arXiv subjects

Jongho Lee

Publications and source records attributed to Jongho Lee.

At least 19 recordsLinked to original sources

arXiv2026

MWF-MIMOSA for efficient simultaneous relaxometry and myelin water fraction mapping

Quantitative magnetic resonance imaging (qMRI) provides improved sensitivity and specificity to tissue composition and pathological alterations compared with conventional contrast-weighted imaging. Among various qMRI biomarkers, myelin water imaging is of particular interest because myelin plays a central role in brain function and its alteration is closely associated with many neurological diseases. However, conventional myelin water fraction (MWF) mapping techniques are often limited by long scan times, low spatial resolution, reduced signal-to-noise ratio (SNR), and high specific absorption rate (SAR). Here, we propose MWF-MIMOSA for efficient simultaneous T1, T2, T2* mapping, magnetic susceptibility source separation, and MWF estimation. To achieve this, multi-contrast and multi-slice zero-shot self-supervised learning (MZS-SSL) was used to jointly reconstruct whole-brain complex-valued images. To improve computational efficiency of the parameter estimation step, a multilayer perceptron (MLP) was trained within the GACELLE GPU-accelerated parameter estimation framework to circumvent the computationally intensive Bloch simulation process, resulting in a >100-fold computational speed-up in MWF estimation. Numerical simulations were performed to evaluate the accuracy and precision of MWF-MIMOSA, and in-vivo results further demonstrated its robustness. Comparison with existing myelin water imaging methods showed that MWF-MIMOSA is highly correlated with established approaches, while providing complementary quantitative parameter maps at higher spatial resolution and with shorter scan times. Notably, simultaneous multi-parametric mapping was achieved in 5 min at 1 mm isotropic resolution, and in 10 min at 0.7 mm isotropic resolution. These results demonstrate the potential of MWF-MIMOSA for fast, high-resolution simultaneous relaxometry and myelin water imaging.

physics.med-ph↗

arXiv2026

Rethinking the Pointer Loss in Table Structure Recognition: Geometry-Aware Pointer Loss for Spatial Locality

Table Structure Recognition (TSR) using a pointer network achieves impressive results by predicting HTML sequences while aligning tags to detected text (or cell) regions. However, our analysis reveals that when pointer networks fail, 79.6% of errors occur between spatially adjacent cells (Manhattan distance <= 2). Despite this, standard cross-entropy loss weights all negative candidates equally. In this work, we propose Geometry-Aware Pointer (GAP) Loss, which reweights the cross-entropy objective based on spatial proximity to ground truth. By applying inverse distance weighting, GAP focuses gradient flow where the model struggles most: immediate neighbors receive stronger gradients than distant cells. Our approach requires only a straightforward modification to the loss computation, maintaining the same model architecture with zero additional inference cost. Extensive experiments on PubTabNet and SynthTabNet demonstrate that GAP consistently reduces adjacent-cell errors, achieving new state-of-the-art performance. Our findings suggest that incorporating geometric inductive biases at the loss level provides a simple yet effective approach to robust TSR. Our code is available at https://github.com/teamreboott/GAP

cs.CV↗

arXiv2026

Longitudinal QSM: Enhancing consistency of multiple time point susceptibility maps via simultaneous reconstruction

Quantitative susceptibility mapping (QSM) has been increasingly applied in longitudinal studies of neurodegenerative diseases and aging to assess temporal alterations in brain iron and myelin. The accuracy of such investigations depends on the repeatability and sensitivity of measurements. However, the ill-posed nature of the QSM processing steps makes the reconstruction vulnerable to background field changes, head orientation changes, noise, and imperfect registration, which compromise repeatability and sensitivity and hinder reliable detection of true changes. To address these limitations, we propose Longitudinal QSM, a simultaneous reconstruction framework that jointly estimates susceptibility maps across time points while enforcing spatial sparsity of temporal changes. The method was evaluated through simulations and in-vivo experiments and compared with conventional reconstruction methods. Longitudinal QSM consistently reduced inter-scan variability and accurately recovered simulated lesion changes. Application to stroke patient and multiple sclerosis patient data further demonstrated that the framework stabilizes non-lesion variability while preserving lesion-related temporal changes. This approach offers a promising tool for monitoring subtle temporal changes in brain iron and myelin in various neurodegenerative diseases as well as throughout aging and development.

