\contentsline {section}{\numberline {1}Section 1: Feature Engineering and Scenario Ablation Analysis}{2}{section.1}%
\contentsline {subsection}{\numberline {1.1}Ablation Study 1: Feature Space Hybridization}{2}{subsection.1.1}%
\contentsline {subsection}{\numberline {1.2}Ablation Study 2: Dimensionality Optimization and Computational Efficiency}{2}{subsection.1.2}%
\contentsline {section}{\numberline {2}Section 2: Comprehensive Performance Evaluation Tables}{4}{section.2}%
\contentsline {subsection}{\numberline {2.1}Evaluation Metrics and Methodological Summary}{4}{subsection.2.1}%
\contentsline {subsection}{\numberline {2.2}Aggregated Performance Profiles Across Disease Modules}{4}{subsection.2.2}%
\contentsline {section}{\numberline {3}Section 3: Top-$K$ Threshold Comparative Analysis}{8}{section.3}%
\contentsline {subsection}{\numberline {3.1}Methodological Context and Robustness Evaluation}{8}{subsection.3.1}%
\contentsline {subsection}{\numberline {3.2}Sequential Threshold Performance Plots}{9}{subsection.3.2}%
\contentsline {section}{\numberline {4}Section 4: Continuous $F_1$-Score Trajectory Analysis across Top-$K$ Thresholds}{14}{section.4}%
\contentsline {subsection}{\numberline {4.1}Methodological Context and Cross-Disease Trends}{14}{subsection.4.1}%
\contentsline {subsection}{\numberline {4.2}Disease-Specific $F_1$-Score Comparison Curves}{14}{subsection.4.2}%
\contentsline {section}{\numberline {5}Section 5: Enrichment Analysis}{19}{section.5}%
