arXiv subjects

Jinah Park

Publications and source records attributed to Jinah Park.

At least 19 recordsLinked to original sources

arXiv2026

Subcortical Shape Variations and Their Associations with Cognition Across the 8th Decade of Life. A Study in the Lothian Birth Cohort 1936

The study of brain morphology changes in normal individuals may capture aspects of functionally-relevant brain aging not fully indicated by gross volumetry. Despite the important role of subcortical brain structures in cognition, the associations between their morphological trajectories and cognitive changes in aging have not been documented. We use neuroimaging, demographic, and cognitive data from a large longitudinal study of cognitive aging, the Lothian Birth Cohort 1936, to explore shape changes in subcortical brain structures of community-dwelling individuals across their 8th decade of life. We investigate the association of these changes with cognitive aging using ANCOVA and mixed linear model analyses. Subcortical shape changes were heterogeneous, with varied atrophy patterns across whole period. The hippocampus and the ventral DC experienced varied morphological deformations (from its baseline point) different in left and right hemispheres, while the thalami and globus pallidi shapes, for example, experienced a more uniform volume contraction, nearly symmetrical throughout different timelines. Changes in general cognition were mainly associated with inwards and outwards vertex displacements between the time-points.

q-bio.NC↗

arXiv2026

Towards Brain MRI Foundation Models for the Clinic: Findings from the FOMO25 Challenge

Clinical deployment of automated brain MRI analysis faces a fundamental challenge: clinical data is heterogeneous and noisy, and high-quality labels are prohibitively costly to obtain. Self-supervised learning (SSL) can address this by leveraging the vast amounts of unlabeled data produced in clinical workflows to train robust \textit{foundation models} that adapt out-of-domain with minimal supervision. However, the development of foundation models for brain MRI has been limited by small pretraining datasets and in-domain benchmarking focused on high-quality, research-grade data. To address this gap, we organized the FOMO25 challenge as a satellite event at MICCAI 2025. FOMO25 provided participants with a large pretraining dataset, FOMO60K, and evaluated models on data sourced directly from clinical workflows in few-shot and out-of-domain settings. Tasks covered infarct classification, meningioma segmentation, and brain age regression, and considered both models trained on FOMO60K (method track) and any data (open track). Nineteen foundation models from sixteen teams were evaluated using a standardized containerized pipeline. Results show that (a) self-supervised pretraining improves generalization on clinical data under domain shift, with the strongest models trained \textit{out-of-domain} surpassing supervised baselines trained \textit{in-domain}. (b) No single pretraining objective benefits all tasks: MAE favors segmentation, hybrid reconstruction-contrastive objectives favor classification, and (c) strong performance was achieved by small pretrained models, and improvements from scaling model size and training duration did not yield reliable benefits.

cs.CV↗

arXiv2026

Neural Particle Automata: Learning Self-Organizing Particle Dynamics

We introduce Neural Particle Automata (NPA), a Lagrangian generalization of Neural Cellular Automata (NCA) from static lattices to dynamic particle systems. Unlike classical Eulerian NCA where cells are pinned to pixels or voxels, NPA model each cell as a particle with a continuous position and internal state, both updated by a shared, learnable neural rule. This particle-based formulation yields clear individuation of cells, allows heterogeneous dynamics, and concentrates computation only on regions where activity is present. At the same time, particle systems pose challenges: neighborhoods are dynamic, and a naive implementation of local interactions scale quadratically with the number of particles. We address these challenges by replacing grid-based neighborhood perception with differentiable Smoothed Particle Hydrodynamics (SPH) operators backed by memory-efficient, CUDA-accelerated kernels, enabling scalable end-to-end training. Across tasks including morphogenesis, point-cloud classification, and particle-based texture synthesis, we show that NPA retain key NCA behaviors such as robustness and self-regeneration, while enabling new behaviors specific to particle systems. Together, these results position NPA as a compact neural model for learning self-organizing particle dynamics.

cs.NE↗

arXiv2025

Cascaded Diffusion Framework for Probabilistic Coarse-to-Fine Hand Pose Estimation

