1. ProsMAE: Multi-Source MAE Pretraining for ISUP Grade Classification

    Authors: Anna Jung, Kyeonghun Kim, Youngung Han, Eunseob Choi, Jiwon Yang, Ken Ying-Kai Liao, Hyuk-Jae Lee, Nam-Joon Kim

    Abstract: Whole slide images (WSIs) provide rich diagnostic information for computational pathology, but their gigapixel scale, stain variation, scanner differences, tissue artifacts, and limited expert annotation make robust model training challenging. This paper presents a multi-source Masked Autoencoder (MAE) framework, named ProsMAE, for histopathology representation learning. Tiles from Prostate cANcer… ▽ More Whole slide images (WSIs) provide rich diagnostic information for computational pathology, but their gigapixel scale, stain variation, scanner differences, tissue artifacts, and limited expert annotation make robust model training challenging. This paper presents a multi-source Masked Autoencoder (MAE) framework, named ProsMAE, for histopathology representation learning. Tiles from Prostate cANcer graDe Assessment (PANDA), CAncer MEtastases in LYmph nOdes challeNge 2017 (CAMELYON17), and BReAst Carcinoma Subtyping (BRACS) are used for ProsMAE pretraining to expose the encoder to diverse tissue morphology and acquisition conditions. The learned encoder is transferred for International Society of Urological Pathology (ISUP) grade classification through ProsCLS, using a frozen encoder and a linear classification head. ProsMAE achieved a higher mean validation quadratic weighted kappa (QWK) than the vanilla MAE frozen linear-probe baseline under the evaluated disjoint PANDA split. Repeated-split evaluation remains necessary to further establish robustness across split compositions. △ Less

    Submitted 9 July, 2026; originally announced July 2026.

  2. LEXIC: Lightweight Eye-tracking eXtension via Injected Complexity

    Authors: Sumin Lee, Kyeonghun Kim, Subeen Lee, Jiwon Yang, Tien Nguyen, Ken Ying-Kai Liao, Nam-Joon Kim

    Abstract: On the recent EyeBench benchmark, predicting reading comprehension from eye movements exposes a stark gap: text-aware models using pretrained language models reach 56--63% AUROC, while gaze-only models operate at chance. We ask how far a gaze-only model can be pushed by lightweight, language-model-free conditioning. Building on the EyeBench AhnCNN baseline, LEXIC-Base, we propose two mechanisms to… ▽ More On the recent EyeBench benchmark, predicting reading comprehension from eye movements exposes a stark gap: text-aware models using pretrained language models reach 56--63% AUROC, while gaze-only models operate at chance. We ask how far a gaze-only model can be pushed by lightweight, language-model-free conditioning. Building on the EyeBench AhnCNN baseline, LEXIC-Base, we propose two mechanisms to inject three precomputed word-level difficulty signals, GPT-2 surprisal, word frequency, and word length, into the per-fixation input: direct concatenation, LEXIC-Concat, and a residual mechanism, LEXIC-Res, where a small head predicts typical-reader gaze response and the encoder is conditioned on the deviation. On the OneStop reading comprehension task, with K=5 seed-ensemble training across ten folds, both mechanisms produce statistically consistent AUROC gains on Unseen Text, +1.8 to +2.2 percentage points, Wilcoxon p <= 0.065. LEXIC-Concat additionally lifts Unseen Reader by +2.9 percentage points, p = 0.010. We trace an architectural boundary in LEXIC-Res on Unseen Reader, +1.8 percentage points, p = 0.19, to the prediction head being calibrated to training readers, transferring imperfectly to out-of-distribution readers. △ Less

    Submitted 9 July, 2026; originally announced July 2026.

