | ensemble_proxy_residual_v1 | 0.1791 | 0.6469 | 0.5284 | 0.7277 | 0.8116 |
+| top50 | strict_all | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1791 | 0.6457 | 0.5289 | 0.6937 | 0.8091 |
+| top50 | strict_all | trainable | logistic_distance_abc | 0.1791 | 0.6383 | 0.5127 | 0.7022 | 0.8124 |
+| top50 | strict_all | trainable | logistic_re2g_extended_highconf_c0003 | 0.1791 | 0.6329 | 0.4942 | 0.7138 | 0.7862 |
+| top50 | strict_all | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1791 | 0.5973 | 0.4745 | 0.6884 | 0.7802 |
+| top50 | very_high_confidence | trainable | residual_deepset_calibrated_gate_v1 | 0.1804 | 0.9868 | 0.9266 | 1.0000 | 0.9878 |
+| top50 | very_high_confidence | trainable | ensemble_proxy_residual_v1 | 0.1804 | 0.9848 | 0.9183 | 1.0000 | 0.9837 |
+| top50 | very_high_confidence | trainable | logistic_re2g_extended_features_c0003 | 0.1804 | 0.9774 | 0.9046 | 1.0000 | 0.9840 |
+| top50 | very_high_confidence | trainable | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | 0.1804 | 0.9718 | 0.8694 | 1.0000 | 0.9714 |
+| top50 | very_high_confidence | trainable | logistic_observed_hic_reabc_c00003 | 0.1804 | 0.9714 | 0.8712 | 1.0000 | 0.9788 |
+| top50 | very_high_confidence | no_training_oracle | mask_abs_delta_atac_target_promoter_sum | 0.1804 | 0.9647 | 0.8301 | 0.9958 | 0.9735 |
+| top50 | very_high_confidence | trainable | logistic_re2g_extended_highconf_c0003 | 0.1804 | 0.9639 | 0.8531 | 0.9981 | 0.9726 |
+| top50 | very_high_confidence | trainable | logistic_distance_abc | 0.1804 | 0.9589 | 0.7980 | 0.9813 | 0.9686 |
+## Paired oracle - best-trainable AUPRC difference (region bootstrap, identical rows)
+| scoreboard | n_pairs | n_regions | n_positive | auprc_a | auprc_b | diff | diff_mean | ci_low | ci_high | p_value | panel | oracle_feature | best_trainable |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| strict_all | 669 | 50 | 111 | 0.6113 | 0.6341 | -0.0228 | -0.0243 | -0.1010 | 0.0493 | 0.5500 | top50 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| high_confidence | 271 | 50 | 47 | 0.8010 | 0.8555 | -0.0544 | -0.0553 | -0.1385 | 0.0116 | 0.1400 | top50 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| field_compatible_e2g | 267 | 50 | 47 | 0.8014 | 0.8557 | -0.0543 | -0.0552 | -0.1385 | 0.0117 | 0.1480 | top50 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| very_high_confidence | 127 | 44 | 19 | 0.9298 | 0.9796 | -0.0498 | -0.0482 | -0.1193 | -0.0038 | 0.0420 | top50 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| strict_all | 1063 | 100 | 164 | 0.5930 | 0.6675 | -0.0745 | -0.0760 | -0.1319 | -0.0213 | 0.0020 | top100 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| high_confidence | 449 | 98 | 74 | 0.8098 | 0.8862 | -0.0764 | -0.0769 | -0.1386 | -0.0236 | 0.0060 | top100 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| field_compatible_e2g | 435 | 97 | 71 | 0.8287 | 0.8928 | -0.0640 | -0.0643 | -0.1224 | -0.0122 | 0.0160 | top100 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| very_high_confidence | 234 | 90 | 46 | 0.8842 | 0.9711 | -0.0870 | -0.0871 | -0.1575 | -0.0328 | 0.0000 | top100 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| strict_all | 2302 | 250 | 314 | 0.6368 | 0.7334 | -0.0966 | -0.0965 | -0.1367 | -0.0535 | 0.0000 | top250 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| high_confidence | 1070 | 246 | 187 | 0.8412 | 0.9205 | -0.0792 | -0.0791 | -0.1171 | -0.0438 | 0.0000 | top250 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| field_compatible_e2g | 1013 | 238 | 173 | 0.8704 | 0.9374 | -0.0670 | -0.0672 | -0.1025 | -0.0341 | 0.0000 | top250 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| very_high_confidence | 530 | 202 | 100 | 0.8674 | 0.9382 | -0.0707 | -0.0705 | -0.1150 | -0.0329 | 0.0000 | top250 | mask_abs_delta_atac_target_promoter_sum | residual_gate |
+| strict_all | 5904 | 600 | 664 | 0.5885 | 0.6958 | -0.1072 | -0.1078 | -0.1392 | -0.0760 | 0.0000 | all_positive | mask_abs_delta_atac_target_promoter_sum | observed_hic_reabc |
+| high_confidence | 2753 | 570 | 308 | 0.8014 | 0.9044 | -0.1030 | -0.1027 | -0.1346 | -0.0729 | 0.0000 | all_positive | mask_abs_delta_atac_target_promoter_sum | observed_hic_reabc |
+| field_compatible_e2g | 2572 | 547 | 291 | 0.8235 | 0.9229 | -0.0994 | -0.0992 | -0.1299 | -0.0666 | 0.0000 | all_positive | mask_abs_delta_atac_target_promoter_sum | observed_hic_reabc |
+| very_high_confidence | 1293 | 465 | 100 | 0.8186 | 0.8858 | -0.0672 | -0.0671 | -0.1151 | -0.0230 | 0.0000 | all_positive | mask_abs_delta_atac_target_promoter_sum | observed_hic_reabc |

