Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access.

Large chest X-rays (CXR) datasets have been collected to train deep learning models to detect thorax pathology on CXR. However, most CXR datasets are from single-center studies and the collected pathologies are often imbalanced. The aim of this study was to automatically construct a public, weakly-labeled CXR database from articles in PubMed Central Open Access (PMC-OA) and to assess model performance on CXR pathology classification by using this database as additional training data. Our framework includes text extraction, CXR pathology verification, subfigure separation, and image modality classification. We have extensively validated the utility of the automatically generated image database on thoracic disease detection tasks, including Hernia, Lung Lesion, Pneumonia, and pneumothorax. We pick these diseases due to their historically poor performance in existing datasets: the NIH-CXR dataset (112,120 CXR) and the MIMIC-CXR dataset (243,324 CXR). We find that classifiers fine-tuned with additional PMC-CXR extracted by the proposed framework consistently and significantly achieved better performance than those without (e.g., Hernia: 0.9335 vs 0.9154; Lung Lesion: 0.7394 vs. 0.7207; Pneumonia: 0.7074 vs. 0.6709; Pneumothorax 0.8185 vs. 0.7517, all in AUC with p< 0.0001) for CXR pathology detection. In contrast to previous approaches that manually submit the medical images to the repository, our framework can automatically collect figures and their accompanied figure legends. Compared to previous studies, the proposed framework improved subfigure segmentation and incorporates our advanced self-developed NLP technique for CXR pathology verification. We hope it complements existing resources and improves our ability to make biomedical image data findable, accessible, interoperable, and reusable.

A new classification method for diagnosing COVID-19 pneumonia based on joint CNN features of chest X-ray images and parallel pyramid MLP-mixer module.

During the past three years, the coronavirus disease 2019 (COVID-19) has swept the world. The rapid and accurate recognition of covid-19 pneumonia are ,therefore, of great importance. To handle this problem, we propose a new pipeline of deep learning framework for diagnosing COVID-19 pneumonia via chest X-ray images from normal, COVID-19, and other pneumonia patients. In detail, the self-trained YOLO-v4 network was first used to locate and segment the thoracic region, and the output images were scaled to the same size. Subsequently, the pre-trained convolutional neural network was adopted to extract the features of X-ray images from 13 convolutional layers, which were fused with the original image to form a 14-dimensional image matrix. It was then put into three parallel pyramid multi-layer perceptron (MLP)-Mixer modules for comprehensive feature extraction through spatial fusion and channel fusion based on different scales so as to grasp more extensive feature correlation. Finally, by combining all image features from the 14-channel output, the classification task was achieved using two fully connected layers as well as Softmax classifier for classification. Extensive simulations based on a total of 4099 chest X-ray images were conducted to verify the effectiveness of the proposed method. Experimental results indicated that our proposed method can achieve the best performance in almost all cases, which is good for auxiliary diagnosis of COVID-19 and has great clinical application potential.

Supervised Pretraining through Contrastive Categorical Positive Samplings to Improve COVID-19 Mortality Prediction.

Clinical EHR data is naturally heterogeneous, where it contains abundant sub-phenotype. Such diversity creates challenges for outcome prediction using a machine learning model since it leads to high intra-class variance. To address this issue, we propose a supervised pre-training model with a unique embedded k-nearest-neighbor positive sampling strategy. We demonstrate the enhanced performance value of this framework theoretically and show that it yields highly competitive experimental results in predicting patient mortality in real-world COVID-19 EHR data with a total of over 7,000 patients admitted to a large, urban health system. Our method achieves a better AUROC prediction score of 0.872, which outperforms the alternative pre-training models and traditional machine learning methods. Additionally, our method performs much better when the training data size is small (345 training instances).