q-bio.QM↗

arXiv2026

A Target-Free Harmonization Method for MRI

In MRI, variations in scan parameters, sequence, or hardware can lead to discrepancies in image appearance, even for the same subject. These inconsistencies, known as domain shifts, can hinder image analysis and degrade the performance of deep learning models trained on data from specific target domains. MRI image harmonization aims to address these issues by aligning source domain images to the target domain images while preserving biological information such as anatomical structures. However, most existing harmonization approaches require access to both source and target domain data in training or test time. This dependence induces data sharing between institutions, raising concerns about patient privacy and substantially limiting the harmonization approaches that can be practically deployed in clinical settings. To overcome these limitations, we introduce TgtFreeHarmony, the harmonization framework tailored for target-free scenarios, eliminating the need for target domain data and any data sharing, enabling privacy-preserving harmonization directly within the source institution. Our approach estimates the target domain style by searching the manifold of MRI domain style constructed via a disentanglement-based generator using Bayesian optimization guided by the performance of a downstream task model, which is trained on target domain data. We evaluated our method on the brain tissue segmentation task across multiple institutes and demonstrated that it effectively harmonizes source images into target images, leading to improved downstream task performance. By enabling harmonization without any access to target-domain data, TgtFreeHarmony establishes a new direction of harmonization preserving data privacy that can be realistically deployed within clinical environments.

eess.IV↗

arXiv2026

Sequence Search: Automated Sequence Design using Neural Architecture Search

Developing an MR sequence is challenging and remains largely constrained by human intuition. Recently, AI-driven approaches have been proposed; however, most require an initial sequence for parameter optimization or extensive training datasets, limiting their general applicability. In this study, we propose "Sequence Search," an automated sequence design framework based on neural architecture search. The method takes tissue properties, imaging parameters, and design objectives as inputs and generates pulse sequences satisfying the design objectives, without requiring prior knowledge of conventional sequence structures. Sequence Search iteratively generates candidate sequences through neural architecture search and optimizes them via a differentiable Bloch simulator and objective-specific loss functions using gradient-based learning. The framework successfully replicated conventional spin-echo, T2-weighted spin-echo, and inversion recovery sequences. Less intuitive solutions were also discovered, such as three-RF spin-echo-like sequences with reduced RF energy and refocusing phases deviating from the conventional Hahn-echo. This work establishes a generalizable framework for automated MR sequence design, highlighting the potential to explore configurations beyond conventional designs based on human intuition.

cs.AI↗

arXiv2025

Deep learning water-unsuppressed MRSI at ultra-high field for simultaneous quantitative metabolic, susceptibility and myelin water imaging

Purpose: Magnetic Resonance Spectroscopic Imaging (MRSI) maps endogenous brain metabolism while suppressing the overwhelming water signal. Water-unsuppressed MRSI (wu-MRSI) allows simultaneous imaging of water and metabolites, but large water sidebands cause challenges for metabolic fitting. We developed an end-to-end deep-learning pipeline to overcome these challenges at ultra-high field. Methods:Fast high-resolution wu-MRSI was acquired at 7T with non-cartesian ECCENTRIC sampling and ultra-short echo time. A water and lipid removal network (WALINET+) was developed to remove lipids, water signal, and sidebands. MRSI reconstruction was performed by DeepER and a physics-informed network for metabolite fitting. Water signal was used for absolute metabolite quantification, quantitative susceptibility mapping (QSM), and myelin water fraction imaging (MWF). Results: WALINET+ provided the lowest NRMSE (< 2%) in simulations and in vivo the smallest bias (< 20%) and limits-of-agreement (+-63%) between wu-MRSI and ws-MRSI scans. Several metabolites such as creatine and glutamate showed higher SNR in wu-MRSI. QSM and MWF obtained from wu-MRSI and GRE showed good agreement with 0 ppm/5.5% bias and +-0.05 ppm/ +- 12.75% limits-of-agreement. Conclusion: High-quality metabolic, QSM, and MWF mapping of the human brain can be obtained simultaneously by ECCENTRIC wu-MRSI at 7T with 2 mm isotropic resolution in 12 min. WALINET+ robustly removes water sidebands while preserving metabolite signal, eliminating the need for water suppression and separate water acquisitions.