results/paper/paper_matched_panel_paired_diff.csv ADDED Viewed

	@@ -0,0 +1,17 @@

+scoreboard,n_pairs,n_regions,n_positive,auprc_a,auprc_b,diff,diff_mean,ci_low,ci_high,p_value,panel,oracle_feature,best_trainable
+strict_all,669,50,111,0.6113252082150445,0.6341481343732525,-0.022822926158207912,-0.02426601709571738,-0.10095789449466176,0.04932632439380514,0.55,top50,mask_abs_delta_atac_target_promoter_sum,residual_gate
+high_confidence,271,50,47,0.8010372600819017,0.8554604404859615,-0.0544231804040598,-0.055339407185123875,-0.1385204220116727,0.011638794516127413,0.14,top50,mask_abs_delta_atac_target_promoter_sum,residual_gate
+field_compatible_e2g,267,50,47,0.8014144828740529,0.8556809338846298,-0.05426645101057692,-0.05520755700553433,-0.13851077648179264,0.011740232251673364,0.148,top50,mask_abs_delta_atac_target_promoter_sum,residual_gate
+very_high_confidence,127,44,19,0.9298221217539536,0.9796264855687606,-0.04980436381480702,-0.048229817449301916,-0.11925328274759477,-0.0037662812333865148,0.042,top50,mask_abs_delta_atac_target_promoter_sum,residual_gate
+strict_all,1063,100,164,0.5930196768479018,0.6675101955554663,-0.07449051870756451,-0.07598462729734698,-0.13191480725186977,-0.02128894664736452,0.002,top100,mask_abs_delta_atac_target_promoter_sum,residual_gate
+high_confidence,449,98,74,0.809758971378422,0.8861500504127767,-0.07639107903435471,-0.07692317743596593,-0.13859077738273856,-0.023555889432349045,0.006,top100,mask_abs_delta_atac_target_promoter_sum,residual_gate
+field_compatible_e2g,435,97,71,0.8287453727892259,0.8927754243723035,-0.06403005158307762,-0.06428385063992169,-0.12236730893895048,-0.012170988356417936,0.016,top100,mask_abs_delta_atac_target_promoter_sum,residual_gate
+very_high_confidence,234,90,46,0.8841845986363874,0.971143561939826,-0.08695896330343855,-0.08707501287611621,-0.1575383340414159,-0.03279020400795553,0.0,top100,mask_abs_delta_atac_target_promoter_sum,residual_gate
+strict_all,2302,250,314,0.6368191161663307,0.7333945206558636,-0.09657540448953295,-0.09653455082777411,-0.13670144489515387,-0.05346607807694203,0.0,top250,mask_abs_delta_atac_target_promoter_sum,residual_gate
+high_confidence,1070,246,187,0.8412454934994064,0.9204585402616607,-0.07921304676225438,-0.07908655618534434,-0.11706454058613341,-0.04382766649382111,0.0,top250,mask_abs_delta_atac_target_promoter_sum,residual_gate
+field_compatible_e2g,1013,238,173,0.8704229890276831,0.9373860097875479,-0.06696302075986482,-0.06724113727158627,-0.1025394054485137,-0.03410293645754148,0.0,top250,mask_abs_delta_atac_target_promoter_sum,residual_gate
+very_high_confidence,530,202,100,0.8674273097482873,0.9381518756205584,-0.07072456587227105,-0.07046313995213078,-0.11498114863534459,-0.03293077892565603,0.0,top250,mask_abs_delta_atac_target_promoter_sum,residual_gate
+strict_all,5904,600,664,0.5885357812553353,0.6957774430989128,-0.10724166184357742,-0.10781956355436191,-0.13918446254857678,-0.0759694338843043,0.0,all_positive,mask_abs_delta_atac_target_promoter_sum,observed_hic_reabc
+high_confidence,2753,570,308,0.8014010451936466,0.9043991047021523,-0.10299805950850571,-0.10265400589387705,-0.13462698863552788,-0.07288447971342318,0.0,all_positive,mask_abs_delta_atac_target_promoter_sum,observed_hic_reabc
+field_compatible_e2g,2572,547,291,0.8234656171861537,0.9229028741297031,-0.09943725694354932,-0.09924636815353412,-0.1299266086839591,-0.06662316434432485,0.0,all_positive,mask_abs_delta_atac_target_promoter_sum,observed_hic_reabc
+very_high_confidence,1293,465,100,0.8186234252586512,0.8858484687873412,-0.06722504352869008,-0.06714334150927968,-0.115133223582139,-0.022996311589286042,0.0,all_positive,mask_abs_delta_atac_target_promoter_sum,observed_hic_reabc

