VLDB 2026 Research / reviewers in the wild / expert
Georges El Fakhri
dblp:02/9372
· DBLP profile ↗
41ranked-venue papers
0as first author
28since 2021 · last 2026
0000-0002-9005-6993ORCID · verified
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 29 · 18 since 2021Graphics, computer vision, multimedia, augmented reality and games · 18 · 14 since 2021Artificial intelligence and machine learning · 10 · 8 since 2021
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2026 | Power Battery Detection
Xiaoqi Zhao 0003, Peiqian Cao, Chenyang Yu, Zonglei Feng, Lihe Zhang, Hanqi Liu, Jiaming Zuo, Youwei Pang, Jinsong Ouyang, Weisi Lin, Georges El Fakhri, Huchuan Lu, Xiaofeng Liu 0001 |
Int. J. Comput. Vis. | 11 |
| 2026 | Anatomically and metabolically informed diffusion for unified denoising and segmentation in low-count PET imaging
Menghua Xia, Kuan-Yin Ko, Der-Shiun Wang, Mingkai Chen 0003, Huidong Xie, Wei Ji 0011, Jinsong Ouyang, Reimund Bayerlein, Benjamin A. Spencer, Quanzheng Li, Ramsey Derek Badawi, Georges El Fakhri, Chi Liu 0001 |
Medical Image Anal. | 14 |
| 2026 | Variance Extrapolated Class-Imbalance-Aware Domain Adaptive Myocardial Segmentation in Multi-Sequence Cardiac MRIabstractFully automated myocardial segmentation from cardiac magnetic resonance imaging (MRI) is vital for efficient diagnosis and treatment planning. Although numerous automated methods have been proposed, they typically focus on single MRI sequences and therefore have difficulties in generalizing across vendors and across cardiac MRI protocols. Simultaneous analysis of complementary cardiac MRI sequences, such as cine, T1 mapping, and late gadolinium enhancement (LGE) MRI, remains challenging due to their distinct image characteristics and scanner-specific variations. To address these issues, we propose an unsupervised domain adaptation approach that allows robust myocardial segmentation across multi-vendor cine, T1, and LGE MRI data. In particular, we introduce a class-imbalance self-training framework to transfer information learned from a source domain with labels to any unlabeled target domain, while maintaining consistent performance across different MRI sequences. Our framework iteratively refines segmentation accuracy by generating pseudo-labels for target data using a hardness-aware strategy, thus effectively addressing the problem of class imbalance in cardiac MRI segmentation. To mitigate data scarcity following pseudo-label selection, we employ a variance-guided vicinal feature extrapolation, which expands data points in the feature space into a probabilistic distribution. This, in turn, facilitates joint source-target training by generating a larger intersection in the feature space. Experimental results demonstrate that our framework outperforms existing methods when assessed using the Dice coefficient and Hausdorff distance. Our framework enables cardiac evaluation across MRI protocols without sequence-specific manual annotations. Fangxu Xing, Xiaofeng Liu 0001, Iman Aganj, Georges El Fakhri, Panki Kim, Jonghye Woo |
IEEE J. Biomed. Health Informatics | 4 |
| 2026 | LeqMod: Adaptable Lesion-Quantification-Consistent Modulation for Deep Learning Low-Count PET Image DenoisingabstractDeep learning-based positron emission tomography (PET) image denoising offers the potential to reduce radiation exposure and scanning time by transforming low-count images into high-count equivalents. However, existing methods typically blur crucial details, leading to inaccurate lesion quantification. This paper proposes a lesion-perceived and quantification-consistent modulation (LeqMod) strategy for enhanced PET image denoising, via employing downstream lesion quantification analysis as auxiliary tools. The LeqMod is a plug-and-play design adaptable to a wide range of model architectures, modulating the sampling and optimization procedures of model training without adding any computational burden to the inference phase. Specifically, the LeqMod consists of two components, the lesion-perceived modulation (LeMod) and the multiscale quantification-consistent modulation (QuMod). The LeMod enhances lesion contrast and visibility by allocating higher sampling weights and stricter loss criteria to lesion-present samples determined by an auxiliary segmentation network than lesion-absent ones. The QuMod further emphasizes quantification accuracy for both the mean and maximum standardized uptake value ( ${\mathrm {SUV}}_{{\textit {mean}}}$ and ${\mathrm {SUV}}_{{\textit {max}}}$ ) across multiscale sub-regions throughout the entire image, thereby reducing biases of denoised results relative to high-count references. Experiments conducted on large PET datasets from multiple centers and vendors, and varying noise levels demonstrated the LeqMod efficacy across various denoising frameworks. Compared to frameworks without LeqMod, the integration of LeqMod reduces the lesion ${\mathrm {SUV}}_{{\textit {max}}}$ bias by 5.92% on average and increases the peak signal-to-noise ratio (PSNR) by 0.36 on average, when denoising images across participating sites. (Code is available at https://github.com/mhxiaaa/LeqMod_PET_denoising). Menghua Xia, Huidong Xie, Bo Zhou 0009, Hanzhong Wang, Axel Rominger, Quanzheng Li, Ramsey Derek Badawi, Kuangyu Shi, Georges El Fakhri, Chi Liu 0001 |
IEEE Trans. Medical Imaging | 11 |
