Automated colorectal cancer (CRC) segmentation in medical imaging is the key to achieving automation of CRC detection, staging, and treatment response monitoring. Compared with magnetic resonance imaging (MRI) and computed tomography colonography (CTC), conventional computed tomography (CT) has enormous potential because of its broad implementation, superiority for the hollow viscera (colon), and convenience without needing bowel preparation. However, the segmentation of CRC in conventional CT is more challenging due to the difficulties presenting with the unprepared bowel, such as distinguishing the colorectum from other structures with similar appearance and distinguishing the CRC from the contents of the colorectum. To tackle these challenges, we introduce DeepCRC-SL, the first automated segmentation algorithm for CRC and colorectum in conventional contrast-enhanced CT scans. We propose a topology-aware deep learning-based approach, which builds a novel 1-D colorectal coordinate system and encodes each voxel of the colorectum with a relative position along the coordinate system. We then induce an auxiliary regression task to predict the colorectal coordinate value of each voxel, aiming to integrate global topology into the segmentation network and thus improve the colorectum's continuity. Self-attention layers are utilized to capture global contexts for the coordinate regression task and enhance the ability to differentiate CRC and colorectum tissues. Moreover, a coordinate-driven self-learning (SL) strategy is introduced to leverage a large amount of unlabeled data to improve segmentation performance. We validate the proposed approach on a dataset including 227 labeled and 585 unlabeled CRC cases by fivefold cross-validation. Experimental results demonstrate that our method outperforms some recent related segmentation methods and achieves the segmentation accuracy in DSC for CRC of 0.669 and colorectum of 0.892, reaching to the performance (at 0.639 and 0.890, respectively) of a medical resident with two years of specialized CRC imaging fellowship.

Radiologists highly desire fully automated versatile AI for medical imaging interpretation. However, the lack of extensively annotated large-scale multi-disease datasets has hindered the achievement of this goal. In this paper, we explore the feasibility of leveraging language as a natu-rally high-quality supervision for chest CT imaging. In light of the limited availability of image-report pairs, we boot-strap the understanding of 3D chest CT images by distilling chest-related diagnostic knowledge from an extensively pre-trained 2D X-ray expert model. Specifically, we propose a language-guided retrieval method to match each 3D CT image with its semantically closest 2D X-ray image, and perform pair-wise and semantic relation knowledge distillation. Subsequently, we use contrastive learning to align images and reports within the same patient while distin-guishing them from the other patients. However, the challenge arises when patients have similar semantic diagnoses, such as healthy patients, potentially confusing if treated as negatives. We introduce a robust contrastive learning that identifies and corrects these false negatives. We train our model with over 12K pairs of chest CT images and radiology reports. Extensive experiments across multiple scenarios, including zero-shot learning, report generation, and fine-tuning processes, demonstrate the model's feasibility in interpreting chest CT images.

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI’s clinical adoption. A certain number of AI models need to be assembled nontrivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (CancerUniT) model to jointly detect tumor existence & location and diagnose tumor characteristics for eight major cancers in CT scans. CancerUniT is a query-based Mask Transformer model with the output of multi-tumor prediction. We decouple the object queries into organ queries, tumor detection queries and tumor diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. CancerUniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, CancerUniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-disease methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. This moves one step closer towards a universal high performance cancer screening tool.

Federated learning is an emerging research paradigm enabling collaborative training of machine learning models among different organizations while keeping data private at each institution. Despite recent progress, there remain fundamental challenges such as the lack of convergence and the potential for catastrophic forgetting across real-world heterogeneous devices. In this paper, we demonstrate that self-attention-based architectures (e.g., Transformers) are more robust to distribution shifts and hence improve federated learning over heterogeneous data. Concretely, we conduct the first rigorous empirical investigation of different neural architectures across a range of federated algorithms, real-world benchmarks, and heterogeneous data splits. Our experiments show that simply replacing convolutional networks with Transformers can greatly reduce catastrophic forgetting of previous devices, accelerate convergence, and reach a better global model, especially when dealing with heterogeneous data. We release our code and pretrained models to encourage future exploration in robust architectures as an alternative to current research efforts on the optimization front.

