arXiv subjects

Jongho Lee

Publications and source records attributed to Jongho Lee.

At least 37 records · Page 2Linked to original sources

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↗

arXiv2024

Adaptive Selection of Sampling-Reconstruction in Fourier Compressed Sensing

Compressed sensing (CS) has emerged to overcome the inefficiency of Nyquist sampling. However, traditional optimization-based reconstruction is slow and can not yield an exact image in practice. Deep learning-based reconstruction has been a promising alternative to optimization-based reconstruction, outperforming it in accuracy and computation speed. Finding an efficient sampling method with deep learning-based reconstruction, especially for Fourier CS remains a challenge. Existing joint optimization of sampling-reconstruction works ($\mathcal{H}_1$) optimize the sampling mask but have low potential as it is not adaptive to each data point. Adaptive sampling ($\mathcal{H}_2$) has also disadvantages of difficult optimization and Pareto sub-optimality. Here, we propose a novel adaptive selection of sampling-reconstruction ($\mathcal{H}_{1.5}$) framework that selects the best sampling mask and reconstruction network for each input data. We provide theorems that our method has a higher potential than $\mathcal{H}_1$ and effectively solves the Pareto sub-optimality problem in sampling-reconstruction by using separate reconstruction networks for different sampling masks. To select the best sampling mask, we propose to quantify the high-frequency Bayesian uncertainty of the input, using a super-resolution space generation model. Our method outperforms joint optimization of sampling-reconstruction ($\mathcal{H}_1$) and adaptive sampling ($\mathcal{H}_2$) by achieving significant improvements on several Fourier CS problems.

eess.IV↗

arXiv2024

Volumetric B1+ field homogenization in 7 Tesla brain MRI using metasurface scattering

Ultrahigh field magnetic resonance imaging (UHF MRI) has become an indispensable tool for human brain imaging, offering excellent diagnostic accuracy while avoiding the risks associated with invasive modalities. When the radiofrequency magnetic field of the UHF MRI encounters the multifaceted complexity of the brain, characterized by wavelength-scale, dissipative, and random heterogeneous materials, detrimental mesoscopic challenges such as B1+ field inhomogeneity and local heating arise. Here we develop the metasurface design inspired by scattering theory to achieve the volumetric field homogeneity in the UHF MRI. The method focuses on finding the scattering ansatz systematically and incorporates a pruning technique to achieve the minimum number of participating modes, which guarantees stable practical implementation. Using full-wave analysis of realistic human brain models under a 7 Tesla MRI, we demonstrate more than a twofold improvement in field homogeneity and suppressed local heating, achieving better performance than even the commercial 3 Tesla MRI. The result shows a noninvasive generalization of constant intensity waves in optics, offering a universal methodology applicable to higher Tesla MRI.

physics.optics↗

arXiv2024

ETROC1: The First Full Chain Precision Timing Prototype ASIC for CMS MTD Endcap Timing Layer Upgrade

We present the design and characterization of the first full chain precision timing prototype ASIC, named ETL Readout Chip version 1 (ETROC1) for the CMS MTD endcap timing layer (ETL) upgrade. The ETL utilizes Low Gain Avalanche Diode (LGAD) sensors to detect charged particles, with the goal to achieve a time resolution of 40 - 50 ps per hit, and 30 - 40 ps per track with hits from two detector layers. The ETROC1 is composed of a 5 x 5 pixel array and peripheral circuits. The pixel array includes a 4 x 4 active pixel array with an H-tree shaped network delivering clock and charge injection signals. Each active pixel is composed of various components, including a bump pad, a charge injection circuit, a pre-amplifier, a discriminator, a digital-to-analog converter, and a time-to-digital converter. These components play essential roles as the front-end link in processing LGAD signals and measuring timing-related information. The peripheral circuits provide clock signals and readout functionalities. The size of the ETROC1 chip is 7 mm x 9 mm. ETROC1 has been fabricated in a 65 nm CMOS process, and extensively tested under stimuli of charge injection, infrared laser, and proton beam. The time resolution of bump-bonded ETROC1 + LGAD chipsets reaches 42 - 46 ps per hit in the beam test.

