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In the modern era of medicine, advancements in data science and biomedical technologies have revolutionized our understanding of diseases. Cancer, being a complex disease, has particularly benefited from the wealth of molecular data available, which can now be analyzed using cutting-edge artificial intelligence (AI) and information science methods. In this context, recent studies have increasingly recognized chronic stress as a significant factor in cancer progression. Utilizing computational methods to address this matter has demonstrated encouraging advancements, providing a hopeful outlook in our efforts to combat cancer. This review focuses on recent computational approaches in understanding the molecular links between stress and cancer metastasis. Specifically, we explore the utilization of single-cell data, an innovative technique in DNA sequencing that allows for detailed analysis. Additionally, we explore the application of AI and data mining techniques to these complex and large-scale datasets. Our findings underscore the potential of these computational pipelines to unravel the intricate relationship between stress and cancer metastasis. However, it is important to note that this field is still in its early stages, and we anticipate a proliferation of similar approaches in the near future, further advancing our understanding and treatment of cancer.

The rapid advancement of high-throughput technologies has led to the generation of vast amounts of omics data, including genomics, epigenomics, and metabolomics. Integrating these diverse datasets has become essential for gaining comprehensive insights into complex biological systems and enhancing personalized healthcare solutions. This critical review examines the current state of multi-omics data integration platforms, highlighting both the strengths and limitations of existing tools. By evaluating the latest digital platforms, such as GraphOmics, OmicsAnalyst, and others, the paper explores how they support seamless integration and analysis of omics data in healthcare applications. Special attention is given to their role in clinical decision-making, disease prediction, and personalized medicine, with a focus on their interoperability, scalability, and usability. The review also discusses the challenges these platforms face, such as data complexity, standardization issues, and the need for improved machine learning and AI-based analytics. Finally, the paper proposes directions for future research and development, emphasizing the importance of more advanced, user-friendly, and secure platforms that can better serve comprehensive healthcare needs.

Lip reading, the art of deciphering spoken words from the visual cues of lip movements, has garnered significant interest for its potential applications in diverse fields, including assistive technologies, human–computer interaction, and security systems. With the rapid advancements in technology and the increasing emphasis on non-verbal communication methods, the significance of lip reading has expanded beyond its traditional boundaries. These technological advancements have led to the generation of large-scale and complex datasets, necessitating the use of cutting-edge deep learning tools that are adept at handling such intricacies. In this study, we propose an innovative approach combining 3D Convolutional Neural Networks (CNNs) and Long Short-Term Memory (LSTM) networks to tackle the challenging task of word recognition from lip movements. Our research leverages a meticulously curated dataset, named MobLip, encompassing various speech patterns, speakers, and environmental conditions. The synergy between the spatial information extracted by 3D CNNs and the temporal dynamics captured by LSTMs yields impressive results, achieving an accuracy rate of up to 87.5%, showcasing robustness to lighting variations and speaker diversity. Comparative experiments demonstrate our model’s superiority over existing lip-reading approaches, underlining its potential for real-world deployment. Furthermore, we discuss ethical considerations and propose avenues for future research, such as multimodal integration with audio data and expanded language support. In conclusion, our 3D CNN-LSTM architecture presents a promising solution to the complex problem of word recognition from lip movements, contributing to the advancement of communication technology and opening doors to innovative applications in an increasingly visual world.

(1) Background: Parkinson’s disease (PD) is a progressively worsening neurodegenerative disorder affecting movement, mental well-being, sleep, and pain. While no cure exists, treatments like hyperbaric oxygen therapy (HBOT) offer potential relief. However, the molecular biology perspective, especially when intertwined with machine learning dynamics, remains underexplored. (2) Methods: We employed machine learning techniques to analyze single-cell RNA-seq data from human PD cell samples. This approach aimed to identify pivotal genes associated with PD and understand their relationship with HBOT. (3) Results: Our analysis indicated genes such as MAP2, CAP2, and WSB1, among others, as being crucially linked with Parkinson’s disease (PD) and showed their significant correlation with Hyperbaric oxygen therapy (HBOT) indicatively. This suggests that certain genomic factors might influence the efficacy of HBOT in PD treatment. (4) Conclusions: HBOT presents promising therapeutic potential for Parkinson’s disease, with certain genomic factors playing a pivotal role in its efficacy. Our findings emphasize the need for further machine learning-driven research harnessing diverse omics data to better understand and treat PD.

