arXiv subjects

Jinming Duan

Publications and source records attributed to Jinming Duan.

At least 55 records · Page 3Linked to original sources

arXiv2021

Learning a Model-Driven Variational Network for Deformable Image Registration

Data-driven deep learning approaches to image registration can be less accurate than conventional iterative approaches, especially when training data is limited. To address this whilst retaining the fast inference speed of deep learning, we propose VR-Net, a novel cascaded variational network for unsupervised deformable image registration. Using the variable splitting optimization scheme, we first convert the image registration problem, established in a generic variational framework, into two sub-problems, one with a point-wise, closed-form solution while the other one is a denoising problem. We then propose two neural layers (i.e. warping layer and intensity consistency layer) to model the analytical solution and a residual U-Net to formulate the denoising problem (i.e. generalized denoising layer). Finally, we cascade the warping layer, intensity consistency layer, and generalized denoising layer to form the VR-Net. Extensive experiments on three (two 2D and one 3D) cardiac magnetic resonance imaging datasets show that VR-Net outperforms state-of-the-art deep learning methods on registration accuracy, while maintains the fast inference speed of deep learning and the data-efficiency of variational model.

cs.CV↗

arXiv2020

Geometry Constrained Weakly Supervised Object Localization

We propose a geometry constrained network, termed GC-Net, for weakly supervised object localization (WSOL). GC-Net consists of three modules: a detector, a generator and a classifier. The detector predicts the object location defined by a set of coefficients describing a geometric shape (i.e. ellipse or rectangle), which is geometrically constrained by the mask produced by the generator. The classifier takes the resulting masked images as input and performs two complementary classification tasks for the object and background. To make the mask more compact and more complete, we propose a novel multi-task loss function that takes into account area of the geometric shape, the categorical cross-entropy and the negative entropy. In contrast to previous approaches, GC-Net is trained end-to-end and predict object location without any post-processing (e.g. thresholding) that may require additional tuning. Extensive experiments on the CUB-200-2011 and ILSVRC2012 datasets show that GC-Net outperforms state-of-the-art methods by a large margin. Our source code is available at https://github.com/lwzeng/GC-Net.

cs.CV↗

arXiv2020

Deep Network Interpolation for Accelerated Parallel MR Image Reconstruction

We present a deep network interpolation strategy for accelerated parallel MR image reconstruction. In particular, we examine the network interpolation in parameter space between a source model that is formulated in an unrolled scheme with L1 and SSIM losses and its counterpart that is trained with an adversarial loss. We show that by interpolating between the two different models of the same network structure, the new interpolated network can model a trade-off between perceptual quality and fidelity.

eess.IV↗

arXiv2020

G2L-Net: Global to Local Network for Real-time 6D Pose Estimation with Embedding Vector Features

In this paper, we propose a novel real-time 6D object pose estimation framework, named G2L-Net. Our network operates on point clouds from RGB-D detection in a divide-and-conquer fashion. Specifically, our network consists of three steps. First, we extract the coarse object point cloud from the RGB-D image by 2D detection. Second, we feed the coarse object point cloud to a translation localization network to perform 3D segmentation and object translation prediction. Third, via the predicted segmentation and translation, we transfer the fine object point cloud into a local canonical coordinate, in which we train a rotation localization network to estimate initial object rotation. In the third step, we define point-wise embedding vector features to capture viewpoint-aware information. To calculate more accurate rotation, we adopt a rotation residual estimator to estimate the residual between initial rotation and ground truth, which can boost initial pose estimation performance. Our proposed G2L-Net is real-time despite the fact multiple steps are stacked via the proposed coarse-to-fine framework. Extensive experiments on two benchmark datasets show that G2L-Net achieves state-of-the-art performance in terms of both accuracy and speed.

cs.CV↗

arXiv2020

Explainable Anatomical Shape Analysis through Deep Hierarchical Generative Models

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating high-throughput analysis of normal anatomy and pathology in large-scale studies of volumetric imaging.

eess.IV↗

arXiv2019

$Σ$-net: Systematic Evaluation of Iterative Deep Neural Networks for Fast Parallel MR Image Reconstruction