physics.ins-det↗

arXiv2024

A Note on LoRA

LoRA (Low-Rank Adaptation) has emerged as a preferred method for efficiently adapting Large Language Models (LLMs) with remarkable simplicity and efficacy. This note extends the original LoRA paper by offering new perspectives that were not initially discussed and presents a series of insights for deploying LoRA at scale. Without introducing new experiments, we aim to improve the understanding and application of LoRA.

cs.LG↗

arXiv2024

A human brain atlas of chi-separation for normative iron and myelin distributions

Iron and myelin are primary susceptibility sources in the human brain. These substances are essential for healthy brain, and their abnormalities are often related to various neurological disorders. Recently, an advanced susceptibility mapping technique, which is referred to as chi-separation, has been proposed, successfully disentangling paramagnetic iron from diamagnetic myelin. This method opened a potential for generating high resolution iron and myelin maps in the brain. Utilizing this technique, this study constructs a normative chi-separation atlas from 106 healthy human brains. The resulting atlas provides detailed anatomical structures associated with the distributions of iron and myelin, clearly delineating subcortical nuclei, thalamic nuclei, and white matter fiber bundles. Additionally, susceptibility values in a number of regions of interest are reported along with age-dependent changes. This atlas may have direct applications such as localization of subcortical structures for deep brain stimulation or high-intensity focused ultrasound and also serve as a valuable resource for future research.

eess.IV↗

arXiv2024

Pixel data real time processing as a next step for HL-LHC upgrades and beyond

The experiments at LHC are implementing novel and challenging detector upgrades for the High Luminosity LHC, among which the tracking systems. This paper reports on performance studies, illustrated by an electron trigger, using a simplified pixel tracker. To achieve a real-time trigger (e.g. processing HL-LHC collision events at 40 MHz), simple algorithms are developed for reconstructing pixel-based tracks and track isolation, utilizing look-up tables based on pixel detector information. Significant gains in electron trigger performance are seen when pixel detector information is included. In particular, a rate reduction up to a factor of 20 is obtained with a signal selection efficiency of more than 95\% over the whole $η$ coverage of this detector. Furthermore, it reconstructs p-p collision points in the beam axis (z) direction, with a high precision of 20 $μ$m resolution in the very central region ($|η| < 0.8$), and, up to 380 $μ$m in the forward region (2.7 $< |η| <$ 3.0). This study as well as the results can easily be adapted to the muon case and to the different tracking systems at LHC and other machines beyond the HL-LHC. The feasibility of such real-time processing of the pixel information is mainly constrained by the Level-1 trigger latency of the experiment. How this might be overcome by the Front-End ASIC design, new processors, and embedded Artificial Intelligence algorithms is briefly tackled as well.

hep-ex↗

arXiv2024

QUICK: Quantization-aware Interleaving and Conflict-free Kernel for efficient LLM inference

We introduce QUICK, a group of novel optimized CUDA kernels for the efficient inference of quantized Large Language Models (LLMs). QUICK addresses the shared memory bank-conflict problem of state-of-the-art mixed precision matrix multiplication kernels. Our method interleaves the quantized weight matrices of LLMs offline to skip the shared memory write-back after the dequantization. We demonstrate up to 1.91x speedup over existing kernels of AutoAWQ on larger batches and up to 1.94x throughput gain on representative LLM models on various NVIDIA GPU devices.

cs.LG↗

arXiv2024

Fast and accurate sparse-view CBCT reconstruction using meta-learned neural attenuation field and hash-encoding regularization