eess.IV↗

arXiv2025

Predicting before Reconstruction: A generative prior framework for MRI acceleration

Recent advancements in artificial intelligence have created transformative capabilities in image synthesis and generation, enabling diverse research fields to innovate at revolutionary speed and spectrum. In this study, we leverage this generative power to introduce a new paradigm for accelerating Magnetic Resonance Imaging (MRI), introducing a shift from image reconstruction to proactive predictive imaging. Despite being a cornerstone of modern patient care, MRI's lengthy acquisition times limit clinical throughput. Our novel framework addresses this challenge by first predicting a target contrast image, which then serves as a data-driven prior for reconstructing highly under-sampled data. This informative prior is predicted by a generative model conditioned on diverse data sources, such as other contrast images, previously scanned images, acquisition parameters, patient information. We demonstrate this approach with two key applications: (1) reconstructing FLAIR images using predictions from T1w and/or T2w scans, and (2) reconstructing T1w images using predictions from previously acquired T1w scans. The framework was evaluated on internal and multiple public datasets (total 14,921 scans; 1,051,904 slices), including multi-channel k-space data, for a range of high acceleration factors (x4, x8 and x12). The results demonstrate that our prediction-prior reconstruction method significantly outperforms other approaches, including those with alternative or no prior information. Through this framework we introduce a fundamental shift from image reconstruction towards a new paradigm of predictive imaging.

cs.CV↗

arXiv2025

Personalized Scientific Figure Caption Generation: An Empirical Study on Author-Specific Writing Style Transfer

We study personalized figure caption generation using author profile data from scientific papers. Our experiments demonstrate that rich author profile data, combined with relevant metadata, can significantly improve the personalization performance of multimodal large language models. However, we also reveal a fundamental trade-off between matching author style and maintaining caption quality. Our findings offer valuable insights and future directions for developing practical caption automation systems that balance both objectives. This work was conducted as part of the 3rd SciCap challenge.

cs.CL↗

arXiv2025

MIMOSA: Multi-parametric Imaging using Multiple-echoes with Optimized Simultaneous Acquisition for highly-efficient quantitative MRI

Purpose: To develop a new sequence, MIMOSA, for highly-efficient T1, T2, T2*, proton density (PD), and source separation quantitative susceptibility mapping (QSM). Methods: MIMOSA was developed based on 3D-quantification using an interleaved Look-Locker acquisition sequence with T2 preparation pulse (3D-QALAS) by combining 3D turbo Fast Low Angle Shot (FLASH) and multi-echo gradient echo acquisition modules with a spiral-like Cartesian trajectory to facilitate highly-efficient acquisition. Simulations were performed to optimize the sequence. Multi-contrast/-slice zero-shot self-supervised learning algorithm was employed for reconstruction. The accuracy of quantitative mapping was assessed by comparing MIMOSA with 3D-QALAS and reference techniques in both ISMRM/NIST phantom and in-vivo experiments. MIMOSA's acceleration capability was assessed at R = 3.3, 6.5, and 11.8 in in-vivo experiments, with repeatability assessed through scan-rescan studies. Beyond the 3T experiments, mesoscale quantitative mapping was performed at 750 um isotropic resolution at 7T. Results: Simulations demonstrated that MIMOSA achieved improved parameter estimation accuracy compared to 3D-QALAS. Phantom experiments indicated that MIMOSA exhibited better agreement with the reference techniques than 3D-QALAS. In-vivo experiments demonstrated that an acceleration factor of up to R = 11.8-fold can be achieved while preserving parameter estimation accuracy, with intra-class correlation coefficients of 0.998 (T1), 0.973 (T2), 0.947 (T2*), 0.992 (QSM), 0.987 (paramagnetic susceptibility), and 0.977 (diamagnetic susceptibility) in scan-rescan studies. Whole-brain T1, T2, T2*, PD, source separation QSM were obtained with 1 mm isotropic resolution in 3 min at 3T and 750 um isotropic resolution in 13 min at 7T. Conclusion: MIMOSA demonstrated potential for highly-efficient multi-parametric mapping.

physics.med-ph↗

arXiv2025

MOST: MR reconstruction Optimization for multiple downStream Tasks via continual learning

Deep learning-based Magnetic Resonance (MR) reconstruction methods have focused on generating high-quality images but often overlook the impact on downstream tasks (e.g., segmentation) that utilize the reconstructed images. Cascading separately trained reconstruction network and downstream task network has been shown to introduce performance degradation due to error propagation and domain gaps between training datasets. To mitigate this issue, downstream task-oriented reconstruction optimization has been proposed for a single downstream task. Expanding this optimization to multi-task scenarios is not straightforward. In this work, we extended this optimization to sequentially introduced multiple downstream tasks and demonstrated that a single MR reconstruction network can be optimized for multiple downstream tasks by deploying continual learning (MOST). MOST integrated techniques from replay-based continual learning and image-guided loss to overcome catastrophic forgetting. Comparative experiments demonstrated that MOST outperformed a reconstruction network without finetuning, a reconstruction network with naïve finetuning, and conventional continual learning methods. The source code is available at: https://github.com/SNU-LIST/MOST.

eess.IV↗

arXiv2025

Self-supervised training of deep denoisers in multi-coil MRI considering noise correlations

Deep learning-based denoising methods have shown powerful results for improving the signal-to-noise ratio of magnetic resonance (MR) images, mostly by leveraging supervised learning with clean ground truth. However, acquiring clean ground truth images is often expensive and time-consuming. Self supervised methods have been widely investigated to mitigate the dependency on clean images, but mostly rely on the suboptimal splitting of K-space measurements of an image to yield input and target images for ensuring statistical independence. In this study, we investigate an alternative self-supervised training method for deep denoisers in multi-coil MRI, dubbed Coil2Coil (C2C), that naturally split and combine the multi-coil data among phased array coils, generating two noise-corrupted images for training. This novel approach allows exploiting multi-coil redundancy, but the images are statistically correlated and may not have the same clean image. To mitigate these issues, we propose the methods to pproximately decorrelate the statistical dependence of these images and match the underlying clean images, thus enabling them to be used as the training pairs. For synthetic denoising experiments, C2C yielded the best performance against prior self-supervised methods, reporting outcome comparable even to supervised methods. For real-world denoising cases, C2C yielded consistent performance as synthetic cases, removing only noise structures.

eess.IV↗

arXiv2025

Efficient and robust 3D blind harmonization for large domain gaps

Blind harmonization has emerged as a promising technique for MR image harmonization to achieve scale-invariant representations, requiring only target domain data (i.e., no source domain data necessary). However, existing methods face limitations such as inter-slice heterogeneity in 3D, moderate image quality, and limited performance for a large domain gap. To address these challenges, we introduce BlindHarmonyDiff, a novel blind 3D harmonization framework that leverages an edge-to-image model tailored specifically to harmonization. Our framework employs a 3D rectified flow trained on target domain images to reconstruct the original image from an edge map, then yielding a harmonized image from the edge of a source domain image. We propose multi-stride patch training for efficient 3D training and a refinement module for robust inference by suppressing hallucination. Extensive experiments demonstrate that BlindHarmonyDiff outperforms prior arts by harmonizing diverse source domain images to the target domain, achieving higher correspondence to the target domain characteristics. Downstream task-based quality assessments such as tissue segmentation and age prediction on diverse MR scanners further confirm the effectiveness of our approach and demonstrate the capability of our robust and generalizable blind harmonization.

