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Multimodal refers to the combination or integration of data from multiple sources or modalities. Multimodal data integration involves merging diverse sources, such as imaging, clinical, and genetic data, to obtain a more comprehensive view of patient health. This process, facilitated by deep learning, has emerged as a transformative technique in the biomedical field, enabling a comprehensive understanding of patient health and leading to improved decision-making. This study provides an overview of the general pipeline for multimodal data integration techniques. We start by examining different types of biomedical data and exploring feature extraction and preprocessing techniques for these modalities. Moreover, we discuss data-level, feature-level, and decision-level fusion methods in detail, specifying scenarios where each fusion approach is most effective. The review also addresses the use cases and existing applications of multimodal data fusion, highlighting their impact on disease diagnosis, prognosis, treatment planning, and personalized medicine. [ABSTRACT FROM AUTHOR]

The fast growth of virtual reality (VR) and augmented reality (AR) head-mounted displays provides a new medium for interactive visualisations and visual analytics. Presence is the experience of consciousness within extended reality, and it has the potential to increase task performance. This project studies the impact that a sense of presence has on data visualisation performance and user experience under AR and VR conditions. A within-subjects design recruited 38 participants to complete interactive visualisation tasks within the novel immersive data analytics system for genomic data in AR and VR, and measured speed, accuracy, preference, presence, and user satisfaction. Open-ended user experience responses were also collected. The results implied that VR was more conducive to efficiency, effectiveness, and user experience as well as offering insight into possible cognitive load benefits for VR users. [ABSTRACT FROM AUTHOR]

This study aims to evaluate the effectiveness and efficiency of various deep learning models in recognizing patterns within diverse biomedical datasets. The methods involved the collection of biomedical data from various public and synthetic sources, including chest radiographs, MRI, CT scans, as well as electrocardiogram (ECG) and electromyography (EMG) signals. The data underwent preprocessing steps such as normalization, noise removal, and data augmentation to improve quality and variability. The deep learning models evaluated included Convolutional Neural Networks (CNN) and Recurrent Neural Networks (RNN), which were trained to identify patterns within the data. The performance evaluation was conducted using metrics like accuracy, sensitivity, specificity, and AUC to ensure the models' generalization capabilities on test datasets. The results revealed that CNNs excelled in medical image analysis, particularly in terms of accuracy and interpretability, while RNNs were more effective in handling sequential data such as medical signals. The primary conclusion of this study is that the selection of deep learning models should be tailored to the type of data and specific application requirements, emphasizing the importance of improving model interpretability and generalization for broader applications in clinical settings.

Biomedical data are generated and collected from various sources, including medical imaging, laboratory tests and genome sequencing. Sharing these data for research can help address unmet health needs, contribute to scientific breakthroughs, accelerate the development of more effective treatments and inform public health policy. Due to the potential sensitivity of such data, however, privacy concerns have led to policies that restrict data sharing. In addition, sharing sensitive data requires a secure and robust infrastructure with appropriate storage solutions. Here, we examine and compare the centralized and federated data sharing models through the prism of five large-scale and real-world use cases of strategic significance within the European data sharing landscape: the French Health Data Hub, the BBMRI-ERIC Colorectal Cancer Cohort, the federated European Genome-phenome Archive, the Observational Medical Outcomes Partnership/OHDSI network and the EBRAINS Medical Informatics Platform. Our analysis indicates that centralized models facilitate data linkage, harmonization and interoperability, while federated models facilitate scaling up and legal compliance, as the data typically reside on the data generator's premises, allowing for better control of how data are shared. This comparative study thus offers guidance on the selection of the most appropriate sharing strategy for sensitive datasets and provides key insights for informed decision-making in data sharing efforts. [ABSTRACT FROM AUTHOR]

