GasHis-Transformer: A Multi-scale Visual Transformer Approach for Gastric Histopathology Image Classification

Existing deep learning methods for diagnosis of gastric cancer commonly use convolutional neural networks (CNN). Recently, the Visual Transformer (VT) has attracted a major attention because of its performance and efficiency, but its applications are mostly in the field of computer vision. In this paper, a multi-scale visual transformer model, referred to as GasHis-Transformer, is proposed for gastric histopathology image classification (GHIC), which enables the automatic classification of microscopic gastric images into abnormal and normal cases. The GasHis-Transformer model consists of two key modules: a global information module (GIM) and a local information module (LIM) to extract pathological features effectively. In our experiments, a public hematoxylin and eosin (H&E) stained gastric histopathology dataset with 280 abnormal or normal images using the GasHis-Transformer model is applied to estimate precision, recall, F1-score, and accuracy on the testing set as 98.0%, 100.0%, 96.0% and 98.0% respectively. Furthermore, a critical study is conducted to evaluate the robustness of GasHis-Transformer according to add ten different noises including adversarial attack and traditional image noise. In addition, a clinically meaningful study is executed to test the gastric cancer identification of GasHis-Transformerwith 420 abnormal images and achieves 96.2% accuracy. Finally, a comparative study is performed to test the generalizability with both H&E and Immunohistochemical (IHC) stained images on a lymphoma image dataset, a breast cancer dataset and a cervical cancer dataset, producing comparable F1-scores (85.6%, 82.8% and 65.7%, respectively) and accuracy (83.9%, 89.4% and 65.7%, respectively) respectively. In conclusion, GasHis-Transformerdemonstrates a high classification performance and shows its significant potential in histopathology image analysis.

Task-Oriented Low-Dose CT Image Denoising

The extensive use of medical CT has raised a public concern over the radiation dose to the patient. Reducing the radiation dose leads to increased CT image noise and artifacts, which can adversely affect not only the radiologists judgement but also the performance of downstream medical image analysis tasks. Various low-dose CT denoising methods, especially the recent deep learning based approaches, have produced impressive results. However, the existing denoising methods are all downstream-task-agnostic and neglect the diverse needs of the downstream applications. In this paper, we introduce a novel Task-Oriented Denoising Network (TOD-Net) with a task-oriented loss leveraging knowledge from the downstream tasks. Comprehensive empirical analysis shows that the task-oriented loss complements other task agnostic losses by steering the denoiser to enhance the image quality in the task related regions of interest. Such enhancement in turn brings general boosts on the performance of various methods for the downstream task. The presented work may shed light on the future development of context-aware image denoising methods.

Image Synthesis for Data Augmentation in Medical CT using Deep Reinforcement Learning

Deep learning has shown great promise for CT image reconstruction, in particular to enable low dose imaging and integrated diagnostics. These merits, however, stand at great odds with the low availability of diverse image data which are needed to train these neural networks. We propose to overcome this bottleneck via a deep reinforcement learning (DRL) approach that is integrated with a style-transfer (ST) methodology, where the DRL generates the anatomical shapes and the ST synthesizes the texture detail. We show that our method bears high promise for generating novel and anatomically accurate high resolution CT images at large and diverse quantities. Our approach is specifically designed to work with even small image datasets which is desirable given the often low amount of image data many researchers have available to them.

SPICE: Semantic Pseudo-labeling for Image Clustering

This paper presents SPICE, a Semantic Pseudo-labeling framework for Image ClustEring. Instead of using indirect loss functions required by the recently proposed methods, SPICE generates pseudo-labels via self-learning and directly uses the pseudo-label-based classification loss to train a deep clustering network. The basic idea of SPICE is to synergize the discrepancy among semantic clusters, the similarity among instance samples, and the semantic consistency of local samples in an embedding space to optimize the clustering network in a semantically-driven paradigm. Specifically, a semantic-similarity-based pseudo-labeling algorithm is first proposed to train a clustering network through unsupervised representation learning. Given the initial clustering results, a local semantic consistency principle is used to select a set of reliably labeled samples, and a semi-pseudo-labeling algorithm is adapted for performance boosting. Extensive experiments demonstrate that SPICE clearly outperforms the state-of-the-art methods on six common benchmark datasets including STL10, Cifar10, Cifar100-20, ImageNet-10, ImageNet-Dog, and Tiny-ImageNet. On average, our SPICE method improves the current best results by about 10% in terms of adjusted rand index, normalized mutual information, and clustering accuracy.