  3. NEMESIS: Noise-suppressed Efficient MAE with Enhanced Superpatch Integration Strategy

    Authors: Kyeonghun Kim, Hyeonseok Jung, Youngung Han, Hyunsu Go, Eunseob Choi, Seongbin Park, Junsu Lim, Jiwon Yang, Sumin Lee, Insung Hwang, Ken Ying-Kai Liao, Nam-Joon Kim

    Abstract: Volumetric CT imaging is essential for clinical diagnosis, yet annotating 3D volumes is expensive and time-consuming, motivating self-supervised learning (SSL) from unlabeled data. However, applying SSL to 3D CT remains challenging due to the high memory cost of full-volume transformers and the anisotropic spatial structure of CT data, which is not well captured by conventional masking strategies.… ▽ More Volumetric CT imaging is essential for clinical diagnosis, yet annotating 3D volumes is expensive and time-consuming, motivating self-supervised learning (SSL) from unlabeled data. However, applying SSL to 3D CT remains challenging due to the high memory cost of full-volume transformers and the anisotropic spatial structure of CT data, which is not well captured by conventional masking strategies. We propose NEMESIS, a masked autoencoder (MAE) framework that operates on local 128x128x128 superpatches, enabling memory-efficient training while preserving anatomical detail. NEMESIS introduces three key components: (i) noise-enhanced reconstruction as a pretext task, (ii) Masked Anatomical Transformer Blocks (MATB) that perform dual-masking through parallel plane-wise and axis-wise token removal, and (iii) NEMESIS Tokens (NT) for cross-scale context aggregation. On the BTCV multi-organ classification benchmark, NEMESIS with a frozen backbone and a linear classifier achieves a mean AUROC of 0.9633, surpassing fully fine-tuned SuPreM (0.9493) and VoCo (0.9387). Under a low-label regime with only 10% of available annotations, it retains an AUROC of 0.9075, demonstrating strong label efficiency. Furthermore, the superpatch-based design reduces computational cost to 31.0 GFLOPs per forward pass, compared to 985.8 GFLOPs for the full-volume baseline, providing a scalable and robust foundation for 3D medical imaging. △ Less

    Submitted 2 April, 2026; originally announced April 2026.

  4. MATHENA: Mamba-based Architectural Tooth Hierarchical Estimator and Holistic Evaluation Network for Anatomy

    Authors: Kyeonghun Kim, Jaehyung Park, Youngung Han, Anna Jung, Seongbin Park, Sumin Lee, Jiwon Yang, Jiyoon Han, Subeen Lee, Junsu Lim, Hyunsu Go, Eunseob Choi, Hyeonseok Jung, Soo Yong Kim, Woo Kyoung Jeong, Won Jae Lee, Pa Hong, Hyuk-Jae Lee, Ken Ying-Kai Liao, Nam-Joon Kim

    Abstract: Dental diagnosis from Orthopantomograms (OPGs) requires coordination of tooth detection, caries segmentation (CarSeg), anomaly detection (AD), and dental developmental staging (DDS). We propose Mamba-based Architectural Tooth Hierarchical Estimator and Holistic Evaluation Network for Anatomy (MATHENA), a unified framework leveraging Mamba's linear-complexity State Space Models (SSM) to address all… ▽ More Dental diagnosis from Orthopantomograms (OPGs) requires coordination of tooth detection, caries segmentation (CarSeg), anomaly detection (AD), and dental developmental staging (DDS). We propose Mamba-based Architectural Tooth Hierarchical Estimator and Holistic Evaluation Network for Anatomy (MATHENA), a unified framework leveraging Mamba's linear-complexity State Space Models (SSM) to address all four tasks. MATHENA integrates MATHE, a multi-resolution SSM-driven detector with four-directional Vision State Space (VSS) blocks for O(N) global context modeling, generating per-tooth crops. These crops are processed by HENA, a lightweight Mamba-UNet with a triple-head architecture and Global Context State Token (GCST). In the triple-head architecture, CarSeg is first trained as an upstream task to establish shared representations, which are then frozen and reused for downstream AD fine-tuning and DDS classification via linear probing, enabling stable, efficient learning. We also curate PARTHENON, a benchmark comprising 15,062 annotated instances from ten datasets. MATHENA achieves 93.78% mAP@50 in tooth detection, 90.11% Dice for CarSeg, 88.35% for AD, and 72.40% ACC for DDS. △ Less

    Submitted 1 April, 2026; originally announced April 2026.