results/paper/paper_oracle_bootstrap_ci.csv ADDED Viewed

	@@ -0,0 +1,29 @@

+model_name,feature_name,scoreboard,n_regions,n_pairs,n_positive,observed_auprc,bootstrap_mean_auprc,ci_low,ci_high,n_iterations
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,strict_all,250,2302,314,0.6368191161663307,0.6381527199334494,0.5916561300599578,0.6878303158775881,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,strict_all,250,2302,314,0.6368191161663307,0.6381527199334494,0.5916561300599578,0.6878303158775881,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,high_confidence,246,1070,187,0.8412454934994064,0.8412865651725324,0.7997195512510122,0.8778344100716805,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,high_confidence,246,1070,187,0.8412454934994064,0.8412865651725324,0.7997195512510122,0.8778344100716805,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,field_compatible_e2g,238,1013,173,0.8704229890276831,0.8700471663301373,0.8281220972867944,0.9103785477422854,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,field_compatible_e2g,238,1013,173,0.8704229890276831,0.8700471663301373,0.8281220972867944,0.9103785477422854,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,very_high_confidence,202,530,100,0.8674273097482873,0.8674487195995607,0.8170730204616092,0.915278679215409,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,very_high_confidence,202,530,100,0.8674273097482873,0.8674487195995607,0.8170730204616092,0.915278679215409,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,re2g_covered_strict,243,2149,289,0.6708511118263218,0.6720615459504836,0.6203097943726611,0.7203358941708583,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,re2g_covered_strict,243,2149,289,0.6708511118263218,0.6720615459504836,0.6203097943726611,0.7203358941708583,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,re2g_covered_high_confidence,238,1013,173,0.8704229890276831,0.8700471663301373,0.8281220972867944,0.9103785477422854,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,re2g_covered_high_confidence,238,1013,173,0.8704229890276831,0.8700471663301373,0.8281220972867944,0.9103785477422854,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_sum,re2g_covered_very_high_confidence,191,493,88,0.9169638689967248,0.9169331316403868,0.8769607220408663,0.954359325342468,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_top250__mask_abs_delta_atac_target_promoter_mean,re2g_covered_very_high_confidence,191,493,88,0.9169638689967248,0.9169331316403868,0.8769607220408663,0.954359325342468,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,strict_all,600,5904,664,0.5885357812553353,0.5883805558377116,0.5533808406960107,0.6235176099600921,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,strict_all,600,5904,664,0.5885357812553353,0.5883805558377116,0.5533808406960107,0.6235176099600921,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,high_confidence,570,2753,308,0.8014010451936466,0.8016266594602566,0.7628939287138962,0.8364749838692832,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,high_confidence,570,2753,308,0.8014010451936466,0.8016266594602566,0.7628939287138962,0.8364749838692832,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,field_compatible_e2g,547,2572,291,0.8234656171861537,0.8245388919123975,0.7850229718325503,0.8599206438948719,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,field_compatible_e2g,547,2572,291,0.8234656171861537,0.8245388919123975,0.7850229718325503,0.8599206438948719,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,very_high_confidence,465,1293,100,0.8186234252586512,0.8197121812880233,0.7555370367119852,0.8740948820135902,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,very_high_confidence,465,1293,100,0.8186234252586512,0.8197121812880233,0.7555370367119852,0.8740948820135902,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,re2g_covered_strict,578,5387,621,0.6094225974398703,0.609231782388191,0.5706806205580913,0.6413178270155414,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,re2g_covered_strict,578,5387,621,0.6094225974398703,0.609231782388191,0.5706806205580913,0.6413178270155414,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,re2g_covered_high_confidence,547,2572,291,0.8234656171861537,0.8245388919123975,0.7850229718325503,0.8599206438948719,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,re2g_covered_high_confidence,547,2572,291,0.8234656171861537,0.8245388919123975,0.7850229718325503,0.8599206438948719,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_sum,re2g_covered_very_high_confidence,436,1194,88,0.878391754712617,0.8797089580624825,0.8264682628212018,0.925234873994,500
+sequence_to_function_oracle__alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,alphagenome_k562_counterfactual_mask_region_complete_all_positive__mask_abs_delta_atac_target_promoter_mean,re2g_covered_very_high_confidence,436,1194,88,0.878391754712617,0.8797089580624825,0.8264682628212018,0.925234873994,500