| 2025 | GlioSurvNet: Multimodal Survival Prediction for Glioblastoma Using Deep Learning and Clinical Variables from Brain MRIabstractAccurate survival prediction using multimodal magnetic resonance imaging (MRI) plays a crucial role in clinical decision-making for patients with glioblastoma (GBM). In this work, we propose a multimodal framework, GlioSurvNet, that integrates deep learning features extracted from Swin UNETR and clinical variables to predict patient survival. Our framework makes use of multiple MRI sequences, including T1, T1 with contrast enhancement, T2-weighted, and FLAIR MRI, to capture diverse tumor characteristics. The Swin UNETR architecture simultaneously carries out tumor segmentation and extracts hierarchical features from multimodal MRI data. These deep learning features are then combined with clinical variables, which are input into a multi-layer perceptron network to yield survival probabilities. We evaluated our framework on a cohort of 287 patients from two independent databases, UPENN-GBM and UCSF-PDGM, demonstrating superior survival prediction performance when compared with existing methods. Our framework achieved a time-dependent concordance index of 0.693 and an integrated brier score of 0.14 with improved risk stratification. GlioSurvNet offers a robust tool for personalized prognosis and treatment planning in GBM patients. Gihyeon Kim, Fangxu Xing, Hyoun-Joong Kong, Emiliano Santarnecchi, Helen A. Shih, Thomas Bortfeld, Georges El Fakhri, Xiaofeng Liu 0001, Jang Hwan Choi 0001, Jonghye Woo |
ICIP | 7 |
| 2025 | Rethinking Evaluation of Infrared Small Target DetectionabstractAs an essential vision task, infrared small target detection (IRSTD) has seen significant advancements through deep learning. However, critical limitations in current evaluation protocols impede further progress. First, existing methods rely on fragmented pixel- and target-level specific metrics, which fails to provide a comprehensive view of model capabilities. Second, an excessive emphasis on overall performance scores obscures crucial error analysis, which is vital for identifying failure modes and improving real-world system performance. Third, the field predominantly adopts dataset-specific training-testing paradigms, hindering the understanding of model robustness and generalization across diverse infrared scenarios. This paper addresses these issues by introducing a hybrid-level metric incorporating pixel- and target-level performance, proposing a systematic error analysis method, and emphasizing the importance of cross-dataset evaluation. These aim to offer a more thorough and rational hierarchical analysis framework, ultimately fostering the development of more effective and robust IRSTD models. An open-source toolkit has be released to facilitate standardized benchmarking. Youwei Pang, Xiaoqi Zhao 0003, Lihe Zhang, Huchuan Lu, Georges El Fakhri, Xiaofeng Liu 0001, Shijian Lu |
NeurIPS | 5 |
| 2025 | UniMRSeg: Unified Modality-Relax Segmentation via Hierarchical Self-Supervised CompensationabstractMulti-modal image segmentation faces real-world deployment challenges from incomplete/corrupted modalities degrading performance. While existing methods address training-inference modality gaps via specialized per-combination models, they introduce high deployment costs by requiring exhaustive model subsets and model-modality matching. In this work, we propose a unified modality-relax segmentation network (UniMRSeg) through hierarchical self-supervised compensation (HSSC). Our approach hierarchically bridges representation gaps between complete and incomplete modalities across input, feature and output levels.
First, we adopt modality reconstruction with the hybrid shuffled-masking augmentation, encouraging the model to learn the intrinsic modality characteristics and generate meaningful representations for missing modalities through cross-modal fusion.
Next, modality-invariant contrastive learning implicitly compensates the feature space distance among incomplete-complete modality pairs. Furthermore, the proposed lightweight reverse attention adapter explicitly compensates for the weak perceptual semantics in the frozen encoder. Last, UniMRSeg is fine-tuned under the hybrid consistency constraint to ensure stable prediction under all modality combinations without large performance fluctuations. Without bells and whistles, UniMRSeg significantly outperforms the state-of-the-art methods under diverse missing modality scenarios on MRI-based brain tumor segmentation, RGB-D semantic segmentation, RGB-D/T salient object segmentation. The code will be released at \url{https://github.com/Xiaoqi-Zhao-DLUT/UniMRSeg}. Xiaoqi Zhao 0003, Youwei Pang, Chenyang Yu, Lihe Zhang, Huchuan Lu, Shijian Lu, Georges El Fakhri, Xiaofeng Liu 0001 |
NeurIPS | 7 |
| 2025 | Bayesian Posterior Distribution Estimation of Kinetic Parameters in Dynamic Brain PET Using Generative Deep Learning ModelsabstractPositron Emission Tomography (PET) is a valuable imaging method for studying molecular-level processes in the body, such as hyperphosphorylated tau (p-tau) protein aggregates, a hallmark of several neurodegenerative diseases including Alzheimer's disease. P-tau density and cerebral perfusion can be quantified from dynamic PET images using tracer kinetic modeling techniques. However, noise in PET images leads to uncertainty in the estimated kinetic parameters, which can be quantified by estimating the posterior distribution of kinetic parameters using Bayesian inference (BI). Markov Chain Monte Carlo (MCMC) techniques are commonly used for posterior estimation but with significant computational needs. This work proposes an Improved Denoising Diffusion Probabilistic Model (iDDPM)-based method to estimate the posterior distribution of kinetic parameters in dynamic PET, leveraging the high computational efficiency of deep learning. The performance of the proposed method was evaluated on a [18F]MK6240 study and compared to a Conditional Variational Autoencoder with dual decoder (CVAE-DD)-based method and a Wasserstein GAN with gradient penalty (WGAN-GP)-based method. Posterior distributions inferred from Metropolis-Hasting MCMC were used as reference. Our approach consistently outperformed the CVAE-DD and WGAN-GP methods and offered significant reduction in computation time than the MCMC method (over 230 times faster), inferring accurate ( $\lt {0}.{67}\,\%$ mean error) and precise ( $\lt {7}.{23}\,\%$ standard deviation error) posterior distributions. Yanis Djebra, Xiaofeng Liu 0001, Thibault Marin, Amal Tiss, Maëva Dhaynaut, Nicolas J. Guehl, Keith A. Johnson, Georges El Fakhri, Chao Ma 0018, Jinsong Ouyang |
