fix: publish MVD 2.2 corrected statistics and verified weight provenance

README.md

@@ -15,3 +15,33 @@ Salidas experimentales del TFM sobre predicción de incompatibilidades de depend
 - `analysis/` — comparación de resolvers, análisis de eficiencia e inferencia repetida, y muestra cualitativa de errores.
 
 Cada subcarpeta se corresponde con una configuración/experimento concreto (p. ej. `results/gnn/graphsage-v2_2/seed-XX/`).
+
+## Versión v0.1.1: cierre estadístico de MVD 2.2
+
+Los pesos de B3 y GraphSAGE de las carpetas `*-v2_2` y sus ablaciones
+corresponden a **MVD 2.2**, tanto en v0.1.0 como en v0.1.1. Los manifiestos de
+las 40 ejecuciones identifican el Parquet final mediante SHA-256:
+
+```text
+7834efc509a38c885fbbbc46cedbbed04b461ad08b6e6243793f8bb6b8ccb20b
+```
+
+Se comprobaron los hashes LFS de los 40 checkpoints, 40 preprocesadores y
+40 ficheros de predicciones contra la etiqueta v0.1.0. Las etiquetas de las
+predicciones se contrastaron con el dataset final. El inventario verificable
+se conserva en `metadata/mvd-v2_2-provenance.json`.
+
+Esta versión **no cambia pesos, predicciones, umbrales ni datos**. Actualiza
+`results/analysis-v2_2/analysis.json` y `wilcoxon_holm.csv` para incorporar la
+corrección de continuidad del contraste aproximado de Wilcoxon cuando hay
+diferencias nulas, según
+[B3 v0.2.1](https://github.com/keyduu/tfm-dependency-baseline-mlp/tree/v0.2.1).
+En la comparación principal GraphSAGE-B3, el valor bruto pasa de
+`0.050612432239184685` a `0.0580240199462214`; el valor ajustado de Holm sigue
+siendo `1.0`. La familia se mantiene en 96 contrastes. Se verificaron los
+valores brutos y ajustados a partir de las diferencias conservadas, sin
+reentrenar modelos ni repetir el bootstrap.
+
+La etiqueta v0.1.0 se conserva intacta como referencia histórica. Para las
+cifras finales de la memoria debe utilizarse v0.1.1, cuyo informe incluye
+las opciones del contraste y coincide con el cierre estadístico documentado.

metadata/mvd-v2_2-provenance.json

@@ -0,0 +1,744 @@
+{
+  "schema_version": 1,
+  "release": "v0.1.1",
+  "dataset": "mvd_v2_2",
+  "dataset_sha256": "7834efc509a38c885fbbbc46cedbbed04b461ad08b6e6243793f8bb6b8ccb20b",
+  "historical_release": "v0.1.0",
+  "historical_commit": "31082ccc824ec09572a4cc2f6c52d49e70243a20",
+  "historical_remote_tag_verified": true,
+  "statistical_code": {
+    "repository": "https://github.com/keyduu/tfm-dependency-baseline-mlp",
+    "version": "v0.2.1",
+    "commit": "a9f90466dbe6084908452404615d49ed9acd4e15"
+  },
+  "verified_runs": 40,
+  "verified_binary_artifacts": 120,
+  "weights_preprocessors_predictions_changed": false,
+  "wilcoxon_holm_tests_verified": 96,
+  "reports": {
+    "results/analysis-v2_2/analysis.json": "ef478f8a82d0dee6aefd110fdbb6f1e94739b00b356096d77f2198ba03511b41",
+    "results/analysis-v2_2/wilcoxon_holm.csv": "e3abe45c587ed4add5d172d46a46c4effb69c41640f5931ad9cecbbb5c632e8c"
+  },
+  "records": [
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+        }
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+    }
+  ]
+}