The progressive aging of the global population and the high impact of neurodegenerative diseases, such as Alzheimer’s disease (AD), underscore the urgent need for innovative diagnostic and therapeutic strategies. AD, the most prevalent neurodegenerative disorder among the elderly, is expected to affect 75 million people in developing countries by 2030. Despite extensive research, the precise etiology of AD remains elusive due to its heterogeneity and complexity. The key pathological features of AD, including amyloid-beta plaques and hyperphosphorylated tau protein, are established years before clinical symptoms appear. Recent studies highlight the pivotal role of neuroinflammation in AD pathogenesis, with the chronic activation of the brain’s immune system contributing to the disease’s progression. Pro-inflammatory cytokines, such as TNF-α, IL-1β, and IL-6, are elevated in AD and mild cognitive impairment (MCI) patients, suggesting a strong link between peripheral inflammation and CNS degeneration. There is a pressing need for minimally invasive, cost-effective diagnostic methods. Buccal mucosa cells and saliva, which share an embryological origin with the CNS, show promise for AD diagnosis and prognosis. This study integrates cellular observations with advanced data processing and machine learning to identify significant biomarkers and patterns, aiming to enhance the early diagnosis and prevention strategies for AD.

Real-world problems often exhibit complex relationships and dependencies, which can be effectively captured by graph learning systems. Graph attention networks (GATs) have emerged as a powerful and versatile framework in this direction, inspiring numerous extensions and applications in several areas. In this review, we present a thorough examination of GATs, covering both diverse approaches and a wide range of applications. We examine the principal GAT-based categories, including Global Attention Networks, Multi-Layer Architectures, graph-embedding techniques, Spatial Approaches, and Variational Models. Furthermore, we delve into the diverse applications of GATs in various systems such as recommendation systems, image analysis, medical domain, sentiment analysis, and anomaly detection. This review seeks to act as a navigational reference for researchers and practitioners aiming to emphasize the capabilities and prospects of GATs.

Advancements in molecular biology have revolutionized our understanding of complex diseases, with Alzheimer’s disease being a prime example. Single-cell sequencing, currently the most suitable technology, facilitates profoundly detailed disease analysis at the cellular level. Prior research has established that the pathology of Alzheimer’s disease varies across different brain regions and cell types. In parallel, only machine learning has the capacity to address the myriad challenges presented by such studies, where the integration of large-scale data and numerous experiments is required to extract meaningful knowledge. Our methodology utilizes single-cell RNA sequencing data from healthy and Alzheimer’s disease (AD) samples, focused on the cortex and hippocampus regions in mice. We designed three distinct case studies and implemented an ensemble feature selection approach through machine learning, also performing an analysis of distinct age-related datasets to unravel age-specific effects, showing differential gene expression patterns within each condition. Important evidence was reported, such as enrichment in central nervous system development and regulation of oligodendrocyte differentiation between the hippocampus and cortex of 6-month-old AD mice as well as regulation of epinephrine secretion and dendritic spine morphogenesis in 15-month-old AD mice. Our outcomes from all three of our case studies illustrate the capacity of machine learning strategies when applied to single-cell data, revealing critical insights into Alzheimer’s disease.