IEEE Trans. Medical Imaging | 8 |
| 2024 | Subtype-Aware Dynamic Unsupervised Domain AdaptationabstractUnsupervised domain adaptation (UDA) has been successfully applied to transfer knowledge from a labeled source domain to target domains without their labels. Recently introduced transferable prototypical networks (TPNs) further address class-wise conditional alignment. In TPN, while the closeness of class centers between source and target domains is explicitly enforced in a latent space, the underlying fine-grained subtype structure and the cross-domain within-class compactness have not been fully investigated. To counter this, we propose a new approach to adaptively perform a fine-grained subtype-aware alignment to improve the performance in the target domain without the subtype label in both domains. The insight of our approach is that the unlabeled subtypes in a class have the local proximity within a subtype while exhibiting disparate characteristics because of different conditional and label shifts. Specifically, we propose to simultaneously enforce subtype-wise compactness and class-wise separation, by utilizing intermediate pseudo-labels. In addition, we systematically investigate various scenarios with and without prior knowledge of subtype numbers and propose to exploit the underlying subtype structure. Furthermore, a dynamic queue framework is developed to evolve the subtype cluster centroids steadily using an alternative processing scheme. Experimental results, carried out with multiview congenital heart disease data and VisDA and DomainNet, show the effectiveness and validity of our subtype-aware UDA, compared with state-of-the-art UDA methods. Xiaofeng Liu 0001, Fangxu Xing, Jane You, Jun Lu 0002, C.-C. Jay Kuo, Georges El Fakhri, Jonghye Woo |
IEEE Trans. Neural Networks Learn. Syst. | 6 |
| 2023 | Motor Control Similarity Between Speakers Saying "A Souk" Using Inverse Atlas Tongue ModelingabstractFinite element models (FEM) of the tongue have facilitated speech studies through analysis of internal muscle forces indirectly derived from imaging data. In this work, we build a uniform hexahedral FEM of a tongue atlas constructed from magnetic resonance imaging data of a healthy population. The FEM is driven by inverse internal tongue tissue kinematics of speakers temporally aligned and deformed into the same atlas space, while performing the speech task "a souk" allowing muscle activation predictions. This work aims to investigate the commonalities in tongue motor strategies in the articulation of "a souk" predicted by the inverse tongue atlas model. Our findings report variability among five speakers for estimated muscle activations with a similarity index using a dynamic time warp function. Two speakers show similarity index > 0.9 and two others < 0.7 with respect to a reference speaker for most tongue muscles. The relative motion tracking error of the model is less than 2% which is promising for speech study applications. Ursa Maity, Fangxu Xing, Jerry L. Prince, Maureen Stone 0001, Georges El Fakhri, Jonghye Woo, Sidney S. Fels |
INTERSPEECH | 5 |
| 2023 | Fine-Tuning Network in Federated Learning for Personalized Skin Diagnosis
Kyungsu Lee, Haeyun Lee, Thiago Coutinho Cavalcanti, Sewoong Kim, Georges El Fakhri, Jonghye Woo, Jae Youn Hwang |
MICCAI (3) | 5 |
| 2023 | Self-Supervised Domain Adaptive Segmentation of Breast Cancer via Test-Time Fine-Tuning
Kyungsu Lee, Haeyun Lee, Georges El Fakhri, Jonghye Woo, Jae Youn Hwang |
MICCAI (1) | 3 |
| 2023 | Incremental Learning for Heterogeneous Structure Segmentation in Brain Tumor MRI
Xiaofeng Liu 0001, Helen A. Shih, Fangxu Xing, Emiliano Santarnecchi, Georges El Fakhri, Jonghye Woo |
MICCAI (2) | 5 |
| 2023 | Speech Audio Synthesis from Tagged MRI and Non-negative Matrix Factorization via Plastic Transformer
Xiaofeng Liu 0001, Fangxu Xing, Maureen Stone 0001, Jiachen Zhuo, Sidney S. Fels, Jerry L. Prince, Georges El Fakhri, Jonghye Woo |
MICCAI (7) | 7 |
| 2023 | Attentive continuous generative self-training for unsupervised domain adaptive medical image translation
Xiaofeng Liu 0001, Jerry L. Prince, Fangxu Xing, Jiachen Zhuo, Timothy G. Reese, Maureen Stone 0001, Georges El Fakhri, Jonghye Woo |
Medical Image Anal. | 7 |
| 2023 | Memory consistent unsupervised off-the-shelf model adaptation for source-relaxed medical image segmentation
Xiaofeng Liu 0001, Fangxu Xing, Georges El Fakhri, Jonghye Woo |
Medical Image Anal. | 3 |
