FROM ALGORITHMS TO AGRICULTURE: APPLYING AI METHODS TO PREDICT KIDNEY DISEASE IN FARMWORKERS

 

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FROM ALGORITHMS TO AGRICULTURE: APPLYING AI METHODS TO PREDICT KIDNEY DISEASE IN FARMWORKERS

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Shuchi
Anand
Yusuf Ashktorab yusufashk@gmail.com Howard University College of Medicine Medicine Washington, D.C. United States -
Santhushya Hewapathiranage santhushya@gmail.com National Hospital Kandy Center for Research Kandy Sri Lanka -
Xue Yu xueyu@stanford.edu Stanford University Division of Nephrology, Department of Medicine Palo Alto, CA United States -
Shuchi Anand sanand2@stanford.edu Stanford University Division of Nephrology, Department of Medicine Palo Alto, CA United States *
Rohana Chandrajith rohanac@sci.pdn.ac.lk National Hospital Kandy Center for Research Kandy Sri Lanka -
Nishantha Nanyakkara nishantha4313@gmail.com National Hospital Kandy Center for Research Kandy Sri Lanka -
Maria Montez-Rath mmrath@stanford.edu Stanford University Division of Nephrology, Department of Medicine Palo Alto, CA United States -
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Chronic Kidney Disease of unknown etiology (CKDu) is a progressive form of kidney damage that disproportionately affects agricultural communities in Sri Lanka, Central America, and parts of India, with emerging hotspots also suspected in the South and Western United States. Despite extensive investigation, the underlying causes of CKDu remain unclear, partly because of a potential long lag between exposure and eventual symptomatic presentation of kidney disease. We applied machine learning (ML) and large language models (LLMs) to explore predictive tools for disease progression in a cohort of persons with CKDu, with the hypothesis that early identification of persons likely to experience kidney function decline will facilitate investigation of proximal (causative) exposures.

We analyzed baseline data (labs demographics) from 244 participants enrolled in Kidney Progression Project (KiPP), a prospective cohort of farmworkers with kidney disease in Sri Lanka launched in 2018. Among these participants, 22 progressed to the study’s primary outcome (eGFR<15 mL/min/1.73 m²) by the year 2024. For model development, we used data from the first 2.5 years of follow-up.

We developed and optimized several ML classifiers including logistic regression, support vector machines, random forests, and XGBoost. Each model was trained using stratified five-fold cross-validation, and class imbalance was addressed using SMOTE-based oversampling. To identify underlying patterns in the dataset, we applied unsupervised models like K-means clustering(k=7), and the resulting cluster labels were included as categorical features in supervised learning models. Model performance was evaluated using standard classification metrics, and interpretability was assessed using SHAP (SHapley Additive exPlanations).

Additionally, we used clinical vignettes from KiPP data to evaluate the predictive capabilities of LLMs. We tested five LLMs through SecureGPT on their ability to predict progression.

The best performing ML model was an XGBoost classifier (ROC-AUC= 0.84; F1 score= 0.48). SHAP analysis identified cluster membership and serum uric acid as key predictors. Among the LLMs, GPT 4.5 performed best (Accuracy= 87%; F1 score of 0.42). Both models outperformed existing methods (eGFR slope, Accuracy=67%, F1 score=0.23).  

 Figure 1. Bar plots comparing LLM’s results across the two prompts: With baseline labs and without

Figure 2. A. UMAP colored by K-Means clusters, using baseline labs and eGFR values

 Figure 2. B. Heatmap showing standardized feature differences across clusters, highlighting distinct profiles in Cluster 2.

Table 1. Best Machine Learning model results.

 Figure 3.  SHAP summary plot showing the top features contributing to the XGBoost model for predicting rapid kidney function decline (CKDu). Each point represents an individual, with SHAP values reflecting the impact of that feature on the model output. Features are ranked by overall importance (top to bottom). Color denotes the feature value for that individual (red = high, blue = low). This plot enables interpretation of feature influence on predictions at both the global and individual level.


Our findings demonstrate that both traditional ML models and LLMs can predict CKDu progression from limited clinical data. Custom-tailored ML models slightly outperformed generative AI models such as GPT-4.5. With continued refinement, these tools may not only support early identification of high risk individuals but also aid in identifying causes of CKDu. Future directions include external validation using ongoing international cohorts and incorporation of longitudinal laboratory data to generate clinically-deployable AI tools.


This abstract has been submitted to the 2025 Interim AMA Poster Showcase.

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