eess.IV↗

arXiv2025

Vessel segmentation for X-separation

$χ$-separation is an advanced quantitative susceptibility mapping (QSM) method that is designed to generate paramagnetic ($χ_{para}$) and diamagnetic ($|χ_{dia}|$) susceptibility maps, reflecting the distribution of iron and myelin in the brain. However, vessels have shown artifacts, interfering with the accurate quantification of iron and myelin in applications. To address this challenge, a new vessel segmentation method for $χ$-separation is developed. The method comprises three steps: 1) Seed generation from $\textit{R}_2^*$ and the product of $χ_{para}$ and $|χ_{dia}|$ maps; 2) Region growing, guided by vessel geometry, creating a vessel mask; 3) Refinement of the vessel mask by excluding non-vessel structures. The performance of the method was compared to conventional vessel segmentation methods both qualitatively and quantitatively. To demonstrate the utility of the method, it was tested in two applications: quantitative evaluation of a neural network-based $χ$-separation reconstruction method ($χ$-sepnet-$\textit{R}_2^*$) and population-averaged region of interest (ROI) analysis. The proposed method demonstrates superior performance to the conventional vessel segmentation methods, effectively excluding the non-vessel structures, achieving the highest Dice score coefficient. For the applications, applying vessel masks report notable improvements for the quantitative evaluation of $χ$-sepnet-$\textit{R}_2^*$ and statistically significant differences in population-averaged ROI analysis. These applications suggest excluding vessels when analyzing the $χ$-separation maps provide more accurate evaluations. The proposed method has the potential to facilitate various applications, offering reliable analysis through the generation of a high-quality vessel mask.

cs.CV↗

arXiv2025

Multi-LLM Collaborative Caption Generation in Scientific Documents

Scientific figure captioning is a complex task that requires generating contextually appropriate descriptions of visual content. However, existing methods often fall short by utilizing incomplete information, treating the task solely as either an image-to-text or text summarization problem. This limitation hinders the generation of high-quality captions that fully capture the necessary details. Moreover, existing data sourced from arXiv papers contain low-quality captions, posing significant challenges for training large language models (LLMs). In this paper, we introduce a framework called Multi-LLM Collaborative Figure Caption Generation (MLBCAP) to address these challenges by leveraging specialized LLMs for distinct sub-tasks. Our approach unfolds in three key modules: (Quality Assessment) We utilize multimodal LLMs to assess the quality of training data, enabling the filtration of low-quality captions. (Diverse Caption Generation) We then employ a strategy of fine-tuning/prompting multiple LLMs on the captioning task to generate candidate captions. (Judgment) Lastly, we prompt a prominent LLM to select the highest quality caption from the candidates, followed by refining any remaining inaccuracies. Human evaluations demonstrate that informative captions produced by our approach rank better than human-written captions, highlighting its effectiveness. Our code is available at https://github.com/teamreboott/MLBCAP

cs.CL↗

arXiv2024

RTP-LX: Can LLMs Evaluate Toxicity in Multilingual Scenarios?

Large language models (LLMs) and small language models (SLMs) are being adopted at remarkable speed, although their safety still remains a serious concern. With the advent of multilingual S/LLMs, the question now becomes a matter of scale: can we expand multilingual safety evaluations of these models with the same velocity at which they are deployed? To this end, we introduce RTP-LX, a human-transcreated and human-annotated corpus of toxic prompts and outputs in 28 languages. RTP-LX follows participatory design practices, and a portion of the corpus is especially designed to detect culturally-specific toxic language. We evaluate 10 S/LLMs on their ability to detect toxic content in a culturally-sensitive, multilingual scenario. We find that, although they typically score acceptably in terms of accuracy, they have low agreement with human judges when scoring holistically the toxicity of a prompt; and have difficulty discerning harm in context-dependent scenarios, particularly with subtle-yet-harmful content (e.g. microaggressions, bias). We release this dataset to contribute to further reduce harmful uses of these models and improve their safe deployment.