Alzheimer’s disease is one of the leading causes of death globally, significantly impacting countless families and communities. In parallel, recent advancements in molecular biology and network approaches, guided by the Network Medicine perspective, offer promising outcomes for Alzheimer’s disease research and treatment. In this study, we aim to discover candidate therapies for AD through drug repurposing. We combined a protein-protein interaction (PPI) network with drug-target interactions. Experimentally validated PPI data were collected from the PICKLE meta-database, while drugs and their protein targets were sourced from the DrugBank database. Then, based on RNA-Seq data, we first assigned weights to edges to indicate co-expression, and secondly, estimated differential gene expression to select a subset of genes potentially related to the disease. Finally, small subgraphs (modules) were extracted from the graph, centered on the genes of interest. The analysis revealed that even if there is no drug targeting several genes of interest directly, an existing drug might target a neighboring node, thus indirectly affecting the aforementioned genes. Our approach offers a promising method for treating various diseases by repurposing existing drugs, thereby reducing the cost and time of experimental procedures and paving the way for more precise Network Medicine strategies.

Mild Cognitive Impairment (MCI) is a cognitive state frequently observed in older adults, characterized by significant alterations in memory, thinking, and reasoning abilities that extend beyond typical cognitive decline. It is worth noting that around 10–15% of individuals with MCI are projected to develop Alzheimer’s disease, effectively positioning MCI as an early stage of Alzheimer’s. In this study, a novel approach is presented involving the utilization of eXtreme Gradient Boosting to predict the onset of Alzheimer’s disease during the MCI stage. The methodology entails utilizing data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Through the analysis of longitudinal data, spanning from the baseline visit to the 12-month follow-up, a predictive model was constructed. The proposed model calculates, over a 36-month period, the likelihood of progression from MCI to Alzheimer’s disease, achieving an accuracy rate of 85%. To further enhance the precision of the model, this study implements feature selection using the Recursive Feature Elimination technique. Additionally, the Shapley method is employed to provide insights into the model’s decision-making process, thereby augmenting the transparency and interpretability of the predictions.

Cancer remains a pervasive and formidable disease within modern societies, necessitating the utilization of advanced techniques in both diagnosis and therapy. Molecular biology has emerged as a crucial tool in deciphering the underlying biological mechanisms that contribute to various types of cancer. Notably, single-cell sequencing has garnered significant attention as a state-of-the-art method for profiling gene expression in individual cells, unveiling previously concealed mechanisms and biological phenomena. With the abundance of single-cell datasets available, there is a pressing need to integrate related datasets into larger ones to enhance our understanding of biological processes and augment predictive capabilities. In this study, we investigated the impact of gene selection, achieved through the implementation of feature selection techniques, on the integration of single-cell datasets. By systematically exploring the effects of gene selection, we aim to enhance the integration process, leading to improved biological insights and enhanced predictive power. The proposed method aims to enhance two cutting-edge data integration methodologies for single-cell RNA sequencing (scRNA-seq). The method utilizes a strategy that combines two key components: a statistical approach to isolate the high variability in gene expression across cells or samples and a feature selection strategy based on XgBoost to keep genes that are important for distinguishing among healthy and cancerous cells.

Post-traumatic stress disorder (PTSD) is a complex psychological disorder that develops following exposure to traumatic events. PTSD is influenced by catalytic factors such as dysregulated hypothalamic-pituitary-adrenal (HPA) axis, neurotransmitter imbalances, and oxidative stress. Genetic variations may act as important catalysts, impacting neurochemical signaling, synaptic plasticity, and stress response systems. Understanding the intricate gene networks and their interactions is vital for comprehending the underlying mechanisms of PTSD. Focusing on the catalytic factors of PTSD is essential because they provide valuable insights into the underlying mechanisms of the disorder. By understanding these factors and their interplay, researchers may uncover potential targets for interventions and therapies, leading to more effective and personalized treatments for individuals with PTSD. The aforementioned gene networks, composed of specific genes associated with the disorder, provide a comprehensive view of the molecular pathways and regulatory mechanisms involved in PTSD. Through this study valuable insights into the disorder’s underlying mechanisms and opening avenues for effective treatments, personalized interventions, and the development of biomarkers for early detection and monitoring are provided.