Deterministic models for 3D hand pose reconstruction, whether single-staged or cascaded, struggle with pose ambiguities caused by self-occlusions and complex hand articulations. Existing cascaded approaches progressively refine pose predictions in a coarse-to-fine manner, but their deterministic nature prevents them from modeling pose uncertainty. Conversely, recent probabilistic methods capture pose distributions but are confined to single-stage estimation, often yielding inaccurate 3D reconstructions without refinement. To address these limitations, we propose a coarse-to-fine cascaded diffusion framework that combines probabilistic modeling with cascaded refinement. The first stage is a joint diffusion model that samples diverse 3D joint hypotheses, and the second stage is a Mesh Latent Diffusion Model (Mesh LDM) that reconstructs a 3D hand mesh conditioned on a joint sample. Our key idea is to use these diverse hypotheses as a training signal rather than as final outputs, so that the Mesh LDM learns distribution-aware joint-mesh relationships and becomes robust to the variation in coarse predictions. Extensive ablations validate the necessity of the cascaded design and the choice of latent-space diffusion. Experiments on FreiHAND, HO3Dv2, and DexYCB show that our method achieves state-of-the-art performance and remains stable under occlusion and pose ambiguity.

cs.CV↗

arXiv2025

LV-Net: Anatomy-aware lateral ventricle shape modeling with a case study on Alzheimer's disease

Lateral ventricle (LV) shape analysis holds promise as a biomarker for neurological diseases; however, challenges remain due to substantial shape variability across individuals and segmentation difficulties arising from limited MRI resolution. We introduce LV-Net, a novel framework for producing individualized 3D LV meshes from brain MRI by deforming an anatomy-aware joint LV-hippocampus template mesh. By incorporating anatomical relationships embedded within the joint template, LV-Net reduces boundary segmentation artifacts and improves reconstruction robustness. In addition, by classifying the vertices of the template mesh based on their anatomical adjacency, our method enhances point correspondence across subjects, leading to more accurate LV shape statistics. We demonstrate that LV-Net achieves superior reconstruction accuracy, even in the presence of segmentation imperfections, and delivers more reliable shape descriptors across diverse datasets. Finally, we apply LV-Net to Alzheimer's disease analysis, identifying LV subregions that show significantly associations with the disease relative to cognitively normal controls. The codes for LV shape modeling are available at https://github.com/PWonjung/LV_Shape_Modeling.

cs.CV↗

arXiv2024

Volumetric Conditioning Module to Control Pretrained Diffusion Models for 3D Medical Images

Spatial control methods using additional modules on pretrained diffusion models have gained attention for enabling conditional generation in natural images. These methods guide the generation process with new conditions while leveraging the capabilities of large models. They could be beneficial as training strategies in the context of 3D medical imaging, where training a diffusion model from scratch is challenging due to high computational costs and data scarcity. However, the potential application of spatial control methods with additional modules to 3D medical images has not yet been explored. In this paper, we present a tailored spatial control method for 3D medical images with a novel lightweight module, Volumetric Conditioning Module (VCM). Our VCM employs an asymmetric U-Net architecture to effectively encode complex information from various levels of 3D conditions, providing detailed guidance in image synthesis. To examine the applicability of spatial control methods and the effectiveness of VCM for 3D medical data, we conduct experiments under single- and multimodal conditions scenarios across a wide range of dataset sizes, from extremely small datasets with 10 samples to large datasets with 500 samples. The experimental results show that the VCM is effective for conditional generation and efficient in terms of requiring less training data and computational resources. We further investigate the potential applications for our spatial control method through axial super-resolution for medical images. Our code is available at \url{https://github.com/Ahn-Ssu/VCM}

cs.CV↗

arXiv2024

Two-Stage Approach for Brain MR Image Synthesis: 2D Image Synthesis and 3D Refinement

Despite significant advancements in automatic brain tumor segmentation methods, their performance is not guaranteed when certain MR sequences are missing. Addressing this issue, it is crucial to synthesize the missing MR images that reflect the unique characteristics of the absent modality with precise tumor representation. Typically, MRI synthesis methods generate partial images rather than full-sized volumes due to computational constraints. This limitation can lead to a lack of comprehensive 3D volumetric information and result in image artifacts during the merging process. In this paper, we propose a two-stage approach that first synthesizes MR images from 2D slices using a novel intensity encoding method and then refines the synthesized MRI. The proposed intensity encoding reduces artifacts when synthesizing MRI on a 2D slice basis. Then, the \textit{Refiner}, which leverages complete 3D volume information, further improves the quality of the synthesized images and enhances their applicability to segmentation methods. Experimental results demonstrate that the intensity encoding effectively minimizes artifacts in the synthesized MRI and improves perceptual quality. Furthermore, using the \textit{Refiner} on synthesized MRI significantly improves brain tumor segmentation results, highlighting the potential of our approach in practical applications.