A crucial stage in eukaryote gene expression involves mRNA splicing by a protein assembly known as the spliceosome. This step significantly contributes to generating and properly operating the ultimate gene product. Since non-coding introns disrupt eukaryotic genes, splicing entails the elimination of introns and joining exons to create a functional mRNA molecule. Nevertheless, accurately finding splice sequence sites using various molecular biology techniques and other biological approaches is complex and time-consuming. This paper presents a precise and reliable computer-aided diagnosis (CAD) technique for the rapid and correct identification of splice site sequences. The proposed deep learning-based framework uses long short-term memory (LSTM) to extract distinct patterns from RNA sequences, enabling rapid and accurate point mutation sequence mapping. The proposed network employs one-hot encodings to find sequential patterns that effectively identify splicing sites. A thorough ablation study of traditional machine learning, one-dimensional convolutional neural networks (1D-CNNs), and recurrent neural networks (RNNs) models was conducted. The proposed LSTM network outperformed existing state-of-the-art approaches, improving accuracy by 3% and 2% for the acceptor and donor sites datasets. [ABSTRACT FROM AUTHOR]

Background: Currently, discriminating Iron Deficiency Anemia (IDA) from other anemia requires an expensive test (serum ferritin). Complete Blood Count (CBC) tests are less costly and more widely available. Machine learning models have not yet been applied to discriminating IDA but do well for similar tasks. Methods: We constructed multiple machine learning methods to classify IDA from CBC data using a US NHANES dataset of over 19,000 instances, calculating accuracy, precision, recall, and precision AUC (PR AUC). We validated the results using an unseen dataset from Kenya, using the same model. We calculated ranked feature importance to explain the global behavior of the model. Results: Our model classifies IDA with a PR AUC of 0.87 and recall/sensitivity of 0.98 and 0.89 for the original dataset and an unseen Kenya dataset, respectively. The explanations indicate that low blood level of hemoglobin, higher age, and higher Red Blood Cell distribution width were most critical. We also found that optimization made only minor changes to the explanations and that the features used remained consistent with professional practice. Conclusions: The overall high performance and consistency of the results suggest that the approach would be acceptable to health professionals and would support enhancements to current automated CBC analyzers.

Biomedical data analysis and visualization often demand data experts for each unique health event. There is a clear lack of automatic tools for semantic visualization of the spread of health risks through biomedical data. Illnesses such as coronavirus disease (COVID-19) and Monkeypox spread rampantly around the world before governments could make decisions based on the analysis of such data. We propose the design of a knowledge graph (KG) for spatio-temporal tracking of public health event propagation. To achieve this, we propose the specialization of the Core Propagation Phenomenon Ontology (PropaPhen) into a health-related propagation phenomenon domain ontology. Data from the UMLS and Open Street Maps are suggested for instantiating the proposed knowledge graph. Finally, the results of a use case on COVID-19 data from the World Health Organization are analyzed to evaluate the possibilities of our approach. [ABSTRACT FROM AUTHOR]

The research of biomedical data is crucial for disease diagnosis, health management, and medicine development. However, biomedical data are usually characterized by high dimensionality and class imbalance, which increase computational cost and affect the classification performance of minority class, making accurate classification difficult. In this paper, we propose a biomedical data classification method based on feature selection and data resampling. First, use the minimal-redundancy maximal-relevance (mRMR) method to select biomedical data features, reduce the feature dimension, reduce the computational cost, and improve the generalization ability; then, a new SMOTE oversampling method (Spectral-SMOTE) is proposed, which solves the noise sensitivity problem of SMOTE by an improved spectral clustering method; finally, the marine predators algorithm is improved using piecewise linear chaotic maps and random opposition-based learning strategy to improve the algorithm's optimization seeking ability and convergence speed, and the key parameters of the spectral-SMOTE are optimized using the improved marine predators algorithm, which effectively improves the performance of the over-sampling approach. In this paper, five real biomedical datasets are selected to test and evaluate the proposed method using four classifiers, and three evaluation metrics are used to compare with seven data resampling methods. The experimental results show that the method effectively improves the classification performance of biomedical data. Statistical test results also show that the proposed PRMPA-Spectral-SMOTE method outperforms other data resampling methods. [ABSTRACT FROM AUTHOR]

