arXiv subjects

Xiaofeng Liu

Publications and source records attributed to Xiaofeng Liu.

At least 127 records · Page 7Linked to original sources

arXiv2023

Synthesizing audio from tongue motion during speech using tagged MRI via transformer

Investigating the relationship between internal tissue point motion of the tongue and oropharyngeal muscle deformation measured from tagged MRI and intelligible speech can aid in advancing speech motor control theories and developing novel treatment methods for speech related-disorders. However, elucidating the relationship between these two sources of information is challenging, due in part to the disparity in data structure between spatiotemporal motion fields (i.e., 4D motion fields) and one-dimensional audio waveforms. In this work, we present an efficient encoder-decoder translation network for exploring the predictive information inherent in 4D motion fields via 2D spectrograms as a surrogate of the audio data. Specifically, our encoder is based on 3D convolutional spatial modeling and transformer-based temporal modeling. The extracted features are processed by an asymmetric 2D convolution decoder to generate spectrograms that correspond to 4D motion fields. Furthermore, we incorporate a generative adversarial training approach into our framework to further improve synthesis quality on our generated spectrograms. We experiment on 63 paired motion field sequences and speech waveforms, demonstrating that our framework enables the generation of clear audio waveforms from a sequence of motion fields. Thus, our framework has the potential to improve our understanding of the relationship between these two modalities and inform the development of treatments for speech disorders.

eess.IV↗

arXiv2023

Pressure Reconstruction from the Measured Pressure Gradient Using Gaussian Process Regression

Many numerical algorithms have been established to reconstruct pressure fields from measured kinematic data with noise by Particle Image Velocimetry (PIV), such as the Pressure Poisson solver and the Omni-Directional Integration (ODI) method. This study adopts Gaussian Process Regression (GPR), a probabilistic framework with an intrinsic de-noising mechanism to tackle drawbacks of traditional Pressure Poisson solver and compares the performance with ODI. To evaluate the accuracy of the algorithm, GPR and ODI are tested in detail in a canonical setup of forced homogeneous isotropic turbulence from the Johns Hopkins Turbulence Database. According to the result, GPR has the same level of accuracy as ODI with optimized hyper-parameters for the isotropic turbulence flow. However, GPR has the tendency to flatten impulsive signals. Therefore, without further modifications, it is not suitable to detect flow structures with impulsive true signals. The error propagation of the proposed framework is also analyzed and discussed in both physical and spectral spaces.

physics.flu-dyn↗

arXiv2023

Successive Subspace Learning for Cardiac Disease Classification with Two-phase Deformation Fields from Cine MRI

Cardiac cine magnetic resonance imaging (MRI) has been used to characterize cardiovascular diseases (CVD), often providing a noninvasive phenotyping tool.~While recently flourished deep learning based approaches using cine MRI yield accurate characterization results, the performance is often degraded by small training samples. In addition, many deep learning models are deemed a ``black box," for which models remain largely elusive in how models yield a prediction and how reliable they are. To alleviate this, this work proposes a lightweight successive subspace learning (SSL) framework for CVD classification, based on an interpretable feedforward design, in conjunction with a cardiac atlas. Specifically, our hierarchical SSL model is based on (i) neighborhood voxel expansion, (ii) unsupervised subspace approximation, (iii) supervised regression, and (iv) multi-level feature integration. In addition, using two-phase 3D deformation fields, including end-diastolic and end-systolic phases, derived between the atlas and individual subjects as input offers objective means of assessing CVD, even with small training samples. We evaluate our framework on the ACDC2017 database, comprising one healthy group and four disease groups. Compared with 3D CNN-based approaches, our framework achieves superior classification performance with 140$\times$ fewer parameters, which supports its potential value in clinical use.