Purpose: To systematically investigate the influence of various data consistency layers, (semi-)supervised learning and ensembling strategies, defined in a $Σ$-net, for accelerated parallel MR image reconstruction using deep learning. Theory and Methods: MR image reconstruction is formulated as learned unrolled optimization scheme with a Down-Up network as regularization and varying data consistency layers. The different architectures are split into sensitivity networks, which rely on explicit coil sensitivity maps, and parallel coil networks, which learn the combination of coils implicitly. Different content and adversarial losses, a semi-supervised fine-tuning scheme and model ensembling are investigated. Results: Evaluated on the fastMRI multicoil validation set, architectures involving raw k-space data outperform image enhancement methods significantly. Semi-supervised fine-tuning adapts to new k-space data and provides, together with reconstructions based on adversarial training, the visually most appealing results although quantitative quality metrics are reduced. The $Σ$-net ensembles the benefits from different models and achieves similar scores compared to the single state-of-the-art approaches. Conclusion: This work provides an open-source framework to perform a systematic wide-range comparison of state-of-the-art reconstruction approaches for parallel MR image reconstruction on the fastMRI knee dataset and explores the importance of data consistency. A suitable trade-off between perceptual image quality and quantitative scores are achieved with the ensembled $Σ$-net.

eess.IV↗

arXiv2019

$Σ$-net: Ensembled Iterative Deep Neural Networks for Accelerated Parallel MR Image Reconstruction

We explore an ensembled $Σ$-net for fast parallel MR imaging, including parallel coil networks, which perform implicit coil weighting, and sensitivity networks, involving explicit sensitivity maps. The networks in $Σ$-net are trained in a supervised way, including content and GAN losses, and with various ways of data consistency, i.e., proximal mappings, gradient descent and variable splitting. A semi-supervised finetuning scheme allows us to adapt to the k-space data at test time, which, however, decreases the quantitative metrics, although generating the visually most textured and sharp images. For this challenge, we focused on robust and high SSIM scores, which we achieved by ensembling all models to a $Σ$-net.

eess.IV↗

arXiv2019

Deep learning for cardiac image segmentation: A review

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.

eess.IV↗

arXiv2019

dAUTOMAP: decomposing AUTOMAP to achieve scalability and enhance performance

AUTOMAP is a promising generalized reconstruction approach, however, it is not scalable and hence the practicality is limited. We present dAUTOMAP, a novel way for decomposing the domain transformation of AUTOMAP, making the model scale linearly. We show dAUTOMAP outperforms AUTOMAP with significantly fewer parameters.

cs.LG↗

arXiv2019

Data consistency networks for (calibration-less) accelerated parallel MR image reconstruction

We present simple reconstruction networks for multi-coil data by extending deep cascade of CNN's and exploiting the data consistency layer. In particular, we propose two variants, where one is inspired by POCSENSE and the other is calibration-less. We show that the proposed approaches are competitive relative to the state of the art both quantitatively and qualitatively.

eess.IV↗

arXiv2019

Data Efficient Unsupervised Domain Adaptation for Cross-Modality Image Segmentation

Deep learning models trained on medical images from a source domain (e.g. imaging modality) often fail when deployed on images from a different target domain, despite imaging common anatomical structures. Deep unsupervised domain adaptation (UDA) aims to improve the performance of a deep neural network model on a target domain, using solely unlabelled target domain data and labelled source domain data. However, current state-of-the-art methods exhibit reduced performance when target data is scarce. In this work, we introduce a new data efficient UDA method for multi-domain medical image segmentation. The proposed method combines a novel VAE-based feature prior matching, which is data-efficient, and domain adversarial training to learn a shared domain-invariant latent space which is exploited during segmentation. Our method is evaluated on a public multi-modality cardiac image segmentation dataset by adapting from the labelled source domain (3D MRI) to the unlabelled target domain (3D CT). We show that by using only one single unlabelled 3D CT scan, the proposed architecture outperforms the state-of-the-art in the same setting. Finally, we perform ablation studies on prior matching and domain adversarial training to shed light on the theoretical grounding of the proposed method.

eess.IV↗

arXiv2019

k-t NEXT: Dynamic MR Image Reconstruction Exploiting Spatio-temporal Correlations

Dynamic magnetic resonance imaging (MRI) exhibits high correlations in k-space and time. In order to accelerate the dynamic MR imaging and to exploit k-t correlations from highly undersampled data, here we propose a novel deep learning based approach for dynamic MR image reconstruction, termed k-t NEXT (k-t NEtwork with X-f Transform). In particular, inspired by traditional methods such as k-t BLAST and k-t FOCUSS, we propose to reconstruct the true signals from aliased signals in x-f domain to exploit the spatio-temporal redundancies. Building on that, the proposed method then learns to recover the signals by alternating the reconstruction process between the x-f space and image space in an iterative fashion. This enables the network to effectively capture useful information and jointly exploit spatio-temporal correlations from both complementary domains. Experiments conducted on highly undersampled short-axis cardiac cine MRI scans demonstrate that our proposed method outperforms the current state-of-the-art dynamic MR reconstruction approaches both quantitatively and qualitatively.