Background: Currently, discriminating Iron Deficiency Anemia (IDA) from other anemia requires an expensive test (serum ferritin). Complete Blood Count (CBC) tests are less costly and more widely available. Machine learning models have not yet been applied to discriminating IDA but do well for similar tasks. Methods: We constructed multiple machine learning methods to classify IDA from CBC data using a US NHANES dataset of over 19,000 instances, calculating accuracy, precision, recall, and precision AUC (PR AUC). We validated the results using an unseen dataset from Kenya, using the same model. We calculated ranked feature importance to explain the global behavior of the model. Results: Our model classifies IDA with a PR AUC of 0.87 and recall/sensitivity of 0.98 and 0.89 for the original dataset and an unseen Kenya dataset, respectively. The explanations indicate that low blood level of hemoglobin, higher age, and higher Red Blood Cell distribution width were most critical. We also found that optimization made only minor changes to the explanations and that the features used remained consistent with professional practice. Conclusions: The overall high performance and consistency of the results suggest that the approach would be acceptable to health professionals and would support enhancements to current automated CBC analyzers. [ABSTRACT FROM AUTHOR]

Typical state-of-the-art flow cytometry data samples typically consist of measures of 10 to 30 features of more than 100,000 cell "events". Artificial intelligence (AI) systems are able to diagnose such data with almost the same accuracy as human experts. However, such systems face one central challenge: their decisions have far-reaching consequences for the health and lives of people. Therefore, the decisions of AI systems need to be understandable and justifiable by humans. In this work, we present a novel explainable AI (XAI) method called algorithmic population descriptions (ALPODS), which is able to classify (diagnose) cases based on subpopulations in high-dimensional data. ALPODS is able to explain its decisions in a form that is understandable to human experts. For the identified subpopulations, fuzzy reasoning rules expressed in the typical language of domain experts are generated. A visualization method based on these rules allows human experts to understand the reasoning used by the AI system. A comparison with a selection of state-of-the-art XAI systems shows that ALPODS operates efficiently on known benchmark data and on everyday routine case data. [ABSTRACT FROM AUTHOR]

Biomedical datasets distill many mechanisms of human diseases, linking diseases to genes and phenotypes (signs and symptoms of disease), genetic mutations to altered protein structures, and altered proteins to changes in molecular functions and biological processes. It is desirable to gain new insights from these data, especially with regard to the uncovering of hierarchical structures relating disease variants. However, analysis to this end has proven difficult due to the complexity of the connections between multi-categorical symbolic data. This article proposes symbolic tree adaptive resonance theory (START), with additional supervised, dual-vigilance (DV-START), and distributed dual-vigilance (DDV-START) formulations, for the clustering of multi-categorical symbolic data from biomedical datasets by demonstrating its utility in clustering variants of Charcot–Marie–Tooth disease using genomic, phenotypic, and proteomic data. [ABSTRACT FROM AUTHOR]

Probability distributions are widely utilized in applied sciences, especially in the field of biomedical science. Biomedical data typically exhibit positive skewness, necessitating the use of flexible, skewed distributions to effectively model such phenomena. In this study, we introduce a novel approach to characterize new lifetime distributions, known as the New Flexible Exponent Power (NFEP) Family of distributions. This involves the addition of a new parameter to existing distributions. A specific sub-model within the proposed class, known as the New Flexible Exponent Power Weibull (NFEP-Wei), is derived to illustrate the concept of flexibility. We employ the well-established Maximum Likelihood Estimation (MLE) method to estimate the unknown parameters in this family of distributions. A simulation study is conducted to assess the behavior of the estimators in various scenarios. To gauge the flexibility and effectiveness of the NFEP-Wei distribution, we compare it with the AP-Wei (alpha power Weibull), MO-Wei (Marshal Olkin Weibull), classical Wei (Weibull), NEP-Wei (new exponent power Weibull), FRLog-Wei (flexible reduced logarithmic Weibull), and Kum-Wei (Kumaraswamy Weibull) distributions by analyzing four distinct biomedical datasets. The results demonstrate that the NFEP-Wei distribution outperforms the compared distributions.