| 2023 | Manifold Learning via Linear Tangent Space Alignment (LTSA) for Accelerated Dynamic MRI With Sparse SamplingabstractThe spatial resolution and temporal frame-rate of dynamic magnetic resonance imaging (MRI) can be improved by reconstructing images from sparsely sampled k -space data with mathematical modeling of the underlying spatiotemporal signals. These models include sparsity models, linear subspace models, and non-linear manifold models. This work presents a novel linear tangent space alignment (LTSA) model-based framework that exploits the intrinsic low-dimensional manifold structure of dynamic images for accelerated dynamic MRI. The performance of the proposed method was evaluated and compared to state-of-the-art methods using numerical simulation studies as well as 2D and 3D in vivo cardiac imaging experiments. The proposed method achieved the best performance in image reconstruction among all the compared methods. The proposed method could prove useful for accelerating many MRI applications, including dynamic MRI, multi-parametric MRI, and MR spectroscopic imaging. Yanis Djebra, Thibault Marin, Paul K. Han, Isabelle Bloch, Georges El Fakhri, Chao Ma 0018 |
IEEE Trans. Medical Imaging | 5 |
| 2022 | Cmri2spec: Cine MRI Sequence to Spectrogram Synthesis via A Pairwise Heterogeneous TranslatorabstractMultimodal representation learning using visual movements from cine magnetic resonance imaging (MRI) and their acoustics has shown great potential to learn shared representation and to predict one modality from another. Here, we propose a new synthesis framework to translate from cine MRI sequences to spectrograms with a limited dataset size. Our framework hinges on a novel fully convolutional heterogeneous translator, with a 3D CNN encoder for efficient sequence encoding and a 2D transpose convolution decoder. In addition, a pairwise correlation of the samples with the same speech word is utilized with a latent space representation disentanglement scheme. Furthermore, an adversarial training approach with generative adversarial networks is incorporated to provide enhanced realism on our generated spectrograms. Our experimental results, carried out with a total of 63 cine MRI sequences alongside speech acoustics, show that our framework improves synthesis accuracy, compared with competing methods. Our framework thereby has shown the potential to aid in better understanding the relationship between the two modalities. Xiaofeng Liu 0001, Fangxu Xing, Maureen Stone 0001, Jerry L. Prince, Jangwon Kim, Georges El Fakhri, Jonghye Woo |
ICASSP | 6 |
| 2022 | Tagged-MRI Sequence to Audio Synthesis via Self Residual Attention Guided Heterogeneous Translator
Xiaofeng Liu 0001, Fangxu Xing, Jerry L. Prince, Jiachen Zhuo, Maureen Stone 0001, Georges El Fakhri, Jonghye Woo |
MICCAI (6) | 6 |
| 2022 | ACT: Semi-supervised Domain-Adaptive Medical Image Segmentation with Asymmetric Co-training
Xiaofeng Liu 0001, Fangxu Xing, Nadya Shusharina, Ruth Lim, C.-C. Jay Kuo, Georges El Fakhri, Jonghye Woo |
MICCAI (5) | 6 |
| 2022 | VoxelHop: Successive Subspace Learning for ALS Disease Classification Using Structural MRIabstractDeep learning has great potential for accurate detection and classification of diseases with medical imaging data, but the performance is often limited by the number of training datasets and memory requirements. In addition, many deep learning models are considered a "black-box," thereby often limiting their adoption in clinical applications. To address this, we present a successive subspace learning model, termed VoxelHop, for accurate classification of Amyotrophic Lateral Sclerosis (ALS) using T2-weighted structural MRI data. Compared with popular convolutional neural network (CNN) architectures, VoxelHop has modular and transparent structures with fewer parameters without any backpropagation, so it is well-suited to small dataset size and 3D imaging data. Our VoxelHop has four key components, including (1) sequential expansion of near-to-far neighborhood for multi-channel 3D data; (2) subspace approximation for unsupervised dimension reduction; (3) label-assisted regression for supervised dimension reduction; and (4) concatenation of features and classification between controls and patients. Our experimental results demonstrate that our framework using a total of 20 controls and 26 patients achieves an accuracy of 93.48 % and an AUC score of 0.9394 in differentiating patients from controls, even with a relatively small number of datasets, showing its robustness and effectiveness. Our thorough evaluations also show its validity and superiority to the state-of-the-art 3D CNN classification approaches. Our framework can easily be generalized to other classification tasks using different imaging modalities. Xiaofeng Liu 0001, Fangxu Xing, Chao Yang 0011, C.-C. Jay Kuo, Suma Babu, Georges El Fakhri, Thomas Jenkins, Jonghye Woo |
IEEE J. Biomed. Health Informatics | 6 |
| 2022 | Brain MR Atlas Construction Using Symmetric Deep Neural InpaintingabstractModeling statistical properties of anatomical structures using magnetic resonance imaging is essential for revealing common information of a target population and unique properties of specific subjects. In brain imaging, a statistical brain atlas is often constructed using a number of healthy subjects. When tumors are present, however, it is difficult to either provide a common space for various subjects or align their imaging data due to the unpredictable distribution of lesions. Here we propose a deep learning-based image inpainting method to replace the tumor regions with normal tissue intensities using only a patient population. Our framework has three major innovations: 1) incompletely distributed datasets with random tumor locations can be used for training; 2) irregularly-shaped tumor regions are properly learned, identified, and corrected; and 3) a symmetry constraint between the two brain hemispheres is applied to regularize inpainted regions. Henceforth, regular atlas construction and image registration methods can be applied using inpainted data to obtain tissue deformation, thereby achieving group-specific statistical atlases and patient-to-atlas registration. Our framework was tested using the public database from the Multimodal Brain Tumor Segmentation challenge. Results showed increased similarity scores as well as reduced reconstruction errors compared with three existing image inpainting methods. Patient-to-atlas registration also yielded better results with improved normalized cross-correlation and mutual information and a reduced amount of deformation over the tumor regions. Fangxu Xing, Xiaofeng Liu 0001, C.-C. Jay Kuo, Georges El Fakhri, Jonghye Woo |
IEEE J. Biomed. Health Informatics | 4 |
| 2021 | Subtype-aware Unsupervised Domain Adaptation for Medical DiagnosisabstractRecent advances in unsupervised domain adaptation (UDA) show that transferable prototypical learning presents a powerful means for class conditional alignment, which encourages the closeness of cross-domain class centroids. However, the cross-domain inner-class compactness and the underlying fine-grained subtype structure remained largely underexplored. In this work, we propose to adaptively carry out the fine-grained subtype-aware alignment by explicitly enforcing the class-wise separation and subtype-wise compactness with intermediate pseudo labels. Our key insight is that the unlabeled subtypes of a class can be divergent to one another with different conditional and label shifts, while inheriting the local proximity within a subtype. The cases with or without the prior information on subtype numbers are investigated to discover the underlying subtype structure in an online fashion. The proposed subtype-aware dynamic UDA achieves promising results on a medical diagnosis task. Xiaofeng Liu 0001, Xiongchang Liu, Wenxuan Ji, Fangxu Xing, Jun Lu 0002, Jane You, C.-C. Jay Kuo, Georges El Fakhri, Jonghye Woo |
AAAI | 9 |
| 2021 | Adversarial Unsupervised Domain Adaptation with Conditional and Label Shift: Infer, Align and IterateabstractIn this work, we propose an adversarial unsupervised domain adaptation (UDA) method under inherent conditional and label shifts, in which we aim to align the distributions w.r.t. both p(x|y) and p(y). Since labels are inaccessible in a target domain, conventional adversarial UDA methods assume that p(y) is invariant across domains and rely on aligning p(x) as an alternative to the p(x|y) alignment. To address this, we provide a thorough theoretical and empirical analysis of the conventional adversarial UDA methods under both conditional and label shifts, and propose a novel and practical alternative optimization scheme for adversarial UDA. Specifically, we infer the marginal p(y) and align p(x|y) iteratively at the training stage, and precisely align the posterior p(y|x) at the testing stage. Our experimental results demonstrate its effectiveness on both classification and segmentation UDA and partial UDA. Xiaofeng Liu 0001, Zhenhua Guo 0001, Site Li, Fangxu Xing, Jane You, C.-C. Jay Kuo, Georges El Fakhri, Jonghye Woo |
ICCV | 7 |
| 2021 | Domain Generalization under Conditional and Label Shifts via Variational Bayesian InferenceabstractIn this work, we propose a domain generalization (DG) approach to learn on several labeled source domains and transfer knowledge to a target domain that is inaccessible in training. Considering the inherent conditional and label shifts, we would expect the alignment of p(x|y) and p(y). However, the widely used domain invariant feature learning (IFL) methods relies on aligning the marginal concept shift w.r.t. p(x), which rests on an unrealistic assumption that p(y) is invariant across domains. We thereby propose a novel variational Bayesian inference framework to enforce the conditional distribution alignment w.r.t. p(x|y) via the prior distribution matching in a latent space, which also takes the marginal label shift w.r.t. p(y) into consideration with the posterior alignment. Extensive experiments on various benchmarks demonstrate that our framework is robust to the label shift and the cross-domain accuracy is significantly improved, thereby achieving superior performance over the conventional IFL counterparts. Xiaofeng Liu 0001, Linghao Jin, Fangxu Xing, Jinsong Ouyang, Jun Lu 0002, Georges El Fakhri, Jonghye Woo |
IJCAI | 8 |
| 2021 | Generative Self-training for Cross-Domain Unsupervised Tagged-to-Cine MRI Synthesis
Xiaofeng Liu 0001, Fangxu Xing, Maureen Stone 0001, Jiachen Zhuo, Timothy G. Reese, Jerry L. Prince, Georges El Fakhri, Jonghye Woo |
MICCAI (3) | 7 |
| 2021 | Adapting Off-the-Shelf Source Segmenter for Target Medical Image Segmentation
Xiaofeng Liu 0001, Fangxu Xing, Chao Yang 0011, Georges El Fakhri, Jonghye Woo |
MICCAI (2) | 4 |
| 2021 | A deep joint sparse non-negative matrix factorization framework for identifying the common and subject-specific functional units of tongue motion during speech
Jonghye Woo, Fangxu Xing, Jerry L. Prince, Maureen Stone 0001, Arnold D. Gomez, Timothy G. Reese, Van J. Wedeen, Georges El Fakhri |
Medical Image Anal. | 8 |
