arXiv subjects

Dohyun Ku

Publications and source records attributed to Dohyun Ku.

2 recordsLinked to original sources

arXiv2026

MetaboLLM: a metabolomics-specialized large language model for biochemical knowledge integration and predictive metabolite graph construction

Metabolomics knowledge is distributed across heterogeneous resources and remains difficult to translate into predictive representations. We developed MetaboLLM, a metabolomics-specialized large language model adapted through continual pretraining, supervised fine-tuning, and structured retrieval, together with MetaboLLM-GIN, which converts generated biochemical descriptions into metabolite graphs for patient-level prediction using a graph isomorphism network. Across four backbone families, MetaboLLM outperformed corresponding base and medically adapted models on metabolomics knowledge, relational, and description tasks, and transferred to an external public benchmark. MetaboLLM-GIN achieved the highest AUC for stress hyperglycemia prediction after coronary artery bypass grafting (0.8616) and postmenopausal hormone-regimen classification (0.8123), outperforming conventional models, alternative graph constructions, and graphs generated from unadapted or non-retrieval LLM configurations. Model interpretation further produced biologically meaningful findings in both applications. These results show that domain-specialized language models can organize heterogeneous biochemical knowledge into predictive and interpretable metabolite graph representations.

cs.LG↗

arXiv2025

MAGIC: Multi-task Gaussian process for joint imputation and classification in healthcare time series

Time series analysis has emerged as an important tool for improving patient diagnosis and management in healthcare applications. However, these applications commonly face two critical challenges: time misalignment and data sparsity. Traditional approaches address these issues through a two-step process of imputation followed by prediction. We propose MAGIC (Multi-tAsk Gaussian Process for Imputation and Classification), a novel unified framework that simultaneously performs class-informed missing value imputation and label prediction within a hierarchical multi-task Gaussian process coupled with functional logistic regression. To handle intractable likelihood components, MAGIC employs Taylor expansion approximations with bounded error analysis, and parameter estimation is performed using EM algorithm with block coordinate optimization supported by convergence analysis. We validate MAGIC through two healthcare applications: prediction of post-traumatic headache improvement following mild traumatic brain injury and prediction of in-hospital mortality within 48 hours after ICU admission. In both applications, MAGIC achieves superior predictive accuracy compared to existing methods. The ability to generate real-time and accurate predictions with limited samples facilitates early clinical assessment and treatment planning, enabling healthcare providers to make more informed treatment decisions.

stat.ML↗