Cone beam computed tomography (CBCT) is an emerging medical imaging technique to visualize the internal anatomical structures of patients. During a CBCT scan, several projection images of different angles or views are collectively utilized to reconstruct a tomographic image. However, reducing the number of projections in a CBCT scan while preserving the quality of a reconstructed image is challenging due to the nature of an ill-posed inverse problem. Recently, a neural attenuation field (NAF) method was proposed by adopting a neural radiance field algorithm as a new way for CBCT reconstruction, demonstrating fast and promising results using only 50 views. However, decreasing the number of projections is still preferable to reduce potential radiation exposure, and a faster reconstruction time is required considering a typical scan time. In this work, we propose a fast and accurate sparse-view CBCT reconstruction (FACT) method to provide better reconstruction quality and faster optimization speed in the minimal number of view acquisitions ($<$ 50 views). In the FACT method, we meta-trained a neural network and a hash-encoder using a few scans (= 15), and a new regularization technique is utilized to reconstruct the details of an anatomical structure. In conclusion, we have shown that the FACT method produced better, and faster reconstruction results over the other conventional algorithms based on CBCT scans of different body parts (chest, head, and abdomen) and CT vendors (Siemens, Phillips, and GE).

eess.IV↗

arXiv2023

BlindHarmony: "Blind" Harmonization for MR Images via Flow model

In MRI, images of the same contrast (e.g., T$_1$) from the same subject can exhibit noticeable differences when acquired using different hardware, sequences, or scan parameters. These differences in images create a domain gap that needs to be bridged by a step called image harmonization, to process the images successfully using conventional or deep learning-based image analysis (e.g., segmentation). Several methods, including deep learning-based approaches, have been proposed to achieve image harmonization. However, they often require datasets from multiple domains for deep learning training and may still be unsuccessful when applied to images from unseen domains. To address this limitation, we propose a novel concept called `Blind Harmonization', which utilizes only target domain data for training but still has the capability to harmonize images from unseen domains. For the implementation of blind harmonization, we developed BlindHarmony using an unconditional flow model trained on target domain data. The harmonized image is optimized to have a correlation with the input source domain image while ensuring that the latent vector of the flow model is close to the center of the Gaussian distribution. BlindHarmony was evaluated on both simulated and real datasets and compared to conventional methods. BlindHarmony demonstrated noticeable performance on both datasets, highlighting its potential for future use in clinical settings. The source code is available at: https://github.com/SNU-LIST/BlindHarmony

eess.IV↗

arXiv2023

Recommended Implementation of Quantitative Susceptibility Mapping for Clinical Research in The Brain: A Consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group

This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with - as a minimum - the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting.

physics.med-ph↗

arXiv2022

Novel Weight Update Scheme for Hardware Neural Network based on Synaptic Devices Having Abrupt LTP or LTD Characteristics

Mitigating nonlinear weight update characteristics is one of the main challenges in designing neural networks based on synaptic devices. This paper presents a novel weight update method named conditional reverse update scheme (CRUS) for hardware neural network (HNN) consisting of synaptic devices with highly nonlinear or abrupt conductance update characteristics. We formulate a linear optimization method of conductance in synaptic devices to reduce the average deviation of weight changes from those calculated by the Stochastic Gradient Rule (SGD) algorithm. We introduce a metric called update noise (UN) to analyze the training dynamics during training. We then design a weight update rule that reduces the UN averaged over the training process. The optimized network achieves >90% accuracy on the MNIST dataset under highly nonlinear long-term potentiation (LTP) and long-term depression (LTD) conditions while using inaccurate and infrequent conductance sensing. Furthermore, the proposed method shows better accuracy than previously reported nonlinear weight update mitigation techniques under the same hardware specifications and device conditions. It also exhibits robustness to temporal variations in conductance updates. We expect our scheme to relieve design requirements in device and circuit engineering and serve as a practical technique that can be applied to future HNNs.