cs.CL↗

arXiv2024

χ-sepnet: Deep neural network for magnetic susceptibility source separation

Magnetic susceptibility source separation ($χ$-separation), an advanced quantitative susceptibility mapping (QSM) method, enables the separate estimation of para- and diamagnetic susceptibility source distributions in the brain. The method utilizes reversible transverse relaxation (R2'=R2*-R2) to complement frequency shift information for estimating susceptibility source concentrations, requiring time-consuming data acquisition for R2 in addition R2*. To address this challenge, we develop a new deep learning network, $χ$-sepnet, and propose two deep learning-based susceptibility source separation pipelines, $χ$-sepnet-R2' for inputs with multi-echo GRE and multi-echo spin-echo, and $χ$-sepnet-R2* for input with multi-echo GRE only. $χ$-sepnet is trained using multiple head orientation data that provide streaking artifact-free labels, generating high-quality $χ$-separation maps. The evaluation of the pipelines encompasses both qualitative and quantitative assessments in healthy subjects, and visual inspection of lesion characteristics in multiple sclerosis patients. The susceptibility source-separated maps of the proposed pipelines delineate detailed brain structures with substantially reduced artifacts compared to those from conventional regularization-based reconstruction methods. In quantitative analysis, $χ$-sepnet-R2' achieves the best outcomes followed by $χ$-sepnet-R2*, outperforming the conventional methods. When the lesions of multiple sclerosis patients are assessed, both pipelines report identical lesion characteristics in most lesions ($χ$para: 99.6% and $χ$dia: 98.4% out of 250 lesions). The $χ$-sepnet-R2* pipeline, which only requires multi-echo GRE data, has demonstrated its potential to offer broad clinical and scientific applications, although further evaluations for various diseases and pathological conditions are necessary.

eess.IV↗

arXiv2024

In-vivo high-resolution χ-separation at 7T

A recently introduced quantitative susceptibility mapping (QSM) technique, $χ$-separation, offers the capability to separate paramagnetic ($χ_{\text{para}}$) and diamagnetic ($χ_{\text{dia}}$) susceptibility distribution within the brain. In-vivo high-resolution mapping of iron and myelin distribution, estimated by $χ$-separation, could provide a deeper understanding of brain substructures, assisting the investigation of their functions and alterations. This can be achieved using 7T MRI, which benefits from a high signal-to-noise ratio and susceptibility effects. However, applying $χ$-separation at 7T presents difficulties due to the requirement of an $R_2$ map, coupled with issues such as high specific absorption rate (SAR), large $B_1$ transmit field inhomogeneities, and prolonged scan time. To address these challenges, we developed a novel deep neural network, R2PRIMEnet7T, designed to convert a 7T $R_2^*$ map into a 3T $R_2'$ map. Building on this development, we present a new pipeline for $χ$-separation at 7T, enabling us to generate high-resolution $χ$-separation maps from multi-echo gradient-echo data. The proposed method is compared with alternative pipelines, such as an end-to-end network and linearly-scaled $R_2'$, and is validated against $χ$-separation maps at 3T, demonstrating its accuracy. The 7T $χ$-separation maps generated by the proposed method exhibit similar contrasts to those from 3T, while 7T high-resolution maps offer enhanced clarity and detail. Quantitative analysis confirms that the proposed method surpasses the alternative pipelines. The proposed method results well delineate the detailed brain structures associated with iron and myelin. This new pipeline holds promise for analyzing iron and myelin concentration changes in various neurodegenerative diseases through precise structural examination.

q-bio.QM↗

arXiv2024

So You Want to Image Myelin Using MRI: Magnetic Susceptibility Source Separation for Myelin Imaging

In MRI, researchers have long endeavored to effectively visualize myelin distribution in the brain, a pursuit with significant implications for both scientific research and clinical applications. Over time, various methods such as myelin water imaging, magnetization transfer imaging, and relaxometric imaging have been developed, each carrying distinct advantages and limitations. Recently, an innovative technique named as magnetic susceptibility source separation has emerged, introducing a novel surrogate biomarker for myelin in the form of a diamagnetic susceptibility map. This paper comprehensively reviews this cutting-edge method, providing the fundamental concepts of magnetic susceptibility, susceptibility imaging, and the validation of the diamagnetic susceptibility map as a myelin biomarker that indirectly measure myelin content. Additionally, the paper explores essential aspects of data acquisition and processing, offering practical insights for readers. A comparison with established myelin imaging methods is also presented, and both current and prospective clinical and scientific applications are discussed to provide a holistic understanding of the technique. This work aims to serve as a foundational resource for newcomers entering this dynamic and rapidly expanding field.

physics.med-ph↗