Differentially private (DP) synthetic data has emerged as a potential solution for sharing sensitive individual-level biomedical data. DP generative models offer a promising approach for generating realistic synthetic data that aims to maintain the original data’s central statistical properties while ensuring privacy by limiting the risk of disclosing sensitive information about individuals. However, the issue regarding how to assess the expected real-world prediction performance of machine learning models trained on synthetic data remains an open question. In this study, we experimentally evaluate two different model evaluation protocols for classifiers trained on synthetic data. The first protocol employs solely synthetic data for downstream model evaluation, whereas the second protocol assumes limited DP access to a private test set consisting of real data managed by a data curator. We also propose a metric for assessing how well the evaluation results of the proposed protocols match the real-world prediction performance of the models. The assessment measures both the systematic error component indicating how optimistic or pessimistic the protocol is on average and the random error component indicating the variability of the protocol’s error. The results of our study suggest that employing the second protocol is advantageous, particularly in biomedical health studies where the precision of the research is of utmost importance. Our comprehensive empirical study offers new insights into the practical feasibility and usefulness of different evaluation protocols for classifiers trained on DP-synthetic data.

Abstract Graph embedding techniques are using deep learning algorithms in data analysis to solve problems of such as node classification, link prediction, community detection, and visualization. Although typically used in the context of guessing friendships in social media, several applications for graph embedding techniques in biomedical data analysis have emerged. While these approaches remain computationally demanding, several developments over the last years facilitate their application to study biomedical data and thus may help advance biological discoveries. Therefore, in this review, we discuss the principles of graph embedding techniques and explore the usefulness for understanding biological network data derived from mass spectrometry and sequencing experiments, the current workhorses of systems biology studies. In particular, we focus on recent examples for characterizing protein–protein interaction networks and predicting novel drug functions.

Typical state-of-the-art flow cytometry data samples typically consist of measures of 10 to 30 features of more than 100,000 cell “events”. Artificial intelligence (AI) systems are able to diagnose such data with almost the same accuracy as human experts. However, such systems face one central challenge: their decisions have far-reaching consequences for the health and lives of people. Therefore, the decisions of AI systems need to be understandable and justifiable by humans. In this work, we present a novel explainable AI (XAI) method called algorithmic population descriptions (ALPODS), which is able to classify (diagnose) cases based on subpopulations in high-dimensional data. ALPODS is able to explain its decisions in a form that is understandable to human experts. For the identified subpopulations, fuzzy reasoning rules expressed in the typical language of domain experts are generated. A visualization method based on these rules allows human experts to understand the reasoning used by the AI system. A comparison with a selection of state-of-the-art XAI systems shows that ALPODS operates efficiently on known benchmark data and on everyday routine case data.

Abstract As a new data management paradigm, knowledge graphs can integrate multiple data sources and achieve quick responses, reasoning and better predictions in drug discovery. Characterized by powerful contagion and a high rate of morbidity and mortality, porcine reproductive and respiratory syndrome (PRRS) is a common infectious disease in the global swine industry that causes economically great losses. Traditional Chinese medicine (TCM) has advantages in low adverse effects and a relatively affordable cost of application, and TCM is therefore conceived as a possibility to treat PRRS under the current circumstance that there is a lack of safe and effective approaches. Here, we constructed a knowledge graph containing common biomedical data from humans and Sus Scrofa as well as information from thousands of TCMs. Subsequently, we validated the effectiveness of the Sus Scrofa knowledge graph by the t-SNE algorithm and selected the optimal model (i.e., transR) from six typical models, namely, transE, transR, DistMult, ComplEx, RESCAL and RotatE, according to five indicators, namely, MRR, MR, HITS@1, HITS@3 and HITS@10. Based on embedding vectors trained by the optimal model, anti-PRRSV TCMs were predicted by two paths, namely, VHC-Herb and VHPC-Herb, and potential anti-PRRSV TCMs were identified by retrieving the HERB database according to the pharmacological properties corresponding to symptoms of PRRS. Ultimately, Dan Shen's (Salvia miltiorrhiza Bunge) capacity to resist PRRSV infection was validated by a cell experiment in which the inhibition rate of PRRSV exceeded 90% when the concentrations of Dan Shen extract were 0.004, 0.008, 0.016 and 0.032 mg/mL. In summary, this is the first report on the Sus Scrofa knowledge graph including TCM information, and our study reflects the important application values of deep learning on graphs in the swine industry as well as providing accessible TCM resources for PRRS.

