Distortion-Corrected Image Reconstruction with Deep Learning on an MRI-Linac

Magnetic resonance imaging (MRI) is increasingly utilized for image-guided radiotherapy due to its outstanding soft-tissue contrast and lack of ionizing radiation. However, geometric distortions caused by gradient nonlinearity (GNL) limit anatomical accuracy, potentially compromising the quality of tumour treatments. In addition, slow MR acquisition and reconstruction limit the potential for real-time image guidance. Here, we demonstrate a deep learning-based method that rapidly reconstructs distortion-corrected images from raw k-space data for real-time MR-guided radiotherapy applications. We leverage recent advances in interpretable unrolling networks to develop a Distortion-Corrected Reconstruction Network (DCReconNet) that applies convolutional neural networks (CNNs) to learn effective regularizations and nonuniform fast Fourier transforms for GNL-encoding. DCReconNet was trained on a public MR brain dataset from eleven healthy volunteers for fully sampled and accelerated techniques including parallel imaging (PI) and compressed sensing (CS). The performance of DCReconNet was tested on phantom and volunteer brain data acquired on a 1.0T MRI-Linac. The DCReconNet, CS- and PI-based reconstructed image quality was measured by structural similarity (SSIM) and root-mean-squared error (RMSE) for numerical comparisons. The computation time for each method was also reported. Phantom and volunteer results demonstrated that DCReconNet better preserves image structure when compared to CS- and PI-based reconstruction methods. DCReconNet resulted in highest SSIM (0.95 median value) and lowest RMSE (<0.04) on simulated brain images with four times acceleration. DCReconNet is over 100-times faster than iterative, regularized reconstruction methods. DCReconNet provides fast and geometrically accurate image reconstruction and has potential for real-time MRI-guided radiotherapy applications.

Integral Migrating Pre-trained Transformer Encoder-decoders for Visual Object Detection

Modern object detectors have taken the advantages of pre-trained vision transformers by using them as backbone networks. However, except for the backbone networks, other detector components, such as the detector head and the feature pyramid network, remain randomly initialized, which hinders the consistency between detectors and pre-trained models. In this study, we propose to integrally migrate the pre-trained transformer encoder-decoders (imTED) for object detection, constructing a feature extraction-operation path that is not only "fully pre-trained" but also consistent with pre-trained models. The essential improvements of imTED over existing transformer-based detectors are twofold: (1) it embeds the pre-trained transformer decoder to the detector head; and (2) it removes the feature pyramid network from the feature extraction path. Such improvements significantly reduce the proportion of randomly initialized parameters and enhance the generation capability of detectors. Experiments on MS COCO dataset demonstrate that imTED consistently outperforms its counterparts by ~2.8% AP. Without bells and whistles, imTED improves the state-of-the-art of few-shot object detection by up to 7.6% AP, demonstrating significantly higher generalization capability. Code will be made publicly available.

Robust Representation via Dynamic Feature Aggregation

Deep convolutional neural network (CNN) based models are vulnerable to the adversarial attacks. One of the possible reasons is that the embedding space of CNN based model is sparse, resulting in a large space for the generation of adversarial samples. In this study, we propose a method, denoted as Dynamic Feature Aggregation, to compress the embedding space with a novel regularization. Particularly, the convex combination between two samples are regarded as the pivot for aggregation. In the embedding space, the selected samples are guided to be similar to the representation of the pivot. On the other side, to mitigate the trivial solution of such regularization, the last fully-connected layer of the model is replaced by an orthogonal classifier, in which the embedding codes for different classes are processed orthogonally and separately. With the regularization and orthogonal classifier, a more compact embedding space can be obtained, which accordingly improves the model robustness against adversarial attacks. An averaging accuracy of 56.91% is achieved by our method on CIFAR-10 against various attack methods, which significantly surpasses a solid baseline (Mixup) by a margin of 37.31%. More surprisingly, empirical results show that, the proposed method can also achieve the state-of-the-art performance for out-of-distribution (OOD) detection, due to the learned compact feature space. An F1 score of 0.937 is achieved by the proposed method, when adopting CIFAR-10 as in-distribution (ID) dataset and LSUN as OOD dataset. Code is available at https://github.com/HaozheLiu-ST/DynamicFeatureAggregation.