eess.IV↗

arXiv2024

Hand-object reconstruction via interaction-aware graph attention mechanism

Estimating the poses of both a hand and an object has become an important area of research due to the growing need for advanced vision computing. The primary challenge involves understanding and reconstructing how hands and objects interact, such as contact and physical plausibility. Existing approaches often adopt a graph neural network to incorporate spatial information of hand and object meshes. However, these approaches have not fully exploited the potential of graphs without modification of edges within and between hand- and object-graphs. We propose a graph-based refinement method that incorporates an interaction-aware graph-attention mechanism to account for hand-object interactions. Using edges, we establish connections among closely correlated nodes, both within individual graphs and across different graphs. Experiments demonstrate the effectiveness of our proposed method with notable improvements in the realm of physical plausibility.

cs.CV↗

arXiv2024

Lateral Ventricle Shape Modeling using Peripheral Area Projection for Longitudinal Analysis

The deformation of the lateral ventricle (LV) shape is widely studied to identify specific morphometric changes associated with diseases. Since LV enlargement is considered a relative change due to brain atrophy, local longitudinal LV deformation can indicate deformation in adjacent brain areas. However, conventional methods for LV shape analysis focus on modeling the solely segmented LV mask. In this work, we propose a novel deep learning-based approach using peripheral area projection, which is the first attempt to analyze LV considering its surrounding areas. Our approach matches the baseline LV mesh by deforming the shape of follow-up LVs, while optimizing the corresponding points of the same adjacent brain area between the baseline and follow-up LVs. Furthermore, we quantitatively evaluated the deformation of the left LV in normal (n=10) and demented subjects (n=10), and we found that each surrounding area (thalamus, caudate, hippocampus, amygdala, and right LV) projected onto the surface of LV shows noticeable differences between normal and demented subjects.

eess.IV↗

arXiv2024

Data-driven Viscosity Solver for Fluid Simulation

We propose a data-driven viscosity solver based on U-shaped convolutional neural network to predict velocity changes due to viscosity. Our solver takes velocity derivatives, fluid volume, and solid indicator quantities as input. The traditional marker-and-cell (MAC) grid stores velocities at the edges of the grid, causing the dimensions of the velocity field vary from axis to axis. In our work, we suggest a symmetric MAC grid that maintains consistent dimensions across axes without interpolation or symmetry breaking. The proposed grid effectively transfers spatial fluid quantities such as partial derivatives of velocity, enabling networks to generate accurate predictions. Additionally, we introduce a physics-based loss inspired by the variational formulation of viscosity to enhance the network's generalization for a wide range of viscosity coefficients. We demonstrate various fluid simulation results, including 2D and 3D fluid-rigid body scenes and a scene exhibiting the buckling effect. Our code is available at \url{https://github.com/SSTDV-Project/python-fluid-simulation.}

cs.GR↗

arXiv2024

Label-Efficient 3D Brain Segmentation via Complementary 2D Diffusion Models with Orthogonal Views

Deep learning-based segmentation techniques have shown remarkable performance in brain segmentation, yet their success hinges on the availability of extensive labeled training data. Acquiring such vast datasets, however, poses a significant challenge in many clinical applications. To address this issue, in this work, we propose a novel 3D brain segmentation approach using complementary 2D diffusion models. The core idea behind our approach is to first mine 2D features with semantic information extracted from the 2D diffusion models by taking orthogonal views as input, followed by fusing them into a 3D contextual feature representation. Then, we use these aggregated features to train multi-layer perceptrons to classify the segmentation labels. Our goal is to achieve reliable segmentation quality without requiring complete labels for each individual subject. Our experiments on training in brain subcortical structure segmentation with a dataset from only one subject demonstrate that our approach outperforms state-of-the-art self-supervised learning methods. Further experiments on the minimum requirement of annotation by sparse labeling yield promising results even with only nine slices and a labeled background region.

cs.CV↗

arXiv2024

Principled Feature Disentanglement for High-Fidelity Unified Brain MRI Synthesis

Multisequence Magnetic Resonance Imaging (MRI) provides a more reliable diagnosis in clinical applications through complementary information across sequences. However, in practice, the absence of certain MR sequences is a common problem that can lead to inconsistent analysis results. In this work, we propose a novel unified framework for synthesizing multisequence MR images, called hybrid-fusion GAN (HF-GAN). The fundamental mechanism of this work is principled feature disentanglement, which aligns the design of the architecture with the complexity of the features. A powerful many-to-one stream is constructed for the extraction of complex complementary features, while utilizing parallel, one-to-one streams to process modality-specific information. These disentangled features are dynamically integrated into a common latent space by a channel attention-based fusion module (CAFF) and then transformed via a modality infuser to generate the target sequence. We validated our framework on public datasets of both healthy and pathological brain MRI. Quantitative and qualitative results show that HF-GAN achieves state-of-the-art performance, with our 2D slice-based framework notably outperforming a leading 3D volumetric model. Furthermore, the utilization of HF-GAN for data imputation substantially improves the performance of the downstream brain tumor segmentation task, demonstrating its clinical relevance.

