Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Chen Chen, Dongjie Wang, Zijun Yao. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Large-scale Electronic Health Record (EHR) databases have become indispensable in supporting clinical decision-making through data-driven treatment recommendations. However, existing medication recommender methods often struggle with a user (i.e., patient) cold-start problem, where recommendations for new patients are usually unreliable due to the lack of sufficient prescription history for patient profiling. While prior studies have utilized medical knowledge graphs to connect medication concepts through pharmacological or chemical relationships, these methods primarily focus on mitigating the item cold-start issue and fall short in providing personalized recommendations that adapt to individual patient characteristics. Meta-learning has shown promise in handling new users with sparse interactions in recommender systems. However, its application to EHRs remains underexplored due to the unique sequential structure of EHR data. To tackle these challenges, we propose MetaDrug, a multi-level, uncertainty-aware meta-learning framework designed to address the patient cold-start problem in medication recommendation. MetaDrug proposes a novel two-level meta-adaptation mechanism, including self-adaptation, which adapts the model to new patients using their own medical events as support sets to capture temporal dependencies; and peer-adaptation, which adapts the model using similar visits from peer patients to enrich new patient representations. Meanwhile, to further improve meta-adaptation outcomes, we introduce an uncertainty quantification module that ranks the support visits and filters out the unrelated information for adaptation consistency. We evaluate our approach on the MIMIC-III and Acute Kidney Injury (AKI) datasets. Experimental results on both datasets demonstrate that MetaDrug consistently outperforms state-of-the-art medication recommendation methods on cold-start patients.

Medical ontology graphs map external knowledge to medical codes in electronic health records (EHRs) via structured relationships. By leveraging domain-approved connections (e.g., parent-child), predictive models can generate richer medical concept representations by incorporating contextual information from related concepts. However, existing literature primarily focuses on incorporating domain knowledge from a single ontology system, or from multiple ontology systems (e.g., diseases, drugs, and procedures) in isolation, without integrating them into a unified learning structure. Consequently, concept representation learning often remains limited to intra-ontology relationships, overlooking cross-ontology connections that could enhance the richness of healthcare representations. In this paper, we propose LINKO, a large language model (LLM)-augmented integrative ontology learning framework that leverages multiple ontology graphs simultaneously by enabling dual-axis knowledge propagation both within and across heterogeneous ontology systems to enhance medical concept representation learning. Specifically, LINKO first employs LLMs to provide a graph-retrieval-augmented initialization for ontology concept embedding, through an engineered prompt that includes concept descriptions, and is further augmented with ontology graph relations and task-specific details. Second, our method jointly learns the medical concepts in diverse ontology graphs by performing knowledge propagation in two axes: (1) intra-ontology vertical propagation across hierarchical ontology levels and (2) inter-ontology horizontal propagation within every level in parallel. Last, through extensive experiments on two public datasets, we validate the superior performance of LINKO over state-of-the-art baselines. As a plug-in encoder compatible with existing EHR predictive models, LINKO further demonstrates enhanced robustness in scenarios involving limited data availability and rare disease prediction.

Over the past decade, significant advancements in mining electronic health records (EHRs) have enabled a broad range of decision-support applications and offered an unprecedented capacity for predicting critical events such as disease prognosis and mortality in healthcare. Despite the availability of comprehensive coding systems in EHRs (e.g., ICD-9), which are designed to record diverse information on diseases, procedures, and medications over time, the complex and dynamic dependencies among the recorded data are usually not captured. This limitation often hinders the contextual understanding of medical observations for effective EHR representation learning. Therefore, there is a compelling need to discover a hidden “EHR graph” that represents the medical relationship between the observed features according to a patient’s history. These hidden graphs consisting of the medical codes from the same visits can offer a comprehensive insight derived from disease-to-disease, disease-to-drug, and drug-to-drug dependencies. However, it is still unclear how to address the challenge that the dependencies may vary from patient to patient, and they can dynamically evolve from one visit to another. To this end, we propose Time-aware Personalized Graph Transformer (TPGT), a novel attention-based time-aware hidden graph model, that captures the personalized graphical structures among observed medical codes and summarizes the temporal code dependencies over time to improve patient representation for outcome prediction. Built upon an intra-visit and an inter-visit dual-attention mechanism to model patients’ EHR graphs, our model offers an interpretability of what diagnosis or medication in a patient’s history can interact, and how those interactions may change over time. We conduct extensive experiments on two real-world EHR datasets for different healthcare predictive tasks: acute kidney injury (AKI) prediction and ICU mortality prediction. The experimental results demonstrate a significant performance improvement of the proposed model over baselines through multi-aspect quantitative evaluation. Furthermore, we perform various qualitative studies to validate the interpretability of the model which highlights the application of the proposed method in the context of personalized medicine.

Recent advancements in sequential modeling applied to Electronic Health Records (EHR) have greatly influenced prescription recommender systems. While the recent literature on drug recommendation has shown promising performance, the study of discovering a diversity of coexisting temporal relationships at the level of medical codes over consecutive visits remains less explored. The goal of this study can be motivated from two perspectives. First, there is a need to develop a sophisticated sequential model capable of disentangling the complex relationships across sequential visits. Second, it is crucial to establish multiple and diverse health profiles for the same patient to ensure a comprehensive consideration of different medical intents in drug recommendation. To achieve this goal, we introduce Attentive Recommendation with Contrasted Intents (ARCI), a multi-level transformer-based method designed to capture the different but coexisting temporal paths across a shared sequence of visits. Specifically, we propose a novel intent-aware method with contrastive learning, that links specialized medical intents of the patients to the transformer heads for extracting distinct temporal paths associated with different health profiles. We conducted experiments on two real-world datasets for the prescription recommendation task using both ranking and classification metrics. Our results demonstrate that ARCI has outperformed the state-of-the-art prescription recommendation methods and is capable of providing interpretable insights for healthcare practitioners.

Survival analysis plays a crucial role in many healthcare decisions, where the risk prediction for the events of interest can support an informative outlook for a patient's medical journey. Given the existence of data censoring, an effective way of survival analysis is to enforce the pairwise temporal concordance between censored and observed data, aiming to utilize the time interval before censoring as partially observed time-to-event labels for supervised learning. Although existing studies mostly employed ranking methods to pursue an ordering objective, contrastive methods which learn a discriminative embedding by having data contrast against each other, have not been explored thoroughly for survival analysis. Therefore, in this paper, we propose a novel Ontology-aware Temporality-based Contrastive Survival (OTCSurv) analysis framework that utilizes survival durations from both censored and observed data to define temporal distinctiveness and construct negative sample pairs with adjustable hardness for contrastive learning. Specifically, we first use an ontological encoder and a sequential self-attention encoder to represent the longitudinal EHR data with rich contexts. Second, we design a temporal contrastive loss to capture varying survival durations in a supervised setting through a hardness-aware negative sampling mechanism. Last, we incorporate the contrastive task into the time-to-event predictive task with multiple loss components. We conduct extensive experiments using a large EHR dataset to forecast the risk of hospitalized patients who are in danger of developing acute kidney injury (AKI), a critical and urgent medical condition. The effectiveness and explainability of the proposed model are validated through comprehensive quantitative and qualitative studies.