| 2020 | Severity-Aware Semantic Segmentation With Reinforced Wasserstein TrainingabstractSemantic segmentation is a class of methods to classify each pixel in an image into semantic classes, which is critical for autonomous vehicles and surgery systems. Cross-entropy (CE) loss-based deep neural networks (DNN) achieved great success w.r.t. the accuracy-based metrics, e.g., mean Intersection-over Union. However, the CE loss has a limitation in that it ignores varying degrees of severity of pair-wise misclassified results. For instance, classifying a car into the road is much more terrible than recognizing it as a bus. To sidestep this, in this work, we propose to incorporate the severity-aware inter-class correlation into our Wasserstein training framework by configuring its ground distance matrix. In addition, our method can adaptively learn the ground metric in a high-fidelity simulator, following a reinforcement alternative optimization scheme. We evaluate our method using the CARLA simulator with the Deeplab backbone, demonstraing that our method significantly improves the survival time in the CARLA simulator. In addition, our method can be readily applied to existing DNN architectures and algorithms while yielding superior performance. We report results from experiments carried out with the CamVid and Cityscapes datasets. Xiaofeng Liu 0001, Wenxuan Ji, Jane You, Georges El Fakhri, Jonghye Woo |
CVPR | 4 |
| 2019 | Iterative PET Image Reconstruction Using Convolutional Neural Network RepresentationabstractPET image reconstruction is challenging due to the ill-poseness of the inverse problem and limited number of detected photons. Recently, the deep neural networks have been widely and successfully used in computer vision tasks and attracted growing interests in medical imaging. In this paper, we trained a deep residual convolutional neural network to improve PET image quality by using the existing inter-patient information. An innovative feature of the proposed method is that we embed the neural network in the iterative reconstruction framework for image representation, rather than using it as a post-processing tool. We formulate the objective function as a constrained optimization problem and solve it using the alternating direction method of multipliers algorithm. Both simulation data and hybrid real data are used to evaluate the proposed method. Quantification results show that our proposed iterative neural network method can outperform the neural network denoising and conventional penalized maximum likelihood methods. Kuang Gong, Jiahui Guan, Kyung Sang Kim, Xuezhu Zhang, Jaewon Yang, Youngho Seo, Georges El Fakhri, Jinyi Qi, Quanzheng Li |
IEEE Trans. Medical Imaging | 7 |
| 2019 | A Sparse Non-Negative Matrix Factorization Framework for Identifying Functional Units of Tongue Behavior From MRIabstractMuscle coordination patterns of lingual behaviors are synergies generated by deforming local muscle groups in a variety of ways. Functional units are functional muscle groups of local structural elements within the tongue that compress, expand, and move in a cohesive and consistent manner. Identifying the functional units using tagged-magnetic resonance imaging (MRI) sheds light on the mechanisms of normal and pathological muscle coordination patterns, yielding improvement in surgical planning, treatment, or rehabilitation procedures. In this paper, to mine this information, we propose a matrix factorization and probabilistic graphical model framework to produce building blocks and their associated weighting map using motion quantities extracted from tagged-MRI. Our tagged-MRI imaging and accurate voxel-level tracking provide previously unavailable internal tongue motion patterns, thus revealing the inner workings of the tongue during speech or other lingual behaviors. We then employ spectral clustering on the weighting map to identify the cohesive regions defined by the tongue motion that may involve multiple or undocumented regions. To evaluate our method, we perform a series of experiments. We first use two-dimensional images and synthetic data to demonstrate the accuracy of our method. We then use three-dimensional synthetic and in vivo tongue motion data using protrusion and simple speech tasks to identify subject-specific and data-driven functional units of the tongue in localized regions. Jonghye Woo, Jerry L. Prince, Maureen Stone 0001, Fangxu Xing, Arnold D. Gomez, Jordan R. Green, Christopher J. Hartnick, Thomas J. Brady, Timothy G. Reese, Van J. Wedeen, Georges El Fakhri |
IEEE Trans. Medical Imaging | 11 |
| 2018 | Penalized PET Reconstruction Using Deep Learning Prior and Local Linear FittingabstractMotivated by the great potential of deep learning in medical imaging, we propose an iterative positron emission tomography reconstruction framework using a deep learning-based prior. We utilized the denoising convolutional neural network (DnCNN) method and trained the network using full-dose images as the ground truth and low dose images reconstructed from downsampled data by Poisson thinning as input. Since most published deep networks are trained at a predetermined noise level, the noise level disparity of training and testing data is a major problem for their applicability as a generalized prior. In particular, the noise level significantly changes in each iteration, which can potentially degrade the overall performance of iterative reconstruction. Due to insufficient existing studies, we conducted simulations and evaluated the degradation of performance at various noise conditions. Our findings indicated that DnCNN produces additional bias induced by the disparity of noise levels. To address this issue, we propose a local linear fitting function incorporated with the DnCNN prior to improve the image quality by preventing unwanted bias. We demonstrate that the resultant method is robust against noise level disparities despite the network being trained at a predetermined noise level. By means of bias and standard deviation studies via both simulations and clinical experiments, we show that the proposed method outperforms conventional methods based on total variation and non-local means penalties. We thereby confirm that the proposed method improves the reconstruction result both quantitatively and qualitatively. Kyung Sang Kim, Dufan Wu, Kuang Gong, Joyita Dutta, Jong Hoon Kim, Young-Don Son, Hang-Keun Kim, Georges El Fakhri, Quanzheng Li |