A novel stereo matching pipeline with robustness and unfixed disparity search range

Stereo matching is an essential basis for various applications, but most stereo matching methods have poor generalization performance and require a fixed disparity search range. Moreover, current stereo matching methods focus on the scenes that only have positive disparities, but ignore the scenes that contain both positive and negative disparities, such as 3D movies. In this paper, we present a new stereo matching pipeline that first computes semi-dense disparity maps based on binocular disparity, and then completes the rest depending on monocular cues. The new stereo matching pipeline have the following advantages: It 1) has better generalization performance than most of the current stereo matching methods; 2) relaxes the limitation of a fixed disparity search range; 3) can handle the scenes that involve both positive and negative disparities, which has more potential applications, such as view synthesis in 3D multimedia and VR/AR. Experimental results demonstrate the effectiveness of our new stereo matching pipeline.

BFRnet: A deep learning-based MR background field removal method for QSM of the brain containing significant pathological susceptibility sources

Introduction: Background field removal (BFR) is a critical step required for successful quantitative susceptibility mapping (QSM). However, eliminating the background field in brains containing significant susceptibility sources, such as intracranial hemorrhages, is challenging due to the relatively large scale of the field induced by these pathological susceptibility sources. Method: This study proposes a new deep learning-based method, BFRnet, to remove background field in healthy and hemorrhagic subjects. The network is built with the dual-frequency octave convolutions on the U-net architecture, trained with synthetic field maps containing significant susceptibility sources. The BFRnet method is compared with three conventional BFR methods and one previous deep learning method using simulated and in vivo brains from 4 healthy and 2 hemorrhagic subjects. Robustness against acquisition field-of-view (FOV) orientation and brain masking are also investigated. Results: For both simulation and in vivo experiments, BFRnet led to the best visually appealing results in the local field and QSM results with the minimum contrast loss and the most accurate hemorrhage susceptibility measurements among all five methods. In addition, BFRnet produced the most consistent local field and susceptibility maps between different sizes of brain masks, while conventional methods depend drastically on precise brain extraction and further brain edge erosions. It is also observed that BFRnet performed the best among all BFR methods for acquisition FOVs oblique to the main magnetic field. Conclusion: The proposed BFRnet improved the accuracy of local field reconstruction in the hemorrhagic subjects compared with conventional BFR algorithms. The BFRnet method was effective for acquisitions of titled orientations and retained whole brains without edge erosion as often required by traditional BFR methods.

Transformer Compressed Sensing via Global Image Tokens

Convolutional neural networks (CNN) have demonstrated outstanding Compressed Sensing (CS) performance compared to traditional, hand-crafted methods. However, they are broadly limited in terms of generalisability, inductive bias and difficulty to model long distance relationships. Transformer neural networks (TNN) overcome such issues by implementing an attention mechanism designed to capture dependencies between inputs. However, high-resolution tasks typically require vision Transformers (ViT) to decompose an image into patch-based tokens, limiting inputs to inherently local contexts. We propose a novel image decomposition that naturally embeds images into low-resolution inputs. These Kaleidoscope tokens (KD) provide a mechanism for global attention, at the same computational cost as a patch-based approach. To showcase this development, we replace CNN components in a well-known CS-MRI neural network with TNN blocks and demonstrate the improvements afforded by KD. We also propose an ensemble of image tokens, which enhance overall image quality and reduces model size. Supplementary material is available: https://github.com/uqmarlonbran/TCS.git

Disentangleing Content and Fine-grained Prosody Information via Hybrid ASR Bottleneck Features for Voice Conversion

