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results/phase1_filtering_summary.txt

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+================================================================================
+PHASE 1: ENVIRONMENTAL FILTERING METRICS
+================================================================================
+
+Provenance:
+  Script: /media/drn2/External/TARA-Oceans/03_analyses/WorldModelApp/scripts/t07_filtering_metrics_20260127_150000.py
+  Input:  /media/drn2/External/TARA-Oceans/03_analyses/WorldModelApp/results/phase1_xgb_predictions.npz
+  Date:   2026-01-27 10:03:39
+  Integrity Check: PASSED
+
+Dataset: 1810 samples, 20 PFAM modules
+Method: Multi-output XGBoost (env -> PFAM modules), leave-one-basin-out CV
+
+--------------------------------------------------------------------------------
+COSINE SIMILARITY (predicted vs true PFAM module vectors)
+--------------------------------------------------------------------------------
+
+  Mean:   0.8788
+  Median: 0.9295
+  Std:    0.1441
+  Min:    -0.3170
+  Max:    0.9972
+
+Percentile distribution:
+  P 5 = 0.5535
+  P10 = 0.6965
+  P25 = 0.8656
+  P50 = 0.9295
+  P75 = 0.9651
+  P90 = 0.9813
+  P95 = 0.9874
+
+Fraction above threshold:
+  > 0.50: 96.0% (1737/1810)
+  > 0.80: 83.0% (1503/1810)
+  > 0.90: 63.7% (1153/1810)
+  > 0.95: 38.0% (687/1810)
+
+--------------------------------------------------------------------------------
+L2 ERROR (Euclidean distance)
+--------------------------------------------------------------------------------
+
+  Mean:   8906.31
+  Median: 5871.31
+  Std:    8406.03
+  Min:    654.80
+  Max:    70019.22
+
+--------------------------------------------------------------------------------
+PER-BASIN COSINE SIMILARITY
+--------------------------------------------------------------------------------
+
+Basin                n     Mean      Std   Median      Min      Max
+---------------------------------------------------------------
+Arctic              38   0.9124   0.0589   0.9093   0.7719   0.9859
+Atlantic           644   0.9084   0.1118   0.9438   0.2581   0.9972
+Indian             195   0.8248   0.1981   0.9011  -0.3170   0.9968
+Mediterranean      242   0.8293   0.1851   0.9061   0.2341   0.9953
+Pacific            617   0.8859   0.1235   0.9340   0.2511   0.9971
+Red_Sea             24   0.6949   0.2134   0.7219   0.1851   0.9809
+Southern            50   0.9207   0.0695   0.9445   0.5978   0.9885
+
+--------------------------------------------------------------------------------
+PER-MODULE R2 (pooled held-out predictions)
+--------------------------------------------------------------------------------
+
+Module               R2
+------------------------
+module_19       +0.0871
+module_14       +0.0568
+module_15       +0.0369
+module_4        +0.0328
+module_17       +0.0269
+module_10       +0.0265
+module_11       +0.0192
+module_12       +0.0153
+module_5        +0.0104
+module_3        +0.0014
+module_18       -0.0004
+module_7        -0.0025
+module_16       -0.0144
+module_8        -0.0153
+module_1        -0.0647
+module_2        -0.0738
+module_20       -0.1492
+module_6        -0.1529
+module_13       -0.1541
+module_9        -0.1877
+
+Mean R2:   -0.0251
+Median R2: +0.0005
+Positive R2: 10/20
+Negative R2: 10/20
+
+--------------------------------------------------------------------------------
+PER-FOLD MEAN R2
+--------------------------------------------------------------------------------
+
+  Arctic          (n=  38): mean R2 = -5.9435
+  Atlantic        (n= 644): mean R2 = +0.0448
+  Indian          (n= 219): mean R2 = -0.1898
+  Mediterranean   (n= 242): mean R2 = +0.0996
+  Pacific         (n= 617): mean R2 = -0.1439
+  Southern        (n=  50): mean R2 = -1.0108
+
+--------------------------------------------------------------------------------
+INTERPRETATION
+--------------------------------------------------------------------------------
+
+Environmental filtering strength is quantified by two metrics:
+
+1. COSINE SIMILARITY (directional match): mean=0.8788
+   - High cosine similarity indicates the environment captures the DIRECTION
+     of PFAM module composition (which modules are relatively up vs down)
+   - 1503/1810 (83.0%) samples have cosine sim > 0.80
+
+2. R2 PER MODULE (magnitude prediction): mean=-0.0251
+   - 10/20 modules have positive R2 (pooled)
+   - R2 near zero indicates the environment captures marginal
+     signal about absolute PFAM module abundances
+
+NOTE: Cosine similarity may be inflated by dominant modules with
+universally high counts. Permutation test (T08) needed to assess
+whether observed cosine similarity exceeds null expectation.