Incremental Learning for Multi-organ Segmentation with Partially Labeled Datasets

There exists a large number of datasets for organ segmentation, which are partially annotated, and sequentially constructed. A typical dataset is constructed at a certain time by curating medical images and annotating the organs of interest. In other words, new datasets with annotations of new organ categories are built over time. To unleash the potential behind these partially labeled, sequentially-constructed datasets, we propose to learn a multi-organ segmentation model through incremental learning (IL). In each IL stage, we lose access to the previous annotations, whose knowledge is assumingly captured by the current model, and gain the access to a new dataset with annotations of new organ categories, from which we learn to update the organ segmentation model to include the new organs. We give the first attempt to conjecture that the different distribution is the key reason for 'catastrophic forgetting' that commonly exists in IL methods, and verify that IL has the natural adaptability to medical image scenarios. Extensive experiments on five open-sourced datasets are conducted to prove the effectiveness of our method and the conjecture mentioned above.

Deep reinforcement learning in medical imaging: A literature review

Deep reinforcement learning (DRL) augments the reinforcement learning framework, which learns a sequence of actions that maximizes the expected reward, with the representative power of deep neural networks. Recent works have demonstrated the great potential of DRL in medicine and healthcare. This paper presents a literature review of DRL in medical imaging. We start with a comprehensive tutorial of DRL, including the latest model-free and model-based algorithms. We then cover existing DRL applications for medical imaging, which are roughly divided into three main categories: (I) parametric medical image analysis tasks including landmark detection, object/lesion detection, registration, and view plane localization; (ii) solving optimization tasks including hyperparameter tuning, selecting augmentation strategies, and neural architecture search; and (iii) miscellaneous applications including surgical gesture segmentation, personalized mobile health intervention, and computational model personalization. The paper concludes with discussions of future perspectives.

A Hierarchical Feature Constraint to Camouflage Medical Adversarial Attacks

Deep neural networks (DNNs) for medical images are extremely vulnerable to adversarial examples (AEs), which poses security concerns on clinical decision making. Luckily, medical AEs are also easy to detect in hierarchical feature space per our study herein. To better understand this phenomenon, we thoroughly investigate the intrinsic characteristic of medical AEs in feature space, providing both empirical evidence and theoretical explanations for the question: why are medical adversarial attacks easy to detect? We first perform a stress test to reveal the vulnerability of deep representations of medical images, in contrast to natural images. We then theoretically prove that typical adversarial attacks to binary disease diagnosis network manipulate the prediction by continuously optimizing the vulnerable representations in a fixed direction, resulting in outlier features that make medical AEs easy to detect. However, this vulnerability can also be exploited to hide the AEs in the feature space. We propose a novel hierarchical feature constraint (HFC) as an add-on to existing adversarial attacks, which encourages the hiding of the adversarial representation within the normal feature distribution. We evaluate the proposed method on two public medical image datasets, namely {Fundoscopy} and {Chest X-Ray}. Experimental results demonstrate the superiority of our adversarial attack method as it bypasses an array of state-of-the-art adversarial detectors more easily than competing attack methods, supporting that the great vulnerability of medical features allows an attacker more room to manipulate the adversarial representations.

CT Film Recovery via Disentangling Geometric Deformation and Illumination Variation: Simulated Datasets and Deep Models

While medical images such as computed tomography (CT) are stored in DICOM format in hospital PACS, it is still quite routine in many countries to print a film as a transferable medium for the purposes of self-storage and secondary consultation. Also, with the ubiquitousness of mobile phone cameras, it is quite common to take pictures of the CT films, which unfortunately suffer from geometric deformation and illumination variation. In this work, we study the problem of recovering a CT film, which marks the first attempt in the literature, to the best of our knowledge. We start with building a large-scale head CT film database CTFilm20K, consisting of approximately 20,000 pictures, using the widely used computer graphics software Blender. We also record all accompanying information related to the geometric deformation (such as 3D coordinate, depth, normal, and UV maps) and illumination variation (such as albedo map). Then we propose a deep framework to disentangle geometric deformation and illumination variation using the multiple maps extracted from the CT films to collaboratively guide the recovery process. Extensive experiments on simulated and real images demonstrate the superiority of our approach over the previous approaches. We plan to open source the simulated images and deep models for promoting the research on CT film recovery (https://anonymous.4open.science/r/e6b1f6e3-9b36-423f-a225-55b7d0b55523/).

Deep Learning to Segment Pelvic Bones: Large-scale CT Datasets and Baseline Models

Purpose: Pelvic bone segmentation in CT has always been an essential step in clinical diagnosis and surgery planning of pelvic bone diseases. Existing methods for pelvic bone segmentation are either hand-crafted or semi-automatic and achieve limited accuracy when dealing with image appearance variations due to the multi-site domain shift, the presence of contrasted vessels, coprolith and chyme, bone fractures, low dose, metal artifacts, etc. Due to the lack of a large-scale pelvic CT dataset with annotations, deep learning methods are not fully explored. Methods: In this paper, we aim to bridge the data gap by curating a large pelvic CT dataset pooled from multiple sources and different manufacturers, including 1, 184 CT volumes and over 320, 000 slices with different resolutions and a variety of the above-mentioned appearance variations. Then we propose for the first time, to the best of our knowledge, to learn a deep multi-class network for segmenting lumbar spine, sacrum, left hip, and right hip, from multiple-domain images simultaneously to obtain more effective and robust feature representations. Finally, we introduce a post-processing tool based on the signed distance function (SDF) to eliminate false predictions while retaining correctly predicted bone fragments. Results: Extensive experiments on our dataset demonstrate the effectiveness of our automatic method, achieving an average Dice of 0.987 for a metal-free volume. SDF post-processor yields a decrease of 10.5% in hausdorff distance by maintaining important bone fragments in post-processing phase. Conclusion: We believe this large-scale dataset will promote the development of the whole community and plan to open source the images, annotations, codes, and trained baseline models at this URL1.

