@inproceedings{kerdabadi-etal-2026-refine,
title = "{REFINE}: {LLM} Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation",
author = "Kerdabadi, Mohsen Nayebi and
Moghaddam, Arya Hadizadeh and
Wang, Dongjie and
Yao, Zijun",
editor = "Lee, Hung-Yi and
Dev, Sunipa and
Li, Jessy and
Elliott, Desmond",
booktitle = "Proceedings of the 2026 Conference on Empirical Methods in Natural Language Processing",
month = oct,
year = "2026",
address = "Budapest, Hungary",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2026.emnlp-main.1919/",
pages = "43714--43730",
ISBN = "979-8-89176-459-0",
abstract = "Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medical relations together with textual semantics. However, most existing encoders process concepts uniformly across patients, despite the fact that a code{'}s meaning and predictive value depend on patient-specific clinical context and trajectory. Learning patient-personalized concept representations from TKGs introduces two key challenges: (1) deciding how much KG context to incorporate for each observed code, and (2) aligning semantic information with the patient-specific relational structure. We propose REFINE, a KG-aware budgeted LLM graph refinement framework for patient-personalized medical concept encoding. Starting from a global TKG, REFINE constructs patient-specific temporal graphs. A sequential reinforcement learning policy selects a personalized KG expansion budget for each observed code. The resulting patient graph is processed by a heterogeneous GNN to capture relation-aware structural dependencies, while a frozen LLM uses graph-aware soft prompts to semantically refine concept representations. Experiments on MIMIC-III and MIMIC-IV show that REFINE consistently improves diverse EHR backbones, outperforms strong baselines, and demonstrates robust gains across component ablation, KG selection, and data insufficiency."
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<abstract>Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medical relations together with textual semantics. However, most existing encoders process concepts uniformly across patients, despite the fact that a code’s meaning and predictive value depend on patient-specific clinical context and trajectory. Learning patient-personalized concept representations from TKGs introduces two key challenges: (1) deciding how much KG context to incorporate for each observed code, and (2) aligning semantic information with the patient-specific relational structure. We propose REFINE, a KG-aware budgeted LLM graph refinement framework for patient-personalized medical concept encoding. Starting from a global TKG, REFINE constructs patient-specific temporal graphs. A sequential reinforcement learning policy selects a personalized KG expansion budget for each observed code. The resulting patient graph is processed by a heterogeneous GNN to capture relation-aware structural dependencies, while a frozen LLM uses graph-aware soft prompts to semantically refine concept representations. Experiments on MIMIC-III and MIMIC-IV show that REFINE consistently improves diverse EHR backbones, outperforms strong baselines, and demonstrates robust gains across component ablation, KG selection, and data insufficiency.</abstract>
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%0 Conference Proceedings
%T REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation
%A Kerdabadi, Mohsen Nayebi
%A Moghaddam, Arya Hadizadeh
%A Wang, Dongjie
%A Yao, Zijun
%Y Lee, Hung-Yi
%Y Dev, Sunipa
%Y Li, Jessy
%Y Elliott, Desmond
%S Proceedings of the 2026 Conference on Empirical Methods in Natural Language Processing
%D 2026
%8 October
%I Association for Computational Linguistics
%C Budapest, Hungary
%@ 979-8-89176-459-0
%F kerdabadi-etal-2026-refine
%X Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medical relations together with textual semantics. However, most existing encoders process concepts uniformly across patients, despite the fact that a code’s meaning and predictive value depend on patient-specific clinical context and trajectory. Learning patient-personalized concept representations from TKGs introduces two key challenges: (1) deciding how much KG context to incorporate for each observed code, and (2) aligning semantic information with the patient-specific relational structure. We propose REFINE, a KG-aware budgeted LLM graph refinement framework for patient-personalized medical concept encoding. Starting from a global TKG, REFINE constructs patient-specific temporal graphs. A sequential reinforcement learning policy selects a personalized KG expansion budget for each observed code. The resulting patient graph is processed by a heterogeneous GNN to capture relation-aware structural dependencies, while a frozen LLM uses graph-aware soft prompts to semantically refine concept representations. Experiments on MIMIC-III and MIMIC-IV show that REFINE consistently improves diverse EHR backbones, outperforms strong baselines, and demonstrates robust gains across component ablation, KG selection, and data insufficiency.
%U https://aclanthology.org/2026.emnlp-main.1919/
%P 43714-43730
Markdown (Informal)
[REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation](https://aclanthology.org/2026.emnlp-main.1919/) (Kerdabadi et al., EMNLP 2026)
ACL