X-amine509: Predicting the Practical Risk Level of Enterprise X.509 Certificates

Abstract: Enterprises managing large X.509 certificate inventories face a prioritization problem: deterministic analysis tools that precisely identify standards violations are indispensable for remediation, but applying them exhaustively across millions of certificates is operationally impractical. We present X-amine509, a two-stage triage system that uses machine learning to rapidly rank certificates by predicted risk and route only the highest-risk items to full deterministic analysis. Certificate risk is quantified as a composite score derived from 177 defect checks grounded in CA/Browser Forum Baseline Requirements, NIST IR 8547/SP 800-57, and cryptographic strength criteria, weighted by security severity across four tiers ranging from cryptographic breaks to minor compliance deviations. We collected 1,027,714 X.509 certificates from Fortune 500, .gov, and .edu domains and scored each using this rubric. On a held-out test set of 201,976 certificates, our best model (Extra Trees) achieves $R<sup>2$ of 0.993 with MAE of 2.26, while Decision Tree scores $R<sup>2$ of 0.986 at 3.7 million certificates per second on a single machine. Ranking quality confirms the triage value: aggregate NDCG exceeds 0.997, and severity-tier classification reports 99.76% accuracy with 98.90% recall on critical-tier defects. Thirteen months later, we retrieved another 571,374 certificates to test our models' durability over time, and the Extra Trees and Decision Tree models maintain MAE below 6.8, $R<sup>2$ of at least 0.915, aggregate NDCG above 0.988, severity-tier accuracy of at least 99.52%, and critical-tier recall of at least 97.03%. Feature importance analysis identifies validity period, Extended Key Usage configuration, negative serial number encoding, and self-signed status as the strongest risk predictors, providing coarse interpretability at the triage stage.