Unsupervised Adaptive Implicit Neural Representation Learning for Scan-Specific MRI Reconstruction

In recent studies on MRI reconstruction, advances have shown significant promise for further accelerating the MRI acquisition. Most state-of-the-art methods require a large amount of fully-sampled data to optimise reconstruction models, which is impractical and expensive under certain clinical settings. On the other hand, for unsupervised scan-specific reconstruction methods, overfitting is likely to happen due to insufficient supervision, while restrictions on acceleration rates and under-sampling patterns further limit their applicability. To this end, we propose an unsupervised, adaptive coarse-to-fine framework that enhances reconstruction quality without being constrained by the sparsity levels or patterns in under-sampling. The framework employs an implicit neural representation for scan-specific MRI reconstruction, learning a mapping from multi-dimensional coordinates to their corresponding signal intensities. Moreover, we integrate a novel learning strategy that progressively refines the use of acquired k-space signals for self-supervision. This approach effectively adjusts the proportion of supervising signals from unevenly distributed information across different frequency bands, thus mitigating the issue of overfitting while improving the overall reconstruction. Comprehensive evaluation on a public dataset, including both 2D and 3D data, has shown that our method outperforms current state-of-the-art scan-specific MRI reconstruction techniques, for up to 8-fold under-sampling.

Dual-Domain Multi-Contrast MRI Reconstruction with Synthesis-based Fusion Network

Purpose: To develop an efficient dual-domain reconstruction framework for multi-contrast MRI, with the focus on minimising cross-contrast misalignment in both the image and the frequency domains to enhance optimisation. Theory and Methods: Our proposed framework, based on deep learning, facilitates the optimisation for under-sampled target contrast using fully-sampled reference contrast that is quicker to acquire. The method consists of three key steps: 1) Learning to synthesise data resembling the target contrast from the reference contrast; 2) Registering the multi-contrast data to reduce inter-scan motion; and 3) Utilising the registered data for reconstructing the target contrast. These steps involve learning in both domains with regularisation applied to ensure their consistency. We also compare the reconstruction performance with existing deep learning-based methods using a dataset of brain MRI scans. Results: Extensive experiments demonstrate the superiority of our proposed framework, for up to an 8-fold acceleration rate, compared to state-of-the-art algorithms. Comprehensive analysis and ablation studies further present the effectiveness of the proposed components. Conclusion:Our dual-domain framework offers a promising approach to multi-contrast MRI reconstruction. It can also be integrated with existing methods to further enhance the reconstruction.

A Comprehensive Survey on Deep Graph Representation Learning

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.

MetaFill: Text Infilling for Meta-Path Generation on Heterogeneous Information Networks

Heterogeneous Information Network (HIN) is essential to study complicated networks containing multiple edge types and node types. Meta-path, a sequence of node types and edge types, is the core technique to embed HINs. Since manually curating meta-paths is time-consuming, there is a pressing need to develop automated meta-path generation approaches. Existing meta-path generation approaches cannot fully exploit the rich textual information in HINs, such as node names and edge type names. To address this problem, we propose MetaFill, a text-infilling-based approach for meta-path generation. The key idea of MetaFill is to formulate meta-path identification problem as a word sequence infilling problem, which can be advanced by Pretrained Language Models (PLMs). We observed the superior performance of MetaFill against existing meta-path generation methods and graph embedding methods that do not leverage meta-paths in both link prediction and node classification on two real-world HIN datasets. We further demonstrated how MetaFill can accurately classify edges in the zero-shot setting, where existing approaches cannot generate any meta-paths. MetaFill exploits PLMs to generate meta-paths for graph embedding, opening up new avenues for language model applications in graph analysis.

KGNN: Harnessing Kernel-based Networks for Semi-supervised Graph Classification

This paper studies semi-supervised graph classification, which is an important problem with various applications in social network analysis and bioinformatics. This problem is typically solved by using graph neural networks (GNNs), which yet rely on a large number of labeled graphs for training and are unable to leverage unlabeled graphs. We address the limitations by proposing the Kernel-based Graph Neural Network (KGNN). A KGNN consists of a GNN-based network as well as a kernel-based network parameterized by a memory network. The GNN-based network performs classification through learning graph representations to implicitly capture the similarity between query graphs and labeled graphs, while the kernel-based network uses graph kernels to explicitly compare each query graph with all the labeled graphs stored in a memory for prediction. The two networks are motivated from complementary perspectives, and thus combing them allows KGNN to use labeled graphs more effectively. We jointly train the two networks by maximizing their agreement on unlabeled graphs via posterior regularization, so that the unlabeled graphs serve as a bridge to let both networks mutually enhance each other. Experiments on a range of well-known benchmark datasets demonstrate that KGNN achieves impressive performance over competitive baselines.

