Kyu Sung Choi

Han Jang, Junhyeok Lee, Heeseong Eum et al.

Precise molecular subtyping of gliomas, including isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion, directly guides surgical and therapeutic decisions, yet currently relies on invasive tissue sampling. Deep learning on structural MRI has emerged as a non-invasive alternative, but anatomy-only approaches cannot capture the hemodynamic signatures that distinguish molecular subtypes. Radiogenomics based on dynamic susceptibility contrast (DSC) MRI holds immense potential for non-invasively characterizing glioma molecular subtypes, yet clinical deployment has been hindered by inter-site variability and the limitations of voxel-wise analysis. We introduce HiPerfGNN, a framework that first learns discrete hemodynamic representations from raw time-intensity curves using a vector-quantized variational autoencoder (VQ-VAE). These quantized perfusion codes define coarse-level graph nodes representing functional tumor habitats, each of which is hierarchically subdivided into fine-level subregions guided by structural MRI. A hierarchical graph neural network then propagates information across scales for molecular prediction. On an internal cohort (n=475), the model achieved AUCs of 0.96 (IDH), 0.89 (1p/19q), and 0.84 (WHO grade), and maintained robust IDH performance (AUC 0.89) on an independent external cohort (n=397) without recalibration. Gradient-based saliency analysis confirms biologically grounded attention patterns aligned with known glioma pathophysiology. Our results demonstrate the added value of integrating perfusion dynamics into radiogenomic pipelines for glioma molecular subtyping. Code is available at https://github.com/janghana/HiPerfGNN.

Han Jang, Junhyeok Lee, Kyu Sung Choi

The explosive growth of AI research has created unprecedented information overload, increasing the demand for scientific summarization at multiple levels of granularity beyond traditional abstracts. While LLMs are increasingly adopted for summarization, existing benchmarks remain limited in scale, target only a single granularity, and predate the LLM era. Moreover, since the release of ChatGPT in November 2022, researchers have rapidly adopted LLMs for drafting manuscripts themselves, fundamentally transforming scientific writing, yet no resource exists to analyze how this writing has evolved. To bridge these gaps, we introduce SciZoom, a benchmark comprising 44,946 papers from four top-tier ML venues (NeurIPS, ICLR, ICML, EMNLP) spanning 2020 to 2025, explicitly stratified into Pre-LLM and Post-LLM eras. SciZoom provides three hierarchical summarization targets (Abstract, Contributions, and TL;DR) achieving compression ratios up to 600:1, enabling both multi-granularity summarization research and temporal mining of scientific writing patterns. Our linguistic analysis reveals striking shifts in phrase patterns (up to 10x for formulaic expressions) and rhetorical style (23% decline in hedging), suggesting that LLM-assisted writing produces more confident yet homogenized prose. SciZoom serves as both a challenging benchmark and a unique resource for mining the evolution of scientific discourse in the generative AI era. Our code and dataset are publicly available on GitHub (https://github.com/janghana/SciZoom) and Hugging Face (https://huggingface.co/datasets/hanjang/SciZoom), respectively.

Junhyeok Lee, Han Jang, Kyu Sung Choi

Precise delineation of meningiomas is crucial for effective radiotherapy (RT) planning, directly influencing treatment efficacy and preservation of adjacent healthy tissues. While automated deep learning approaches have demonstrated considerable potential, achieving consistently accurate clinical segmentation remains challenging due to tumor heterogeneity. Interactive Medical Image Segmentation (IMIS) addresses this challenge by integrating advanced AI techniques with clinical input. However, generic segmentation tools, despite widespread applicability, often lack the specificity required for clinically critical and disease-specific tasks like meningioma RT planning. To overcome these limitations, we introduce Interactive-MEN-RT, a dedicated IMIS tool specifically developed for clinician-assisted 3D meningioma segmentation in RT workflows. The system incorporates multiple clinically relevant interaction methods, including point annotations, bounding boxes, lasso tools, and scribbles, enhancing usability and clinical precision. In our evaluation involving 500 contrast-enhanced T1-weighted MRI scans from the BraTS 2025 Meningioma RT Segmentation Challenge, Interactive-MEN-RT demonstrated substantial improvement compared to other segmentation methods, achieving Dice similarity coefficients of up to 77.6\% and Intersection over Union scores of 64.8\%. These results emphasize the need for clinically tailored segmentation solutions in critical applications such as meningioma RT planning. The code is publicly available at: https://github.com/snuh-rad-aicon/Interactive-MEN-RT

Joon Jang, Eunho Jeong, Kyu Sung Choi et al.