eess.IV↗

arXiv2019

VS-Net: Variable splitting network for accelerated parallel MRI reconstruction

In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data. We formulate the generalized parallel compressed sensing reconstruction as an energy minimization problem, for which a variable splitting optimization method is derived. Based on this formulation we propose a novel, end-to-end trainable deep neural network architecture by unrolling the resulting iterative process of such variable splitting scheme. VS-Net is evaluated on complex valued multi-coil knee images for 4-fold and 6-fold acceleration factors. We show that VS-Net outperforms state-of-the-art deep learning reconstruction algorithms, in terms of reconstruction accuracy and perceptual quality. Our code is publicly available at https://github.com/j-duan/VS-Net.

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arXiv2019

Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach

Deep learning approaches have achieved state-of-the-art performance in cardiac magnetic resonance (CMR) image segmentation. However, most approaches have focused on learning image intensity features for segmentation, whereas the incorporation of anatomical shape priors has received less attention. In this paper, we combine a multi-task deep learning approach with atlas propagation to develop a shape-constrained bi-ventricular segmentation pipeline for short-axis CMR volumetric images. The pipeline first employs a fully convolutional network (FCN) that learns segmentation and landmark localisation tasks simultaneously. The architecture of the proposed FCN uses a 2.5D representation, thus combining the computational advantage of 2D FCNs networks and the capability of addressing 3D spatial consistency without compromising segmentation accuracy. Moreover, the refinement step is designed to explicitly enforce a shape constraint and improve segmentation quality. This step is effective for overcoming image artefacts (e.g. due to different breath-hold positions and large slice thickness), which preclude the creation of anatomically meaningful 3D cardiac shapes. The proposed pipeline is fully automated, due to network's ability to infer landmarks, which are then used downstream in the pipeline to initialise atlas propagation. We validate the pipeline on 1831 healthy subjects and 649 subjects with pulmonary hypertension. Extensive numerical experiments on the two datasets demonstrate that our proposed method is robust and capable of producing accurate, high-resolution and anatomically smooth bi-ventricular 3D models, despite the artefacts in input CMR volumes.

cs.CV↗

arXiv2019

Self-Supervised Learning for Cardiac MR Image Segmentation by Anatomical Position Prediction

In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manually annotated data, which is expensive to acquire and limited by the available resources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.

cs.CV↗

arXiv2019

A new nonlocal forward model for diffuse optical tomography

The forward model in diffuse optical tomography (DOT) describes how light propagates through a turbid medium. It is often approximated by a diffusion equation (DE) that is numerically discretized by the classical finite element method (FEM). We propose a nonlocal diffusion equation (NDE) as a new forward model for DOT, the discretization of which is carried out with an efficient graph-based numerical method (GNM). To quantitatively evaluate the new forward model, we first conduct experiments on a homogeneous slab, where the numerical accuracy of both NDE and DE is compared against the existing analytical solution. We further evaluate NDE by comparing its image reconstruction performance (inverse problem) to that of DE. Our experiments show that NDE is quantitatively comparable to DE and is up to 64% faster due to the efficient graph-based representation that can be implemented identically for geometries in different dimensions.

physics.comp-ph↗

arXiv2019

Graph- and finite element-based total variation models for the inverse problem in diffuse optical tomography

Total variation (TV) is a powerful regularization method that has been widely applied in different imaging applications, but is difficult to apply to diffuse optical tomography (DOT) image reconstruction (inverse problem) due to complex and unstructured geometries, non-linearity of the data fitting and regularization terms, and non-differentiability of the regularization term. We develop several approaches to overcome these difficulties by: i) defining discrete differential operators for unstructured geometries using both finite element and graph representations; ii) developing an optimization algorithm based on the alternating direction method of multipliers (ADMM) for the non-differentiable and non-linear minimization problem; iii) investigating isotropic and anisotropic variants of TV regularization, and comparing their finite element- and graph-based implementations. These approaches are evaluated on experiments on simulated data and real data acquired from a tissue phantom. Our results show that both FEM and graph-based TV regularization is able to accurately reconstruct both sparse and non-sparse distributions without the over-smoothing effect of Tikhonov regularization and the over-sparsifying effect of L$_1$ regularization. The graph representation was found to out-perform the FEM method for low-resolution meshes, and the FEM method was found to be more accurate for high-resolution meshes.

cs.CV↗

arXiv2018

Deep learning cardiac motion analysis for human survival prediction

Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrell's C-index) was significantly higher (p < .0001) for our model C=0.73 (95$\%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$\%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival.

cs.LG↗