Alzheimer’s disease (AD) represents one of the most important healthcare challenges of the current century, characterized as an expanding, “silent pandemic”. Recent studies suggest that the peripheral immune system may participate in AD development; however, the molecular components of these cells in AD remain poorly understood. Although single-cell RNA sequencing (scRNA-seq) offers a sufficient exploration of various biological processes at the cellular level, the number of existing works is limited, and no comprehensive machine learning (ML) analysis has yet been conducted to identify effective biomarkers in AD. Herein, we introduced a computational workflow using both deep learning and ML processes examining scRNA-seq data obtained from the peripheral blood of both Alzheimer’s disease patients with an amyloid-positive status and healthy controls with an amyloid-negative status, totaling 36,849 cells. The output of our pipeline contained transcripts ranked by their level of significance, which could serve as reliable genetic signatures of AD pathophysiology. The comprehensive functional analysis of the most dominant genes in terms of biological relevance to AD demonstrates that the proposed methodology has great potential for discovering blood-based fingerprints of the disease. Furthermore, the present approach paves the way for the application of ML techniques to scRNA-seq data from complex disorders, providing new challenges to identify key biological processes from a molecular perspective.

Alzheimer’s disease (AD) is now classified as a silent pandemic due to concerning current statistics and future predictions. Despite this, no effective treatment or accurate diagnosis currently exists. The negative impacts of invasive techniques and the failure of clinical trials have prompted a shift in research towards non-invasive treatments. In light of this, there is a growing need for early detection of AD through non-invasive approaches. The abundance of data generated by non-invasive techniques such as blood component monitoring, imaging, wearable sensors, and bio-sensors not only offers a platform for more accurate and reliable bio-marker developments but also significantly reduces patient pain, psychological impact, risk of complications, and cost. Nevertheless, there are challenges concerning the computational analysis of the large quantities of data generated, which can provide crucial information for the early diagnosis of AD. Hence, the integration of artificial intelligence and deep learning is critical to addressing these challenges. This work attempts to examine some of the facts and the current situation of these approaches to AD diagnosis by leveraging the potential of these tools and utilizing the vast amount of non-invasive data in order to revolutionize the early detection of AD according to the principles of a new non-invasive medicine era.

Data-driven analysis and characterization of molecular phenotypes comprises an efficient way to decipher complex disease mechanisms. Using emerging next generation sequencing technologies, important disease-relevant outcomes are extracted, offering the potential for precision diagnosis and therapeutics in progressive disorders. Single-cell RNA sequencing (scRNA-seq) allows the inherent heterogeneity between individual cellular environments to be exploited and provides one of the most promising platforms for quantifying cell-to-cell gene expression variability. However, the high-dimensional nature of scRNA-seq data poses a significant challenge for downstream analysis, particularly in identifying genes that are dominant across cell populations. Feature selection is a crucial step in scRNA-seq data analysis, reducing the dimensionality of data and facilitating the identification of genes most relevant to the biological question. Herein, we present a need for an ensemble feature selection methodology for scRNA-seq data, specifically in the context of Alzheimer’s disease (AD). We combined various feature selection strategies to obtain the most dominant differentially expressed genes (DEGs) in an AD scRNA-seq dataset, providing a promising approach to identify potential transcriptome biomarkers through scRNA-seq data analysis, which can be applied to other diseases. We anticipate that feature selection techniques, such as our ensemble methodology, will dominate analysis options for transcriptome data, especially as datasets increase in volume and complexity, leading to more accurate classification and the generation of differentially significant features.

