mmFormer: Multimodal Medical Transformer for Incomplete Multimodal Learning of Brain Tumor Segmentation

Accurate brain tumor segmentation from Magnetic Resonance Imaging (MRI) is desirable to joint learning of multimodal images. However, in clinical practice, it is not always possible to acquire a complete set of MRIs, and the problem of missing modalities causes severe performance degradation in existing multimodal segmentation methods. In this work, we present the first attempt to exploit the Transformer for multimodal brain tumor segmentation that is robust to any combinatorial subset of available modalities. Concretely, we propose a novel multimodal Medical Transformer (mmFormer) for incomplete multimodal learning with three main components: the hybrid modality-specific encoders that bridge a convolutional encoder and an intra-modal Transformer for both local and global context modeling within each modality; an inter-modal Transformer to build and align the long-range correlations across modalities for modality-invariant features with global semantics corresponding to tumor region; a decoder that performs a progressive up-sampling and fusion with the modality-invariant features to generate robust segmentation. Besides, auxiliary regularizers are introduced in both encoder and decoder to further enhance the model's robustness to incomplete modalities. We conduct extensive experiments on the public BraTS $2018$ dataset for brain tumor segmentation. The results demonstrate that the proposed mmFormer outperforms the state-of-the-art methods for incomplete multimodal brain tumor segmentation on almost all subsets of incomplete modalities, especially by an average 19.07% improvement of Dice on tumor segmentation with only one available modality. The code is available at https://github.com/YaoZhang93/mmFormer.

Myocardial Segmentation of Late Gadolinium Enhanced MR Images by Propagation of Contours from Cine MR Images

Automatic segmentation of myocardium in Late Gadolinium Enhanced (LGE) Cardiac MR (CMR) images is often difficult due to the intensity heterogeneity resulting from accumulation of contrast agent in infarcted areas. In this paper, we propose an automatic segmentation framework that fully utilizes shared information between corresponding cine and LGE images of a same patient. Given myocardial contours in cine CMR images, the proposed framework achieves accurate segmentation of LGE CMR images in a coarse-to-fine manner. Affine registration is first performed between the corresponding cine and LGE image pair, followed by nonrigid registration, and finally local deformation of myocardial contours driven by forces derived from local features of the LGE image. Experimental results on real patient data with expert outlined ground truth show that the proposed framework can generate accurate and reliable results for myocardial segmentation of LGE CMR images.

A Comprehensive 3-D Framework for Automatic Quantification of Late Gadolinium Enhanced Cardiac Magnetic Resonance Images

Late gadolinium enhanced (LGE) cardiac magnetic resonance (CMR) can directly visualize nonviable myocardium with hyperenhanced intensities with respect to normal myocardium. For heart attack patients, it is crucial to facilitate the decision of appropriate therapy by analyzing and quantifying their LGE CMR images. To achieve accurate quantification, LGE CMR images need to be processed in two steps: segmentation of the myocardium followed by classification of infarcts within the segmented myocardium. However, automatic segmentation is difficult usually due to the intensity heterogeneity of the myocardium and intensity similarity between the infarcts and blood pool. Besides, the slices of an LGE CMR dataset often suffer from spatial and intensity distortions, causing further difficulties in segmentation and classification. In this paper, we present a comprehensive 3-D framework for automatic quantification of LGE CMR images. In this framework, myocardium is segmented with a novel method that deforms coupled endocardial and epicardial meshes and combines information in both short- and long-axis slices, while infarcts are classified with a graph-cut algorithm incorporating intensity and spatial information. Moreover, both spatial and intensity distortions are effectively corrected with specially designed countermeasures. Experiments with 20 sets of real patient data show visually good segmentation and classification results that are quantitatively in strong agreement with those manually obtained by experts.

