Contextual Phenotyping of Pediatric Sepsis Cohort Using Large Language Models

Abstract

The clustering of patient subgroups is essential for personalized care and efficient use of resources. Traditional clustering methods struggle with high-dimensional heterogeneous healthcare data and lack contextual understanding. This study evaluates clustering based on the Large Language Model (LLM) against classical methods using a pediatric sepsis dataset from a low-income country (LIC), containing 2,686 records with 28 numerical variables and 119 categorical variables. Patient records were serialized into text with and without a clustering objective. Embeddings were generated using quantized LLAMA 3.1 8B, DeepSeek-R1-Distill-Llama-8B with low-rank adaptation(LoRA), and Stella-En-400M-V5 models. K-means clustering was applied to these embeddings. Classical comparisons included K-Medoids clustering on UMAP and FAMD-reduced mixed data. Silhouette scores and statistical tests evaluated the quality and distinctiveness of the cluster. Stella-En-400M-V5 achieved the highest Silhouette Score (0.86). LLAMA 3.1 8B with the clustering objective performed better with a higher number of clusters, identifying subgroups with distinct nutritional, clinical, and socioeconomic profiles. LLM-based methods outperformed classical techniques by capturing richer context and prioritizing key features. These results highlight the potential of LLMs for contextual phenotyping and informed decision making in resource-limited settings.