IEEE Trans. Medical Imaging | 8 |
| 2017 | Speaker-Specific Biomechanical Model-Based Investigation of a Simple Speech Task Based on Tagged-MRI
Keyi Tang, Negar M. Harandi, Jonghye Woo, Georges El Fakhri, Maureen Stone 0001, Sidney S. Fels |
INTERSPEECH | 4 |
| 2017 | Guest Editorial Low-Dose CT: What Has Been Done, and What Challenges Remain?abstractThe introduction of computed tomography (CT) in 1972 was among the most significant development in medical imaging since the discovery of X-rays in 1895. In addition, the innovation of computationally reconstructing tomographic images from projection data significantly influenced the development of other medical imaging modalities, such as magnetic resonance imaging and single photon and positron emission tomography. With the advent of helical and multi-detector-row CT (MDCT) scanners in the 1990s and 2000s along with innovations in cone-beam CT (CBCT) in many forms, CT gained unmatched speed and adaptability for volumetric imaging, leading to widespread use for diagnostic imaging, emergency examination, image-guided interventions, treatment planning, and monitoring of therapeutic response. Zhengrong Liang, Patrick J. La Rivière, Georges El Fakhri, Stephen J. Glick, Jeffrey H. Siewerdsen |
IEEE Trans. Medical Imaging | 3 |
| 2017 | Iterative Low-Dose CT Reconstruction With Priors Trained by Artificial Neural NetworkabstractDose reduction in computed tomography (CT) is essential for decreasing radiation risk in clinical applications. Iterative reconstruction algorithms are one of the most promising way to compensate for the increased noise due to reduction of photon flux. Most iterative reconstruction algorithms incorporate manually designed prior functions of the reconstructed image to suppress noises while maintaining structures of the image. These priors basically rely on smoothness constraints and cannot exploit more complex features of the image. The recent development of artificial neural networks and machine learning enabled learning of more complex features of image, which has the potential to improve reconstruction quality. In this letter, K-sparse auto encoder was used for unsupervised feature learning. A manifold was learned from normal-dose images and the distance between the reconstructed image and the manifold was minimized along with data fidelity during reconstruction. Experiments on 2016 Low-dose CT Grand Challenge were used for the method verification, and results demonstrated the noise reduction and detail preservation abilities of the proposed method. Dufan Wu, Kyung Sang Kim, Georges El Fakhri, Quanzheng Li |
IEEE Trans. Medical Imaging | 3 |
| 2015 | Sparse-View Spectral CT Reconstruction Using Spectral Patch-Based Low-Rank PenaltyabstractSpectral computed tomography (CT) is a promising technique with the potential for improving lesion detection, tissue characterization, and material decomposition. In this paper, we are interested in kVp switching-based spectral CT that alternates distinct kVp X-ray transmissions during gantry rotation. This system can acquire multiple X-ray energy transmissions without additional radiation dose. However, only sparse views are generated for each spectral measurement; and the spectra themselves are limited in number. To address these limitations, we propose a penalized maximum likelihood method using spectral patch-based low-rank penalty, which exploits the self-similarity of patches that are collected at the same position in spectral images. The main advantage is that the relatively small number of materials within each patch allows us to employ the low-rank penalty that is less sensitive to intensity changes while preserving edge directions. In our optimization formulation, the cost function consists of the Poisson log-likelihood for X-ray transmission and the nonconvex patch-based low-rank penalty. Since the original cost function is difficult to minimize directly, we propose an optimization method using separable quadratic surrogate and concave convex procedure algorithms for the log-likelihood and penalty terms, which results in an alternating minimization that provides a computational advantage because each subproblem can be solved independently. We performed computer simulations and a real experiment using a kVp switching-based spectral CT with sparse-view measurements, and compared the proposed method with conventional algorithms. We confirmed that the proposed method improves spectral images both qualitatively and quantitatively. Furthermore, our GPU implementation significantly reduces the computational cost. Kyung Sang Kim, Jong Chul Ye, William Worstell, Jinsong Ouyang, Yothin Rakvongthai, Georges El Fakhri, Quanzheng Li |
IEEE Trans. Medical Imaging | 6 |