eess.IV↗

arXiv2022

Plug-Play Plasmonic Metafibers for Ultrafast Fiber Lasers

Metafibers expand the functionalities of conventional optical fibers to unprecedented nanoscale light manipulations by integrating metasurfaces on the fiber tips, becoming an emerging light-coupling platform for both nanoscience and fiber optics communities. Mostly exploring the isolated bare fibers, current metafibers remain as proof-of-concept demonstrations due to a lack of standard interfaces with the universal fiber networks. Here, we develop new methodologies to fabricate well-defined plasmonic metasurfaces directly on the end facets of commercial single mode fiber jumpers using standard planar technologies and provide a first demonstration of their practical applications in the nonlinear optics regime. Featuring plug-play connections with fiber circuitry and arbitrary metasurfaces landscapes, the metafibers with tunable plasmonic resonances are implemented into fiber laser cavities, yielding all-fiber sub-picosecond (minimum 513 fs) soliton mode locked lasers at optical wavelengths of 1.5 micrometer and 2 micrometer, demonstrating their unusual polarimetric nonlinear transfer functions and superior saturation absorption responses. Novel insights into the physical mechanisms behind the saturable absorption of plasmonic metasurfaces are provided. The nanofabrication process flow is compatible with existing cleanroom technologies, offering metafibers an avenue to be a regular member of functionalized fiber components. The work paves the way towards next generation of ultrafast fiber lasers, optical frequency combs, optical neural networks and ultracompact "all-in-fibers" optical systems for sensing, imaging, communications, and many others.

physics.optics↗

arXiv2022

Tagged-MRI Sequence to Audio Synthesis via Self Residual Attention Guided Heterogeneous Translator

Understanding the underlying relationship between tongue and oropharyngeal muscle deformation seen in tagged-MRI and intelligible speech plays an important role in advancing speech motor control theories and treatment of speech related-disorders. Because of their heterogeneous representations, however, direct mapping between the two modalities -- i.e., two-dimensional (mid-sagittal slice) plus time tagged-MRI sequence and its corresponding one-dimensional waveform -- is not straightforward. Instead, we resort to two-dimensional spectrograms as an intermediate representation, which contains both pitch and resonance, from which to develop an end-to-end deep learning framework to translate from a sequence of tagged-MRI to its corresponding audio waveform with limited dataset size.~Our framework is based on a novel fully convolutional asymmetry translator with guidance of a self residual attention strategy to specifically exploit the moving muscular structures during speech.~In addition, we leverage a pairwise correlation of the samples with the same utterances with a latent space representation disentanglement strategy.~Furthermore, we incorporate an adversarial training approach with generative adversarial networks to offer improved realism on our generated spectrograms.~Our experimental results, carried out with a total of 63 tagged-MRI sequences alongside speech acoustics, showed that our framework enabled the generation of clear audio waveforms from a sequence of tagged-MRI, surpassing competing methods. Thus, our framework provides the great potential to help better understand the relationship between the two modalities.

cs.SD↗

arXiv2022

ACT: Semi-supervised Domain-adaptive Medical Image Segmentation with Asymmetric Co-training

Unsupervised domain adaptation (UDA) has been vastly explored to alleviate domain shifts between source and target domains, by applying a well-performed model in an unlabeled target domain via supervision of a labeled source domain. Recent literature, however, has indicated that the performance is still far from satisfactory in the presence of significant domain shifts. Nonetheless, delineating a few target samples is usually manageable and particularly worthwhile, due to the substantial performance gain. Inspired by this, we aim to develop semi-supervised domain adaptation (SSDA) for medical image segmentation, which is largely underexplored. We, thus, propose to exploit both labeled source and target domain data, in addition to unlabeled target data in a unified manner. Specifically, we present a novel asymmetric co-training (ACT) framework to integrate these subsets and avoid the domination of the source domain data. Following a divide-and-conquer strategy, we explicitly decouple the label supervisions in SSDA into two asymmetric sub-tasks, including semi-supervised learning (SSL) and UDA, and leverage different knowledge from two segmentors to take into account the distinction between the source and target label supervisions. The knowledge learned in the two modules is then adaptively integrated with ACT, by iteratively teaching each other, based on the confidence-aware pseudo-label. In addition, pseudo label noise is well-controlled with an exponential MixUp decay scheme for smooth propagation. Experiments on cross-modality brain tumor MRI segmentation tasks using the BraTS18 database showed, even with limited labeled target samples, ACT yielded marked improvements over UDA and state-of-the-art SSDA methods and approached an "upper bound" of supervised joint training.

cs.CV↗

arXiv2022

Memory Consistent Unsupervised Off-the-Shelf Model Adaptation for Source-Relaxed Medical Image Segmentation

