Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions

Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology

The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.

Machine Learning Meets Meta-Heuristics: Bald Eagle Search Optimization and Red Deer Optimization for Feature Selection in Type II Diabetes Diagnosis

This article investigates the effectiveness of feature extraction and selection techniques in enhancing the performance of classifier accuracy in Type II Diabetes Mellitus (DM) detection using microarray gene data. To address the inherent high dimensionality of the data, three feature extraction (FE) methods are used, namely Short-Time Fourier Transform (STFT), Ridge Regression (RR), and Pearson's Correlation Coefficient (PCC). To further refine the data, meta-heuristic algorithms like Bald Eagle Search Optimization (BESO) and Red Deer Optimization (RDO) are utilized for feature selection. The performance of seven classification techniques, Non-Linear Regression-NLR, Linear Regression-LR, Gaussian Mixture Models-GMMs, Expectation Maximization-EM, Logistic Regression-LoR, Softmax Discriminant Classifier-SDC, and Support Vector Machine with Radial Basis Function kernel-SVM-RBF, are evaluated with and without feature selection. The analysis reveals that the combination of PCC with SVM-RBF achieved a promising accuracy of 92.85% even without feature selection. Notably, employing BESO with PCC and SVM-RBF maintained this high accuracy. However, the highest overall accuracy of 97.14% was achieved when RDO was used for feature selection alongside PCC and SVM-RBF. These findings highlight the potential of feature extraction and selection techniques, particularly RDO with PCC, in improving the accuracy of DM detection using microarray gene data.