results/analysis-v2_2/analysis.json

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@@ -74,10 +76,12 @@
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@@ -142,10 +148,12 @@
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@@ -5311,10 +5395,12 @@
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@@ -6064,10 +6160,12 @@
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@@ -6166,10 +6268,12 @@
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             "method": "exact",
             "pvalue": 0.009765625,
-            "statistic": 3.0
+            "statistic": 3.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -6200,10 +6304,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -6234,10 +6340,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -6817,10 +6925,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -6851,10 +6961,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -6885,10 +6997,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -6919,10 +7033,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -6953,10 +7069,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -6987,10 +7105,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -7570,10 +7690,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "exact",
             "pvalue": 0.193359375,
-            "statistic": 14.0
+            "statistic": 14.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -7604,10 +7726,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "exact",
             "pvalue": 0.01953125,
-            "statistic": 5.0
+            "statistic": 5.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -7638,10 +7762,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": true,
             "holm_adjusted_pvalue": 1.0,
             "method": "approx",
-            "pvalue": 0.050612432239184685,
-            "statistic": 6.0
+            "pvalue": 0.0580240199462214,
+            "statistic": 6.0,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -7672,10 +7798,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "exact",
             "pvalue": 0.625,
-            "statistic": 22.0
+            "statistic": 22.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -7706,10 +7834,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -7740,10 +7870,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -8323,10 +8455,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "exact",
             "pvalue": 0.322265625,
-            "statistic": 17.0
+            "statistic": 17.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -8357,10 +8491,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -8391,10 +8527,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -8425,10 +8563,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "exact",
             "pvalue": 0.037109375,
-            "statistic": 7.0
+            "statistic": 7.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -8459,10 +8599,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -8493,10 +8635,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -9076,10 +9220,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -9110,10 +9256,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -9144,10 +9292,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
-            "holm_adjusted_pvalue": 0.5974223587648595,
+            "correction": true,
+            "holm_adjusted_pvalue": 0.7068182103123081,
             "method": "approx",
-            "pvalue": 0.010862224704815628,
-            "statistic": 1.0
+            "pvalue": 0.01285124018749651,
+            "statistic": 1.0,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -9178,10 +9328,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -9212,10 +9364,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -9246,10 +9400,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -9829,10 +9985,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -9863,10 +10021,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -9897,10 +10057,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": true,
             "holm_adjusted_pvalue": 1.0,
             "method": "approx",
-            "pvalue": 0.08446903225325182,
-            "statistic": 2.5
+            "pvalue": 0.10577220785075259,
+            "statistic": 2.5,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -9931,10 +10093,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -9965,10 +10129,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -9999,10 +10165,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -10582,10 +10750,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -10616,10 +10786,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -10650,10 +10822,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -10684,10 +10858,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -10718,10 +10894,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -10752,10 +10930,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -11335,10 +11515,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "ece": {
@@ -11369,10 +11551,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "f1_incompatible": {
@@ -11403,10 +11587,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "log_loss": {
@@ -11437,10 +11623,12 @@
           },
           "direction": "lower_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 0.1875,
             "method": "exact",
             "pvalue": 0.001953125,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_10": {
@@ -11471,10 +11659,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         },
         "precision_at_50": {
@@ -11505,10 +11695,12 @@
           },
           "direction": "higher_is_better",
           "wilcoxon_two_sided": {
+            "correction": false,
             "holm_adjusted_pvalue": 1.0,
             "method": "all_deltas_zero",
             "pvalue": 1.0,
-            "statistic": 0.0
+            "statistic": 0.0,
+            "zero_method": "wilcox"
           }
         }
       },
@@ -23468,9 +23660,12 @@
       "unit": "test pair"
     },
     "paired_seed_test": {
+      "continuity_correction": "applied only with the normal approximation",
       "family_size": 96,
+      "method_selection": "exact without zeros; normal approximation with zeros",
       "multiple_testing": "Holm step-down over all comparison-metric hypotheses",
-      "test": "two-sided Wilcoxon signed-rank over right-minus-left seed deltas"
+      "test": "two-sided Wilcoxon signed-rank over right-minus-left seed deltas",
+      "zero_method": "wilcox: zero differences are excluded from the ranks"
     },
     "precision_at_k": {
       "k": [

results/analysis-v2_2/wilcoxon_holm.csv

@@ -1,5 +1,5 @@
 comparison,metric,direction,raw_pvalue,holm_adjusted_pvalue,family_size
-principal_xgboost_minus_random_forest,f1_incompatible,higher_is_better,0.08446903225325182,1.0,96
+principal_xgboost_minus_random_forest,f1_incompatible,higher_is_better,0.10577220785075259,1.0,96
 principal_xgboost_minus_random_forest,precision_at_10,higher_is_better,1.0,1.0,96
 principal_xgboost_minus_random_forest,precision_at_50,higher_is_better,1.0,1.0,96
 principal_xgboost_minus_random_forest,brier,lower_is_better,0.001953125,0.1875,96
@@ -23,13 +23,13 @@ principal_b3_minus_xgboost,precision_at_50,higher_is_better,1.0,1.0,96
 principal_b3_minus_xgboost,brier,lower_is_better,0.001953125,0.1875,96
 principal_b3_minus_xgboost,log_loss,lower_is_better,0.001953125,0.1875,96
 principal_b3_minus_xgboost,ece,lower_is_better,0.001953125,0.1875,96
-principal_graphsage_minus_xgboost,f1_incompatible,higher_is_better,0.010862224704815628,0.5974223587648595,96
+principal_graphsage_minus_xgboost,f1_incompatible,higher_is_better,0.01285124018749651,0.7068182103123081,96
 principal_graphsage_minus_xgboost,precision_at_10,higher_is_better,1.0,1.0,96
 principal_graphsage_minus_xgboost,precision_at_50,higher_is_better,1.0,1.0,96
 principal_graphsage_minus_xgboost,brier,lower_is_better,0.001953125,0.1875,96
 principal_graphsage_minus_xgboost,log_loss,lower_is_better,0.001953125,0.1875,96
 principal_graphsage_minus_xgboost,ece,lower_is_better,0.001953125,0.1875,96
-principal_graphsage_minus_b3,f1_incompatible,higher_is_better,0.050612432239184685,1.0,96
+principal_graphsage_minus_b3,f1_incompatible,higher_is_better,0.0580240199462214,1.0,96
 principal_graphsage_minus_b3,precision_at_10,higher_is_better,1.0,1.0,96
 principal_graphsage_minus_b3,precision_at_50,higher_is_better,1.0,1.0,96
 principal_graphsage_minus_b3,brier,lower_is_better,0.193359375,1.0,96