As a new data management paradigm, knowledge graphs can integrate multiple data sources and achieve quick responses, reasoning and better predictions in drug discovery. Characterized by powerful contagion and a high rate of morbidity and mortality, porcine reproductive and respiratory syndrome (PRRS) is a common infectious disease in the global swine industry that causes economically great losses. Traditional Chinese medicine (TCM) has advantages in low adverse effects and a relatively affordable cost of application, and TCM is therefore conceived as a possibility to treat PRRS under the current circumstance that there is a lack of safe and effective approaches. Here, we constructed a knowledge graph containing common biomedical data from humans and Sus Scrofa as well as information from thousands of TCMs. Subsequently, we validated the effectiveness of the Sus Scrofa knowledge graph by the t-SNE algorithm and selected the optimal model (i.e., transR) from six typical models, namely, transE, transR, DistMult, ComplEx, RESCAL and RotatE, according to five indicators, namely, MRR, MR, HITS@1, HITS@3 and HITS@10. Based on embedding vectors trained by the optimal model, anti-PRRSV TCMs were predicted by two paths, namely, VHC-Herb and VHPC-Herb, and potential anti-PRRSV TCMs were identified by retrieving the HERB database according to the pharmacological properties corresponding to symptoms of PRRS. Ultimately, Dan Shen's (Salvia miltiorrhiza Bunge) capacity to resist PRRSV infection was validated by a cell experiment in which the inhibition rate of PRRSV exceeded 90% when the concentrations of Dan Shen extract were 0.004, 0.008, 0.016 and 0.032 mg/mL. In summary, this is the first report on the Sus Scrofa knowledge graph including TCM information, and our study reflects the important application values of deep learning on graphs in the swine industry as well as providing accessible TCM resources for PRRS. [ABSTRACT FROM AUTHOR]

Graph embedding techniques are using deep learning algorithms in data analysis to solve problems of such as node classification, link prediction, community detection, and visualization. Although typically used in the context of guessing friendships in social media, several applications for graph embedding techniques in biomedical data analysis have emerged. While these approaches remain computationally demanding, several developments over the last years facilitate their application to study biomedical data and thus may help advance biological discoveries. Therefore, in this review, we discuss the principles of graph embedding techniques and explore the usefulness for understanding biological network data derived from mass spectrometry and sequencing experiments, the current workhorses of systems biology studies. In particular, we focus on recent examples for characterizing protein–protein interaction networks and predicting novel drug functions. [ABSTRACT FROM AUTHOR]

Researchers increasingly turn to explainable artificial intelligence (XAI) to analyze omics data and gain insights into the underlying biological processes. Yet, given the interdisciplinary nature of the field, many findings have only been shared in their respective research community. An overview of XAI for omics data is needed to highlight promising approaches and help detect common issues. Toward this end, we conducted a systematic mapping study. To identify relevant literature, we queried Scopus, PubMed, Web of Science, BioRxiv, MedRxiv and arXiv. Based on keywording, we developed a coding scheme with 10 facets regarding the studies' AI methods, explainability methods and omics data. Our mapping study resulted in 405 included papers published between 2010 and 2023. The inspected papers analyze DNA-based (mostly genomic), transcriptomic, proteomic or metabolomic data by means of neural networks, tree-based methods, statistical methods and further AI methods. The preferred post-hoc explainability methods are feature relevance (n  = 166) and visual explanation (n  = 52), while papers using interpretable approaches often resort to the use of transparent models (n  = 83) or architecture modifications (n  = 72). With many research gaps still apparent for XAI for omics data, we deduced eight research directions and discuss their potential for the field. We also provide exemplary research questions for each direction. Many problems with the adoption of XAI for omics data in clinical practice are yet to be resolved. This systematic mapping study outlines extant research on the topic and provides research directions for researchers and practitioners. [ABSTRACT FROM AUTHOR]

