Dense regression activation maps for lesion segmentation in CT scans of COVID-19 patients

Modeling Chickpea Productivity with Artificial Image Objects and Convolutional Neural Network

The chickpea plays a significant role in global agriculture and occupies an increasing share in the human diet. The main aim of the research was to develop a model for the prediction of two chickpea productivity traits in the available dataset. Genomic data for accessions were encoded in Artificial Image Objects, and a model for the thousand-seed weight (TSW) and number of seeds per plant (SNpP) prediction was constructed using a Convolutional Neural Network, dictionary learning and sparse coding for feature extraction, and extreme gradient boosting for regression. The model was capable of predicting both traits with an acceptable accuracy of 84-85%. The most important factors for model solution were identified using the dense regression attention maps method. The SNPs important for the SNpP and TSW traits were found in 34 and 49 genes, respectively. Genomic prediction with a constructed model can help breeding programs harness genotypic and phenotypic diversity to more effectively produce varieties with a desired phenotype.

Weakly-Supervised Segmentation-Based Quantitative Characterization of Pulmonary Cavity Lesions in CT Scans

OBJECTIVE

Pulmonary cavity lesion is one of the commonly seen lesions in lung caused by a variety of malignant and non-malignant diseases. Diagnosis of a cavity lesion is commonly based on accurate recognition of the typical morphological characteristics. A deep learning-based model to automatically detect, segment, and quantify the region of cavity lesion on CT scans has potential in clinical diagnosis, monitoring, and treatment efficacy assessment.

METHODS

A weakly-supervised deep learning-based method named CSA2-ResNet was proposed to quantitatively characterize cavity lesions in this paper. The lung parenchyma was firstly segmented using a pretrained 2D segmentation model, and then the output with or without cavity lesions was fed into the developed deep neural network containing hybrid attention modules. Next, the visualized lesion was generated from the activation region of the classification network using gradient-weighted class activation mapping, and image processing was applied for post-processing to obtain the expected segmentation results of cavity lesions. Finally, the automatic characteristic measurement of cavity lesions (e.g., area and thickness) was developed and verified.

RESULTS

the proposed weakly-supervised segmentation method achieved an accuracy, precision, specificity, recall, and F1-score of 98.48%, 96.80%, 97.20%, 100%, and 98.36%, respectively. There is a significant improvement (P < 0.05) compared to other methods. Quantitative characterization of morphology also obtained good analysis effects.

CONCLUSIONS

The proposed easily-trained and high-performance deep learning model provides a fast and effective way for the diagnosis and dynamic monitoring of pulmonary cavity lesions in clinic. Clinical and Translational Impact Statement: This model used artificial intelligence to achieve the detection and quantitative analysis of pulmonary cavity lesions in CT scans. The morphological features revealed in experiments can be utilized as potential indicators for diagnosis and dynamic monitoring of patients with cavity lesions.

Automatic Quantification of COVID-19 Pulmonary Edema by Self-supervised Contrastive Learning

We proposed a self-supervised machine learning method to automatically rate the severity of pulmonary edema in the frontal chest X-ray radiographs (CXR) which could be potentially related to COVID-19 viral pneumonia. For this we use the modified radiographic assessment of lung edema (mRALE) scoring system. The new model was first optimized with the simple Siamese network (SimSiam) architecture where a ResNet-50 pretrained by ImageNet database was used as the backbone. The encoder projected a 2048-dimension embedding as representation features to a downstream fully connected deep neural network for mRALE score prediction. A 5-fold cross-validation with 2,599 frontal CXRs was used to examine the new model's performance with comparison to a non-pretrained SimSiam encoder and a ResNet-50 trained from scratch. The mean absolute error (MAE) of the new model is 5.05 (95%CI 5.03-5.08), the mean squared error (MSE) is 66.67 (95%CI 66.29-67.06), and the Spearman's correlation coefficient (Spearman ρ) to the expert-annotated scores is 0.77 (95%CI 0.75-0.79). All the performance metrics of the new model are superior to the two comparators (P<0.01), and the scores of MSE and Spearman ρ of the two comparators have no statistical difference (P>0.05). The model also achieved a prediction probability concordance of 0.811 and a quadratic weighted kappa of 0.739 with the medical expert annotations in external validation. We conclude that the self-supervised contrastive learning method is an effective strategy for mRALE automated scoring. It provides a new approach to improve machine learning performance and minimize the expert knowledge involvement in quantitative medical image pattern learning.

Emphysema subtyping on thoracic computed tomography scans using deep neural networks

Accurate identification of emphysema subtypes and severity is crucial for effective management of COPD and the study of disease heterogeneity. Manual analysis of emphysema subtypes and severity is laborious and subjective. To address this challenge, we present a deep learning-based approach for automating the Fleischner Society's visual score system for emphysema subtyping and severity analysis. We trained and evaluated our algorithm using 9650 subjects from the COPDGene study. Our algorithm achieved the predictive accuracy at 52%, outperforming a previously published method's accuracy of 45%. In addition, the agreement between the predicted scores of our method and the visual scores was good, where the previous method obtained only moderate agreement. Our approach employs a regression training strategy to generate categorical labels while simultaneously producing high-resolution localized activation maps for visualizing the network predictions. By leveraging these dense activation maps, our method possesses the capability to compute the percentage of emphysema involvement per lung in addition to categorical severity scores. Furthermore, the proposed method extends its predictive capabilities beyond centrilobular emphysema to include paraseptal emphysema subtypes.

Semi-Supervised COVID-19 Volumetric Pulmonary Lesion Estimation on CT Images using Probabilistic Active Contour and CNN Segmentation

Purpose

A semi-supervised two-step methodology is proposed to obtain a volumetric estimation of COVID-19-related lesions on Computed Tomography (CT) images.

Methods

First, damaged tissue was segmented from CT images using a probabilistic active contours approach. Second, lung parenchyma was extracted using a previously trained U-Net. Finally, volumetric estimation of COVID-19 lesions was calculated considering the lung parenchyma masks.

Our approach was validated using a publicly available dataset containing 20 CT COVID-19 images previously labeled and manually segmented. Then, it was applied to 295 COVID-19 patients CT scans admitted to an intensive care unit. We compared the lesion estimation between deceased and survived patients for high and low-resolution images.

Results

A comparable median Dice similarity coefficient of 0.66 for the 20 validation images was achieved. For the 295 images dataset, results show a significant difference in lesion percentages between deceased and survived patients, with a p-value of 9.1×10⁻⁴ in low-resolution and 5.1×10⁻⁵ for high-resolution images. Furthermore, the difference in lesion percentages between high and low-resolution images was 10% on average.

Conclusion

The proposed approach could help estimate the lesion size caused by COVID-19 in CT images and may be considered as an alternative to getting a volumetric segmentation for this novel disease without the requirement of large amounts of COVID-19 labeled data to train an artificial intelligence algorithm. The low variation between the estimated percentage of lesions in high and low-resolution CT images suggests that the proposed approach is robust and It may provide valuable information to differentiate between survived and deceased patients.