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Predicting Antimicrobial Resistance (AMR) in Campylobacter, a Foodborne Pathogen, and Cost Burden Analysis Using Machine Learning
Mishra, Shubham, Han, The Anh, Lopes, Bruno Silvester, Ghareeb, Shatha, Shamszaman, Zia Ush
Antimicrobial resistance (AMR) poses a significant public health and economic challenge, increasing treatment costs and reducing antibiotic effectiveness. This study employs machine learning to analyze genomic and epidemiological data from the public databases for molecular typing and microbial genome diversity (PubMLST), incorporating data from UK government-supported AMR surveillance by the Food Standards Agency and Food Standards Scotland. We identify AMR patterns in Campylobacter jejuni and Campylobacter coli isolates collected in the UK from 2001 to 2017. The research integrates whole-genome sequencing (WGS) data, epidemiological metadata, and economic projections to identify key resistance determinants and forecast future resistance trends and healthcare costs. We investigate gyrA mutations for fluoroquinolone resistance and the tet(O) gene for tetracycline resistance, training a Random Forest model validated with bootstrap resampling (1,000 samples, 95% confidence intervals), achieving 74% accuracy in predicting AMR phenotypes. Time-series forecasting models (SARIMA, SIR, and Prophet) predict a rise in campylobacteriosis cases, potentially exceeding 130 cases per 100,000 people by 2050, with an economic burden projected to surpass 1.9 billion GBP annually if left unchecked. An enhanced Random Forest system, analyzing 6,683 isolates, refines predictions by incorporating temporal patterns, uncertainty estimation, and resistance trend modeling, indicating sustained high beta-lactam resistance, increasing fluoroquinolone resistance, and fluctuating tetracycline resistance.
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- Europe > United Kingdom > England > Oxfordshire > Oxford (0.04)
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- Research Report > New Finding (1.00)
- Research Report > Experimental Study (0.89)
- Information Technology > Artificial Intelligence > Machine Learning > Ensemble Learning (0.57)
- Information Technology > Artificial Intelligence > Machine Learning > Decision Tree Learning (0.57)
- Information Technology > Artificial Intelligence > Machine Learning > Neural Networks > Deep Learning (0.48)
Return of EM: Entity-driven Answer Set Expansion for QA Evaluation
Lee, Dongryeol, Lee, Minwoo, Min, Kyungmin, Park, Joonsuk, Jung, Kyomin
Recently, directly using large language models (LLMs) has been shown to be the most reliable method to evaluate QA models. However, it suffers from limited interpretability, high cost, and environmental harm. To address these, we propose to use soft exact match (EM) with entitydriven answer set expansion. Our approach expands the gold answer set to include diverse surface forms, based on the observation that the surface forms often follow particular patterns depending on the entity type. The experimental results show that our method outperforms traditional evaluation methods by a large margin. Moreover, the reliability of our evaluation method is comparable to that of LLM-based ones, while offering the benefits of high interpretability and reduced environmental harm.
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- North America > Canada > British Columbia > Metro Vancouver Regional District > Vancouver (0.28)
- North America > Canada > Ontario > Toronto (0.14)
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- Media > Television (1.00)
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