Faster Diffusion Cardiac MRI with Deep Learning-based breath hold reduction

Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) enables us to probe the microstructural arrangement of cardiomyocytes within the myocardium in vivo and non-invasively, which no other imaging modality allows. This innovative technology could revolutionise the ability to perform cardiac clinical diagnosis, risk stratification, prognosis and therapy follow-up. However, DT-CMR is currently inefficient with over six minutes needed to acquire a single 2D static image. Therefore, DT-CMR is currently confined to research but not used clinically. We propose to reduce the number of repetitions needed to produce DT-CMR datasets and subsequently de-noise them, decreasing the acquisition time by a linear factor while maintaining acceptable image quality. Our proposed approach, based on Generative Adversarial Networks, Vision Transformers, and Ensemble Learning, performs significantly and considerably better than previous proposed approaches, bringing single breath-hold DT-CMR closer to reality.

CS$^2$: A Controllable and Simultaneous Synthesizer of Images and Annotations with Minimal Human Intervention

The destitution of image data and corresponding expert annotations limit the training capacities of AI diagnostic models and potentially inhibit their performance. To address such a problem of data and label scarcity, generative models have been developed to augment the training datasets. Previously proposed generative models usually require manually adjusted annotations (e.g., segmentation masks) or need pre-labeling. However, studies have found that these pre-labeling based methods can induce hallucinating artifacts, which might mislead the downstream clinical tasks, while manual adjustment could be onerous and subjective. To avoid manual adjustment and pre-labeling, we propose a novel controllable and simultaneous synthesizer (dubbed CS$^2$) in this study to generate both realistic images and corresponding annotations at the same time. Our CS$^2$ model is trained and validated using high resolution CT (HRCT) data collected from COVID-19 patients to realize an efficient infections segmentation with minimal human intervention. Our contributions include 1) a conditional image synthesis network that receives both style information from reference CT images and structural information from unsupervised segmentation masks, and 2) a corresponding segmentation mask synthesis network to automatically segment these synthesized images simultaneously. Our experimental studies on HRCT scans collected from COVID-19 patients demonstrate that our CS$^2$ model can lead to realistic synthesized datasets and promising segmentation results of COVID infections compared to the state-of-the-art nnUNet trained and fine-tuned in a fully supervised manner.

Towards Reliable and Explainable AI Model for Solid Pulmonary Nodule Diagnosis

Lung cancer has the highest mortality rate of deadly cancers in the world. Early detection is essential to treatment of lung cancer. However, detection and accurate diagnosis of pulmonary nodules depend heavily on the experiences of radiologists and can be a heavy workload for them. Computer-aided diagnosis (CAD) systems have been developed to assist radiologists in nodule detection and diagnosis, greatly easing the workload while increasing diagnosis accuracy. Recent development of deep learning, greatly improved the performance of CAD systems. However, lack of model reliability and interpretability remains a major obstacle for its large-scale clinical application. In this work, we proposed a multi-task explainable deep-learning model for pulmonary nodule diagnosis. Our neural model can not only predict lesion malignancy but also identify relevant manifestations. Further, the location of each manifestation can also be visualized for visual interpretability. Our proposed neural model achieved a test AUC of 0.992 on LIDC public dataset and a test AUC of 0.923 on our in-house dataset. Moreover, our experimental results proved that by incorporating manifestation identification tasks into the multi-task model, the accuracy of the malignancy classification can also be improved. This multi-task explainable model may provide a scheme for better interaction with the radiologists in a clinical environment.

Data and Physics Driven Learning Models for Fast MRI -- Fundamentals and Methodologies from CNN, GAN to Attention and Transformers

Research studies have shown no qualms about using data driven deep learning models for downstream tasks in medical image analysis, e.g., anatomy segmentation and lesion detection, disease diagnosis and prognosis, and treatment planning. However, deep learning models are not the sovereign remedy for medical image analysis when the upstream imaging is not being conducted properly (with artefacts). This has been manifested in MRI studies, where the scanning is typically slow, prone to motion artefacts, with a relatively low signal to noise ratio, and poor spatial and/or temporal resolution. Recent studies have witnessed substantial growth in the development of deep learning techniques for propelling fast MRI. This article aims to (1) introduce the deep learning based data driven techniques for fast MRI including convolutional neural network and generative adversarial network based methods, (2) survey the attention and transformer based models for speeding up MRI reconstruction, and (3) detail the research in coupling physics and data driven models for MRI acceleration. Finally, we will demonstrate through a few clinical applications, explain the importance of data harmonisation and explainable models for such fast MRI techniques in multicentre and multi-scanner studies, and discuss common pitfalls in current research and recommendations for future research directions.

ME-Net: Multi-Encoder Net Framework for Brain Tumor Segmentation

Glioma is the most common and aggressive brain tumor. Magnetic resonance imaging (MRI) plays a vital role to evaluate tumors for the arrangement of tumor surgery and the treatment of subsequent procedures. However, the manual segmentation of the MRI image is strenuous, which limits its clinical application. With the development of deep learning, a large number of automatic segmentation methods have been developed, but most of them stay in 2D images, which leads to subpar performance. Moreover, the serious voxel imbalance between the brain tumor and the background as well as the different sizes and locations of the brain tumor makes the segmentation of 3D images a challenging problem. Aiming at segmenting 3D MRI, we propose a model for brain tumor segmentation with multiple encoders. The structure contains four encoders and one decoder. The four encoders correspond to the four modalities of the MRI image, perform one-to-one feature extraction, and then merge the feature maps of the four modalities into the decoder. This method reduces the difficulty of feature extraction and greatly improves model performance. We also introduced a new loss function named "Categorical Dice", and set different weights for different segmented regions at the same time, which solved the problem of voxel imbalance. We evaluated our approach using the online BraTS 2020 Challenge verification. Our proposed method can achieve promising results in the validation set compared to the state-of-the-art approaches with Dice scores of 0.70249, 0.88267, and 0.73864 for the intact tumor, tumor core, and enhanced tumor, respectively.