Aggregative Self-Supervised Feature Learning

Self-supervised learning (SSL) is an efficient approach that addresses the issue of annotation shortage. The key part in SSL is its proxy task that defines the supervisory signals and drives the learning toward effective feature representations. However, most SSL approaches usually focus on a single proxy task, which greatly limits the expressive power of the learned features and therefore deteriorates the network generalization capacity. In this regard, we hereby propose three strategies of aggregation in terms of complementarity of various forms to boost the robustness of self-supervised learned features. In spatial context aggregative SSL, we contribute a heuristic SSL method that integrates two ad-hoc proxy tasks with spatial context complementarity, modeling global and local contextual features, respectively. We then propose a principled framework of multi-task aggregative self-supervised learning to form a unified representation, with an intent of exploiting feature complementarity among different tasks. Finally, in self-aggregative SSL, we propose to self-complement an existing proxy task with an auxiliary loss function based on a linear centered kernel alignment metric, which explicitly promotes the exploring of where are uncovered by the features learned from a proxy task at hand to further boost the modeling capability. Our extensive experiments on 2D natural image and 3D medical image classification tasks under limited annotation scenarios confirm that the proposed aggregation strategies successfully boost the classification accuracy.

Label-Free Segmentation of COVID-19 Lesions in Lung CT

Scarcity of annotated images hampers the building of automated solution for reliable COVID-19 diagnosis and evaluation from CT. To alleviate the burden of data annotation, we herein present a label-free approach for segmenting COVID-19 lesions in CT via pixel-level anomaly modeling that mines out the relevant knowledge from normal CT lung scans. Our modeling is inspired by the observation that the parts of tracheae and vessels, which lay in the high-intensity range where lesions belong to, exhibit strong patterns. To facilitate the learning of such patterns at a pixel level, we synthesize `lesions' using a set of surprisingly simple operations and insert the synthesized `lesions' into normal CT lung scans to form training pairs, from which we learn a normalcy-converting network (NormNet) that turns an 'abnormal' image back to normal. Our experiments on three different datasets validate the effectiveness of NormNet, which conspicuously outperforms a variety of unsupervised anomaly detection (UAD) methods.

Limited View Tomographic Reconstruction Using a Deep Recurrent Framework with Residual Dense Spatial-Channel Attention Network and Sinogram Consistency

Limited view tomographic reconstruction aims to reconstruct a tomographic image from a limited number of sinogram or projection views arising from sparse view or limited angle acquisitions that reduce radiation dose or shorten scanning time. However, such a reconstruction suffers from high noise and severe artifacts due to the incompleteness of sinogram. To derive quality reconstruction, previous state-of-the-art methods use UNet-like neural architectures to directly predict the full view reconstruction from limited view data; but these methods leave the deep network architecture issue largely intact and cannot guarantee the consistency between the sinogram of the reconstructed image and the acquired sinogram, leading to a non-ideal reconstruction. In this work, we propose a novel recurrent reconstruction framework that stacks the same block multiple times. The recurrent block consists of a custom-designed residual dense spatial-channel attention network. Further, we develop a sinogram consistency layer interleaved in our recurrent framework in order to ensure that the sampled sinogram is consistent with the sinogram of the intermediate outputs of the recurrent blocks. We evaluate our methods on two datasets. Our experimental results on AAPM Low Dose CT Grand Challenge datasets demonstrate that our algorithm achieves a consistent and significant improvement over the existing state-of-the-art neural methods on both limited angle reconstruction (over 5dB better in terms of PSNR) and sparse view reconstruction (about 4dB better in term of PSNR). In addition, our experimental results on Deep Lesion datasets demonstrate that our method is able to generate high-quality reconstruction for 8 major lesion types.

A review of deep learning in medical imaging: Image traits, technology trends, case studies with progress highlights, and future promises

Since its renaissance, deep learning has been widely used in various medical imaging tasks and has achieved remarkable success in many medical imaging applications, thereby propelling us into the so-called artificial intelligence (AI) era. It is known that the success of AI is mostly attributed to the availability of big data with annotations for a single task and the advances in high performance computing. However, medical imaging presents unique challenges that confront deep learning approaches. In this survey paper, we first highlight both clinical needs and technical challenges in medical imaging and describe how emerging trends in deep learning are addressing these issues. We cover the topics of network architecture, sparse and noisy labels, federating learning, interpretability, uncertainty quantification, etc. Then, we present several case studies that are commonly found in clinical practice, including digital pathology and chest, brain, cardiovascular, and abdominal imaging. Rather than presenting an exhaustive literature survey, we instead describe some prominent research highlights related to these case study applications. We conclude with a discussion and presentation of promising future directions.