eess.IV↗

arXiv2024

Disentangled Multimodal Brain MR Image Translation via Transformer-based Modality Infuser

Multimodal Magnetic Resonance (MR) Imaging plays a crucial role in disease diagnosis due to its ability to provide complementary information by analyzing a relationship between multimodal images on the same subject. Acquiring all MR modalities, however, can be expensive, and, during a scanning session, certain MR images may be missed depending on the study protocol. The typical solution would be to synthesize the missing modalities from the acquired images such as using generative adversarial networks (GANs). Yet, GANs constructed with convolutional neural networks (CNNs) are likely to suffer from a lack of global relationships and mechanisms to condition the desired modality. To address this, in this work, we propose a transformer-based modality infuser designed to synthesize multimodal brain MR images. In our method, we extract modality-agnostic features from the encoder and then transform them into modality-specific features using the modality infuser. Furthermore, the modality infuser captures long-range relationships among all brain structures, leading to the generation of more realistic images. We carried out experiments on the BraTS 2018 dataset, translating between four MR modalities, and our experimental results demonstrate the superiority of our proposed method in terms of synthesis quality. In addition, we conducted experiments on a brain tumor segmentation task and different conditioning methods.

eess.IV↗

arXiv2023

Hybrid-Fusion Transformer for Multisequence MRI

Medical segmentation has grown exponentially through the advent of a fully convolutional network (FCN), and we have now reached a turning point through the success of Transformer. However, the different characteristics of the modality have not been fully integrated into Transformer for medical segmentation. In this work, we propose the novel hybrid fusion Transformer (HFTrans) for multisequence MRI image segmentation. We take advantage of the differences among multimodal MRI sequences and utilize the Transformer layers to integrate the features extracted from each modality as well as the features of the early fused modalities. We validate the effectiveness of our hybrid-fusion method in three-dimensional (3D) medical segmentation. Experiments on two public datasets, BraTS2020 and MRBrainS18, show that the proposed method outperforms previous state-of-the-art methods on the task of brain tumor segmentation and brain structure segmentation.

eess.IV↗

arXiv2023

FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI.

cs.CY↗

arXiv2023

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

cs.CV↗

arXiv2022

Joint Embedding of 2D and 3D Networks for Medical Image Anomaly Detection

Obtaining ground truth data in medical imaging has difficulties due to the fact that it requires a lot of annotating time from the experts in the field. Also, when trained with supervised learning, it detects only the cases included in the labels. In real practice, we want to also open to other possibilities than the named cases while examining the medical images. As a solution, the need for anomaly detection that can detect and localize abnormalities by learning the normal characteristics using only normal images is emerging. With medical image data, we can design either 2D or 3D networks of self-supervised learning for anomaly detection task. Although 3D networks, which learns 3D structures of the human body, show good performance in 3D medical image anomaly detection, they cannot be stacked in deeper layers due to memory problems. While 2D networks have advantage in feature detection, they lack 3D context information. In this paper, we develop a method for combining the strength of the 3D network and the strength of the 2D network through joint embedding. We also propose the pretask of self-supervised learning to make it possible for the networks to learn efficiently. Through the experiments, we show that the proposed method achieves better performance in both classification and segmentation tasks compared to the SoTA method.

cs.CV↗

arXiv2022

WG-VITON: Wearing-Guide Virtual Try-On for Top and Bottom Clothes

Studies of virtual try-on (VITON) have been shown their effectiveness in utilizing the generative neural network for virtually exploring fashion products, and some of recent researches of VITON attempted to synthesize human image wearing given multiple types of garments (e.g., top and bottom clothes). However, when replacing the top and bottom clothes of the target human, numerous wearing styles are possible with a certain combination of the clothes. In this paper, we address the problem of variation in wearing style when simultaneously replacing the top and bottom clothes of the model. We introduce Wearing-Guide VITON (i.e., WG-VITON) which utilizes an additional input binary mask to control the wearing styles of the generated image. Our experiments show that WG-VITON effectively generates an image of the model wearing given top and bottom clothes, and create complicated wearing styles such as partly tucking in the top to the bottom

cs.CV↗