Three-Dimensional Segmentation of the Left Ventricle in Late Gadolinium Enhanced MR Images of Chronic Infarction Combining Long- and Short-Axis Information

Automatic segmentation of the left ventricle (LV) in late gadolinium enhanced (LGE) cardiac MR (CMR) images is difficult due to the intensity heterogeneity arising from accumulation of contrast agent in infarcted myocardium. In this paper, we present a comprehensive framework for automatic 3D segmentation of the LV in LGE CMR images. Given myocardial contours in cine images as a priori knowledge, the framework initially propagates the a priori segmentation from cine to LGE images via 2D translational registration. Two meshes representing respectively endocardial and epicardial surfaces are then constructed with the propagated contours. After construction, the two meshes are deformed towards the myocardial edge points detected in both short-axis and long-axis LGE images in a unified 3D coordinate system. Taking into account the intensity characteristics of the LV in LGE images, we propose a novel parametric model of the LV for consistent myocardial edge points detection regardless of pathological status of the myocardium (infarcted or healthy) and of the type of the LGE images (short-axis or long-axis). We have evaluated the proposed framework with 21 sets of real patient and 4 sets of simulated phantom data. Both distance- and region-based performance metrics confirm the observation that the framework can generate accurate and reliable results for myocardial segmentation of LGE images. We have also tested the robustness of the framework with respect to varied a priori segmentation in both practical and simulated settings. Experimental results show that the proposed framework can greatly compensate variations in the given a priori knowledge and consistently produce accurate segmentations.

Learning Shape Priors by Pairwise Comparison for Robust Semantic Segmentation

Semantic segmentation is important in medical image analysis. Inspired by the strong ability of traditional image analysis techniques in capturing shape priors and inter-subject similarity, many deep learning (DL) models have been recently proposed to exploit such prior information and achieved robust performance. However, these two types of important prior information are usually studied separately in existing models. In this paper, we propose a novel DL model to model both type of priors within a single framework. Specifically, we introduce an extra encoder into the classic encoder-decoder structure to form a Siamese structure for the encoders, where one of them takes a target image as input (the image-encoder), and the other concatenates a template image and its foreground regions as input (the template-encoder). The template-encoder encodes the shape priors and appearance characteristics of each foreground class in the template image. A cosine similarity based attention module is proposed to fuse the information from both encoders, to utilize both types of prior information encoded by the template-encoder and model the inter-subject similarity for each foreground class. Extensive experiments on two public datasets demonstrate that our proposed method can produce superior performance to competing methods.

Domain Adaptation Meets Zero-Shot Learning: An Annotation-Efficient Approach to Multi-Modality Medical Image Segmentation

Due to the lack of properly annotated medical data, exploring the generalization capability of the deep model is becoming a public concern. Zero-shot learning (ZSL) has emerged in recent years to equip the deep model with the ability to recognize unseen classes. However, existing studies mainly focus on natural images, which utilize linguistic models to extract auxiliary information for ZSL. It is impractical to apply the natural image ZSL solutions directly to medical images, since the medical terminology is very domain-specific, and it is not easy to acquire linguistic models for the medical terminology. In this work, we propose a new paradigm of ZSL specifically for medical images utilizing cross-modality information. We make three main contributions with the proposed paradigm. First, we extract the prior knowledge about the segmentation targets, called relation prototypes, from the prior model and then propose a cross-modality adaptation module to inherit the prototypes to the zero-shot model. Second, we propose a relation prototype awareness module to make the zero-shot model aware of information contained in the prototypes. Last but not least, we develop an inheritance attention module to recalibrate the relation prototypes to enhance the inheritance process. The proposed framework is evaluated on two public cross-modality datasets including a cardiac dataset and an abdominal dataset. Extensive experiments show that the proposed framework significantly outperforms the state of the arts.

Deep Convolutional Neural Networks for Molecular Subtyping of Gliomas Using Magnetic Resonance Imaging

Knowledge of molecular subtypes of gliomas can provide valuable information for tailored therapies. This study aimed to investigate the use of deep convolutional neural networks (DCNNs) for noninvasive glioma subtyping with radiological imaging data according to the new taxonomy announced by the World Health Organization in 2016. Methods: A DCNN model was developed for the prediction of the five glioma subtypes based on a hierarchical classification paradigm. This model used three parallel, weight-sharing, deep residual learning networks to process 2.5-dimensional input of trimodal MRI data, including T1-weighted, T1-weighted with contrast enhancement, and T2-weighted images. A data set comprising 1,016 real patients was collected for evaluation of the developed DCNN model. The predictive performance was evaluated via the area under the curve (AUC) from the receiver operating characteristic analysis. For comparison, the performance of a radiomics-based approach was also evaluated. Results: The AUCs of the DCNN model for the four classification tasks in the hierarchical classification paradigm were 0.89, 0.89, 0.85, and 0.66, respectively, as compared to 0.85, 0.75, 0.67, and 0.59 of the radiomics approach. Conclusion: The results showed that the developed DCNN model can predict glioma subtypes with promising performance, given sufficient, non-ill-balanced training data.