Unsupervised domain adaptation (UDA) has been a vital protocol for migrating information learned from a labeled source domain to facilitate the implementation in an unlabeled heterogeneous target domain. Although UDA is typically jointly trained on data from both domains, accessing the labeled source domain data is often restricted, due to concerns over patient data privacy or intellectual property. To sidestep this, we propose "off-the-shelf (OS)" UDA (OSUDA), aimed at image segmentation, by adapting an OS segmentor trained in a source domain to a target domain, in the absence of source domain data in adaptation. Toward this goal, we aim to develop a novel batch-wise normalization (BN) statistics adaptation framework. In particular, we gradually adapt the domain-specific low-order BN statistics, e.g., mean and variance, through an exponential momentum decay strategy, while explicitly enforcing the consistency of the domain shareable high-order BN statistics, e.g., scaling and shifting factors, via our optimization objective. We also adaptively quantify the channel-wise transferability to gauge the importance of each channel, via both low-order statistics divergence and a scaling factor.~Furthermore, we incorporate unsupervised self-entropy minimization into our framework to boost performance alongside a novel queued, memory-consistent self-training strategy to utilize the reliable pseudo label for stable and efficient unsupervised adaptation. We evaluated our OSUDA-based framework on both cross-modality and cross-subtype brain tumor segmentation and cardiac MR to CT segmentation tasks. Our experimental results showed that our memory consistent OSUDA performs better than existing source-relaxed UDA methods and yields similar performance to UDA methods with source data.

cs.CV↗

arXiv2022

Tensor Decomposition based Personalized Federated Learning

Federated learning (FL) is a new distributed machine learning framework that can achieve reliably collaborative training without collecting users' private data. However, due to FL's frequent communication and average aggregation strategy, they experience challenges scaling to statistical diversity data and large-scale models. In this paper, we propose a personalized FL framework, named Tensor Decomposition based Personalized Federated learning (TDPFed), in which we design a novel tensorized local model with tensorized linear layers and convolutional layers to reduce the communication cost. TDPFed uses a bi-level loss function to decouple personalized model optimization from the global model learning by controlling the gap between the personalized model and the tensorized local model. Moreover, an effective distributed learning strategy and two different model aggregation strategies are well designed for the proposed TDPFed framework. Theoretical convergence analysis and thorough experiments demonstrate that our proposed TDPFed framework achieves state-of-the-art performance while reducing the communication cost.

cs.LG↗

arXiv2022

Constraining Pseudo-label in Self-training Unsupervised Domain Adaptation with Energy-based Model

Deep learning is usually data starved, and the unsupervised domain adaptation (UDA) is developed to introduce the knowledge in the labeled source domain to the unlabeled target domain. Recently, deep self-training presents a powerful means for UDA, involving an iterative process of predicting the target domain and then taking the confident predictions as hard pseudo-labels for retraining. However, the pseudo-labels are usually unreliable, thus easily leading to deviated solutions with propagated errors. In this paper, we resort to the energy-based model and constrain the training of the unlabeled target sample with an energy function minimization objective. It can be achieved via a simple additional regularization or an energy-based loss. This framework allows us to gain the benefits of the energy-based model, while retaining strong discriminative performance following a plug-and-play fashion. The convergence property and its connection with classification expectation minimization are investigated. We deliver extensive experiments on the most popular and large-scale UDA benchmarks of image classification as well as semantic segmentation to demonstrate its generality and effectiveness.

cs.CV↗

arXiv2022

Subtype-Aware Dynamic Unsupervised Domain Adaptation

Unsupervised 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 (TPN) further addresses 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 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 multi-view 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.

cs.CV↗

arXiv2022

Unsupervised Domain Adaptation for Segmentation with Black-box Source Model

Unsupervised domain adaptation (UDA) has been widely used to transfer knowledge from a labeled source domain to an unlabeled target domain to counter the difficulty of labeling in a new domain. The training of conventional solutions usually relies on the existence of both source and target domain data. However, privacy of the large-scale and well-labeled data in the source domain and trained model parameters can become the major concern of cross center/domain collaborations. In this work, to address this, we propose a practical solution to UDA for segmentation with a black-box segmentation model trained in the source domain only, rather than original source data or a white-box source model. Specifically, we resort to a knowledge distillation scheme with exponential mixup decay (EMD) to gradually learn target-specific representations. In addition, unsupervised entropy minimization is further applied to regularization of the target domain confidence. We evaluated our framework on the BraTS 2018 database, achieving performance on par with white-box source model adaptation approaches.

cs.CV↗

arXiv2022

Deep Unsupervised Domain Adaptation: A Review of Recent Advances and Perspectives