results/paper/paper_reporting_inputs_included.csv ADDED Viewed

	@@ -0,0 +1,14 @@

+source_name,path,n_rows
+distance_abc,results/s2t/gasperini_gse120861/learned_logistic_distance_abc_predictions_labeled.parquet,403220
+re2g_extended_features,results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_features_c0003_predictions_labeled.parquet,403220
+observed_hic_reabc,results/s2t/gasperini_gse120861/learned_logistic_observed_hic_reabc_c00003_predictions_labeled.parquet,403220
+residual_gate,results/s2t/gasperini_gse120861/learned_residual_deepset_calibrated_gate_v1_predictions_labeled.parquet,403220
+field_leader,results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_highconf_c0003_predictions_labeled.parquet,403220
+proxy_v1,results/s2t/gasperini_gse120861/learned_logistic_counterfactual_proxy_highconf_c0003_predictions_labeled.parquet,403220
+proxy_v2,results/s2t/gasperini_gse120861/learned_logistic_counterfactual_proxy_v2_highconf_c0003_predictions_labeled.parquet,403220
+proxy_v2_rich,results/s2t/gasperini_gse120861/learned_logistic_counterfactual_proxy_v2_rich_highconf_c0003_predictions_labeled.parquet,403220
+proxy_v2_rich_without_contact,results/s2t/gasperini_gse120861/learned_s2t_proxy_v2_without_contact_logistic_predictions_labeled.parquet,403220
+proxy_v2_rich_without_contact_field_tuned,results/s2t/gasperini_gse120861/learned_proxy_v2_rich_without_contact_high_confidence_c0p01_predictions_labeled.parquet,403220
+residual_proxy_v2_rich,results/s2t/gasperini_gse120861/learned_molecular_residual_proxy_v2_rich_highconf_c003_predictions_labeled.parquet,403220
+residual_proxy_v2_rich_strict,results/s2t/gasperini_gse120861/learned_molecular_residual_proxy_v2_rich_strict_broad_c001_predictions_labeled.parquet,403220
+ensemble_proxy_residual_v1,results/s2t/gasperini_gse120861/ensemble_proxy_residual_v1_predictions_labeled.parquet,403220