Conquering Data Variations in Resolution: A Slice-Aware Multi-Branch Decoder Network

Fully convolutional neural networks have made promising progress in joint liver and liver tumor segmentation. Instead of following the debates over 2D versus 3D networks (for example, pursuing the balance between large-scale 2D pretraining and 3D context), in this paper, we novelly identify the wide variation in the ratio between intra- and inter-slice resolutions as a crucial obstacle to the performance. To tackle the mismatch between the intra- and inter-slice information, we propose a slice-aware 2.5D network that emphasizes extracting discriminative features utilizing not only in-plane semantics but also out-of-plane coherence for each separate slice. Specifically, we present a slice-wise multi-input multi-output architecture to instantiate such a design paradigm, which contains a Multi-Branch Decoder (MD) with a Slice-centric Attention Block (SAB) for learning slice-specific features and a Densely Connected Dice (DCD) loss to regularize the inter-slice predictions to be coherent and continuous. Based on the aforementioned innovations, we achieve state-of-the-art results on the MICCAI 2017 Liver Tumor Segmentation (LiTS) dataset. Besides, we also test our model on the ISBI 2019 Segmentation of THoracic Organs at Risk (SegTHOR) dataset, and the result proves the robustness and generalizability of the proposed method in other segmentation tasks.

Simultaneous Alignment and Surface Regression Using Hybrid 2D-3D Networks for 3D Coherent Layer Segmentation of Retina OCT Images

Automated surface segmentation of retinal layer is important and challenging in analyzing optical coherence tomography (OCT). Recently, many deep learning based methods have been developed for this task and yield remarkable performance. However, due to large spatial gap and potential mismatch between the B-scans of OCT data, all of them are based on 2D segmentation of individual B-scans, which may loss the continuity information across the B-scans. In addition, 3D surface of the retina layers can provide more diagnostic information, which is crucial in quantitative image analysis. In this study, a novel framework based on hybrid 2D-3D convolutional neural networks (CNNs) is proposed to obtain continuous 3D retinal layer surfaces from OCT. The 2D features of individual B-scans are extracted by an encoder consisting of 2D convolutions. These 2D features are then used to produce the alignment displacement field and layer segmentation by two 3D decoders, which are coupled via a spatial transformer module. The entire framework is trained end-to-end. To the best of our knowledge, this is the first study that attempts 3D retinal layer segmentation in volumetric OCT images based on CNNs. Experiments on a publicly available dataset show that our framework achieves superior results to state-of-the-art 2D methods in terms of both layer segmentation accuracy and cross-B-scan 3D continuity, thus offering more clinical values than previous works.

Revisiting Experience Replay: Continual Learning by Adaptively Tuning Task-wise Relationship

Continual learning requires models to learn new tasks while maintaining previously learned knowledge. Various algorithms have been proposed to address this real challenge. Till now, rehearsal-based methods, such as experience replay, have achieved state-of-the-art performance. These approaches save a small part of the data of the past tasks as a memory buffer to prevent models from forgetting previously learned knowledge. However, most of them treat every new task equally, i.e., fixed the hyperparameters of the framework while learning different new tasks. Such a setting lacks the consideration of the relationship/similarity between past and new tasks. For example, the previous knowledge/features learned from dogs are more beneficial for the identification of cats (new task), compared to those learned from buses. In this regard, we propose a meta learning algorithm based on bi-level optimization to adaptively tune the relationship between the knowledge extracted from the past and new tasks. Therefore, the model can find an appropriate direction of gradient during continual learning and avoid the serious overfitting problem on memory buffer. Extensive experiments are conducted on three publicly available datasets (i.e., CIFAR-10, CIFAR-100, and Tiny ImageNet). The experimental results demonstrate that the proposed method can consistently improve the performance of all baselines.