Transformers Improve Breast Cancer Diagnosis from Unregistered Multi-View Mammograms

Deep convolutional neural networks (CNNs) have been widely used in various medical imaging tasks. However, due to the intrinsic locality of convolution operation, CNNs generally cannot model long-range dependencies well, which are important for accurately identifying or mapping corresponding breast lesion features computed from unregistered multiple mammograms. This motivates us to leverage the architecture of Multi-view Vision Transformers to capture long-range relationships of multiple mammograms from the same patient in one examination. For this purpose, we employ local Transformer blocks to separately learn patch relationships within four mammograms acquired from two-view (CC/MLO) of two-side (right/left) breasts. The outputs from different views and sides are concatenated and fed into global Transformer blocks, to jointly learn patch relationships between four images representing two different views of the left and right breasts. To evaluate the proposed model, we retrospectively assembled a dataset involving 949 sets of mammograms, which include 470 malignant cases and 479 normal or benign cases. We trained and evaluated the model using a five-fold cross-validation method. Without any arduous preprocessing steps (e.g., optimal window cropping, chest wall or pectoral muscle removal, two-view image registration, etc.), our four-image (two-view-two-side) Transformer-based model achieves case classification performance with an area under ROC curve (AUC = 0.818), which significantly outperforms AUC = 0.784 achieved by the state-of-the-art multi-view CNNs (p = 0.009). It also outperforms two one-view-two-side models that achieve AUC of 0.724 (CC view) and 0.769 (MLO view), respectively. The study demonstrates the potential of using Transformers to develop high-performing computer-aided diagnosis schemes that combine four mammograms.

Virtual Adversarial Training for Semi-supervised Breast Mass Classification

This study aims to develop a novel computer-aided diagnosis (CAD) scheme for mammographic breast mass classification using semi-supervised learning. Although supervised deep learning has achieved huge success across various medical image analysis tasks, its success relies on large amounts of high-quality annotations, which can be challenging to acquire in practice. To overcome this limitation, we propose employing a semi-supervised method, i.e., virtual adversarial training (VAT), to leverage and learn useful information underlying in unlabeled data for better classification of breast masses. Accordingly, our VAT-based models have two types of losses, namely supervised and virtual adversarial losses. The former loss acts as in supervised classification, while the latter loss aims at enhancing model robustness against virtual adversarial perturbation, thus improving model generalizability. To evaluate the performance of our VAT-based CAD scheme, we retrospectively assembled a total of 1024 breast mass images, with equal number of benign and malignant masses. A large CNN and a small CNN were used in this investigation, and both were trained with and without the adversarial loss. When the labeled ratios were 40% and 80%, VAT-based CNNs delivered the highest classification accuracy of 0.740 and 0.760, respectively. The experimental results suggest that the VAT-based CAD scheme can effectively utilize meaningful knowledge from unlabeled data to better classify mammographic breast mass images.

Recent advances and clinical applications of deep learning in medical image analysis

Deep learning has become the mainstream technology in computer vision, and it has received extensive research interest in developing new medical image processing algorithms to support disease detection and diagnosis. As compared to conventional machine learning technologies, the major advantage of deep learning is that models can automatically identify and recognize representative features through the hierarchal model architecture, while avoiding the laborious development of hand-crafted features. In this paper, we reviewed and summarized more than 200 recently published papers to provide a comprehensive overview of applying deep learning methods in various medical image analysis tasks. Especially, we emphasize the latest progress and contributions of state-of-the-art unsupervised and semi-supervised deep learning in medical images, which are summarized based on different application scenarios, including lesion classification, segmentation, detection, and image registration. Additionally, we also discussed the major technical challenges and suggested the possible solutions in future research efforts.

Automatic Pulmonary Artery and Vein Separation Algorithm Based on Multitask Classification Network and Topology Reconstruction in Chest CT Images

