REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation

In electronic health record (EHR) mining, learning high-quality representations of medical concepts (e.g., standardized diagnosis, medication, and procedure codes) is fundamental for downstream clinical prediction. However, ro bust concept representation learning is hindered by two key challenges: (i) clinically important cross-type dependencies (e.g., diagnosis medication and medication-procedure relations) are often missing or incomplete in existing ontology resources, limiting the ability to model complex EHR patterns; and (ii) rich clinical semantics are often missing from structured resources, and even when available as text, are difficult to integrate with KG structure for representation learning. To address these challenges, we present MedCo, an LLM empowered graph learning framework for medical concept representation. MedCo first builds a global knowledge graph (KG) over medical codes by combining statistically reliable associations mined from EHRs with type-constrained LLM prompting to infer semantic relations. It then utilizes LLMs to enrich the KG into a text-attributed graph by generating node descriptions and edge rationales, providing semantic signals for both concepts and their relationships. Finally, MedCo jointly trains a LoRA-tuned LLaMA text encoder with a heterogeneous GNN, fusing text semantics and graph structure into unified concept embeddings. Extensive experiments on MIMIC-III and MIMIC-IV show that MedCo consistently improves prediction performance and serves as an effective plug-in concept encoder for standard EHR pipelines.

Language models (LMs) offer strong textual representations for electronic health records (EHRs), but they encode patient sequences in isolation and provide limited explainability. Graph neural networks (GNNs) complement LMs by incorporating inter-patient relationships and enabling reference-patient attribution, yet they rely on high-quality patient representations. We propose Patients-like-me (PLM), a unified LM--GNN framework that integrates local patient semantics with global cohort structure. To train PLM efficiently, we introduce a Variational Expectation-Maximization algorithm that alternates LM and GNN updates under a supervised variational objective. Extensive experiments on MIMIC-III and MIMIC-IV show that PLM consistently outperforms state-of-the-art methods, with improvements generalizing across encoder-only and decoder-only LM backbones. These gains are achieved with only modest additional computational overhead. PLM also provides reference-patient explanations by retrieving influential similar patients, while edge-masking experiments confirm that the highest-ranked references have the greatest impact on model predictions.

Post-discharge risk prediction from electronic health records (EHRs) is difficult because many dependencies that link discharge-time observations to downstream complications, such as comorbidity cascades and drug-disease interactions, are absent from the record. External medical knowledge graphs (KGs) can supply these missing dependencies, but tracing them demands three properties: KG exploration must remain cost-bounded, retrieved evidence must be differentiated by source quality, and the resulting rationale must be citable for retrospective review. Large language models (LLMs) can plan and verify over structured evidence, making them natural candidates for KG reasoning, but existing LLM-based methods do not satisfy these three properties jointly. In this paper, we propose BAR, a Budget-Aware LLM Reasoning framework over medical KGs with three contributions. First, BAR refines the raw KG into disease-specific evidence graphs whose edges carry support scores and provenance records, turning the KG into a quality-annotated reasoning space rather than a static feature source. Second, an LLM then reasons over this graph through a plan-navigate-verify loop that decomposes the question into steps, retrieves evidence under a patient-specific budget, and revises when verification fails. Third, a reasoning policy is trained with a reward that compares predictions with and without acquired evidence, combined with acquisition cost and citation-integrity terms. Across 8 diseases and 3 prediction horizons on MIMIC-III and MIMIC-IV, BAR improves AUPRC by 3.4 points over the strongest baseline, raises citation precision from 59.8% to 77.9%, and consumes only 62-65% of the budget cap.