arXiv subjects

Dicheng Chen

Publications and source records attributed to Dicheng Chen.

7 recordsLinked to original sources

arXiv2025

An artificially intelligent magnetic resonance spectroscopy quantification method: Comparison between QNet and LCModel on the cloud computing platform CloudBrain-MRS

Objctives: This work aimed to statistically compare the metabolite quantification of human brain magnetic resonance spectroscopy (MRS) between the deep learning method QNet and the classical method LCModel through an easy-to-use intelligent cloud computing platform CloudBrain-MRS. Materials and Methods: In this retrospective study, two 3 T MRI scanners Philips Ingenia and Achieva collected 61 and 46 in vivo 1H magnetic resonance (MR) spectra of healthy participants, respectively, from the brain region of pregenual anterior cingulate cortex from September to October 2021. The analyses of Bland-Altman, Pearson correlation and reasonability were performed to assess the degree of agreement, linear correlation and reasonability between the two quantification methods. Results: Fifteen healthy volunteers (12 females and 3 males, age range: 21-35 years, mean age/standard deviation = 27.4/3.9 years) were recruited. The analyses of Bland-Altman, Pearson correlation and reasonability showed high to good consistency and very strong to moderate correlation between the two methods for quantification of total N-acetylaspartate (tNAA), total choline (tCho), and inositol (Ins) (relative half interval of limits of agreement = 3.04%, 9.3%, and 18.5%, respectively; Pearson correlation coefficient r = 0.775, 0.927, and 0.469, respectively). In addition, quantification results of QNet are more likely to be closer to the previous reported average values than those of LCModel. Conclusion: There were high or good degrees of consistency between the quantification results of QNet and LCModel for tNAA, tCho, and Ins, and QNet generally has more reasonable quantification than LCModel.

physics.med-ph↗

arXiv2023

Magnetic Resonance Spectroscopy Quantification Aided by Deep Estimations of Imperfection Factors and Macromolecular Signal

Objective: Magnetic Resonance Spectroscopy (MRS) is an important technique for biomedical detection. However, it is challenging to accurately quantify metabolites with proton MRS due to serious overlaps of metabolite signals, imperfections because of non-ideal acquisition conditions, and interference with strong background signals mainly from macromolecules. The most popular method, LCModel, adopts complicated non-linear least square to quantify metabolites and addresses these problems by designing empirical priors such as basis-sets, imperfection factors. However, when the signal-to-noise ratio of MRS signal is low, the solution may have large deviation. Methods: Linear Least Squares (LLS) is integrated with deep learning to reduce the complexity of solving this overall quantification. First, a neural network is designed to explicitly predict the imperfection factors and the overall signal from macromolecules. Then, metabolite quantification is solved analytically with the introduced LLS. In our Quantification Network (QNet), LLS takes part in the backpropagation of network training, which allows the feedback of the quantification error into metabolite spectrum estimation. This scheme greatly improves the generalization to metabolite concentrations unseen for training compared to the end-to-end deep learning method. Results: Experiments show that compared with LCModel, the proposed QNet, has smaller quantification errors for simulated data, and presents more stable quantification for 20 healthy in vivo data at a wide range of signal-to-noise ratio. QNet also outperforms other end-to-end deep learning methods. Conclusion: This study provides an intelligent, reliable and robust MRS quantification. Significance: QNet is the first LLS quantification aided by deep learning.

physics.med-ph↗

arXiv2023

CloudBrain-MRS: An Intelligent Cloud Computing Platform for in vivo Magnetic Resonance Spectroscopy Preprocessing, Quantification, and Analysis

Magnetic resonance spectroscopy (MRS) is an important clinical imaging method for diagnosis of diseases. MRS spectrum is used to observe the signal intensity of metabolites or further infer their concentrations. Although the magnetic resonance vendors commonly provide basic functions of spectra plots and metabolite quantification, the widespread clinical research of MRS is still limited due to the lack of easy-to-use processing software or platform. To address this issue, we have developed CloudBrain-MRS, a cloud-based online platform that provides powerful hardware and advanced algorithms. The platform can be accessed simply through a web browser, without the need of any program installation on the user side. CloudBrain-MRS also integrates the classic LCModel and advanced artificial intelligence algorithms and supports batch preprocessing, quantification, and analysis of MRS data from different vendors. Additionally, the platform offers useful functions: 1) Automatically statistical analysis to find biomarkers for diseases; 2) Consistency verification between the classic and artificial intelligence quantification algorithms; 3) Colorful three-dimensional visualization for easy observation of individual metabolite spectrum. Last, both healthy and mild cognitive impairment patient data are used to demonstrate the functions of the platform. To the best of our knowledge, this is the first cloud computing platform for in vivo MRS with artificial intelligence processing. We have shared our cloud platform at MRSHub, providing free access and service for two years. Please visit https://mrshub.org/software_all/#CloudBrain-MRS or https://csrc.xmu.edu.cn/CloudBrain.html.