Parkinson’s disease (PD) is a progressive neurodegenerative disorder associated with dysfunction of dopaminergic neurons in the brain, lack of dopamine and the formation of abnormal Lewy body protein particles. PD is an idiopathic disease of the nervous system, characterized by motor and nonmotor manifestations without a discrete onset of symptoms until a substantial loss of neurons has already occurred, enabling early diagnosis very challenging. Sensor-based platforms have gained much attention in clinical practice screening various biological signals simultaneously and allowing researchers to quickly receive a huge number of biomarkers for diagnostic and prognostic purposes. The integration of machine learning into medical systems provides the potential for optimization of data collection, disease prediction through classification of symptoms and can strongly support data-driven clinical decisions. This work attempts to examine some of the facts and current situation of sensor-based approaches in PD diagnosis and discusses ensemble techniques using sensor-based data for developing machine learning models for personalized risk prediction. Additionally, a biosensing platform combined with clinical data processing and appropriate software is proposed in order to implement a complete diagnostic system for PD monitoring.

Nowadays, biomedical data are generated exponentially, creating datasets for analysis with ultra-high dimensionality and complexity. An indicative example is emerging single-cell RNA-sequencing (scRNA-seq) technology, which isolates and measures individual cells. The analysis of scRNA-seq data consists of a major challenge because of its ultra-high dimensionality and complexity. Towards this direction, we study the generalization of the MRPV, a recently published ensemble classification algorithm, which combines multiple ultra-low dimensional random projected spaces with a voting scheme, while exposing its ability to enhance the performance of base classifiers. We empirically showed that we can design a reliable ensemble classification technique using random projected subspaces in an extremely small fixed number of dimensions, without following the restrictions of the classical random projection method. Therefore, the MPRV acquires the ability to efficiently and rapidly perform classification tasks even for data with extremely high dimensionality. Furthermore, through the experimental analysis in six scRNA-seq data, we provided evidence that the most critical advantage of MRPV is the dramatic reduction in data dimensionality that allows for the utilization of computational demanding classifiers that are considered as non-practical in real-life applications. The scalability, the simplicity, and the capabilities of our proposed framework render it as a tool-guide for single-cell RNA-seq data which are characterized by ultra-high dimensionality. MRPV is available on GitHub in MATLAB implementation.

Biomedicine is a pillar of the collective, scientific effort of human self-discovery, as well as a major source of humanistic data codified primarily in biomedical documents. Despite their rigid structure, maintaining and updating a considerably-sized collection of such documents is a task of overwhelming complexity mandating efficient information retrieval for the purpose of the integration of clustering schemes. The latter should work natively with inherently multidimensional data and higher order interdependencies. Additionally, past experience indicates that clustering should be semantically enhanced. Tensor algebra is the key to extending the current term-document model to more dimensions. In this article, an alternative keyword-term-document strategy, based on scientometric observations that keywords typically possess more expressive power than ordinary text terms, whose algorithmic cornerstones are third order tensors and MeSH ontological functions, is proposed. This strategy has been compared against a baseline using two different biomedical datasets, the TREC (Text REtrieval Conference) genomics benchmark and a large custom set of cognitive science articles from PubMed.

It has already been established by the systems-level approaches that the future of predictive disease biomarkers will not be sketched by plain lists of genes or proteins or other biological entities but rather integrated entities that consider all underlying component relationships. Towards this orientation, early pathway-based approaches coupled expression data with whole pathway interaction topologies but it was the recent approaches that zoomed into subpathways (local areas of the entire biological pathway) that provided more targeted and context-specific candidate disease biomarkers. Here, we explore the application potential of PerSubs, a graph-based algorithm which identifies differentially activated disease-specific subpathways. PerSubs is applicable both for microarray and RNA-Seq data and utilizes the Kyoto Encyclopedia of Genes and Genomes (KEGG) database as reference for biological pathways. PerSubs operates in two stages: first, identifies differentially expressed genes (or uses any list of disease-related genes) and in second stage, treating each gene of the list as start point, it scans the pathway topology around to build meaningful subpathway topologies. Here, we apply PerSubs to investigate which pathways are perturbed towards mouse lung regeneration following H1N1 influenza infection.