  5. MAESIL: Masked Autoencoder for Enhanced Self-supervised Medical Image Learning

    Authors: Kyeonghun Kim, Hyeonseok Jung, Youngung Han, Junsu Lim, YeonJu Jean, Seongbin Park, Eunseob Choi, Hyunsu Go, SeoYoung Ju, Seohyoung Park, Gyeongmin Kim, MinJu Kwon, KyungSeok Yuh, Soo Yong Kim, Ken Ying-Kai Liao, Nam-Joon Kim, Hyuk-Jae Lee

    Abstract: Training deep learning models for three-dimensional (3D) medical imaging, such as Computed Tomography (CT), is fundamentally challenged by the scarcity of labeled data. While pre-training on natural images is common, it results in a significant domain shift, limiting performance. Self-Supervised Learning (SSL) on unlabeled medical data has emerged as a powerful solution, but prominent frameworks o… ▽ More Training deep learning models for three-dimensional (3D) medical imaging, such as Computed Tomography (CT), is fundamentally challenged by the scarcity of labeled data. While pre-training on natural images is common, it results in a significant domain shift, limiting performance. Self-Supervised Learning (SSL) on unlabeled medical data has emerged as a powerful solution, but prominent frameworks often fail to exploit the inherent 3D nature of CT scans. These methods typically process 3D scans as a collection of independent 2D slices, an approach that fundamentally discards critical axial coherence and the 3D structural context. To address this limitation, we propose the autoencoder for enhanced self-supervised medical image learning(MAESIL), a novel self-supervised learning framework designed to capture 3D structural information efficiently. The core innovation is the 'superpatch', a 3D chunk-based input unit that balances 3D context preservation with computational efficiency. Our framework partitions the volume into superpatches and employs a 3D masked autoencoder strategy with a dual-masking strategy to learn comprehensive spatial representations. We validated our approach on three diverse large-scale public CT datasets. Our experimental results show that MAESIL demonstrates significant improvements over existing methods such as AE, VAE and VQ-VAE in key reconstruction metrics such as PSNR and SSIM. This establishes MAESIL as a robust and practical pre-training solution for 3D medical imaging tasks. △ Less

    Submitted 1 April, 2026; originally announced April 2026.

  6. NeoNet: An End-to-End 3D MRI-Based Deep Learning Framework for Non-Invasive Prediction of Perineural Invasion via Generation-Driven Classification

    Authors: Youngung Han, Minkyung Cha, Kyeonghun Kim, Induk Um, Myeongbin Sho, Joo Young Bae, Jaewon Jung, Jung Hyeok Park, Seojun Lee, Nam-Joon Kim, Woo Kyoung Jeong, Won Jae Lee, Pa Hong, Ken Ying-Kai Liao, Hyuk-Jae Lee

    Abstract: Minimizing invasive diagnostic procedures to reduce the risk of patient injury and infection is a central goal in medical imaging. And yet, noninvasive diagnosis of perineural invasion (PNI), a critical prognostic factor involving infiltration of tumor cells along the surrounding nerve, still remains challenging, due to the lack of clear and consistent imaging criteria criteria for identifying PNI… ▽ More Minimizing invasive diagnostic procedures to reduce the risk of patient injury and infection is a central goal in medical imaging. And yet, noninvasive diagnosis of perineural invasion (PNI), a critical prognostic factor involving infiltration of tumor cells along the surrounding nerve, still remains challenging, due to the lack of clear and consistent imaging criteria criteria for identifying PNI. To address this challenge, we present NeoNet, an integrated end-to-end 3D deep learning framework for PNI prediction in cholangiocarcinoma that does not rely on predefined image features. NeoNet integrates three modules: (1) NeoSeg, utilizing a Tumor-Localized ROI Crop (TLCR) algorithm; (2) NeoGen, a 3D Latent Diffusion Model (LDM) with ControlNet, conditioned on anatomical masks to generate synthetic image patches, specifically balancing the dataset to a 1:1 ratio; and (3) NeoCls, the final prediction module. For NeoCls, we developed the PNI-Attention Network (PattenNet), which uses the frozen LDM encoder and specialized 3D Dual Attention Blocks (DAB) designed to detect subtle intensity variations and spatial patterns indicative of PNI. In 5-fold cross-validation, NeoNet outperformed baseline 3D models and achieved the highest performance with a maximum AUC of 0.7903. △ Less

    Submitted 31 March, 2026; originally announced March 2026.