results/paper/paper_reporting_inputs_skipped.csv ADDED Viewed

	@@ -0,0 +1 @@


1	+

results/paper/paper_reporting_summary.md ADDED Viewed

	@@ -0,0 +1,135 @@

+# Paper Reporting Summary
+This directory is the paper-facing result snapshot generated from existing Seq2State artifacts.
+## Headline Comparison
+Only full-benchmark trainable rows are included here, so AUPRCs are directly comparable within each scoreboard.
+| result_type | comparison_scope | source_name | model_or_feature | scoreboard | evaluation_universe | auprc | ci_low | ci_high | auroc | mrr | recall_at_1 | terms_ok_for_training |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | field_compatible_e2g | full_benchmark_138k | 0.6515 | 0.5661 | 0.6866 | 0.9790 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | field_compatible_e2g | full_benchmark_138k | 0.6440 | 0.5547 | 0.6778 | 0.9750 | 0.0613 | 0.0606 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | field_compatible_e2g | full_benchmark_138k | 0.6379 | 0.5414 | 0.6664 | 0.9741 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | field_compatible_e2g | full_benchmark_138k | 0.6349 | 0.5590 | 0.6736 | 0.9768 | 0.0613 | 0.0605 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.6286 | 0.5341 | 0.6553 | 0.9747 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | field_compatible_e2g | full_benchmark_138k | 0.6250 | 0.5470 | 0.6608 | 0.9761 | 0.0611 | 0.0603 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | field_compatible_e2g | full_benchmark_138k | 0.6163 | 0.5266 | 0.6481 | 0.9747 | 0.0611 | 0.0603 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.6125 | 0.5291 | 0.6570 | 0.9743 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | field_compatible_e2g | full_benchmark_138k | 0.6084 | 0.5184 | 0.6431 | 0.9761 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | field_compatible_e2g | full_benchmark_138k | 0.5951 | 0.5036 | 0.6294 | 0.9768 | 0.0613 | 0.0605 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.5730 | 0.4814 | 0.6018 | 0.9715 | 0.0609 | 0.0598 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.4898 | 0.4202 | 0.5399 | 0.9636 | 0.0604 | 0.0592 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | field_compatible_e2g | full_benchmark_138k | 0.3860 | 0.3147 | 0.4282 | 0.9501 | 0.0598 | 0.0578 | True |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | high_confidence | full_benchmark_138k | 0.6286 | 0.5443 | 0.6640 | 0.9742 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | high_confidence | full_benchmark_138k | 0.6215 | 0.5333 | 0.6598 | 0.9705 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | high_confidence | full_benchmark_138k | 0.6163 | 0.5211 | 0.6444 | 0.9702 | 0.0591 | 0.0579 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | high_confidence | full_benchmark_138k | 0.6121 | 0.5295 | 0.6500 | 0.9725 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | high_confidence | full_benchmark_138k | 0.6042 | 0.5052 | 0.6352 | 0.9694 | 0.0591 | 0.0577 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | high_confidence | full_benchmark_138k | 0.6022 | 0.5200 | 0.6393 | 0.9713 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | high_confidence | full_benchmark_138k | 0.5936 | 0.5131 | 0.6351 | 0.9704 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | high_confidence | full_benchmark_138k | 0.5931 | 0.5050 | 0.6267 | 0.9701 | 0.0591 | 0.0581 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | high_confidence | full_benchmark_138k | 0.5846 | 0.4925 | 0.6212 | 0.9699 | 0.0591 | 0.0579 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | high_confidence | full_benchmark_138k | 0.5750 | 0.4818 | 0.6083 | 0.9712 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | high_confidence | full_benchmark_138k | 0.5552 | 0.4622 | 0.5897 | 0.9686 | 0.0589 | 0.0575 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | high_confidence | full_benchmark_138k | 0.4762 | 0.4075 | 0.5253 | 0.9622 | 0.0587 | 0.0573 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | high_confidence | full_benchmark_138k | 0.3672 | 0.3054 | 0.4129 | 0.9465 | 0.0580 | 0.0559 | True |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | strict_all | full_benchmark_138k | 0.2965 | 0.2543 | 0.3232 | 0.8816 | 0.0886 | 0.0806 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | strict_all | full_benchmark_138k | 0.2900 | 0.2416 | 0.3172 | 0.8831 | 0.0886 | 0.0805 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | strict_all | full_benchmark_138k | 0.2879 | 0.2426 | 0.3165 | 0.8790 | 0.0886 | 0.0809 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | strict_all | full_benchmark_138k | 0.2849 | 0.2430 | 0.3101 | 0.8817 | 0.0887 | 0.0803 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | strict_all | full_benchmark_138k | 0.2817 | 0.2366 | 0.3088 | 0.8660 | 0.0879 | 0.0799 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | strict_all | full_benchmark_138k | 0.2784 | 0.2366 | 0.3047 | 0.8776 | 0.0884 | 0.0804 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | strict_all | full_benchmark_138k | 0.2784 | 0.2338 | 0.3000 | 0.8830 | 0.0885 | 0.0806 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | strict_all | full_benchmark_138k | 0.2734 | 0.2339 | 0.3019 | 0.8649 | 0.0869 | 0.0783 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | strict_all | full_benchmark_138k | 0.2730 | 0.2306 | 0.2975 | 0.8672 | 0.0878 | 0.0799 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | strict_all | full_benchmark_138k | 0.2601 | 0.2180 | 0.2824 | 0.8647 | 0.0884 | 0.0808 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | strict_all | full_benchmark_138k | 0.2594 | 0.2248 | 0.2909 | 0.8682 | 0.0873 | 0.0790 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | strict_all | full_benchmark_138k | 0.2256 | 0.1924 | 0.2521 | 0.8601 | 0.0875 | 0.0796 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | strict_all | full_benchmark_138k | 0.1842 | 0.1527 | 0.2024 | 0.8511 | 0.0866 | 0.0781 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | very_high_confidence | full_benchmark_138k | 0.7136 | 0.5814 | 0.7727 | 0.9842 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | very_high_confidence | full_benchmark_138k | 0.7117 | 0.5867 | 0.7695 | 0.9803 | 0.0255 | 0.0249 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.6984 | 0.5645 | 0.7625 | 0.9831 | 0.0258 | 0.0255 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | very_high_confidence | full_benchmark_138k | 0.6924 | 0.5508 | 0.7464 | 0.9844 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | very_high_confidence | full_benchmark_138k | 0.6751 | 0.5392 | 0.7317 | 0.9804 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | very_high_confidence | full_benchmark_138k | 0.6741 | 0.5416 | 0.7376 | 0.9773 | 0.0255 | 0.0249 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.6708 | 0.5406 | 0.7307 | 0.9816 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | very_high_confidence | full_benchmark_138k | 0.6614 | 0.5348 | 0.7251 | 0.9776 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | very_high_confidence | full_benchmark_138k | 0.6440 | 0.5037 | 0.7074 | 0.9724 | 0.0255 | 0.0249 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | very_high_confidence | full_benchmark_138k | 0.6179 | 0.5028 | 0.7055 | 0.9727 | 0.0254 | 0.0249 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.6096 | 0.4687 | 0.6710 | 0.9816 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.5192 | 0.3782 | 0.5887 | 0.9774 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | very_high_confidence | full_benchmark_138k | 0.3723 | 0.2717 | 0.4553 | 0.9607 | 0.0252 | 0.0246 | True |
+## Unmatched Oracle-Panel Context
+> WARNING: The table below intentionally mixes evaluation universes for context.
+> Trainable rows are scored on the full 138k-pair benchmark (low prevalence) while
+> oracle rows are scored on positive-region panels (high prevalence), so AUPRCs
+> must not be interpreted as a leaderboard. For the prevalence-matched,
+> apples-to-apples comparison see `paper_matched_panel_comparison.csv` / `.md`
+> and `paper_matched_panel_paired_diff.csv` produced by
+> `scripts/build_matched_panel_comparison.py`.
+| result_type | comparison_scope | source_name | model_or_feature | scoreboard | evaluation_universe | auprc | ci_low | ci_high | auroc | mrr | recall_at_1 | terms_ok_for_training |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| no_training_oracle_all_positive | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | field_compatible_e2g | oracle_panel_all_positive | 0.8282 | 0.7850 | 0.8599 | 0.9358 | 0.4789 | 0.4608 | False |
+| no_training_oracle_top250 | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | field_compatible_e2g | oracle_panel_top250 | 0.8724 | 0.8281 | 0.9104 | 0.9405 | 0.6440 | 0.6198 | False |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | field_compatible_e2g | full_benchmark_138k | 0.6515 | 0.5661 | 0.6866 | 0.9790 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | field_compatible_e2g | full_benchmark_138k | 0.6440 | 0.5547 | 0.6778 | 0.9750 | 0.0613 | 0.0606 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | field_compatible_e2g | full_benchmark_138k | 0.6379 | 0.5414 | 0.6664 | 0.9741 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | field_compatible_e2g | full_benchmark_138k | 0.6349 | 0.5590 | 0.6736 | 0.9768 | 0.0613 | 0.0605 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.6286 | 0.5341 | 0.6553 | 0.9747 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | field_compatible_e2g | full_benchmark_138k | 0.6250 | 0.5470 | 0.6608 | 0.9761 | 0.0611 | 0.0603 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | field_compatible_e2g | full_benchmark_138k | 0.6163 | 0.5266 | 0.6481 | 0.9747 | 0.0611 | 0.0603 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.6125 | 0.5291 | 0.6570 | 0.9743 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | field_compatible_e2g | full_benchmark_138k | 0.6084 | 0.5184 | 0.6431 | 0.9761 | 0.0612 | 0.0603 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | field_compatible_e2g | full_benchmark_138k | 0.5951 | 0.5036 | 0.6294 | 0.9768 | 0.0613 | 0.0605 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.5730 | 0.4814 | 0.6018 | 0.9715 | 0.0609 | 0.0598 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | field_compatible_e2g | full_benchmark_138k | 0.4898 | 0.4202 | 0.5399 | 0.9636 | 0.0604 | 0.0592 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | field_compatible_e2g | full_benchmark_138k | 0.3860 | 0.3147 | 0.4282 | 0.9501 | 0.0598 | 0.0578 | True |
+| no_training_oracle_all_positive | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | high_confidence | oracle_panel_all_positive | 0.8064 | 0.7629 | 0.8365 | 0.9201 | 0.4821 | 0.4602 | False |
+| no_training_oracle_top250 | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | high_confidence | oracle_panel_top250 | 0.8443 | 0.7997 | 0.8778 | 0.9156 | 0.6654 | 0.6322 | False |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | high_confidence | full_benchmark_138k | 0.6286 | 0.5443 | 0.6640 | 0.9742 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | high_confidence | full_benchmark_138k | 0.6215 | 0.5333 | 0.6598 | 0.9705 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | high_confidence | full_benchmark_138k | 0.6163 | 0.5211 | 0.6444 | 0.9702 | 0.0591 | 0.0579 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | high_confidence | full_benchmark_138k | 0.6121 | 0.5295 | 0.6500 | 0.9725 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | high_confidence | full_benchmark_138k | 0.6042 | 0.5052 | 0.6352 | 0.9694 | 0.0591 | 0.0577 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | high_confidence | full_benchmark_138k | 0.6022 | 0.5200 | 0.6393 | 0.9713 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | high_confidence | full_benchmark_138k | 0.5936 | 0.5131 | 0.6351 | 0.9704 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | high_confidence | full_benchmark_138k | 0.5931 | 0.5050 | 0.6267 | 0.9701 | 0.0591 | 0.0581 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | high_confidence | full_benchmark_138k | 0.5846 | 0.4925 | 0.6212 | 0.9699 | 0.0591 | 0.0579 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | high_confidence | full_benchmark_138k | 0.5750 | 0.4818 | 0.6083 | 0.9712 | 0.0592 | 0.0581 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | high_confidence | full_benchmark_138k | 0.5552 | 0.4622 | 0.5897 | 0.9686 | 0.0589 | 0.0575 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | high_confidence | full_benchmark_138k | 0.4762 | 0.4075 | 0.5253 | 0.9622 | 0.0587 | 0.0573 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | high_confidence | full_benchmark_138k | 0.3672 | 0.3054 | 0.4129 | 0.9465 | 0.0580 | 0.0559 | True |