Deep learning has become the method of choice to tackle real-world problems in different domains, partly because of its ability to learn from data and achieve impressive performance on a wide range of applications. However, its success usually relies on two assumptions: (i) vast troves of labeled datasets are required for accurate model fitting, and (ii) training and testing data are independent and identically distributed. Its performance on unseen target domains, thus, is not guaranteed, especially when encountering out-of-distribution data at the adaptation stage. The performance drop on data in a target domain is a critical problem in deploying deep neural networks that are successfully trained on data in a source domain. Unsupervised domain adaptation (UDA) is proposed to counter this, by leveraging both labeled source domain data and unlabeled target domain data to carry out various tasks in the target domain. UDA has yielded promising results on natural image processing, video analysis, natural language processing, time-series data analysis, medical image analysis, etc. In this review, as a rapidly evolving topic, we provide a systematic comparison of its methods and applications. In addition, the connection of UDA with its closely related tasks, e.g., domain generalization and out-of-distribution detection, has also been discussed. Furthermore, deficiencies in current methods and possible promising directions are highlighted.

cs.CV↗

arXiv2022

Feasibility study of clinical target volume definition for soft-tissue sarcoma using muscle fiber orientations derived from diffusion tensor imaging

Objective: Soft-tissue sarcoma spreads preferentially along muscle fibers. We explore the utility of deriving muscle fiber orientations from diffusion tensor MRI (DT-MRI) for defining the boundary of the clinical target volume in muscle tissue. Approach: We recruited eight healthy volunteers to acquire MR images of the left and right thigh. The imaging session consisted of (a) two MRI spin-echo-based scans, T1- and T2-weighted; (b) a diffusion weighted (DW) spin-echo-based scan using an echo planar acquisition with fat suppression. The thigh muscles were auto-segmented using CNN. DT-MRI data was used as a geometry encoding input to solve the anisotropic Eikonal equation with Hamiltonian Fast-Marching method. The isosurfaces of the solution modeled the CTV boundary. Main results: The auto-segmented muscles of the thigh agreed with manually delineated with the Dice score ranging from 0.8 to 0.94 for different muscles. Anisotropy of the isosurfaces was compared across muscles with different anatomical orientations within a thigh, between muscles in left and right thighs of each subject, and between different subjects. Analysis showed a high degree of consistency across all comparisons. The distance from the GTV to the isosurface and the eigenvalues ratio are two controlling parameters for the extent and shape of the CTV. Significance: Our feasibility study with healthy volunteers shows the promise of using muscle fiber orientations derived from diffusion weighted MRI data for automated generation of anisotropic CTV boundary in soft tissue sarcoma. Our contribution is significant as it is expected to lead to the improvements in the treatment outcomes of soft-tissue sarcoma patients undergoing radiotherapy and decrease amputation rate for a subset of patients. We expect such improvements to have a strong positive impact for the cancer centers with small volume of sarcoma patients.

physics.med-ph↗

arXiv2022

AI Enlightens Wireless Communication: A Transformer Backbone for CSI Feedback

This paper is based on the background of the 2nd Wireless Communication Artificial Intelligence (AI) Competition (WAIC) which is hosted by IMT-2020(5G) Promotion Group 5G+AIWork Group, where the framework of the eigenvector-based channel state information (CSI) feedback problem is firstly provided. Then a basic Transformer backbone for CSI feedback referred to EVCsiNet-T is proposed. Moreover, a series of potential enhancements for deep learning based (DL-based) CSI feedback including i) data augmentation, ii) loss function design, iii) training strategy, and iv) model ensemble are introduced. The experimental results involving the comparison between EVCsiNet-T and traditional codebook methods over different channels are further provided, which show the advanced performance and a promising prospect of Transformer on DL-based CSI feedback problem.

eess.SP↗

arXiv2022

Bathymetry Inversion using a Deep-Learning-Based Surrogate for Shallow Water Equations Solvers

River bathymetry is critical for many aspects of water resources management. We propose and demonstrate a bathymetry inversion method using a deep-learning-based surrogate for shallow water equations solvers. The surrogate uses the convolutional autoencoder with a shared-encoder, separate-decoder architecture. It encodes the input bathymetry and decodes to separate outputs for flow-field variables. A gradient-based optimizer is used to perform bathymetry inversion with the trained surrogate. Two physically-based constraints on both bed elevation value and slope have to be added as inversion loss regularizations to obtain usable inversion results. Using the "L-curve" criterion, a heuristic approach was proposed to determine the regularization parameters. Both the surrogate model and the inversion algorithm show good performance. We found the bathymetry inversion process has two distinctive stages, which resembles the sculptural process of initial broad-brush calving and final detailing. The inversion loss due to flow prediction error reaches its minimum in the first stage and remains almost constant afterward. The bed elevation value and slope regularizations play the dominant role in the second stage in selecting the most probable solution. We also found the surrogate architecture (whether with both velocity and water surface elevation or velocity only as outputs) does not show significant impact on inversion result.