Recently, there emerges a series of vision Transformers, which show superior performance with a more compact model size than conventional convolutional neural networks, thanks to the strong ability of Transformers to model long-range dependencies. However, the advantages of vision Transformers also come with a price: Self-attention, the core part of Transformer, has a quadratic complexity to the input sequence length. This leads to a dramatic increase of computation and memory cost with the increase of sequence length, thus introducing difficulties when applying Transformers to the vision tasks that require dense predictions based on high-resolution feature maps.In this paper, we propose a new vision Transformer, named Glance-and-Gaze Transformer (GG-Transformer), to address the aforementioned issues. It is motivated by the Glance and Gaze behavior of human beings when recognizing objects in natural scenes, with the ability to efficiently model both long-range dependencies and local context. In GG-Transformer, the Glance and Gaze behavior is realized by two parallel branches: The Glance branch is achieved by performing self-attention on the adaptively-dilated partitions of the input, which leads to a linear complexity while still enjoying a global receptive field; The Gaze branch is implemented by a simple depth-wise convolutional layer, which compensates local image context to the features obtained by the Glance mechanism. We empirically demonstrate our method achieves consistently superior performance over previous state-of-the-art Transformers on various vision tasks and benchmarks.

While making a tremendous impact in various fields, deep neural networks usually require large amounts of labeled data for training which are expensive to collect in many applications, especially in the medical domain. Un-labeled data, on the other hand, is much more abundant. Semi-supervised learning techniques, such as co-training, could provide a powerful tool to leverage unlabeled data. In this paper, we propose a novel framework, uncertainty-aware multi-view co-training (UMCT), to address semi-supervised learning on 3D data, such as volumetric data from medical imaging. In our work, co-training is achieved by exploiting multi-viewpoint consistency of 3D data. We generate different views by rotating or permuting the 3D data and utilize asymmetrical 3D kernels to encourage diversified features in different sub-networks. In addition, we propose an uncertainty-weighted label fusion mechanism to estimate the reliability of each view's prediction with Bayesian deep learning. As one view requires the supervision from other views in co-training, our self-adaptive approach computes a confidence score for the prediction of each unlabeled sample in order to assign a reliable pseudo label. Thus, our approach can take advantage of unlabeled data during training. We show the effectiveness of our proposed semi-supervised method on several public datasets from medical image segmentation tasks (NIH pancreas & LiTS liver tumor dataset). Meanwhile, a fully-supervised method based on our approach achieved state-of-the-art performances on both the LiTS liver tumor segmentation and the Medical Segmentation Decathlon (MSD) challenge, demonstrating the robustness and value of our framework, even when fully supervised training is feasible.

Learning visual features from unlabeled image data is an important yet challenging task, which is often achieved by training a model on some annotation-free information. We consider spatial contexts, for which we solve so-called jigsaw puzzles, i.e., each image is cut into grids and then disordered, and the goal is to recover the correct configuration. Existing approaches formulated it as a classification task by defining a fixed mapping from a small subset of configurations to a class set, but these approaches ignore the underlying relationship between different configurations and also limit their applications to more complex scenarios. This paper presents a novel approach which applies to jigsaw puzzles with an arbitrary grid size and dimensionality. We provide a fundamental and generalized principle, that weaker cues are easier to be learned in an unsupervised manner and also transfer better. In the context of puzzle recognition, we use an iterative manner which, instead of solving the puzzle all at once, adjusts the order of the patches in each step until convergence. In each step, we combine both unary and binary features of each patch into a cost function judging the correctness of the current configuration. Our approach, by taking similarity between puzzles into consideration, enjoys a more efficient way of learning visual knowledge. We verify the effectiveness of our approach from two aspects. First, it solves arbitrarily complex puzzles, including high-dimensional puzzles, that prior methods are difficult to handle. Second, it serves as a reliable way of network initialization, which leads to better transfer performance in visual recognition tasks including classification, detection and segmentation.

It is usually hard for a learning system to predict correctly on rare events that never occur in the training data, and there is no exception for segmentation algorithms. Meanwhile, manual inspection of each case to locate the failures becomes infeasible due to the trend of large data scale and limited human resource. Therefore, we build an alarm system that will set off alerts when the segmentation result is possibly unsatisfactory, assuming no corresponding ground truth mask is provided. One plausible solution is to project the segmentation results into a low dimensional feature space; then learn classifiers/regressors to predict their qualities. Motivated by this, in this paper, we learn a feature space using the shape information which is a strong prior shared among different datasets and robust to the appearance variation of input data. The shape feature is captured using a Variational Auto-Encoder (VAE) network that trained with only the ground truth masks. During testing, the segmentation results with bad shapes shall not fit the shape prior well, resulting in large loss values. Thus, the VAE is able to evaluate the quality of segmentation result on unseen data, without using ground truth. Finally, we learn a regressor in the one-dimensional feature space to predict the qualities of segmentation results. Our alarm system is evaluated on several recent state-of-art segmentation algorithms for 3D medical segmentation tasks. Compared with other standard quality assessment methods, our system consistently provides more reliable prediction on the qualities of segmentation results.

In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial information along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-Sørensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.