Boosting t-SNE Efficiency for Sequencing Data: Insights from Kernel Selection

Dimensionality reduction techniques are essential for visualizing and analyzing high-dimensional biological sequencing data. t-distributed Stochastic Neighbor Embedding (t-SNE) is widely used for this purpose, traditionally employing the Gaussian kernel to compute pairwise similarities. However, the Gaussian kernel's lack of data-dependence and computational overhead limit its scalability and effectiveness for categorical biological sequences. Recent work proposed the isolation kernel as an alternative, yet it may not optimally capture sequence similarities. In this study, we comprehensively evaluate nine different kernel functions for t-SNE applied to molecular sequences, using three embedding methods: One-Hot Encoding, Spike2Vec, and minimizers. Through both subjective visualization and objective metrics (including neighborhood preservation scores), we demonstrate that the cosine similarity kernel in general outperforms other kernels, including Gaussian and isolation kernels, achieving superior runtime efficiency and better preservation of pairwise distances in low-dimensional space. We further validate our findings through extensive classification and clustering experiments across six diverse biological datasets (Spike7k, Host, ShortRead, Rabies, Genome, and Breast Cancer), employing multiple machine learning algorithms and evaluation metrics. Our results show that kernel selection significantly impacts not only visualization quality but also downstream analytical tasks, with the cosine similarity kernel providing the most robust performance across different data types and embedding strategies, making it particularly suitable for large-scale biological sequence analysis.

EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis

Cardiac arrest is one of the biggest global health problems, and early identification and management are key to enhancing the patient's prognosis. In this paper, we propose a novel framework that combines an EfficientNet-based deep learning model with a digital twin system to improve the early detection and analysis of cardiac arrest. We use compound scaling and EfficientNet to learn the features of cardiovascular images. In parallel, the digital twin creates a realistic and individualized cardiovascular system model of the patient based on data received from the Internet of Things (IoT) devices attached to the patient, which can help in the constant assessment of the patient and the impact of possible treatment plans. As shown by our experiments, the proposed system is highly accurate in its prediction abilities and, at the same time, efficient. Combining highly advanced techniques such as deep learning and digital twin (DT) technology presents the possibility of using an active and individual approach to predicting cardiac disease.

Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based Computed Tomography Scan Analysis

The application of Digital Twin (DT) technology and Federated Learning (FL) has great potential to change the field of biomedical image analysis, particularly for Computed Tomography (CT) scans. This paper presents Federated Transfer Learning (FTL) as a new Digital Twin-based CT scan analysis paradigm. FTL uses pre-trained models and knowledge transfer between peer nodes to solve problems such as data privacy, limited computing resources, and data heterogeneity. The proposed framework allows real-time collaboration between cloud servers and Digital Twin-enabled CT scanners while protecting patient identity. We apply the FTL method to a heterogeneous CT scan dataset and assess model performance using convergence time, model accuracy, precision, recall, F1 score, and confusion matrix. It has been shown to perform better than conventional FL and Clustered Federated Learning (CFL) methods with better precision, accuracy, recall, and F1-score. The technique is beneficial in settings where the data is not independently and identically distributed (non-IID), and it offers reliable, efficient, and secure solutions for medical diagnosis. These findings highlight the possibility of using FTL to improve decision-making in digital twin-based CT scan analysis, secure and efficient medical image analysis, promote privacy, and open new possibilities for applying precision medicine and smart healthcare systems.