arXiv subjects

Min Gu Kwak

Publications and source records attributed to Min Gu Kwak.

6 recordsLinked to original sources

arXiv2026

MedRAGChecker: Claim-Level Verification for Biomedical Retrieval-Augmented Generation

Biomedical retrieval-augmented generation (RAG) can ground LLM answers in medical literature, yet long-form outputs often contain isolated unsupported or contradictory claims with safety implications. We introduce MedRAGChecker, a claim-level verification and diagnostic framework for biomedical RAG. Given a question, retrieved evidence, and a generated answer, MedRAGChecker decomposes the answer into atomic claims and estimates claim support by combining evidence-grounded natural language inference (NLI) with biomedical knowledge-graph (KG) consistency signals. Aggregating claim decisions yields answer-level diagnostics that help disentangle retrieval and generation failures, including faithfulness, under-evidence, contradiction, and safety-critical error rates. To enable scalable evaluation, we distill the pipeline into compact biomedical models and use an ensemble verifier with class-specific reliability weighting. Experiments on four biomedical QA benchmarks show that MedRAGChecker reliably flags unsupported and contradicted claims and reveals distinct risk profiles across generators, particularly on safety-critical biomedical relations.

cs.CL↗

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↗

arXiv2026

BrainNormalizer: Anatomy-Informed Pseudo-Healthy Brain Reconstruction from Tumor MRI via Edge-Guided ControlNet

Brain tumors induce complex structural deformations that obscure the patient' s original neuroanatomy, making it difficult to distinguish tumor-induced changes from inherent anatomical variability. Reconstructing a subject-specific pseudo-healthy brain can provide a critical reference for such analysis, but this task is inherently counterfactual, as paired pre-tumor scans and explicit healthy guidance are unavailable. We propose BrainNormalizer, a diffusion-based framework for subject-specific pseudo-healthy brain MRI reconstruction that enables anatomy-informed reconstruction without requiring paired data or explicit healthy references. The framework learns anatomical priors and edge-based structural conditioning through a two-stage training strategy consisting of inpainting-based diffusion fine-tuning and ControlNet-based edge conditioning. At inference, counterfactual pseudo-healthy reconstruction is achieved through a deliberate misalignment strategy, where tumorous inputs are paired with non-tumorous prompts and mirrored contralateral edge maps. This allows subject-specific anatomical guidance to be constructed from the patient's own anatomy, enabling anatomically consistent pseudo-healthy reconstruction that preserves individual structural characteristics. Experiments on the BraTS2020 dataset demonstrate that BrainNormalizer achieves improved distributional realism, symmetry-based structural consistency, and reduced false positive detection compared to existing methods. These results indicate that the proposed framework provides a principled approach for subject-specific counterfactual reconstruction and supports downstream analysis of tumor-induced deformation.

eess.IV↗

arXiv2026

What Makes a Medical Checker Trainable? Diagnosing Signal Collapse and Reward Hacking in Checker-Guided RAG for Biomedical QA

Medical RAG needs evidence-grounded claims, so plugging a claim-level NLI checker into retrieval-augmented RL is intuitive. \textbf{We find that the checker's \emph{output distribution} during training, not its held-out accuracy, decides whether it provides trainable gradient.} We compare four NLI checker back-ends as process rewards inside a GRPO-trained medical RAG agent (Qwen2.5-7B, replicated on Qwen3-4B and Llama-3.1-8B) across four held-out medical QA benchmarks. Three diagnostic findings emerge. \textbf{(i)} Signal collapse is log-prob-specific: LLM log-probability scoring labels over 97\% of claims neutral -- collapsing the RL gradient to zero -- while a calibrated MedNLI classifier scores the same pairs non-degenerately. \textbf{(ii)} Moderate signal beats strong signal on answer quality: a strong proprietary checker triggers a three-step reward-hacking cascade -- ultra-short answers, search avoidance, language collapse -- so a moderate-signal local classifier trains a higher-quality model (\textbf{+12\% BERTScore over zero-shot, no GPT dependency}). \textbf{(iii)} Signal strength is policy-dependent: the same checker registers as moderate on one policy but strong on another without triggering the cascade end-state. We frame these as boundary conditions for verifier-as-reward systems.

cs.CL↗

arXiv2025

Generative Foundation Model for Structured and Unstructured Electronic Health Records

Electronic health records (EHRs) are rich clinical data sources but complex repositories of patient data, spanning structured elements (demographics, vitals, lab results, codes), unstructured clinical notes and other modalities of data. Harnessing this heterogeneity is critical for improving patient outcomes. Recent advances in large language models (LLMs) have enabled foundation models that can learn from multiple data modalities and support clinical tasks. However, most current approaches simply serialize numeric EHR data into text, which risks losing temporal and quantitative detail. We introduce Generative Deep Patient (GDP), a multimodal foundation model that natively encodes structured EHR time-series via a CNN-Transformer encoder and fuses it with unstructured EHRs through cross-modal attention into a LLaMA-based decoder. GDP is trained in two stages: (1) generative pretraining, where it learns to produce clinical narratives from raw patient timelines while also performing masked feature prediction (MFP) and next time-step prediction (NTP) to capture temporal dynamics; and (2) multi-task fine-tuning for clinically meaningful predictions (e.g., heart failure, type 2 diabetes, 30-day readmission). In clinical prediction, GDP demonstrated superior performance on MIMIC-IV: heart failure AUROC = 0.923, type 2 diabetes AUROC = 0.817, and 30-day readmission AUROC = 0.627. For narrative generation, GDP achieved ROUGE-L = 0.135 and BERTScore-F1 = 0.545. In a blinded human evaluation, GDP-Instruct scored highest on faithfulness, fluency, and overall clinical utility, suggesting reduced hospital documentation workload without sacrificing accuracy. Our results demonstrate that a single multimodal foundation model can both predict clinically actionable events and generate high-quality clinical narratives. Furthermore, GDP's flexible architecture can be extended to additional modalities.

cs.AI↗

arXiv2024

Safe Semi-Supervised Contrastive Learning Using In-Distribution Data as Positive Examples

Semi-supervised learning methods have shown promising results in solving many practical problems when only a few labels are available. The existing methods assume that the class distributions of labeled and unlabeled data are equal; however, their performances are significantly degraded in class distribution mismatch scenarios where out-of-distribution (OOD) data exist in the unlabeled data. Previous safe semi-supervised learning studies have addressed this problem by making OOD data less likely to affect training based on labeled data. However, even if the studies effectively filter out the unnecessary OOD data, they can lose the basic information that all data share regardless of class. To this end, we propose to apply a self-supervised contrastive learning approach to fully exploit a large amount of unlabeled data. We also propose a contrastive loss function with coefficient schedule to aggregate as an anchor the labeled negative examples of the same class into positive examples. To evaluate the performance of the proposed method, we conduct experiments on image classification datasets - CIFAR-10, CIFAR-100, Tiny ImageNet, and CIFAR-100+Tiny ImageNet - under various mismatch ratios. The results show that self-supervised contrastive learning significantly improves classification accuracy. Moreover, aggregating the in-distribution examples produces better representation and consequently further improves classification accuracy.

cs.LG↗