Noise Entangled GAN For Low-Dose CT Simulation

We propose a Noise Entangled GAN (NE-GAN) for simulating low-dose computed tomography (CT) images from a higher dose CT image. First, we present two schemes to generate a clean CT image and a noise image from the high-dose CT image. Then, given these generated images, an NE-GAN is proposed to simulate different levels of low-dose CT images, where the level of generated noise can be continuously controlled by a noise factor. NE-GAN consists of a generator and a set of discriminators, and the number of discriminators is determined by the number of noise levels during training. Compared with the traditional methods based on the projection data that are usually unavailable in real applications, NE-GAN can directly learn from the real and/or simulated CT images and may create low-dose CT images quickly without the need of raw data or other proprietary CT scanner information. The experimental results show that the proposed method has the potential to simulate realistic low-dose CT images.

Noise2Sim -- Similarity-based Self-Learning for Image Denoising

The key idea behind denoising methods is to perform a mean/averaging operation, either locally or non-locally. An observation on classic denoising methods is that non-local mean (NLM) outcomes are typically superior to locally denoised results. Despite achieving the best performance in image denoising, the supervised deep denoising methods require paired noise-clean data which are often unavailable. To address this challenge, Noise2Noise methods are based on the fact that paired noise-clean images can be replaced by paired noise-noise images which are easier to collect. However, in many scenarios the collection of paired noise-noise images are still impractical. To bypass labeled images, Noise2Void methods predict masked pixels from their surroundings in a single noisy image only. It is pitiful that neither Noise2Noise nor Noise2Void methods utilize self-similarities in an image as NLM methods do, while self-similarities/symmetries play a critical role in modern sciences. Here we propose Noise2Sim, an NLM-inspired self-learning method for image denoising. Specifically, Noise2Sim leverages self-similarities of image patches and learns to map between the center pixels of similar patches for self-consistent image denoising. Our statistical analysis shows that Noise2Sim tends to be equivalent to Noise2Noise under mild conditions. To accelerate the process of finding similar image patches, we design an efficient two-step procedure to provide data for Noise2Sim training, which can be iteratively conducted if needed. Extensive experiments demonstrate the superiority of Noise2Sim over Noise2Noise and Noise2Void on common benchmark datasets.

Stabilizing Deep Tomographic Reconstruction Networks

Tomographic image reconstruction with deep learning is an emerging field of applied artificial intelligence but a recent study reveals that deep reconstruction networks, such as well-known AUTOMAP, are unstable for computed tomography (CT) and magnetic resonance imaging (MRI). Specifically, three kinds of instabilities were identified: (1) strong output artefacts from tiny perturbation, (2) poor detection of small features, and (3) decreased performance with increased input data. These instabilities are believed to be from lacking kernel awareness and nontrivial to overcome, but compressed sensing (CS) reconstruction was reported to be stable due to its kernel awareness. Since deep reconstruction may potentially become the main driving force to achieve better image quality, stabilizing deep reconstruction networks is an urgent challenge. Here we propose an Analytic, Compressive, Iterative Deep (ACID) network to fundamentally address this challenge. Instead of only using deep learning or compressed sensing, ACID consists of four modules including deep reconstruction, CS, analytic mapping, and iterative refinement. In our experiments, ACID eliminated all three kinds of instabilities and significantly improved image quality relative to the methods in the aforementioned PNAS study. ACID is only an example of integrating diverse algorithmic ingredients but it has clearly demonstrated that data-driven reconstruction can be stabilized to outperform reconstruction using CS alone. The power of ACID comes from a unique combination of a deep reconstruction network trained on big data, CS via advanced optimization, and iterative refinement that stabilizes the whole workflow. We anticipate that this integrative closed-loop data driven approach will add great value to clinical and other applications.

Deep Learning Predicts Cardiovascular Disease Risks from Lung Cancer Screening Low Dose Computed Tomography

The high risk population of cardiovascular disease (CVD) is simultaneously at high risk of lung cancer. Given the dominance of low dose computed tomography (LDCT) for lung cancer screening, the feasibility of extracting information on CVD from the same LDCT scan would add major value to patients at no additional radiation dose. However, with strong noise in LDCT images and without electrocardiogram (ECG) gating, CVD risk analysis from LDCT is highly challenging. Here we present an innovative deep learning model to address this challenge. Our deep model was trained with 30,286 LDCT volumes and achieved the state-of-the-art performance (area under the curve (AUC) of 0.869) on 2,085 National Lung Cancer Screening Trial (NLST) subjects, and effectively identified patients with high CVD mortality risks (AUC of 0.768). Our deep model was further calibrated against the clinical gold standard CVD risk scores from ECG-gated dedicated cardiac CT, including coronary artery calcification (CAC) score, CAD-RADS score and MESA 10-year CHD risk score from an independent dataset of 106 subjects. In this validation study, our model achieved AUC of 0.942, 0.809 and 0.817 for CAC, CAD-RADS and MESA scores, respectively. Our deep learning model has the potential to convert LDCT for lung cancer screening into dual-screening quantitative tool for CVD risk estimation.