Non-parallel data voice conversion (VC) have achieved considerable breakthroughs recently through introducing bottleneck features (BNFs) extracted by the automatic speech recognition(ASR) model. However, selection of BNFs have a significant impact on VC result. For example, when extracting BNFs from ASR trained with Cross Entropy loss (CE-BNFs) and feeding into neural network to train a VC system, the timbre similarity of converted speech is significantly degraded. If BNFs are extracted from ASR trained using Connectionist Temporal Classification loss (CTC-BNFs), the naturalness of the converted speech may decrease. This phenomenon is caused by the difference of information contained in BNFs. In this paper, we proposed an any-to-one VC method using hybrid bottleneck features extracted from CTC-BNFs and CE-BNFs to complement each other advantages. Gradient reversal layer and instance normalization were used to extract prosody information from CE-BNFs and content information from CTC-BNFs. Auto-regressive decoder and Hifi-GAN vocoder were used to generate high-quality waveform. Experimental results show that our proposed method achieves higher similarity, naturalness, quality than baseline method and reveals the differences between the information contained in CE-BNFs and CTC-BNFs as well as the influence they have on the converted speech.

Undersampled MRI Reconstruction with Side Information-Guided Normalisation

Magnetic resonance (MR) images exhibit various contrasts and appearances based on factors such as different acquisition protocols, views, manufacturers, scanning parameters, etc. This generally accessible appearance-related side information affects deep learning-based undersampled magnetic resonance imaging (MRI) reconstruction frameworks, but has been overlooked in the majority of current works. In this paper, we investigate the use of such side information as normalisation parameters in a convolutional neural network (CNN) to improve undersampled MRI reconstruction. Specifically, a Side Information-Guided Normalisation (SIGN) module, containing only few layers, is proposed to efficiently encode the side information and output the normalisation parameters. We examine the effectiveness of such a module on two popular reconstruction architectures, D5C5 and OUCR. The experimental results on both brain and knee images under various acceleration rates demonstrate that the proposed method improves on its corresponding baseline architectures with a significant margin.

Multi-channel deep convolutional neural networks for multi-classifying thyroid disease

Thyroid disease instances have been continuously increasing since the 1990s, and thyroid cancer has become the most rapidly rising disease among all the malignancies in recent years. Most existing studies focused on applying deep convolutional neural networks for detecting thyroid cancer. Despite their satisfactory performance on binary classification tasks, limited studies have explored multi-class classification of thyroid disease types; much less is known of the diagnosis of co-existence situation for different types of thyroid diseases. Therefore, this study proposed a novel multi-channel convolutional neural network (CNN) architecture to address the multi-class classification task of thyroid disease. The multi-channel CNN merits from computed tomography to drive a comprehensive diagnostic decision for the overall thyroid gland, emphasizing the disease co-existence circumstance. Moreover, this study also examined alternative strategies to enhance the diagnostic accuracy of CNN models through concatenation of different scales of feature maps. Benchmarking experiments demonstrate the improved performance of the proposed multi-channel CNN architecture compared with the standard single-channel CNN architecture. More specifically, the multi-channel CNN achieved an accuracy of 0.909, precision of 0.944, recall of 0.896, specificity of 0.994, and F1 of 0.917, in contrast to the single-channel CNN, which obtained 0.902, 0.892, 0.909, 0.993, 0.898, respectively. In addition, the proposed model was evaluated in different gender groups; it reached a diagnostic accuracy of 0.908 for the female group and 0.901 for the male group. Collectively, the results highlight that the proposed multi-channel CNN has excellent generalization and has the potential to be deployed to provide computational decision support in clinical settings.

Adversarial Attacks and Defense for Non-Parametric Two-Sample Tests

Non-parametric two-sample tests (TSTs) that judge whether two sets of samples are drawn from the same distribution, have been widely used in the analysis of critical data. People tend to employ TSTs as trusted basic tools and rarely have any doubt about their reliability. This paper systematically uncovers the failure mode of non-parametric TSTs through adversarial attacks and then proposes corresponding defense strategies. First, we theoretically show that an adversary can upper-bound the distributional shift which guarantees the attack's invisibility. Furthermore, we theoretically find that the adversary can also degrade the lower bound of a TST's test power, which enables us to iteratively minimize the test criterion in order to search for adversarial pairs. To enable TST-agnostic attacks, we propose an ensemble attack (EA) framework that jointly minimizes the different types of test criteria. Second, to robustify TSTs, we propose a max-min optimization that iteratively generates adversarial pairs to train the deep kernels. Extensive experiments on both simulated and real-world datasets validate the adversarial vulnerabilities of non-parametric TSTs and the effectiveness of our proposed defense.