BioGeMT · zacharopoulou · Apr 29, 2026 · May 10, 2026 · May 10, 2026 · May 10, 2026
diff --git a/README.md b/README.md
@@ -297,9 +297,12 @@ normal workflow is just to edit or uncomment filters.
 
 ## Outputs
 
-After a benchmark run, `results/` contains one new run folder, for example:
+After a benchmark run, `results/` contains one new run folder named with the run date. For example:
 
-- `results/tag-demo__exp3__pred2__oe1__ko1__kd0__cell3/`
+- `results/20260510/`
+
+Detailed dataset, miRNA, predictor, perturbation, cell-line, and evaluation-threshold metadata is
+recorded inside the run folder.
 
 Inside each run folder you get:
 
@@ -312,7 +315,7 @@ Inside each run folder you get:
 - `datasets/<dataset_id>/reports/`: per-dataset Markdown/PDF reports and correlation TSVs
 - `tables/per_experiment/`: per-experiment metric tables
 - `tables/combined/`: cross-dataset predictor summary table
-- `plots/combined/metrics/`, `plots/combined/coverage/`, `plots/combined/ranks/`: cross-dataset comparison plots grouped by theme
+- `plots/combined/metrics/`, `plots/combined/ranks/`, `plots/combined/combinations/`: cross-dataset comparison plots grouped by theme
 - `summary.json`: run summary
 
 When 2 or more predictors are selected, each dataset gets:
@@ -321,7 +324,7 @@ When 2 or more predictors are selected, each dataset gets:
 - one combined PR curve on common scored pairs
 - one combined ROC curve on common scored pairs
 - one algorithms-vs-genes heatmap
-- one predictor-correlation heatmap
+- common-prediction overlap summaries for comparable predictor sets
 
 ## Commands
 

diff --git a/benchmark.yaml b/benchmark.yaml
@@ -11,7 +11,7 @@ predictions_tsv: metadata/predictions_info.tsv
 # The default repo config ships with a small 3-dataset demo selection.
 # Edit or comment these active rows to benchmark other subsets.
 experiments:
-  id: [GSE109725_OE_miR_204_5p, GSE118315_KO_miR_124_3p, GSE210778_OE_miR_375_3p]
+  id: [GSE124411_OE_miR_150_5p_2, GSE129076_OE_miR_450a_5p_1]
   # mirna_name: [hsa-miR-375-3p]
   # mirna_sequence: [UUUGUUCGUUCGGCUCGCGUGA]
   # article_pubmed_id: [https://pubmed.ncbi.nlm.nih.gov/36074222]
@@ -25,9 +25,9 @@ experiments:
 
 # Filter predictors by ANY column in the predictions TSV.
 # The default repo config compares two random baselines, the cheating and perfect
-# demo predictors, and TargetScan.
+# demo predictors, TargetScan, miRDB, and TEC-miTarget.
 predictors:
-  tool_id: [random, random_3000, cheating, perfect, targetscan, microt_cnn]
+  tool_id: [random, random_3000, cheating, perfect, targetscan, mirdb_mirtarget, tec-mitarget, microt_cnn, mirbind2, miraw]
   # official_name: [Random, Random (3000 per dataset), Cheating, Perfect]
   # organism: [Homo sapiens]
   # score_type: [probability]
@@ -40,8 +40,11 @@ predictors:
   # predictor_output_path: [data/predictions/random/random_standardized.tsv]
 
 evaluation:
-  fdr_threshold: 0.05
-  abs_logfc_threshold: 1.0
+  fdr_threshold: null
+  effect_threshold: 1.0
   predictor_top_fraction: 0.10
+  write_top_prediction_cdfs: true
+  report_min_common_coverage: 0.10
+  figure_dpi: 600
 
