Forecasting Bacterial Antimicrobial Resistance Trends Using Machine Learning on WHO GLASS Surveillance Data: A Retrieval-Augmented Generation Approach for Policy Decision Support

Public health forecasts must respond to abrupt changes in surveillance data without over-extrapolating noise, reporting artifacts, or temporary trends. We evaluated autoregressive integrated moving average (ARIMA), random forest, and extreme gradient boosting (XGBoost) models using 190 weekly observations of publicly available Ontario COVID-19 case counts from January 2020 to October 2023. Rolling-origin time-series cross-validation preserved temporal order during model tuning and evaluation. Performance was assessed across three operating dimensions: responsiveness following selected turning points, forecast horizons of one to six weeks, and the amount of historical training data. We also developed Machine Learning and ARIMA Model Averaging (MLAMA), a non-negative performance-weighted ensemble with weights that vary by forecast horizon and responsiveness setting. Retrospective comparisons showed that ARIMA adapted rapidly after turning points but its normalized error increased at longer horizons. Random forest and XGBoost were less responsive initially but maintained more stable normalized error over longer horizons. For two-week forecasts at the end of the study period, training on the most recent data outperformed using longer historical periods, particularly for XGBoost. MLAMA achieved the lowest normalized mean absolute percentage error across most forecast horizons and ranked among the best-performing methods across responsiveness settings. These findings support selecting forecasting models according to operating conditions rather than relying on a single universally preferred approach. MLAMA provides a practical framework for combining complementary statistical and machine-learning forecasts. The accompanying Python package is currently maintained in a private repository while software validation and reproducibility testing are completed.

Antimicrobial resistance (AMR) poses a global health threat, reducing the effectiveness of antibiotics and complicating clinical decision-making. To address this challenge, we introduce abx_amr_simulator, a Python-based simulation package designed to model antibiotic prescribing and AMR dynamics within a controlled, reinforcement learning (RL)-compatible environment. The simulator allows users to specify patient populations, antibiotic-specific AMR response curves, and reward functions that balance immedi- ate clinical benefit against long-term resistance management. Key features include a modular design for configuring patient attributes, antibiotic resistance dynamics modeled via a leaky-balloon abstraction, and tools to explore partial observability through noise, bias, and delay in observations. The package is compatible with the Gymnasium RL API, enabling users to train and test RL agents under diverse clinical scenarios. From an ML perspective, the package provides a configurable benchmark environment for sequential decision-making under uncertainty, including partial observability induced by noisy, biased, and delayed observations. By providing a customizable and extensible framework, abx_amr_simulator offers a valuable tool for studying AMR dynamics and optimizing antibiotic stewardship strategies under realistic uncertainty.

Accurate blood glucose forecasting using continuous glucose monitoring (CGM) data can support the early prediction of dysglycemic risk. However, current neural-network-based forecasting models treat CGM data as a purely numerical sequence without integrating the contextual information contained in CGM signal morphology. Recently, large language models (LLMs) have shown promise for time-series forecasting, yet their role as agentic context extractors in diabetes care remains largely unexplored. In this study, we bridge glucose forecasting and LLM-based contextualization by developing GlyRAG, a context-aware, retrieval-augmented forecasting framework that uses an LLM as a contextualization agent to summarize glucose morphology directly from a timed CGM window. The generated CGM-only narrative is embedded and fused with patch-based glucose representations, while a retrieval module incorporates similar historical training episodes through cross-attention. We evaluate GlyRAG on the OhioT1DM and AZT1D datasets for 5-, 30-, and 60-minute forecasting horizons. Compared with strong CGM-only baselines, GPT-4 GlyRAG significantly improves long-horizon root mean square error (RMSE) over PatchTST on both datasets. For example, RMSE decreases from 13.8 to 10.6 at 30 minutes and from 23.1 to 20.2 at 60 minutes on OhioT1DM. LLaMA 3.1 produces smaller but significant long-horizon gains, suggesting that the contextualization pipeline is not limited to GPT-4. Clinical error-grid analyses further show that approximately 85 percent of predictions fall within the clinically acceptable Clarke Error Grid Zones A and B. These results suggest that CGM-derived linguistic context and case-based retrieval can improve long-horizon glucose forecasting without requiring additional sensing modalities.