Developing Sustainable Classification of Diseases via Deep Learning and Semi-Supervised Learning

Transformer Architecture and Attention Mechanisms in Genome Data Analysis: A Comprehensive Review

The emergence and rapid development of deep learning, specifically transformer-based architectures and attention mechanisms, have had transformative implications across several domains, including bioinformatics and genome data analysis. The analogous nature of genome sequences to language texts has enabled the application of techniques that have exhibited success in fields ranging from natural language processing to genomic data. This review provides a comprehensive analysis of the most recent advancements in the application of transformer architectures and attention mechanisms to genome and transcriptome data. The focus of this review is on the critical evaluation of these techniques, discussing their advantages and limitations in the context of genome data analysis. With the swift pace of development in deep learning methodologies, it becomes vital to continually assess and reflect on the current standing and future direction of the research. Therefore, this review aims to serve as a timely resource for both seasoned researchers and newcomers, offering a panoramic view of the recent advancements and elucidating the state-of-the-art applications in the field. Furthermore, this review paper serves to highlight potential areas of future investigation by critically evaluating studies from 2019 to 2023, thereby acting as a stepping-stone for further research endeavors.

Machine Learning Methods for Small Data Challenges in Molecular Science

Small data are often used in scientific and engineering research due to the presence of various constraints, such as time, cost, ethics, privacy, security, and technical limitations in data acquisition. However, big data have been the focus for the past decade, small data and their challenges have received little attention, even though they are technically more severe in machine learning (ML) and deep learning (DL) studies. Overall, the small data challenge is often compounded by issues, such as data diversity, imputation, noise, imbalance, and high-dimensionality. Fortunately, the current big data era is characterized by technological breakthroughs in ML, DL, and artificial intelligence (AI), which enable data-driven scientific discovery, and many advanced ML and DL technologies developed for big data have inadvertently provided solutions for small data problems. As a result, significant progress has been made in ML and DL for small data challenges in the past decade. In this review, we summarize and analyze several emerging potential solutions to small data challenges in molecular science, including chemical and biological sciences. We review both basic machine learning algorithms, such as linear regression, logistic regression (LR), k-nearest neighbor (KNN), support vector machine (SVM), kernel learning (KL), random forest (RF), and gradient boosting trees (GBT), and more advanced techniques, including artificial neural network (ANN), convolutional neural network (CNN), U-Net, graph neural network (GNN), Generative Adversarial Network (GAN), long short-term memory (LSTM), autoencoder, transformer, transfer learning, active learning, graph-based semi-supervised learning, combining deep learning with traditional machine learning, and physical model-based data augmentation. We also briefly discuss the latest advances in these methods. Finally, we conclude the survey with a discussion of promising trends in small data challenges in molecular science.

A Lightweight Convolutional Neural Network Architecture Applied for Bone Metastasis Classification in Nuclear Medicine: A Case Study on Prostate Cancer Patients

Bone metastasis is among the most frequent in diseases to patients suffering from metastatic cancer, such as breast or prostate cancer. A popular diagnostic method is bone scintigraphy where the whole body of the patient is scanned. However, hot spots that are presented in the scanned image can be misleading, making the accurate and reliable diagnosis of bone metastasis a challenge. Artificial intelligence can play a crucial role as a decision support tool to alleviate the burden of generating manual annotations on images and therefore prevent oversights by medical experts. So far, several state-of-the-art convolutional neural networks (CNN) have been employed to address bone metastasis diagnosis as a binary or multiclass classification problem achieving adequate accuracy (higher than 90%). However, due to their increased complexity (number of layers and free parameters), these networks are severely dependent on the number of available training images that are typically limited within the medical domain. Our study was dedicated to the use of a new deep learning architecture that overcomes the computational burden by using a convolutional neural network with a significantly lower number of floating-point operations (FLOPs) and free parameters. The proposed lightweight look-behind fully convolutional neural network was implemented and compared with several well-known powerful CNNs, such as ResNet50, VGG16, Inception V3, Xception, and MobileNet on an imaging dataset of moderate size (778 images from male subjects with prostate cancer). The results prove the superiority of the proposed methodology over the current state-of-the-art on identifying bone metastasis. The proposed methodology demonstrates a unique potential to revolutionize image-based diagnostics enabling new possibilities for enhanced cancer metastasis monitoring and treatment.