physics.flu-dyn↗

arXiv2022

Structure-aware Unsupervised Tagged-to-Cine MRI Synthesis with Self Disentanglement

Cycle reconstruction regularized adversarial training -- e.g., CycleGAN, DiscoGAN, and DualGAN -- has been widely used for image style transfer with unpaired training data. Several recent works, however, have shown that local distortions are frequent, and structural consistency cannot be guaranteed. Targeting this issue, prior works usually relied on additional segmentation or consistent feature extraction steps that are task-specific. To counter this, this work aims to learn a general add-on structural feature extractor, by explicitly enforcing the structural alignment between an input and its synthesized image. Specifically, we propose a novel input-output image patches self-training scheme to achieve a disentanglement of underlying anatomical structures and imaging modalities. The translator and structure encoder are updated, following an alternating training protocol. In addition, the information w.r.t. imaging modality can be eliminated with an asymmetric adversarial game. We train, validate, and test our network on 1,768, 416, and 1,560 unpaired subject-independent slices of tagged and cine magnetic resonance imaging from a total of twenty healthy subjects, respectively, demonstrating superior performance over competing methods.

eess.IV↗

arXiv2022

A Multi-modal Fusion Framework Based on Multi-task Correlation Learning for Cancer Prognosis Prediction

Morphological attributes from histopathological images and molecular profiles from genomic data are important information to drive diagnosis, prognosis, and therapy of cancers. By integrating these heterogeneous but complementary data, many multi-modal methods are proposed to study the complex mechanisms of cancers, and most of them achieve comparable or better results from previous single-modal methods. However, these multi-modal methods are restricted to a single task (e.g., survival analysis or grade classification), and thus neglect the correlation between different tasks. In this study, we present a multi-modal fusion framework based on multi-task correlation learning (MultiCoFusion) for survival analysis and cancer grade classification, which combines the power of multiple modalities and multiple tasks. Specifically, a pre-trained ResNet-152 and a sparse graph convolutional network (SGCN) are used to learn the representations of histopathological images and mRNA expression data respectively. Then these representations are fused by a fully connected neural network (FCNN), which is also a multi-task shared network. Finally, the results of survival analysis and cancer grade classification output simultaneously. The framework is trained by an alternate scheme. We systematically evaluate our framework using glioma datasets from The Cancer Genome Atlas (TCGA). Results demonstrate that MultiCoFusion learns better representations than traditional feature extraction methods. With the help of multi-task alternating learning, even simple multi-modal concatenation can achieve better performance than other deep learning and traditional methods. Multi-task learning can improve the performance of multiple tasks not just one of them, and it is effective in both single-modal and multi-modal data.

cs.LG↗

arXiv2022

Variational Inference for Quantifying Inter-observer Variability in Segmentation of Anatomical Structures

Lesions or organ boundaries visible through medical imaging data are often ambiguous, thus resulting in significant variations in multi-reader delineations, i.e., the source of aleatoric uncertainty. In particular, quantifying the inter-observer variability of manual annotations with Magnetic Resonance (MR) Imaging data plays a crucial role in establishing a reference standard for various diagnosis and treatment tasks. Most segmentation methods, however, simply model a mapping from an image to its single segmentation map and do not take the disagreement of annotators into consideration. In order to account for inter-observer variability, without sacrificing accuracy, we propose a novel variational inference framework to model the distribution of plausible segmentation maps, given a specific MR image, which explicitly represents the multi-reader variability. Specifically, we resort to a latent vector to encode the multi-reader variability and counteract the inherent information loss in the imaging data. Then, we apply a variational autoencoder network and optimize its evidence lower bound (ELBO) to efficiently approximate the distribution of the segmentation map, given an MR image. Experimental results, carried out with the QUBIQ brain growth MRI segmentation datasets with seven annotators, demonstrate the effectiveness of our approach.

cs.CV↗