cs.ET↗

arXiv2021

Deep reinforcement learning-designed radiofrequency waveform in MRI

Carefully engineered radiofrequency (RF) pulses play a key role in a number of systems such as mobile phone, radar, and magnetic resonance imaging. The design of an RF waveform, however, is often posed as an inverse problem with no general solution. As a result, various design methods each with a specific purpose have been developed based on the intuition of human experts. In this work, we propose an artificial intelligence (AI)-powered RF pulse design framework, DeepRF, which utilizes the self-learning characteristics of deep reinforcement learning to generate a novel RF pulse. The effectiveness of DeepRF is demonstrated using four types of RF pulses that are commonly used. The DeepRF-designed pulses successfully satisfy the design criteria while reporting reduced energy. Analyses demonstrate the pulses utilize new mechanisms of magnetization manipulation, suggesting the potentials of DeepRF in discovering unseen design dimensions beyond human intuition. This work may lay the foundation for an emerging field of AI-driven RF waveform design.

eess.IV↗

arXiv2021

BUDA-SAGE with self-supervised denoising enables fast, distortion-free, high-resolution T2, T2*, para- and dia-magnetic susceptibility mapping

To rapidly obtain high resolution T2, T2* and quantitative susceptibility mapping (QSM) source separation maps with whole-brain coverage and high geometric fidelity. We propose Blip Up-Down Acquisition for Spin And Gradient Echo imaging (BUDA-SAGE), an efficient echo-planar imaging (EPI) sequence for quantitative mapping. The acquisition includes multiple T2*-, T2'- and T2-weighted contrasts. We alternate the phase-encoding polarities across the interleaved shots in this multi-shot navigator-free acquisition. A field map estimated from interim reconstructions was incorporated into the joint multi-shot EPI reconstruction with a structured low rank constraint to eliminate geometric distortion. A self-supervised MR-Self2Self (MR-S2S) neural network (NN) was utilized to perform denoising after BUDA reconstruction to boost SNR. Employing Slider encoding allowed us to reach 1 mm isotropic resolution by performing super-resolution reconstruction on BUDA-SAGE volumes acquired with 2 mm slice thickness. Quantitative T2 and T2* maps were obtained using Bloch dictionary matching on the reconstructed echoes. QSM was estimated using nonlinear dipole inversion (NDI) on the gradient echoes. Starting from the estimated R2 and R2* maps, R2' information was derived and used in source separation QSM reconstruction, which provided additional para- and dia-magnetic susceptibility maps. In vivo results demonstrate the ability of BUDA-SAGE to provide whole-brain, distortion-free, high-resolution multi-contrast images and quantitative T2 and T2* maps, as well as yielding para- and dia-magnetic susceptibility maps. Derived quantitative maps showed comparable values to conventional mapping methods in phantom and in vivo measurements. BUDA-SAGE acquisition with self-supervised denoising and Slider encoding enabled rapid, distortion-free, whole-brain T2, T2* mapping at 1 mm3 isotropic resolution in 90 seconds.

physics.med-ph↗

arXiv2021

DIFFnet: Diffusion parameter mapping network generalized for input diffusion gradient schemes and bvalues

In MRI, deep neural networks have been proposed to reconstruct diffusion model parameters. However, the inputs of the networks were designed for a specific diffusion gradient scheme (i.e., diffusion gradient directions and numbers) and a specific b-value that are the same as the training data. In this study, a new deep neural network, referred to as DIFFnet, is developed to function as a generalized reconstruction tool of the diffusion-weighted signals for various gradient schemes and b-values. For generalization, diffusion signals are normalized in a q-space and then projected and quantized, producing a matrix (Qmatrix) as an input for the network. To demonstrate the validity of this approach, DIFFnet is evaluated for diffusion tensor imaging (DIFFnetDTI) and for neurite orientation dispersion and density imaging (DIFFnetNODDI). In each model, two datasets with different gradient schemes and b-values are tested. The results demonstrate accurate reconstruction of the diffusion parameters at substantially reduced processing time (approximately 8.7 times and 2240 times faster processing time than conventional methods in DTI and NODDI, respectively; less than 4% mean normalized root-mean-square errors (NRMSE) in DTI and less than 8% in NODDI). The generalization capability of the networks was further validated using reduced numbers of diffusion signals from the datasets. Different from previously proposed deep neural networks, DIFFnet does not require any specific gradient scheme and b-value for its input. As a result, it can be adopted as an online reconstruction tool for various complex diffusion imaging.