eess.SP↗

arXiv2023

A Dynamics Theory of Implicit Regularization in Deep Low-Rank Matrix Factorization

Implicit regularization is an important way to interpret neural networks. Recent theory starts to explain implicit regularization with the model of deep matrix factorization (DMF) and analyze the trajectory of discrete gradient dynamics in the optimization process. These discrete gradient dynamics are relatively small but not infinitesimal, thus fitting well with the practical implementation of neural networks. Currently, discrete gradient dynamics analysis has been successfully applied to shallow networks but encounters the difficulty of complex computation for deep networks. In this work, we introduce another discrete gradient dynamics approach to explain implicit regularization, i.e. landscape analysis. It mainly focuses on gradient regions, such as saddle points and local minima. We theoretically establish the connection between saddle point escaping (SPE) stages and the matrix rank in DMF. We prove that, for a rank-R matrix reconstruction, DMF will converge to a second-order critical point after R stages of SPE. This conclusion is further experimentally verified on a low-rank matrix reconstruction problem. This work provides a new theory to analyze implicit regularization in deep learning.

cs.LG↗

arXiv2022

Magnetic Resonance Spectroscopy Deep Learning Denoising Using Few In Vivo Data

Magnetic Resonance Spectroscopy (MRS) is a noninvasive tool to reveal metabolic information. One challenge of 1H-MRS is the low Signal-Noise Ratio (SNR). To improve the SNR, a typical approach is to perform Signal Averaging (SA) with M repeated samples. The data acquisition time, however, is increased by M times accordingly, and a complete clinical MRS scan takes approximately 10 minutes at a common setting M=128. Recently, deep learning has been introduced to improve the SNR but most of them use the simulated data as the training set. This may hinder the MRS applications since some potential differences, such as acquisition system imperfections, and physiological and psychologic conditions may exist between the simulated and in vivo data. Here, we proposed a new scheme that purely used the repeated samples of realistic data. A deep learning model, Refusion Long Short-Term Memory (ReLSTM), was designed to learn the mapping from the low SNR time-domain data (24 SA) to the high SNR one (128 SA). Experiments on the in vivo brain spectra of 7 healthy subjects, 2 brain tumor patients and 1 cerebral infarction patient showed that only using 20% repeated samples, the denoised spectra by ReLSTM could provide comparable estimated concentrations of metabolites to 128 SA. Compared with the state-of-the-art low-rank denoising method, the ReLSTM achieved the lower relative error and the Cramér-Rao lower bounds in quantifying some important biomarkers. In summary, ReLSTM can perform high-fidelity denoising of the spectra under fast acquisition (24 SA), which would be valuable to MRS clinical studies.

physics.med-ph↗

arXiv2020

Spatiotemporal Flexible Sparse Reconstruction for Rapid Dynamic Contrast-enhanced MRI

Dynamic Contrast-enhanced magnetic resonance imaging (DCE-MRI) is a tissue perfusion imaging technique. Some versatile free-breathing DCE-MRI techniques combining compressed sensing (CS) and parallel imaging with golden-angle radial sampling have been developed to improve motion robustness with high spatial and temporal resolution. These methods have demonstrated good diagnostic performance in clinical setting, but the reconstruction quality will degrade at high acceleration rates and overall reconstruction time remains long. In this paper, we proposed a new parallel CS reconstruction model for DCE-MRI that enforces flexible weighted sparse constraint along both spatial and temporal dimensions. Weights were introduced to flexibly adjust the importance of time and space sparsity, and we derived a fast thresholding algorithm which was proven to be simple and efficient for solving the proposed reconstruction model. Results on in vivo liver DCE datasets show that the proposed method outperforms the state-of-the-art methods in terms of visual image quality assessment and reconstruction speed without introducing significant temporal blurring.

physics.med-ph↗

arXiv2020

Review and Prospect: Deep Learning in Nuclear Magnetic Resonance Spectroscopy

Since the concept of Deep Learning (DL) was formally proposed in 2006, it had a major impact on academic research and industry. Nowadays, DL provides an unprecedented way to analyze and process data with demonstrated great results in computer vision, medical imaging, natural language processing, etc. In this Minireview, we summarize applications of DL in Nuclear Magnetic Resonance (NMR) spectroscopy and outline a perspective for DL as entirely new approaches that are likely to transform NMR spectroscopy into a much more efficient and powerful technique in chemistry and life science.

physics.med-ph↗