With the development of medical computer-aided diagnostic systems, pulmonary artery-vein(A/V) reconstruction plays a crucial role in assisting doctors in preoperative planning for lung cancer surgery. However, distinguishing arterial from venous irrigation in chest CT images remains a challenge due to the similarity and complex structure of the arteries and veins. We propose a novel method for automatic separation of pulmonary arteries and veins from chest CT images. The method consists of three parts. First, global connection information and local feature information are used to construct a complete topological tree and ensure the continuity of vessel reconstruction. Second, the multitask classification network proposed can automatically learn the differences between arteries and veins at different scales to reduce classification errors caused by changes in terminal vessel characteristics. Finally, the topology optimizer considers interbranch and intrabranch topological relationships to maintain spatial consistency to avoid the misclassification of A/V irrigations. We validate the performance of the method on chest CT images. Compared with manual classification, the proposed method achieves an average accuracy of 96.2% on noncontrast chest CT. In addition, the method has been proven to have good generalization, that is, the accuracies of 93.8% and 94.8% are obtained for CT scans from other devices and other modes, respectively. The result of pulmonary artery-vein reconstruction obtained by the proposed method can provide better assistance for preoperative planning of lung cancer surgery.

Coarse-to-fine Airway Segmentation Using Multi information Fusion Network and CNN-based Region Growing

Automatic airway segmentation from chest computed tomography (CT) scans plays an important role in pulmonary disease diagnosis and computer-assisted therapy. However, low contrast at peripheral branches and complex tree-like structures remain as two mainly challenges for airway segmentation. Recent research has illustrated that deep learning methods perform well in segmentation tasks. Motivated by these works, a coarse-to-fine segmentation framework is proposed to obtain a complete airway tree. Our framework segments the overall airway and small branches via the multi-information fusion convolution neural network (Mif-CNN) and the CNN-based region growing, respectively. In Mif-CNN, atrous spatial pyramid pooling (ASPP) is integrated into a u-shaped network, and it can expend the receptive field and capture multi-scale information. Meanwhile, boundary and location information are incorporated into semantic information. These information are fused to help Mif-CNN utilize additional context knowledge and useful features. To improve the performance of the segmentation result, the CNN-based region growing method is designed to focus on obtaining small branches. A voxel classification network (VCN), which can entirely capture the rich information around each voxel, is applied to classify the voxels into airway and non-airway. In addition, a shape reconstruction method is used to refine the airway tree.

Interpretative Computer-aided Lung Cancer Diagnosis: from Radiology Analysis to Malignancy Evaluation

Background and Objective:Computer-aided diagnosis (CAD) systems promote diagnosis effectiveness and alleviate pressure of radiologists. A CAD system for lung cancer diagnosis includes nodule candidate detection and nodule malignancy evaluation. Recently, deep learning-based pulmonary nodule detection has reached satisfactory performance ready for clinical application. However, deep learning-based nodule malignancy evaluation depends on heuristic inference from low-dose computed tomography volume to malignant probability, which lacks clinical cognition. Methods:In this paper, we propose a joint radiology analysis and malignancy evaluation network (R2MNet) to evaluate the pulmonary nodule malignancy via radiology characteristics analysis. Radiological features are extracted as channel descriptor to highlight specific regions of the input volume that are critical for nodule malignancy evaluation. In addition, for model explanations, we propose channel-dependent activation mapping to visualize the features and shed light on the decision process of deep neural network. Results:Experimental results on the LIDC-IDRI dataset demonstrate that the proposed method achieved area under curve of 96.27% on nodule radiology analysis and AUC of 97.52% on nodule malignancy evaluation. In addition, explanations of CDAM features proved that the shape and density of nodule regions were two critical factors that influence a nodule to be inferred as malignant, which conforms with the diagnosis cognition of experienced radiologists. Conclusion:Incorporating radiology analysis with nodule malignant evaluation, the network inference process conforms to the diagnostic procedure of radiologists and increases the confidence of evaluation results. Besides, model interpretation with CDAM features shed light on the regions which DNNs focus on when they estimate nodule malignancy probabilities.

Evaluation of company investment value based on machine learning

In this paper, company investment value evaluation models are established based on comprehensive company information. After data mining and extracting a set of 436 feature parameters, an optimal subset of features is obtained by dimension reduction through tree-based feature selection, followed by the 5-fold cross-validation using XGBoost and LightGBM models. The results show that the Root-Mean-Square Error (RMSE) reached 3.098 and 3.059, respectively. In order to further improve the stability and generalization capability, Bayesian Ridge Regression has been used to train a stacking model based on the XGBoost and LightGBM models. The corresponding RMSE is up to 3.047. Finally, the importance of different features to the LightGBM model is analysed.