+| no_training_oracle_all_positive | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | strict_all | oracle_panel_all_positive | 0.5952 | 0.5534 | 0.6235 | 0.8268 | 0.7764 | 0.6852 | False |
+| no_training_oracle_top250 | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | strict_all | oracle_panel_top250 | 0.6438 | 0.5917 | 0.6878 | 0.8155 | 0.8155 | 0.7366 | False |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | strict_all | full_benchmark_138k | 0.2965 | 0.2543 | 0.3232 | 0.8816 | 0.0886 | 0.0806 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | strict_all | full_benchmark_138k | 0.2900 | 0.2416 | 0.3172 | 0.8831 | 0.0886 | 0.0805 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | strict_all | full_benchmark_138k | 0.2879 | 0.2426 | 0.3165 | 0.8790 | 0.0886 | 0.0809 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | strict_all | full_benchmark_138k | 0.2849 | 0.2430 | 0.3101 | 0.8817 | 0.0887 | 0.0803 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | strict_all | full_benchmark_138k | 0.2817 | 0.2366 | 0.3088 | 0.8660 | 0.0879 | 0.0799 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | strict_all | full_benchmark_138k | 0.2784 | 0.2366 | 0.3047 | 0.8776 | 0.0884 | 0.0804 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | strict_all | full_benchmark_138k | 0.2784 | 0.2338 | 0.3000 | 0.8830 | 0.0885 | 0.0806 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | strict_all | full_benchmark_138k | 0.2734 | 0.2339 | 0.3019 | 0.8649 | 0.0869 | 0.0783 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | strict_all | full_benchmark_138k | 0.2730 | 0.2306 | 0.2975 | 0.8672 | 0.0878 | 0.0799 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | strict_all | full_benchmark_138k | 0.2601 | 0.2180 | 0.2824 | 0.8647 | 0.0884 | 0.0808 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | strict_all | full_benchmark_138k | 0.2594 | 0.2248 | 0.2909 | 0.8682 | 0.0873 | 0.0790 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | strict_all | full_benchmark_138k | 0.2256 | 0.1924 | 0.2521 | 0.8601 | 0.0875 | 0.0796 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | strict_all | full_benchmark_138k | 0.1842 | 0.1527 | 0.2024 | 0.8511 | 0.0866 | 0.0781 | True |
+| no_training_oracle_all_positive | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | very_high_confidence | oracle_panel_all_positive | 0.8396 | 0.7555 | 0.8741 | 0.9296 | 0.2016 | 0.1947 | False |
+| no_training_oracle_top250 | context_only_unmatched_oracle_panel | alphagenome_counterfactual | mask_abs_delta_atac_target_promoter_sum | very_high_confidence | oracle_panel_top250 | 0.8881 | 0.8171 | 0.9153 | 0.9222 | 0.4669 | 0.4510 | False |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact_field_tuned | proxy_v2_rich_without_contact_high_confidence_c0p01 | very_high_confidence | full_benchmark_138k | 0.7136 | 0.5814 | 0.7727 | 0.9842 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | ensemble_proxy_residual_v1 | ensemble_proxy_residual_v1 | very_high_confidence | full_benchmark_138k | 0.7117 | 0.5867 | 0.7695 | 0.9803 | 0.0255 | 0.0249 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich | logistic_counterfactual_proxy_v2_rich_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.6984 | 0.5645 | 0.7625 | 0.9831 | 0.0258 | 0.0255 | True |
+| trainable | headline_full_benchmark | proxy_v2_rich_without_contact | s2t_proxy_v2_without_contact_logistic | very_high_confidence | full_benchmark_138k | 0.6924 | 0.5508 | 0.7464 | 0.9844 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich | molecular_residual_proxy_v2_rich_highconf_c003 | very_high_confidence | full_benchmark_138k | 0.6751 | 0.5392 | 0.7317 | 0.9804 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | residual_proxy_v2_rich_strict | molecular_residual_proxy_v2_rich_strict_broad_c001 | very_high_confidence | full_benchmark_138k | 0.6741 | 0.5416 | 0.7376 | 0.9773 | 0.0255 | 0.0249 | True |
+| trainable | headline_full_benchmark | field_leader | logistic_re2g_extended_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.6708 | 0.5406 | 0.7307 | 0.9816 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | residual_gate | residual_deepset_calibrated_gate_v1 | very_high_confidence | full_benchmark_138k | 0.6614 | 0.5348 | 0.7251 | 0.9776 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | observed_hic_reabc | logistic_observed_hic_reabc_c00003 | very_high_confidence | full_benchmark_138k | 0.6440 | 0.5037 | 0.7074 | 0.9724 | 0.0255 | 0.0249 | True |
+| trainable | headline_full_benchmark | re2g_extended_features | logistic_re2g_extended_features_c0003 | very_high_confidence | full_benchmark_138k | 0.6179 | 0.5028 | 0.7055 | 0.9727 | 0.0254 | 0.0249 | True |
+| trainable | headline_full_benchmark | proxy_v2 | logistic_counterfactual_proxy_v2_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.6096 | 0.4687 | 0.6710 | 0.9816 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | proxy_v1 | logistic_counterfactual_proxy_highconf_c0003 | very_high_confidence | full_benchmark_138k | 0.5192 | 0.3782 | 0.5887 | 0.9774 | 0.0256 | 0.0252 | True |
+| trainable | headline_full_benchmark | distance_abc | logistic_distance_abc | very_high_confidence | full_benchmark_138k | 0.3723 | 0.2717 | 0.4553 | 0.9607 | 0.0252 | 0.0246 | True |