DRAG: Dynamic Region-Aware GCN for Privacy-Leaking Image Detection

The daily practice of sharing images on social media raises a severe issue about privacy leakage. To address the issue, privacy-leaking image detection is studied recently, with the goal to automatically identify images that may leak privacy. Recent advance on this task benefits from focusing on crucial objects via pretrained object detectors and modeling their correlation. However, these methods have two limitations: 1) they neglect other important elements like scenes, textures, and objects beyond the capacity of pretrained object detectors; 2) the correlation among objects is fixed, but a fixed correlation is not appropriate for all the images. To overcome the limitations, we propose the Dynamic Region-Aware Graph Convolutional Network (DRAG) that dynamically finds out crucial regions including objects and other important elements, and models their correlation adaptively for each input image. To find out crucial regions, we cluster spatially-correlated feature channels into several region-aware feature maps. Further, we dynamically model the correlation with the self-attention mechanism and explore the interaction among the regions with a graph convolutional network. The DRAG achieved an accuracy of 87% on the largest dataset for privacy-leaking image detection, which is 10 percentage points higher than the state of the art. The further case study demonstrates that it found out crucial regions containing not only objects but other important elements like textures.

Delta Tuning: A Comprehensive Study of Parameter Efficient Methods for Pre-trained Language Models

Despite the success, the process of fine-tuning large-scale PLMs brings prohibitive adaptation costs. In fact, fine-tuning all the parameters of a colossal model and retaining separate instances for different tasks are practically infeasible. This necessitates a new branch of research focusing on the parameter-efficient adaptation of PLMs, dubbed as delta tuning in this paper. In contrast with the standard fine-tuning, delta tuning only fine-tunes a small portion of the model parameters while keeping the rest untouched, largely reducing both the computation and storage costs. Recent studies have demonstrated that a series of delta tuning methods with distinct tuned parameter selection could achieve performance on a par with full-parameter fine-tuning, suggesting a new promising way of stimulating large-scale PLMs. In this paper, we first formally describe the problem of delta tuning and then comprehensively review recent delta tuning approaches. We also propose a unified categorization criterion that divide existing delta tuning methods into three groups: addition-based, specification-based, and reparameterization-based methods. Though initially proposed as an efficient method to steer large models, we believe that some of the fascinating evidence discovered along with delta tuning could help further reveal the mechanisms of PLMs and even deep neural networks. To this end, we discuss the theoretical principles underlying the effectiveness of delta tuning and propose frameworks to interpret delta tuning from the perspective of optimization and optimal control, respectively. Furthermore, we provide a holistic empirical study of representative methods, where results on over 100 NLP tasks demonstrate a comprehensive performance comparison of different approaches. The experimental results also cover the analysis of combinatorial, scaling and transferable properties of delta tuning.

Automatic Fine-grained Glomerular Lesion Recognition in Kidney Pathology

Recognition of glomeruli lesions is the key for diagnosis and treatment planning in kidney pathology; however, the coexisting glomerular structures such as mesangial regions exacerbate the difficulties of this task. In this paper, we introduce a scheme to recognize fine-grained glomeruli lesions from whole slide images. First, a focal instance structural similarity loss is proposed to drive the model to locate all types of glomeruli precisely. Then an Uncertainty Aided Apportionment Network is designed to carry out the fine-grained visual classification without bounding-box annotations. This double branch-shaped structure extracts common features of the child class from the parent class and produces the uncertainty factor for reconstituting the training dataset. Results of slide-wise evaluation illustrate the effectiveness of the entire scheme, with an 8-22% improvement of the mean Average Precision compared with remarkable detection methods. The comprehensive results clearly demonstrate the effectiveness of the proposed method.

HDL: Hybrid Deep Learning for the Synthesis of Myocardial Velocity Maps in Digital Twins for Cardiac Analysis

Synthetic digital twins based on medical data accelerate the acquisition, labelling and decision making procedure in digital healthcare. A core part of digital healthcare twins is model-based data synthesis, which permits the generation of realistic medical signals without requiring to cope with the modelling complexity of anatomical and biochemical phenomena producing them in reality. Unfortunately, algorithms for cardiac data synthesis have been so far scarcely studied in the literature. An important imaging modality in the cardiac examination is three-directional CINE multi-slice myocardial velocity mapping (3Dir MVM), which provides a quantitative assessment of cardiac motion in three orthogonal directions of the left ventricle. The long acquisition time and complex acquisition produce make it more urgent to produce synthetic digital twins of this imaging modality. In this study, we propose a hybrid deep learning (HDL) network, especially for synthetic 3Dir MVM data. Our algorithm is featured by a hybrid UNet and a Generative Adversarial Network with a foreground-background generation scheme. The experimental results show that from temporally down-sampled magnitude CINE images (six times), our proposed algorithm can still successfully synthesise high temporal resolution 3Dir MVM CMR data (PSNR=42.32) with precise left ventricle segmentation (DICE=0.92). These performance scores indicate that our proposed HDL algorithm can be implemented in real-world digital twins for myocardial velocity mapping data simulation. To the best of our knowledge, this work is the first one in the literature investigating digital twins of the 3Dir MVM CMR, which has shown great potential for improving the efficiency of clinical studies via synthesised cardiac data.