Simulation-based inference (SBI) provides amortized Bayesian parameter inference from simulator-generated data without requiring explicit likelihood evaluation. Its reliability can degrade under model misspecification, where real-world observations are not well represented by the simulator used for training. Existing methods using unlabeled real-world data often align simulated and real-world data distributions, but marginal alignment alone does not directly preserve parameter-relevant information needed for posterior inference. We propose SPIN, an SBI framework with parameter-relevant information-preserving domain transfer using unlabeled, unpaired real-world observations. During training, SPIN translates labeled simulator observations toward the real-world domain and back to the simulator domain, using the original simulator labels to encourage domain transfer that preserves parameter-relevant mutual information. At test time, the learned real-to-simulator transport maps real-world observations into the simulator domain for posterior inference, without requiring real-world parameter labels or paired real--simulator observations. Across controlled synthetic and physical real-world benchmarks, SPIN improves real-world posterior inference, with the improvement becoming clearer as misspecification increases.

Junhyeok Lee, Han Jang, Heeseong Eum et al.

Multiplex immunofluorescence (mIF) enables simultaneous single-cell quantification of multiple biomarkers within intact tissue architecture, yet its high reagent cost, multi-round staining protocols, and need for specialized imaging platforms limit routine clinical adoption. Virtual staining can synthesize mIF channels from widely available brightfield immunohistochemistry (IHC), but current translators optimize pixel-level fidelity without explicitly constraining nuclear morphology. In pathology, this gap is clinically consequential: subtle distortions in nuclei count, shape, or spatial arrangement propagate directly to quantification endpoints such as the Ki67 proliferation index, where errors of a few percent can shift treatment-relevant risk categories. This work introduces a supervision-free, architecture-agnostic conditioning strategy that injects a continuous cell probability map from a pretrained nuclei segmentation foundation model as an explicit input prior, together with a variance-preserving regularization term that matches local intensity statistics to maintain cell-level heterogeneity in synthesized fluorescence channels. The soft prior retains gradient-level boundary information lost by binary thresholding, providing a richer conditioning signal without task-specific tuning. Controlled experiments across Pix2Pix with U-Net and ResNet generators, deterministic regression U-Net, and conditional diffusion on two independent datasets demonstrate consistent improvements in nuclei count fidelity and perceptual quality, as the sole modifications. Code will be made publicly available upon acceptance.

Junhyeok Lee, Minseo Choi, Han Jang et al.

Physics-informed neural networks (PINNs) have shown promise in addressing the ill-posed deconvolution problem in computed tomography perfusion (CTP) imaging for acute ischemic stroke assessment. However, existing PINN-based approaches remain deterministic and do not quantify uncertainty associated with violations of physics constraints, limiting reliability assessment. We propose Evidential Perfusion Physics-Informed Neural Networks (EPPINN), a framework that integrates evidential deep learning with physics-informed modeling to enable uncertainty-aware perfusion parameter estimation. EPPINN models arterial input, tissue concentration, and perfusion parameters using coordinate-based networks, and places a Normal--Inverse--Gamma distribution over the physics residual to characterize voxel-wise aleatoric and epistemic uncertainty in physics consistency without requiring Bayesian sampling or ensemble inference. The framework further incorporates physiologically constrained parameterization and stabilization strategies to promote robust per-case optimization. We evaluate EPPINN on digital phantom data, the ISLES 2018 benchmark, and a clinical cohort. On the evaluated datasets, EPPINN achieves lower normalized mean absolute error than classical deconvolution and PINN baselines, particularly under sparse temporal sampling and low signal-to-noise conditions, while providing conservative uncertainty estimates with high empirical coverage. On clinical data, EPPINN attains the highest voxel-level and case-level infarct-core detection sensitivity. These results suggest that evidential physics-informed learning can improve both accuracy and reliability of CTP analysis for time-critical stroke assessment.

Junhyeok Lee, Han Jang, Kyu Sung Choi

Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems are increasingly integrated into clinical workflows; however, prompt injection attacks can steer these systems toward clinically unsafe or misleading outputs. We introduce the Medical Prompt Injection Benchmark (MPIB), a dataset-and-benchmark suite for evaluating clinical safety under both direct prompt injection and indirect, RAG-mediated injection across clinically grounded tasks. MPIB emphasizes outcome-level risk via the Clinical Harm Event Rate (CHER), which measures high-severity clinical harm events under a clinically grounded taxonomy, and reports CHER alongside Attack Success Rate (ASR) to disentangle instruction compliance from downstream patient risk. The benchmark comprises 9,697 curated instances constructed through multi-stage quality gates and clinical safety linting. Evaluating MPIB across a diverse set of baseline LLMs and defense configurations, we find that ASR and CHER can diverge substantially, and that robustness depends critically on whether adversarial instructions appear in the user query or in retrieved context. We release MPIB with evaluation code, adversarial baselines, and comprehensive documentation to support reproducible and systematic research on clinical prompt injection. Code and data are available at GitHub (code) and Hugging Face (data).

