Prepare BMC Oral Health submission package

.gitignore

@@ -58,6 +58,7 @@ artifacts/*.db
 logs/*.log
 reports/*.pdf
 reports/*.html
+reports/*.docx
 
 # Keep .gitkeep files
 !.gitkeep

CITATION.cff

@@ -1,8 +1,8 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 title: "NHANES Periodontitis Prediction Benchmark"
-version: 1.3.1
-date-released: 2026-06-02
+version: 1.3.2
+date-released: 2026-06-04
 url: "https://github.com/Tuminha/NHANES-Periodontitis-Machine-Learning-Project"
 repository-code: "https://github.com/Tuminha/NHANES-Periodontitis-Machine-Learning-Project"
 license: MIT
@@ -11,7 +11,13 @@ authors:
   - family-names: "Barbosa"
     given-names: "Francisco Teixeira"
     email: "cisco@periospot.com"
-    affiliation: "Oral Rehabilitation Foundation"
+    affiliation: "Foundation for Oral Rehabilitation; DENS-ia Research Group, Faculty of Health Sciences, Miguel de Cervantes European University"
+  - family-names: "Brizuela-Velasco"
+    given-names: "Aritza"
+    affiliation: "DENS-ia Research Group, Faculty of Health Sciences, Miguel de Cervantes European University"
+  - family-names: "Robles Cantero"
+    given-names: "Daniel"
+    affiliation: "DENS-ia Research Group, Faculty of Health Sciences, Miguel de Cervantes European University"
 keywords:
   - periodontitis
   - machine learning
@@ -33,5 +39,9 @@ preferred-citation:
     - family-names: "Barbosa"
       given-names: "Francisco Teixeira"
       email: "cisco@periospot.com"
+    - family-names: "Brizuela-Velasco"
+      given-names: "Aritza"
+    - family-names: "Robles Cantero"
+      given-names: "Daniel"
   title: "Machine Learning for Periodontitis Prediction: A Realistic Benchmark with Same-Source Temporal Validation on NHANES"
   year: 2026

MODEL_CARD.md

@@ -78,4 +78,4 @@ The consistency check enforces agreement between result artifacts, README, this
 
 ## AI-Use Disclosure
 
-AI systems were used as drafting and code-review aids during project development. The author remains responsible for study design, code, analysis decisions, interpretation, and manuscript claims.
+AI systems were used as drafting, figure-label review, critique, and code-review aids during project development. No AI system is listed as an author. The authors remain responsible for study design, code, analysis decisions, interpretation, and manuscript claims.

Makefile

@@ -111,7 +111,7 @@ notebook:
 
 figures:
 	@echo "Generating publication figures..."
-	@echo "Figure regeneration remains notebook-backed; see notebooks/00_nhanes_periodontitis_end_to_end.ipynb"
+	$(PYTHON) scripts/06_generate_publication_figures.py
 
 manuscript:
 	@echo "Rendering manuscript if pandoc is installed..."
@@ -128,6 +128,9 @@ manuscript:
 			exit 1; \
 		fi; \
 		mkdir -p reports; \
+		pandoc docs/publication/ARTICLE_DRAFT.md \
+			-o reports/manuscript_bmc_submission.docx; \
+		echo "Rendered reports/manuscript_bmc_submission.docx"; \
 		pandoc docs/publication/ARTICLE_DRAFT.md \
 			--pdf-engine=$$ENGINE \
 			-V geometry:margin=1in \
@@ -145,7 +148,7 @@ clean:
 	rm -rf artifacts/*.npy
 	rm -rf artifacts/*.db
 	rm -rf logs/*.log
-	rm -rf reports/*.pdf reports/*.html
+	rm -rf reports/*.pdf reports/*.html reports/*.docx
 	@echo "Clean complete"
 
 lock:

README.md

@@ -74,7 +74,10 @@ The legacy notebooks are retired as source-of-truth artifacts. The maintained pu
 | `scripts/reproduce_v13_primary.py` | Regenerates internal v1.3 benchmark result artifacts |
 | `scripts/run_temporal_validation.py` | Regenerates same-source temporal validation artifacts |
 | `scripts/04_publication_analyses.py` | Generates publication sensitivity tables from processed predictions |
+| `scripts/06_generate_publication_figures.py` | Generates submission figures from canonical result artifacts |
 | `results/publication_sensitivity_tables.md` | Survey-weighted prevalence and subgroup performance summary generated by the full reproduction |
+| `figures/19_publication_performance_summary.png` | Main performance and operating-point figure |
+| `figures/20_publication_sensitivity_summary.png` | Survey-weighted prevalence, subgroup AUC, and missingness figure |
 | `results/` | Saved result artifacts used by the manuscript and model card |
 | `docs/publication/ARTICLE_DRAFT.md` | Current manuscript source |
 
@@ -90,7 +93,7 @@ The legacy notebooks are retired as source-of-truth artifacts. The maintained pu
 
 ```bibtex
 @software{barbosa_nhanes_periodontitis_benchmark,
-  author = {Barbosa, Francisco Teixeira},
+  author = {Barbosa, Francisco Teixeira and Brizuela-Velasco, Aritza and Robles Cantero, Daniel},
   title = {NHANES Periodontitis Prediction Benchmark},
   year = {2026},
   url = {https://github.com/Tuminha/NHANES-Periodontitis-Machine-Learning-Project}