iLoRA: Bayesian Low-Rank Adaptation with Latent Interaction Graphs for Microbiome Diagnosis

Parameter-efficient adaptation has made LLMs practical for domain prediction, but standard LoRA still relies on a static low-rank update and does not expose the latent interactions that often drive scientific labels. We introduce iLoRA. To our knowledge, it is the first Bayesian graph-conditioned LoRA framework. It infers a latent interaction graph from the input and uses it to generate input-conditioned LoRA updates. As a result, iLoRA learns prediction and latent interaction structure jointly, rather than training a predictor and applying interaction analysis only post hoc. We instantiate this idea for microbiome diagnosis, where disease state can depend on both species-level abundance and microbe-microbe cross-talk, and evaluate it in two complementary settings: interactive QA with human-annotated graphs, which tests latent structure recovery, and multi-cohort IBD diagnosis, which tests biomedical utility. Across both settings, iLoRA improves over strong LoRA and Bayesian adaptation baselines, recovers graphs aligned with human annotations and cohort-level microbiome associations, and provides calibrated uncertainty with moderate graph-branch overhead.