| 2015 | Spectral CT Using Multiple Balanced K-Edge FiltersabstractOur goal is to validate a spectral computed tomography (CT) system design that uses a conventional X-ray source with multiple balanced K-edge filters. By performing a simultaneously synthetic reconstruction in multiple energy bins, we obtained a good agreement between measurements and model expectations for a reasonably complex phantom. We performed simulation and data acquisition on a phantom containing multiple rods of different materials using a NeuroLogica CT scanner. Five balanced K-edge filters including Molybdenum, Cerium, Dysprosium, Erbium, and Tungsten were used separately proximal to the X-ray tube. For each sinogram bin, measured filtered vector can be defined as a product of a transmission matrix, which is determined by the filters and is independent of the imaging object, and energy-binned intensity vector. The energy-binned sinograms were then obtained by inverting the transmission matrix followed by a multiplication of the filter measurement vector. For each energy bin defined by two consecutive K-edges, a synthesized energy-binned attenuation image was obtained using filtered back-projection reconstruction. The reconstructed attenuation coefficients for each rod obtained from the experiment was in good agreement with the corresponding simulated results. Furthermore, the reconstructed attenuation coefficients for a given energy bin, agreed with National Institute of Standards and Technology reference values when beam hardening within the energy bin is small. The proposed cost-effective system design using multiple balanced K-edge filters can be used to perform spectral CT imaging at clinically relevant flux rates using conventional detectors and integrating electronics. Yothin Rakvongthai, William Worstell, Georges El Fakhri, Junguo Bian, Auranuch Lorsakul, Jinsong Ouyang |
IEEE Trans. Medical Imaging | 3 |
| 2014 | Evaluating Structural Symmetry of Weighted Brain Networks via Graph Matching
Chenhui Hu, Georges El Fakhri, Quanzheng Li |
MICCAI (2) | 2 |
| 2014 | Erratum: Evaluating Structural Symmetry of Weighted Brain Networks via Graph Matching
Chenhui Hu, Georges El Fakhri, Quanzheng Li |
MICCAI (2) | 2 |
| 2011 | Novel Scatter Compensation of List-Mode PET Data Using Spatial and Energy Dependent CorrectionsabstractWith the widespread use of positron emission tomography (PET) crystals with greatly improved energy resolution (e.g., 11.5% with LYSO as compared to 20% with BGO) and of list-mode acquisitions, the use of the energy of individual events in scatter correction schemes becomes feasible. We propose a novel scatter approach that incorporates the energy of individual photons in the scatter correction and reconstruction of list-mode PET data in addition to the spatial information presently used in clinical scanners. First, we rewrite the Poisson likelihood function of list-mode PET data including the energy distributions of primary and scatter coincidences and show that this expression yields an MLEM reconstruction algorithm containing both energy and spatial dependent corrections. To estimate the spatial distribution of scatter coincidences we use the single scatter simulation (SSS). Next, we derive two new formulae which allow estimation of the 2-D (coincidences) energy probability density functions (E-PDF) of primary and scatter coincidences from the 1-D (photons) E-PDFs associated with each photon. We also describe an accurate and robust object-specific method for estimating these 1-D E-PDFs based on a decomposition of the total energy spectra detected across the scanner into primary and scattered components. Finally, we show that the energy information can be used to accurately normalize the scatter sinogram to the data. We compared the performance of this novel scatter correction incorporating both the position and energy of detected coincidences to that of the traditional approach modeling only the spatial distribution of scatter coincidences in 3-D Monte Carlo simulations of a medium cylindrical phantom and a large, nonuniform NCAT phantom. Incorporating the energy information in the scatter correction decreased bias in the activity distribution estimation by ~20% and ~40% in the cold regions of the large NCAT phantom at energy resolutions 11.5% and 20% at 511 keV, respectively, compared to when using the spatial information alone. Brigitte Guérin, Georges El Fakhri |
IEEE Trans. Medical Imaging | 2 |
| 2005 | Collimator optimization for detection and quantitation tasks: application to gallium-67 imagingabstractWe describe a new approach to the problem of collimator optimization in nuclear medicine; our methodology is illustrated for the challenging case of gallium-67 imaging. Collimator-design methods based on empirical rules, such as specification of an allowable level of single-septal penetration (SSP) at a fixed energy, are especially inappropriate for radionuclides characterized by an abundance of high-energy contaminant photons that scatter in the patient, collimator, and/or detector before detection within one of a few photopeak energy windows. Lead X-rays produced in the collimator are an additional source of contamination. We designed optimal collimation for 67Ga based on relevant clinical imaging tasks and a realistic simulation of photon transport in a phantom, collimator, and detector. Collimator designs were compared on the basis of performance in lesion detection, as predicted by a three-channel Hotelling observer (CHO), as well as in tumor and background activity estimation (EST), quantified by task-specific signal-to-noise ratios (SNRs). The optimal values of collimator lead content were 22.0 and 23.8 g/cm2, respectively, for CHO and EST, while the optimal geometric resolution values were 1.8 and 1.6 cm full-width at half-maximum (FWHM), respectively, at a distance of 23.5 cm. The resolution of a commercially available medium-energy low-penetration collimator (MELP) is 1.9 cm FWHM at this distance. The optimal values for SSP at 300 keV were 7.3% and 5.8% based on CHO and EST, respectively, compared to 5.2% for the MELP collimator. Compared with the commercial MELP collimator, the 67Ga collimator optimized for tumor detection or activity estimation tasks provided improved geometric spatial resolution with reduced geometric efficiency and, surprisingly, allowed an increased level of single-septal penetration. Stephen C. Moore, Marie Foley Kijewski, Georges El Fakhri |
IEEE Trans. Medical Imaging | 3 |