Applying a random projection algorithm to optimize machine learning model for breast lesion classification

Machine learning is widely used in developing computer-aided diagnosis (CAD) schemes of medical images. However, CAD usually computes large number of image features from the targeted regions, which creates a challenge of how to identify a small and optimal feature vector to build robust machine learning models. In this study, we investigate feasibility of applying a random projection algorithm to build an optimal feature vector from the initially CAD-generated large feature pool and improve performance of machine learning model. We assemble a retrospective dataset involving 1,487 cases of mammograms in which 644 cases have confirmed malignant mass lesions and 843 have benign lesions. A CAD scheme is first applied to segment mass regions and initially compute 181 features. Then, support vector machine (SVM) models embedded with several feature dimensionality reduction methods are built to predict likelihood of lesions being malignant. All SVM models are trained and tested using a leave-one-case-out cross-validation method. SVM generates a likelihood score of each segmented mass region depicting on one-view mammogram. By fusion of two scores of the same mass depicting on two-view mammograms, a case-based likelihood score is also evaluated. Comparing with the principle component analyses, nonnegative matrix factorization, and Chi-squared methods, SVM embedded with the random projection algorithm yielded a significantly higher case-based lesion classification performance with the area under ROC curve of 0.84+0.01 (p<0.02). The study demonstrates that the random project algorithm is a promising method to generate optimal feature vectors to help improve performance of machine learning models of medical images.

Applying a random projection algorithm to optimize machine learning model for predicting peritoneal metastasis in gastric cancer patients using CT images

Background and Objective: Non-invasively predicting the risk of cancer metastasis before surgery plays an essential role in determining optimal treatment methods for cancer patients (including who can benefit from neoadjuvant chemotherapy). Although developing radiomics based machine learning (ML) models has attracted broad research interest for this purpose, it often faces a challenge of how to build a highly performed and robust ML model using small and imbalanced image datasets. Methods: In this study, we explore a new approach to build an optimal ML model. A retrospective dataset involving abdominal computed tomography (CT) images acquired from 159 patients diagnosed with gastric cancer is assembled. Among them, 121 cases have peritoneal metastasis (PM), while 38 cases do not have PM. A computer-aided detection (CAD) scheme is first applied to segment primary gastric tumor volumes and initially computes 315 image features. Then, two Gradient Boosting Machine (GBM) models embedded with two different feature dimensionality reduction methods, namely, the principal component analysis (PCA) and a random projection algorithm (RPA) and a synthetic minority oversampling technique, are built to predict the risk of the patients having PM. All GBM models are trained and tested using a leave-one-case-out cross-validation method. Results: Results show that the GBM embedded with RPA yielded a significantly higher prediction accuracy (71.2%) than using PCA (65.2%) (p<0.05). Conclusions: The study demonstrated that CT images of the primary gastric tumors contain discriminatory information to predict the risk of PM, and RPA is a promising method to generate optimal feature vector, improving the performance of ML models of medical images.

Improving performance of CNN to predict likelihood of COVID-19 using chest X-ray images with preprocessing algorithms

As the rapid spread of coronavirus disease (COVID-19) worldwide, chest X-ray radiography has also been used to detect COVID-19 infected pneumonia and assess its severity or monitor its prognosis in the hospitals due to its low cost, low radiation dose, and wide accessibility. However, how to more accurately and efficiently detect COVID-19 infected pneumonia and distinguish it from other community-acquired pneumonia remains a challenge. In order to address this challenge, we in this study develop and test a new computer-aided diagnosis (CAD) scheme. It includes several image pre-processing algorithms to remove diaphragms, normalize image contrast-to-noise ratio, and generate three input images, then links to a transfer learning based convolutional neural network (a VGG16 based CNN model) to classify chest X-ray images into three classes of COVID-19 infected pneumonia, other community-acquired pneumonia and normal (non-pneumonia) cases. To this purpose, a publicly available dataset of 8,474 chest X-ray images is used, which includes 415 confirmed COVID-19 infected pneumonia, 5,179 community-acquired pneumonia, and 2,880 non-pneumonia cases. The dataset is divided into two subsets with 90% and 10% of images in each subset to train and test the CNN-based CAD scheme. The testing results achieve 94.0% of overall accuracy in classifying three classes and 98.6% accuracy in detecting Covid-19 infected cases. Thus, the study demonstrates the feasibility of developing a CAD scheme of chest X-ray images and providing radiologists useful decision-making supporting tools in detecting and diagnosis of COVID-19 infected pneumonia.