  7. FOSCU: Feasibility of Synthetic MRI Generation via Duo-Diffusion Models for Enhancement of 3D U-Nets in Hepatic Segmentation

    Authors: Youngung Han, Kyeonghun Kim, Seoyoung Ju, Yeonju Jean, Minkyung Cha, Seohyoung Park, Hyeonseok Jung, Nam-Joon Kim, Woo Kyoung Jeong, Ken Ying-Kai Liao, Hyuk-Jae Lee

    Abstract: Medical image segmentation faces fundamental challenges including restricted access, costly annotation, and data shortage to clinical datasets through Picture Archiving and Communication Systems (PACS). These systemic barriers significantly impede the development of robust segmentation algorithms. To address these challenges, we propose FOSCU, which integrates Duo-Diffusion, a 3D latent diffusion… ▽ More Medical image segmentation faces fundamental challenges including restricted access, costly annotation, and data shortage to clinical datasets through Picture Archiving and Communication Systems (PACS). These systemic barriers significantly impede the development of robust segmentation algorithms. To address these challenges, we propose FOSCU, which integrates Duo-Diffusion, a 3D latent diffusion model with ControlNet that simultaneously generates high-resolution, anatomically realistic synthetic MRI volumes and corresponding segmentation labels, and an enhanced 3D U-Net training pipeline. Duo-Diffusion employs segmentation-conditioned diffusion to ensure spatial consistency and precise anatomical detail in the generated data. Experimental evaluation on 720 abdominal MRI scans shows that models trained with combined real and synthetic data yield a mean Dice score gain of 0.67% over those using only real data, and achieve a 36.4% reduction in Fréchet Inception Distance (FID), reflecting enhanced image fidelity. △ Less

    Submitted 31 March, 2026; originally announced March 2026.

  8. 3D-LLDM: Label-Guided 3D Latent Diffusion Model for Improving High-Resolution Synthetic MR Imaging in Hepatic Structure Segmentation

    Authors: Kyeonghun Kim, Jaehyeok Bae, Youngung Han, Joo Young Bae, Seoyoung Ju, Junsu Lim, Gyeongmin Kim, Nam-Joon Kim, Woo Kyoung Jeong, Ken Ying-Kai Liao, Won Jae Lee, Pa Hong, Hyuk-Jae Lee

    Abstract: Deep learning and generative models are advancing rapidly, with synthetic data increasingly being integrated into training pipelines for downstream analysis tasks. However, in medical imaging, their adoption remains constrained by the scarcity of reliable annotated datasets. To address this limitation, we propose 3D-LLDM, a label-guided 3D latent diffusion model that generates high-quality synthet… ▽ More Deep learning and generative models are advancing rapidly, with synthetic data increasingly being integrated into training pipelines for downstream analysis tasks. However, in medical imaging, their adoption remains constrained by the scarcity of reliable annotated datasets. To address this limitation, we propose 3D-LLDM, a label-guided 3D latent diffusion model that generates high-quality synthetic magnetic resonance (MR) volumes with corresponding anatomical segmentation masks. Our approach uses hepatobiliary phase MR images enhanced with the Gd-EOB-DTPA contrast agent to derive structural masks for the liver, portal vein, hepatic vein, and hepatocellular carcinoma, which then guide volumetric synthesis through a ControlNet-based architecture. Trained on 720 real clinical hepatobiliary phase MR scans from Samsung Medical Center, 3D-LLDM achieves a Fréchet Inception Distance (FID) of 28.31, improving over GANs by 70.9% and over state-of-the-art diffusion baselines by 26.7%. When used for data augmentation, the synthetic volumes improve hepatocellular carcinoma segmentation by up to 11.153% Dice score across five CNN architectures. △ Less

    Submitted 24 March, 2026; originally announced March 2026.