eess.IV↗

arXiv2021

Expression of Interest for the CODEX-b Detector

This document presents the physics case and ancillary studies for the proposed CODEX-b long-lived particle (LLP) detector, as well as for a smaller proof-of-concept demonstrator detector, CODEX-$β$, to be operated during Run 3 of the LHC. Our development of the CODEX-b physics case synthesizes `top-down' and `bottom-up' theoretical approaches, providing a detailed survey of both minimal and complete models featuring LLPs. Several of these models have not been studied previously, and for some others we amend studies from previous literature: In particular, for gluon and fermion-coupled axion-like particles. We moreover present updated simulations of expected backgrounds in CODEX-b's actively shielded environment, including the effects of shielding propagation uncertainties, high-energy tails and variation in the shielding design. Initial results are also included from a background measurement and calibration campaign. A design overview is presented for the CODEX-$β$ demonstrator detector, which will enable background calibration and detector design studies. Finally, we lay out brief studies of various design drivers of the CODEX-b experiment and potential extensions of the baseline design, including the physics case for a calorimeter element, precision timing, event tagging within LHCb, and precision low-momentum tracking.

hep-ex↗

arXiv2020

The Analog Front-end for the LGAD Based Precision Timing Application in CMS ETL

The analog front-end for the Low Gain Avalanche Detector (LGAD) based precision timing application in the CMS Endcap Timing Layer (ETL) has been prototyped in a 65 nm CMOS mini-ASIC named ETROC0. Serving as the very first prototype of ETL readout chip (ETROC), ETROC0 aims to study and demonstrate the performance of the analog frontend, with the goal to achieve 40 to 50 ps time resolution per hit with LGAD (therefore reach about 30ps per track with two detector-layer hits per track). ETROC0 consists of preamplifier and discriminator stages, which amplifies the LGAD signal and generates digital pulses containing time of arrival and time over threshold information. This paper will focus on the design considerations that lead to the ETROC front-end architecture choice, the key design features of the building blocks, the methodology of using the LGAD simulation data to evaluate and optimize the front-end design. The ETROC0 prototype chips have been extensively tested using charge injection and the measured performance agrees well with simulation. The initial beam test results are also presented, with time resolution of around 33 ps observed from the preamplifier waveform analysis and around 41 ps from the discriminator pulses analysis. A subset of ETROC0 chips have also been tested to a total ionizing dose of 100 MRad with X-ray and no performance degradation been observed.

physics.ins-det↗

arXiv2020

Background studies for the CODEX-b experiment: measurements and simulation

This report presents results from a background measurement campaign for the CODEX-b proposal undertaken in August, 2018. The data were recorded in the DELPHI side of the LHCb cavern behind a 3.2~m concrete shield wall, during Run~2 proton-proton collisions with the goal of calibrating the simulation for the full CODEX-b detector. The maximum flux rate in the DELPHI side of the cavern was found to be around 0.6~mHz/cm$^2$ across a vertical plane just behind the shield wall, parallel to the beam line. A detailed simulation under development within the LHCb {\tt Gauss} framework is described. This includes shielding elements pertinent for CODEX-b's acceptance -- the LHCb detector, the shield wall and cavern infrastructure. Additional flux from tracks not in the line of sight from the interaction point, but bent by the magnetic fields, are incorporated. Overall, the simulation overestimates the background flux compared to the measurement. Several cross-checks and avenues for further investigations are described.

physics.ins-det↗