Forecasting Bacterial Antimicrobial Resistance Trends Using Machine Learning on WHO GLASS Surveillance Data: A Retrieval-Augmented Generation Approach for Policy Decision Support
cs.LG, q-bio.QM
Submitted: 2026-02-26
Updated: 2026-09-26
Comments: v3: correction. A leakage audit found four defects in the v2 feature construction; on the corrected panel a persistence forecast (MAE 5.79 pp) significantly beats XGBoost (6.55 pp, p = 0.001) and the v2 claim of an 85.3% improvement is withdrawn. See the Correction notice. Code and corrected panel: github.com/TanvirTurja/amr-forecasting-rag ; full reanalysis under journal review
Code: https://github.com/TanvirTurja/amr-forecasting-rag
License: http://creativecommons.org/licenses/by/4.0/
The gist: Background: Antimicrobial resistance (AMR) is a global health threat.
Terminology
Abstract
Background: Antimicrobial resistance (AMR) is a global health threat. While the WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) provides standardized data, population-level machine learning forecasting of resistance trends remains limited. Translating forecasts into policy also requires transparent interpretation. Methods: Surveillance data (2021-2023) comprising 5,909 observations across 44 countries and five WHO regions were processed. Six models (Naive, Linear, Ridge, XGBoost, LightGBM, LSTM) were benchmarked to forecast one-year-ahead resistance rates using prior-year resistance, antibiotic consumption, and related features. MAE, RMSE, and sMAPE were computed with 95% bootstrap confidence intervals for MAE. A local Retrieval-Augmented Generation (RAG) system (Gemma 4) translated forecast findings into policy guidance grounded in WHO documents. Results: XGBoost achieved the best predictive performance (test MAE = 6.13% [95% CI: 5.83-6.44]), an 85.3% error reduction versus the naive baseline (MAE = 41.79%). SHAP analysis identified prior-year resistance as the dominant predictor (50.5% gain). Regional forecast error tracked surveillance coverage, from 3.65% in the European Region to 8.61% in South-East Asia. The RAG pipeline generated source-attributed policy responses without fabricated citations. Conclusion: Short-term AMR resistance rates exhibit strong temporal autocorrelation that can be accurately forecasted using gradient boosting. Coupling these forecasts with a hallucination-resistant RAG system provides a scalable, evidence-based decision-support framework for AMR governance. v3 correction: a leakage audit found feature-construction defects; on the corrected panel a persistence forecast (MAE 5.79) significantly outperforms XGBoost (6.55), and the 85.3% claim is withdrawn (see Correction).
Sources
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