 out_dir: results/
diff --git a/data/experiments/processed/18745741/GSE109725_edger_out_oe_hsa_miR_204_5p_525.tsv b/data/experiments/processed/18745741/GSE109725_edger_out_oe_hsa_miR_204_5p_525.tsv
diff --git a/data/experiments/processed/18745741/GSE112859_edger_out_oe_hsa_miR_574_3p_oe_3p.tsv b/data/experiments/processed/18745741/GSE112859_edger_out_oe_hsa_miR_574_3p_oe_3p.tsv
diff --git a/data/experiments/processed/18745741/GSE112859_edger_out_oe_hsa_miR_574_5p_oe_5p.tsv b/data/experiments/processed/18745741/GSE112859_edger_out_oe_hsa_miR_574_5p_oe_5p.tsv
diff --git a/data/experiments/processed/18745741/GSE118315_edger_out_ko_hsa_miR_124_3p_2.tsv b/data/experiments/processed/18745741/GSE118315_edger_out_ko_hsa_miR_124_3p_2.tsv
diff --git a/data/experiments/processed/18745741/GSE124411_edger_out_oe_hsa_miR_150_5p_oe_line1.tsv b/data/experiments/processed/18745741/GSE124411_edger_out_oe_hsa_miR_150_5p_oe_line1.tsv
diff --git a/data/experiments/processed/18745741/GSE124411_edger_out_oe_hsa_miR_150_5p_oe_line2.tsv b/data/experiments/processed/18745741/GSE124411_edger_out_oe_hsa_miR_150_5p_oe_line2.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_let_7c_5p_oe_7c5p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_let_7c_5p_oe_7c5p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_107_oe_107.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_107_oe_107.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_10a_5p_oe_10a5p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_10a_5p_oe_10a5p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_124_3p_oe_1243p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_124_3p_oe_1243p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_126_3p_oe_1263p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_126_3p_oe_1263p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_126_5p_oe_1265p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_126_5p_oe_1265p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_133b_oe_133b.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_133b_oe_133b.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_142_3p_oe_1423p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_142_3p_oe_1423p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_145_5p_oe_1455p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_145_5p_oe_1455p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_146a_5p_oe_146a5p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_146a_5p_oe_146a5p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_155_5p_oe_1555p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_155_5p_oe_1555p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_15a_5p_oe_15a5p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_15a_5p_oe_15a5p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_16_5p_oe_165p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_16_5p_oe_165p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_17_5p_oe_175p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_17_5p_oe_175p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_193b_3p_oe_193b3p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_193b_3p_oe_193b3p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_200a_3p_oe_200a3p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_200a_3p_oe_200a3p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_200b_3p_oe_200b3p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_200b_3p_oe_200b3p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_200c_3p_oe_200c.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_200c_3p_oe_200c.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_206_oe_206.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_206_oe_206.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_210_3p_oe_2103p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_210_3p_oe_2103p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_21_5p_oe_215p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_21_5p_oe_215p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_31_5p_oe_315p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_31_5p_oe_315p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_34a_5p_oe_34a5p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_34a_5p_oe_34a5p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_9_3p_oe_93p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_9_3p_oe_93p.tsv
diff --git a/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_9_5p_oe_95p.tsv b/data/experiments/processed/18745741/GSE124530_edger_out_oe_hsa_miR_9_5p_oe_95p.tsv
diff --git a/data/experiments/processed/18745741/GSE129076_edger_out_oe_hsa_miR_450a_5p_line_1.tsv b/data/experiments/processed/18745741/GSE129076_edger_out_oe_hsa_miR_450a_5p_line_1.tsv
diff --git a/data/experiments/processed/18745741/GSE129076_edger_out_oe_hsa_miR_450a_5p_line_2.tsv b/data/experiments/processed/18745741/GSE129076_edger_out_oe_hsa_miR_450a_5p_line_2.tsv
diff --git a/data/experiments/processed/18745741/GSE148827_edger_out_ko_hsa_miR_1271_5p_mrna_ko.tsv b/data/experiments/processed/18745741/GSE148827_edger_out_ko_hsa_miR_1271_5p_mrna_ko.tsv
diff --git a/data/experiments/processed/18745741/GSE148827_edger_out_oe_hsa_miR_1271_5p_mrna_oe.tsv b/data/experiments/processed/18745741/GSE148827_edger_out_oe_hsa_miR_1271_5p_mrna_oe.tsv
diff --git a/data/experiments/processed/18745741/GSE154968_edger_out_oe_hsa_miR_21_3p.tsv b/data/experiments/processed/18745741/GSE154968_edger_out_oe_hsa_miR_21_3p.tsv
diff --git a/data/experiments/processed/18745741/GSE160736_edger_out_oe_hsa_miR_642a_5p.tsv b/data/experiments/processed/18745741/GSE160736_edger_out_oe_hsa_miR_642a_5p.tsv
diff --git a/data/experiments/processed/18745741/GSE160906_edger_out_ko_hsa_miR_378a_3p_24h_inhibitor.tsv b/data/experiments/processed/18745741/GSE160906_edger_out_ko_hsa_miR_378a_3p_24h_inhibitor.tsv
diff --git a/data/experiments/processed/18745741/GSE160906_edger_out_ko_hsa_miR_378a_3p_48h_inhibitor.tsv b/data/experiments/processed/18745741/GSE160906_edger_out_ko_hsa_miR_378a_3p_48h_inhibitor.tsv
diff --git a/data/experiments/processed/18745741/GSE160906_edger_out_oe_hsa_miR_378a_3p_24h_mimic.tsv b/data/experiments/processed/18745741/GSE160906_edger_out_oe_hsa_miR_378a_3p_24h_mimic.tsv
diff --git a/data/experiments/processed/18745741/GSE160906_edger_out_oe_hsa_miR_378a_3p_48h_mimic.tsv b/data/experiments/processed/18745741/GSE160906_edger_out_oe_hsa_miR_378a_3p_48h_mimic.tsv
diff --git a/data/experiments/processed/18745741/GSE165469_edger_out_ko_hsa_miR_340_5p_ko.tsv b/data/experiments/processed/18745741/GSE165469_edger_out_ko_hsa_miR_340_5p_ko.tsv
diff --git a/data/experiments/processed/18745741/GSE165469_edger_out_oe_hsa_miR_340_5p_oe.tsv b/data/experiments/processed/18745741/GSE165469_edger_out_oe_hsa_miR_340_5p_oe.tsv