Taste perception plays a pivotal role in guiding nutrient intake and aiding in the avoidance of potentially harmful substances through five basic tastes - sweet, bitter, umami, salty, and sour. Taste perception originates from molecular interactions in the oral cavity between taste receptors and chemical tastants. Hence, the recognition of taste receptors and the subsequent perception of taste heavily rely on the physicochemical properties of food ingredients. In recent years, several advances have been made towards the development of machine learning-based algorithms to classify chemical compounds’ tastes using their molecular structures. Despite the great efforts, there remains significant room for improvement in developing multi-class models to predict the entire spectrum of basic tastes. Here, we present a multi-class predictor aimed at distinguishing bitter, sweet, and umami, from other taste sensations. The development of a multi-class taste predictor paves the way for a comprehensive understanding of the chemical attributes associated with each fundamental taste. It also opens the potential for integration into the evolving realm of multi-sensory perception, which encompasses visual, tactile, and olfactory sensations to holistically characterize flavour perception. This concept holds promise for introducing innovative methodologies in the rational design of foods, including pre-determining specific tastes and engineering complementary diets to augment traditional pharmacological treatments.

The development of machine learning-based models that can be used for the prediction of severe diseases has been one of the main concerns of the scientific community. The current study seeks to expand a highly sophisticated tool, the Convolutional Neural Networks, making it applicable in multidimensional omics data classification problems and testing the newly introduced method on publicly available transcriptomics and proteomics data. In this study, we introduce Omics-CNN, a Convolutional Neural Network-based pipeline, which couples Convolutional Neural Networks with dimensionality reduction, preprocessing, clustering, and explainability techniques to make them suitable to build highly accurate and interpretable classification models from high-throughput omics data. The developed tool has the potential to classify patients depending on the expression of genetic and clinical factors and identify features that can act as diagnostic biomarkers. Regarding dimensionality reduction, univariate and multivariate techniques were explored and compared. Gradient Weighted Class Activation Mapping analysis was performed to determine the most important features in the classification of the samples after training the model. The newly introduced pipeline was applied to one transcriptomics and one proteomics dataset for the identification of diagnostic models and biosignatures for Ischemic Stroke (IS) and COVID-19 infection, reporting highly accurate biosignatures with accuracies of 96 % and 95.41 %, respectively. Meanwhile, classification models based solely on a small part of attributes provided lower predictive accuracy, but identified compact transcript biosignature (KRT15, VPRBP, TNFRSF4, GORASP2) for Ischemic Stroke and protein biosignature (ADGRB3, VNN2, AGER, CIAPIN1) for Covid-19 infection diagnosis, respectively. Omics-CNN, overcame the inherent problems of applying Convolutional Neural Networks for the training diagnostic models with quantitative omics data, outperforming previous models of machine learning developed using the same datasets for Ischemic Stroke and Covid-19 infection diagnosis, determining the most contributing biomarkers for both diseases.

Purpose: Chronic pain is a life changing condition, and non-opioid treatments have been lately introduced to overcome the addictive nature of opioid therapies and their side effects. In the present study, we explore the potential of machine learning methods to discriminate chronic pain patients into ones who will benefit from such a treatment and ones who will not, aiming to personalize their treatment. Patients and Methods: In the current study, data from the OPERA study were used, with 631 chronic pain patients answering the Brief Pain Inventory (BPI) validated questionnaire along with supplemental questions before and after a follow-up period. A novel machine learning approach combining multi-objective optimization and support vector regression was used to build prediction models which can predict, using responses in the baseline, the four different outcomes of the study: total drugs change, total interference change, total severity change, and total complaints change. Data were split to training (504 patients) and testing (127 patients) sets and all results are measured on the independent test set. Results: The machine learning models extracted in the present study significantly overcame other state of the art machine learning methods which were deployed for comparative purposes. The experimental results indicated that the machine learning models can predict the outcomes of this study with considerably high accuracy (AUC 73.8– 87.2%) and this allowed their incorporation in a decision support system for the selection of the treatment of chronic pain patients. Conclusion: Results of this study revealed the potential of machine learning for an individualized medicine application for chronic pain therapies. Topical analgesics treatment were proven to be, in general, beneficial but carefully selecting with the suggested individualized medicine decision support system was able to decrease by approximately 10% the patients which would have been subscribed with topical analgesics without having benefits from it.

Motivation: Biomarker discovery is one of the most frequent pursuits in bioinformatics and is crucial for precision medicine, disease prognosis, and drug discovery. A common challenge of biomarker discovery applications is the low ratio of samples over features for the selection of a reliable not-redundant subset of features, but despite the development of efficient tree-based classification methods, such as the extreme gradient boosting (XGBoost), this limitation is still relevant. Moreover, existing approaches for optimizing XGBoost do not deal effectively with the class imbalance nature of the biomarker discovery problems, and the presence of multiple conflicting objectives, since they focus on the training of a single-objective model. In the current work, we introduce MEvA-X, a novel hybrid ensemble for feature selection (FS) and classification, combining a niche-based multiobjective evolutionary algorithm (EA) with the XGBoost classifier. MEvA-X deploys a multiobjective EA to optimize the hyperparameters of the classifier and perform FS, identifying a set of Pareto-optimal solutions and optimizing multiple objectives, including classification and model simplicity metrics. Results: The performance of the MEvA-X tool was benchmarked using one omics dataset coming from a microarray gene expression experiment, and one clinical questionnaire-based dataset combined with demographic information. MEvA-X tool outperformed the state-of-the-art methods in the balanced categorization of classes, creating multiple low-complexity models and identifying important nonredundant biomarkers. The best-performing run of MEvA-X for the prediction of weight loss using gene expression data yields a small set of blood circulatory markers which are sufficient for this precision nutrition application but need further validation. Availability and implementation: https://github.com/PanKonstantinos/MEvA-X.

Electroencephalography (EEG) has transitioned from a subjective observational method into a data-intensive analytical field that utilises sophisticated algorithms and mathematical models. This review provides a holistic foundation by detailing the neurophysiological basis, recording techniques, and applications of EEG before providing a rigorous examination of traditional and modern analytical pillars. Statistical and Time-Series Analysis, Spectral and Time-Frequency Analysis, Spatial Analysis and Source Modelling, Connectivity and Network Analysis, and Nonlinear and Chaotic Analysis are explored. Afterwards, while acknowledging the historical role of Machine Learning (ML) and Deep Learning (DL) architectures, such as Support Vector Machines (SVMs) and Convolutional Neural Networks (CNNs), this review shifts the primary focus toward current state-of-the-art Artificial Intelligence (AI) trends. We place emphasis on the emergence of Foundation Models, including Large Language Models (LLMs) and Large Vision Models (LVMs), adapted for high-dimensional neural sequences. Finally, we explore the integration of Generative AI for data augmentation and review Explainable AI (XAI) frameworks designed to bridge the gap between “black-box” decoding and clinical interpretability. We conclude that the next generation of EEG analysis will likely converge into Neuro-Symbolic architectures, synergising the massive generative power of foundation models with the rigorous, rule-based interpretability of classical signal theory.

Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs.