fix evaluation path mismatches and prune unreachable artefact checks

Author: wa5rx3

Makefile

@@ -36,24 +36,32 @@ bootstrap_delta:
 	$(PYTHON) -m src.evaluation.bootstrap_eval \
 	  --model-a artifacts/models/multimodal_pneumonia_densenet121_triage_u_ignore_temporal_stronger_lr_v3/test_predictions.csv \
 	  --model-b artifacts/models/image_pneumonia_finetune_densenet121_u_ignore_temporal_stronger_lr_v3/test_predictions.csv \
-	  --output-json artifacts/evaluation/bootstrap_multimodal_vs_image.json \
+	  --output-json artifacts/evaluation/bootstrap_multimodal_vs_image_stronger_lr_v3.json \
 	  --n-bootstrap 2000 --seed $(SEED)
 
 calibration:
 	$(PYTHON) -m src.evaluation.calibration_analysis \
-	  --output-dir artifacts/evaluation/calibration_final \
+	  --output-dir artifacts/evaluation/calibration_stronger_lr_v3 \
 	  --n-bins 10 --bootstrap --n-bootstrap 2000 \
 	  --model "Image" artifacts/models/image_pneumonia_finetune_densenet121_u_ignore_temporal_stronger_lr_v3/test_predictions.csv \
 	  --model "Multimodal" artifacts/models/multimodal_pneumonia_densenet121_triage_u_ignore_temporal_stronger_lr_v3/test_predictions.csv
 
+dca:
+	$(PYTHON) -m src.evaluation.decision_curve_analysis \
+	  --output-dir artifacts/evaluation/dca \
+	  --model "Image" artifacts/models/image_pneumonia_finetune_densenet121_u_ignore_temporal_stronger_lr_v3/test_predictions.csv \
+	  --model "Multimodal" artifacts/models/multimodal_pneumonia_densenet121_triage_u_ignore_temporal_stronger_lr_v3/test_predictions.csv
+
 feature_ablation:
 	$(PYTHON) scripts/collect_feature_ablation_results.py
 
-evaluate: bootstrap_delta calibration feature_ablation
+evaluate: bootstrap_delta calibration dca feature_ablation
 
 # ─── SHAP ────────────────────────────────────────────────────────────────────
 shap:
-	$(PYTHON) scripts/generate_shap_clinical.py
+	$(PYTHON) scripts/generate_shap_clinical.py \
+	  --model-dir artifacts/models/clinical_xgb_u_ignore_temporal_strong_v2 \
+	  --feature-groups all
 
 # ─── Publication report ───────────────────────────────────────────────────────
 report:
@@ -68,4 +76,4 @@ all: pretrain finetune_image finetune_multimodal train_clinical evaluate shap re
 
 .PHONY: preprocess preprocess_labs pretrain finetune_image finetune_multimodal \
         train_clinical_lr train_clinical_xgb train_clinical bootstrap_delta \
-        calibration feature_ablation evaluate shap report all test
+        calibration dca feature_ablation evaluate shap report all test

scripts/regenerate_all_results.py

@@ -25,6 +25,12 @@
     # Source of truth — all numerical results
     ("artifacts/evaluation/final_publication_report.json", MIN_JSON_BYTES, "json"),
 
+    # Bootstrap comparison
+    (
+        "artifacts/evaluation/bootstrap_multimodal_vs_image_stronger_lr_v3.json",
+        MIN_JSON_BYTES, "json"
+    ),
+
     # Feature ablation
     ("artifacts/evaluation/feature_ablation_results.csv", MIN_CSV_BYTES, "csv"),
 
@@ -46,58 +52,6 @@
 
     # DCA
     ("artifacts/evaluation/dca/decision_curve_standardized.png", MIN_PNG_BYTES, "png"),
-
-    # Generated thesis figures (from scripts/generate_thesis_figures.py)
-    (
-        "thesis_new_docs/figures/generated_results/fig_a1_pr_curves.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/generated_results/fig_a3_ablation_bars.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/generated_results/fig_a4_label_sensitivity.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/generated_results/fig_a5_training_curves.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/generated_results/fig_a6_missing_heatmap.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/generated_results/fig_a7_vital_distributions.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/generated_results/fig_a8_label_distribution.png",
-        MIN_PNG_BYTES, "png"
-    ),
-
-    # Original result figures
-    (
-        "thesis_new_docs/figures/original_results/"
-        "roc_curve_all_models.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/original_results/"
-        "calibration_stronger_lr_v3_reliability_diagram_all_models.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/original_results/"
-        "shap_summary_beeswarm.png",
-        MIN_PNG_BYTES, "png"
-    ),
-    (
-        "thesis_new_docs/figures/original_results/"
-        "decision_curve_standardized.png",
-        MIN_PNG_BYTES, "png"
-    ),
 ]