results/paper/paper_s2t_bootstrap_ci.csv ADDED Viewed

	@@ -0,0 +1,92 @@

+source_name,model_name,scoreboard,n_regions,n_pairs,n_positive,observed_auprc,bootstrap_mean_auprc,ci_low,ci_high,bootstrap_iterations
+distance_abc,logistic_distance_abc,strict_all,5545,40322,664,0.1764834850369487,0.1772262367150376,0.1527315521253184,0.20236306638294238,500
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+distance_abc,logistic_distance_abc,field_compatible_e2g,4483,16778,291,0.37039229043836713,0.37209382164021815,0.3147494869304455,0.4281753434726135,500
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+distance_abc,logistic_distance_abc,re2g_covered_strict,5114,34465,621,0.18801284500957444,0.188367400025439,0.1633213635986692,0.21703091772730165,500
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+distance_abc,logistic_distance_abc,re2g_covered_very_high_confidence,3487,8237,88,0.39610619352364473,0.40002151774066025,0.30051873918711197,0.5052178116485823,500
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results/paper/paper_s2t_scoreboard_metrics.csv ADDED Viewed

The diff for this file is too large to render. See raw diff

results/paper/paper_s2t_scoreboard_summary.csv ADDED Viewed

	@@ -0,0 +1,92 @@

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results/paper/paper_s2t_slice_summary.csv ADDED Viewed

	@@ -0,0 +1,131 @@

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results/paper/paper_unmatched_oracle_context.csv ADDED Viewed

	@@ -0,0 +1,61 @@

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results/s2t/fulco2019_k562/generalization_summary.csv ADDED Viewed

	@@ -0,0 +1,4 @@

+model_name,recall_at_1,mrr,auroc,auprc,n_pairs,n_positive
+distance,0.033374857161489406,0.04237318929184211,0.9536023169940855,0.33296299820095876,874.0,11.75
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results/s2t/fulco2019_k562/generalization_summary.md ADDED Viewed

	@@ -0,0 +1,11 @@

+# External Screen Generalization
+Screen: `fulco2019_k562` (K562, hg38).
+Balanced chromosome-fold test means on an independent CRISPRi screen.
+| model | recall@1 | mrr | auroc | auprc | n_pairs | n_positive |
+| --- | --- | --- | --- | --- | --- | --- |
+| distance | 0.0334 | 0.0424 | 0.9536 | 0.3330 | 874 | 11 |
+| logistic_molecular | 0.0334 | 0.0424 | 0.9341 | 0.3178 | 874 | 11 |
+| nearest_gene | 0.0334 | 0.0395 | 0.6604 | 0.0347 | 874 | 11 |

results/s2t/fulco2019_k562/screen_deconfounding_comparison.csv ADDED Viewed

	@@ -0,0 +1,7 @@

+screen,result_type,model_name,scoreboard,prevalence,auprc,auroc,ci_low,ci_high
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results/s2t/fulco2019_k562/screen_deconfounding_paired_diff.csv ADDED Viewed

	@@ -0,0 +1,3 @@

+scoreboard,n_pairs,n_regions,n_positive,auprc_a,auprc_b,diff,diff_mean,ci_low,ci_high,p_value,screen,best_trained
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results/s2t/gasperini_gse120861/ensemble_proxy_residual_rank_slice_metrics.csv ADDED Viewed

The diff for this file is too large to render. See raw diff

results/s2t/gasperini_gse120861/ensemble_proxy_residual_regime_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/ensemble_proxy_residual_score_strictfloor_slice_metrics.csv ADDED Viewed

The diff for this file is too large to render. See raw diff

results/s2t/gasperini_gse120861/learned_ensemble_logistic_deepset_nonnearest_raw_weights.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_lightgbm_distance_abc_jaspar2026_pilot_filtered_interactions_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_lightgbm_e2g_competition_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/learned_lightgbm_e2g_competition_permutation_importance.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_lightgbm_e2g_competition_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_lightgbm_gene_group_k562_expr_molecular_ranker_feature_importance.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_listwise_observed_hic_l2_001_b01_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_abc_contact_c0003_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/learned_logistic_counterfactual_proxy_v2_rich_highconf_c0003_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_distance_abc_jaspar2026_pilot_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_e2g_activity_contact_c01.log ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_e2g_activity_contact_c01_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_e2g_molecular_c003_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_e2g_molecular_fixed_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/learned_logistic_e2g_molecular_fixed_slice_metrics.csv ADDED Viewed

The diff for this file is too large to render. See raw diff

results/s2t/gasperini_gse120861/learned_logistic_k562_expr_molecular_c001_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/learned_logistic_k562_expr_molecular_c001_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_lifted_ccre_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_features_c001_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_features_c003_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_features_c003_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_highconf_c00003_slice_metrics.csv ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_re2g_extended_vhighconf_c0001.log ADDED Viewed

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results/s2t/gasperini_gse120861/learned_logistic_recomputed_abc_c00003_metrics.csv ADDED Viewed

	@@ -0,0 +1,151 @@

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results/s2t/gasperini_gse120861/learned_molecular_residual_fieldleader_highconf_c001_candidate_metrics.csv ADDED Viewed

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