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Brain tissue segmentation has demonstrated great utility in quantifying MRI data through Voxel-Based Morphometry and highlighting subtle structural changes associated with various conditions within the brain. However, manual segmentation is highly labor-intensive, and automated approaches have struggled due to properties inherent to MRI acquisition, leaving a great need for an effective segmentation tool. Despite the recent success of deep convolutional neural networks (CNNs) for brain tissue segmentation, many such solutions do not generalize well to new datasets, which is critical for a reliable solution. Transformers have demonstrated success in natural image segmentation and have recently been applied to 3D medical image segmentation tasks due to their ability to capture long-distance relationships in the input where the local receptive fields of CNNs struggle. This study introduces a novel CNN-Transformer hybrid architecture designed for brain tissue segmentation. We validate our model's performance across four multi-site T1w MRI datasets, covering different vendors, field strengths, scan parameters, time points, and neuropsychiatric conditions. In all situations, our model achieved the greatest generality and reliability. Out method is inherently robust and can serve as a valuable tool for brain-related T1w MRI studies. The code for the TABS network is available at: //github.com/raovish6/TABS.

Recent medical imaging studies have given rise to distinct but inter-related datasets corresponding to multiple experimental tasks or longitudinal visits. Standard scalar-on-image regression models that fit each dataset separately are not equipped to leverage information across inter-related images, and existing multi-task learning approaches are compromised by the inability to account for the noise that is often observed in images. We propose a novel joint scalar-on-image regression framework involving wavelet-based image representations with grouped penalties that are designed to pool information across inter-related images for joint learning, and which explicitly accounts for noise in high-dimensional images via a projection-based approach. In the presence of non-convexity arising due to noisy images, we derive non-asymptotic error bounds under non-convex as well as convex grouped penalties, even when the number of voxels increases exponentially with sample size. A projected gradient descent algorithm is used for computation, which is shown to approximate the optimal solution via well-defined non-asymptotic optimization error bounds under noisy images. Extensive simulations and application to a motivating longitudinal Alzheimer's disease study illustrate significantly improved predictive ability and greater power to detect true signals, that are simply missed by existing methods without noise correction due to the attenuation to null phenomenon.

There has been increasing interest in the potential of multi-modal imaging to obtain more robust estimates of Functional Connectivity (FC) in high-dimensional settings. We develop novel algorithms adapting graphical methods incorporating diffusion tensor imaging (DTI) and statistically rigorous control to FC estimation with computational efficiency and scalability. Our proposed algorithm leverages a graphical random walk on DTI data to define a new measure of structural influence that highlights connected components of interest. We then test for minimum subnetwork size and find the subnetwork topology using permutation testing before the discovered components are tested for significance. Extensive simulations demonstrate that our method has comparable power to other currently used methods, with the advantage of greater speed, equal or more robustness, and simple implementation. To verify our approach, we analyze task-based fMRI data obtained from the Human Connectome Project database, which reveal novel insights into brain interactions during performance of a motor task. We expect that the transparency and flexibility of our approach will prove valuable as further understanding of the structure-function relationship informs the future of network estimation. Scalability will also only become more important as neurological data become more granular and grow in dimension.

Unsupervised domain adaptation has recently emerged as an effective paradigm for generalizing deep neural networks to new target domains. However, there is still enormous potential to be tapped to reach the fully supervised performance. In this paper, we present a novel active learning strategy to assist knowledge transfer in the target domain, dubbed active domain adaptation. We start from an observation that energy-based models exhibit free energy biases when training (source) and test (target) data come from different distributions. Inspired by this inherent mechanism, we empirically reveal that a simple yet efficient energy-based sampling strategy sheds light on selecting the most valuable target samples than existing approaches requiring particular architectures or computation of the distances. Our algorithm, Energy-based Active Domain Adaptation (EADA), queries groups of targe data that incorporate both domain characteristic and instance uncertainty into every selection round. Meanwhile, by aligning the free energy of target data compact around the source domain via a regularization term, domain gap can be implicitly diminished. Through extensive experiments, we show that EADA surpasses state-of-the-art methods on well-known challenging benchmarks with substantial improvements, making it a useful option in the open world. Code is available at //github.com/BIT-DA/EADA.

Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively.

Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.

Biomedical image segmentation is an important task in many medical applications. Segmentation methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling datasets of medical images requires significant expertise and time, and is infeasible at large scales. To tackle the lack of labeled data, researchers use techniques such as hand-engineered preprocessing steps, hand-tuned architectures, and data augmentation. However, these techniques involve costly engineering efforts, and are typically dataset-specific. We present an automated data augmentation method for medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans, focusing on the one-shot segmentation scenario -- a practical challenge in many medical applications. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transforms from the images, and use the model along with the labeled example to synthesize additional labeled training examples for supervised segmentation. Each transform is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. Augmenting the training of a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at //github.com/xamyzhao/brainstorm.

Accurate segmentation of the prostate from magnetic resonance (MR) images provides useful information for prostate cancer diagnosis and treatment. However, automated prostate segmentation from 3D MR images still faces several challenges. For instance, a lack of clear edge between the prostate and other anatomical structures makes it challenging to accurately extract the boundaries. The complex background texture and large variation in size, shape and intensity distribution of the prostate itself make segmentation even further complicated. With deep learning, especially convolutional neural networks (CNNs), emerging as commonly used methods for medical image segmentation, the difficulty in obtaining large number of annotated medical images for training CNNs has become much more pronounced that ever before. Since large-scale dataset is one of the critical components for the success of deep learning, lack of sufficient training data makes it difficult to fully train complex CNNs. To tackle the above challenges, in this paper, we propose a boundary-weighted domain adaptive neural network (BOWDA-Net). To make the network more sensitive to the boundaries during segmentation, a boundary-weighted segmentation loss (BWL) is proposed. Furthermore, an advanced boundary-weighted transfer leaning approach is introduced to address the problem of small medical imaging datasets. We evaluate our proposed model on the publicly available MICCAI 2012 Prostate MR Image Segmentation (PROMISE12) challenge dataset. Our experimental results demonstrate that the proposed model is more sensitive to boundary information and outperformed other state-of-the-art methods.

Multi-task learning (MTL) allows deep neural networks to learn from related tasks by sharing parameters with other networks. In practice, however, MTL involves searching an enormous space of possible parameter sharing architectures to find (a) the layers or subspaces that benefit from sharing, (b) the appropriate amount of sharing, and (c) the appropriate relative weights of the different task losses. Recent work has addressed each of the above problems in isolation. In this work we present an approach that learns a latent multi-task architecture that jointly addresses (a)--(c). We present experiments on synthetic data and data from OntoNotes 5.0, including four different tasks and seven different domains. Our extension consistently outperforms previous approaches to learning latent architectures for multi-task problems and achieves up to 15% average error reductions over common approaches to MTL.

This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.