InsCon:Instance Consistency Feature Representation via Self-Supervised Learning

Feature representation via self-supervised learning has reached remarkable success in image-level contrastive learning, which brings impressive performances on image classification tasks. While image-level feature representation mainly focuses on contrastive learning in single instance, it ignores the objective differences between pretext and downstream prediction tasks such as object detection and instance segmentation. In order to fully unleash the power of feature representation on downstream prediction tasks, we propose a new end-to-end self-supervised framework called InsCon, which is devoted to capturing multi-instance information and extracting cell-instance features for object recognition and localization. On the one hand, InsCon builds a targeted learning paradigm that applies multi-instance images as input, aligning the learned feature between corresponding instance views, which makes it more appropriate for multi-instance recognition tasks. On the other hand, InsCon introduces the pull and push of cell-instance, which utilizes cell consistency to enhance fine-grained feature representation for precise boundary localization. As a result, InsCon learns multi-instance consistency on semantic feature representation and cell-instance consistency on spatial feature representation. Experiments demonstrate the method we proposed surpasses MoCo v2 by 1.1% AP^{bb} on COCO object detection and 1.0% AP^{mk} on COCO instance segmentation using Mask R-CNN R50-FPN network structure with 90k iterations, 2.1% APbb on PASCAL VOC objection detection using Faster R-CNN R50-C4 network structure with 24k iterations.

Fast T2w/FLAIR MRI Acquisition by Optimal Sampling of Information Complementary to Pre-acquired T1w MRI

Recent studies on T1-assisted MRI reconstruction for under-sampled images of other modalities have demonstrated the potential of further accelerating MRI acquisition of other modalities. Most of the state-of-the-art approaches have achieved improvement through the development of network architectures for fixed under-sampling patterns, without fully exploiting the complementary information between modalities. Although existing under-sampling pattern learning algorithms can be simply modified to allow the fully-sampled T1-weighted MR image to assist the pattern learning, no significant improvement on the reconstruction task can be achieved. To this end, we propose an iterative framework to optimize the under-sampling pattern for MRI acquisition of another modality that can complement the fully-sampled T1-weighted MR image at different under-sampling factors, while jointly optimizing the T1-assisted MRI reconstruction model. Specifically, our proposed method exploits the difference of latent information between the two modalities for determining the sampling patterns that can maximize the assistance power of T1-weighted MR image in improving the MRI reconstruction. We have demonstrated superior performance of our learned under-sampling patterns on a public dataset, compared to commonly used under-sampling patterns and state-of-the-art methods that can jointly optimize both the reconstruction network and the under-sampling pattern, up to 8-fold under-sampling factor.

MIASSR: An Approach for Medical Image Arbitrary Scale Super-Resolution

Single image super-resolution (SISR) aims to obtain a high-resolution output from one low-resolution image. Currently, deep learning-based SISR approaches have been widely discussed in medical image processing, because of their potential to achieve high-quality, high spatial resolution images without the cost of additional scans. However, most existing methods are designed for scale-specific SR tasks and are unable to generalise over magnification scales. In this paper, we propose an approach for medical image arbitrary-scale super-resolution (MIASSR), in which we couple meta-learning with generative adversarial networks (GANs) to super-resolve medical images at any scale of magnification in (1, 4]. Compared to state-of-the-art SISR algorithms on single-modal magnetic resonance (MR) brain images (OASIS-brains) and multi-modal MR brain images (BraTS), MIASSR achieves comparable fidelity performance and the best perceptual quality with the smallest model size. We also employ transfer learning to enable MIASSR to tackle SR tasks of new medical modalities, such as cardiac MR images (ACDC) and chest computed tomography images (COVID-CT). The source code of our work is also public. Thus, MIASSR has the potential to become a new foundational pre-/post-processing step in clinical image analysis tasks such as reconstruction, image quality enhancement, and segmentation.

Deep Local Trajectory Replanning and Control for Robot Navigation

We present a navigation system that combines ideas from hierarchical planning and machine learning. The system uses a traditional global planner to compute optimal paths towards a goal, and a deep local trajectory planner and velocity controller to compute motion commands. The latter components of the system adjust the behavior of the robot through attention mechanisms such that it moves towards the goal, avoids obstacles, and respects the space of nearby pedestrians. Both the structure of the proposed deep models and the use of attention mechanisms make the system's execution interpretable. Our simulation experiments suggest that the proposed architecture outperforms baselines that try to map global plan information and sensor data directly to velocity commands. In comparison to a hand-designed traditional navigation system, the proposed approach showed more consistent performance.