Cross-attention enables deep learning on limited omics-imaging-clinical data of 130 lung cancer patients.

Deep-learning tools that extract prognostic factors derived from multi-omics data have recently contributed to individualized predictions of survival outcomes. However, the limited size of integrated omics-imaging-clinical datasets poses challenges. Here, we propose two biologically interpretable and robust deep-learning architectures for survival prediction of non-small cell lung cancer (NSCLC) patients, learning simultaneously from computed tomography (CT) scan images, gene expression data, and clinical information. The proposed models integrate patient-specific clinical, transcriptomic, and imaging data and incorporate Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway information, adding biological knowledge within the learning process to extract prognostic gene biomarkers and molecular pathways. While both models accurately stratify patients in high- and low-risk groups when trained on a dataset of only 130 patients, introducing a cross-attention mechanism in a sparse autoencoder significantly improves the performance, highlighting tumor regions and NSCLC-related genes as potential biomarkers and thus offering a significant methodological advancement when learning from small imaging-omics-clinical samples.

Microaneurysm detection in fundus images using a two-step convolutional neural network.

BACKGROUND AND OBJECTIVES: Diabetic retinopathy (DR) is the leading cause of blindness worldwide, and therefore its early detection is important in order to reduce disease-related eye injuries. DR is diagnosed by inspecting fundus images. Since microaneurysms (MA) are one of the main symptoms of the disease, distinguishing this complication within the fundus images facilitates early DR detection. In this paper, an automatic analysis of retinal images using convolutional neural network (CNN) is presented. METHODS: Our method incorporates a novel technique utilizing a two-stage process with two online datasets which results in accurate detection while solving the imbalance data problem and decreasing training time in comparison with previous studies. We have implemented our proposed CNNs using the Keras library. RESULTS: In order to evaluate our proposed method, an experiment was conducted on two standard publicly available datasets, i.e., Retinopathy Online Challenge dataset and E-Ophtha-MA dataset. Our results demonstrated a promising sensitivity value of about 0.8 for an average of >6 false positives per image, which is competitive with state of the art approaches. CONCLUSION: Our method indicates significant improvement in MA-detection using retinal fundus images for monitoring diabetic retinopathy.

A new dataset of computed-tomography angiography images for computer-aided detection of pulmonary embolism.

The lack of publicly available datasets of computed-tomography angiography (CTA) images for pulmonary embolism (PE) is a problem felt by physicians and researchers. Although a number of computer-aided detection (CAD) systems have been developed for PE diagnosis, their performance is often evaluated using private datasets. In this paper, we introduce a new public dataset called FUMPE (standing for Ferdowsi University of Mashhad's PE dataset) which consists of three-dimensional PE-CTA images of 35 different subjects with 8792 slices in total. For each benchmark image, two expert radiologists provided the ground-truth with the assistance of a semi-automated image processing software tool. FUMPE is a challenging benchmark for CAD methods because of the large number (i.e., 3438) of PE regions and, more especially, because of the location of most of them (i.e., 67%) in lung peripheral arteries. Moreover, due to the reporting of the Qanadli score for each PE-CTA image, FUMPE is the first public dataset which can be used for the analysis of mortality and morbidity risks associated with PE. We also report some complementary prognosis information for each subject.