Junhyeok Lee, Kyu Sung Choi

Mixture-of-Experts (MoE) language models are universally sensitive to demographic content at the routing level, yet exploiting this sensitivity for fairness control is structurally limited. We introduce Fairness-Aware Routing Equilibrium (FARE), a diagnostic framework designed to probe the limits of routing-level stereotype intervention across diverse MoE architectures. FARE reveals that routing-level preference shifts are either unachievable (Mixtral, Qwen1.5, Qwen3), statistically non-robust (DeepSeekMoE), or accompanied by substantial utility cost (OLMoE, -4.4%p CrowS-Pairs at -6.3%p TQA). Critically, even where log-likelihood preference shifts are robust, they do not transfer to decoded generation: expanded evaluations on both non-null models yield null results across all generation metrics. Group-level expert masking reveals why: bias and core knowledge are deeply entangled within expert groups. These findings indicate that routing sensitivity is necessary but insufficient for stereotype control, and identify specific architectural conditions that can inform the design of more controllable future MoE systems.

Junhyeok Lee, Yujin Oh, Dahyoun Lee et al.

Acute ischemic stroke (AIS) requires time-critical management, with hours of delayed intervention leading to an irreversible disability of the patient. Since diffusion weighted imaging (DWI) using the magnetic resonance image (MRI) plays a crucial role in the detection of AIS, automated prediction of AIS from DWI has been a research topic of clinical importance. While text radiology reports contain the most relevant clinical information from the image findings, the difficulty of mapping across different modalities has limited the factuality of conventional direct DWI-to-report generation methods. Here, we propose paired image-domain retrieval and text-domain augmentation (PIRTA), a cross-modal retrieval-augmented generation (RAG) framework for providing clinician-interpretative AIS radiology reports with improved factuality. PIRTA mitigates the need for learning cross-modal mapping, which poses difficulty in image-to-text generation, by casting the cross-modal mapping problem as an in-domain retrieval of similar DWI images that have paired ground-truth text radiology reports. By exploiting the retrieved radiology reports to augment the report generation process of the query image, we show by experiments with extensive in-house and public datasets that PIRTA can accurately retrieve relevant reports from 3D DWI images. This approach enables the generation of radiology reports with significantly higher accuracy compared to direct image-to-text generation using state-of-the-art multimodal language models.

Han Jang, Junhyeok Lee, Heeseong Eum et al.

Medical Vision-Language Models (Med-VLMs) have achieved expert-level proficiency in interpreting diagnostic imaging. However, current models are predominantly trained on professional literature, limiting their ability to communicate findings in the lay register required for patient-centered care. While text-centric research has actively developed resources for simplifying medical jargon, there is a critical absence of large-scale multimodal benchmarks designed to facilitate lay-accessible medical image understanding. To bridge this resource gap, we introduce MedLayBench-V, the first large-scale multimodal benchmark dedicated to expert-lay semantic alignment. Unlike naive simplification approaches that risk hallucination, our dataset is constructed via a Structured Concept-Grounded Refinement (SCGR) pipeline. This method enforces strict semantic equivalence by integrating Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs) with micro-level entity constraints. MedLayBench-V provides a verified foundation for training and evaluating next-generation Med-VLMs capable of bridging the communication divide between clinical experts and patients.

Junhyeok Lee, Hyunwoong Kim, Hyungjin Chung et al.

Image-to-Image translation models can help mitigate various challenges inherent to medical image acquisition. Latent diffusion models (LDMs) leverage efficient learning in compressed latent space and constitute the core of state-of-the-art generative image models. However, this efficiency comes with a trade-off, potentially compromising crucial pixel-level detail essential for high-fidelity medical images. This limitation becomes particularly critical when generating clinically significant structures, such as lesions, which often occupy only a small portion of the image. Failure to accurately reconstruct these regions can severely impact diagnostic reliability and clinical decision-making. To overcome this limitation, we propose a novel post-training framework for LDMs in medical image-to-image translation by incorporating lesion-aware medical pixel space objectives. This approach is essential, as it not only enhances overall image quality but also improves the precision of lesion delineation. We evaluate our framework on brain CT-to-MRI translation in acute ischemic stroke patients, where early and accurate diagnosis is critical for optimal treatment selection and improved patient outcomes. While diffusion MRI is the gold standard for stroke diagnosis, its clinical utility is often constrained by high costs and low accessibility. Using a dataset of 817 patients, we demonstrate that our framework improves overall image quality and enhances lesion delineation when synthesizing DWI and ADC images from CT perfusion scans, outperforming existing image-to-image translation models. Furthermore, our post-training strategy is easily adaptable to pre-trained LDMs and exhibits substantial potential for broader applications across diverse medical image translation tasks.