Getting highly accurate output in biomedical data processing concerning biomedical signals and images is impossible because biomedical data are generated from various electronic and electrical resources that can deliver the data with noise. Filtering is widely used for signal and image processing applications in medical, multimedia, communications, biomedical electronics, and computer vision. The biggest problem in biomedical signal and image processing is developing a perfect filter for the system. Digital filters are more advanced in precision and stability than analog filters. Digital filters are getting more attention due to the increasing advancements in digital technologies. Hence, most medical image and signal processing techniques use digital filters for preprocessing tasks. This paper briefly explains various filters used in medical image and signal processing. Matlab is a famous mathematical, analytical software with a platform and built-in tools to design filters and experiment with different inputs. Even though this paper implements filters like, Mean, Median, Weighted Average, Guassian, and Bilateral in Python to verify their performance, a suitable filter can be selected for biomedical applications by comparing their performance. [ABSTRACT FROM AUTHOR]

Biomedical datasets are usually large and complex, containing biological information about a disease. Computational analytics and the interactive visualisation of such data are essential decision-making tools for disease diagnosis and treatment. Oncology data models were observed in a virtual reality environment to analyse gene expression and clinical data from a cohort of cancer patients. The technology enables a new way to view information from the outside in (exocentric view) and the inside out (egocentric view), which is otherwise not possible on ordinary displays. This paper presents a usability study on the exocentric and egocentric views of biomedical data visualisation in virtual reality and their impact on usability on human behaviour and perception. Our study revealed that the performance time was faster in the exocentric view than in the egocentric view. The exocentric view also received higher ease-of-use scores than the egocentric view. However, the influence of usability on time performance was only evident in the egocentric view. The findings of this study could be used to guide future development and refinement of visualisation tools in virtual reality. [ABSTRACT FROM AUTHOR]

In an increasingly interconnected world, the convergence of power system networks and biometric-based biomedical applications presents unique challenges for data protection and privacy. This research endeavors to conceptualize and design an intelligent countermeasure system that serves as a robust defense mechanism for enhancing security in this complex ecosystem. The proposed system incorporates biometric authentication techniques to fortify user access controls, implements advanced encryption methods for safeguarding sensitive biomedical data, and intrusion detection and prevention mechanisms to thwart cyber threats. This paper proposed an Integrated Probabilistic Regression Cryptographic Classifier (IPRCC) for data protection and privacy in biometric data for power system devices for biomedical applications. The IPRCC combines probabilistic regression techniques for data analysis with cryptographic methods to fortify the security and privacy of biometric data used within power system devices for biomedical applications. To secure biometric data, IPRCC integrates cryptographic techniques. Cryptography involves encoding information in a way that only authorized parties can decode and understand it. IPRCC incorporates a classifier as part of its security framework. The classifier is used to make decisions or classifications based on the analyzed biometric data. The IPRCC includes enhanced data protection, improved privacy, and increased security for biometric data. The Integrated Probabilistic Regression Cryptographic Classifier (IPRCC) is a sophisticated security system that combines probabilistic regression modeling and cryptographic techniques to protect biometric data used in biomedical applications, especially when integrated with power system devices. Simulation results demonstrated that the proposed IPRCC model exhibits an improved attack detection rate of 99%. [ABSTRACT FROM AUTHOR]

Existing cardiovascular studies tend to suffer from small sample sizes and unaddressed confounders. Re-profiling of 9 microarray datasets revealed significant global gene expression differences between 358 failing and 191 non-failing left ventricles independent of age and sex (p = 5.1e-10). Covariate-adjusted mixed-effect regression revealed 17 % (945/5553) genes with >1.5-fold changes. The extracellular matrix and integral membrane ontologies were significantly enriched and depleted in failing ventricles, respectively. Furthermore, MTSS1 implicated in cardiovascular dysfunction showed the greatest change in ischemic compared to dilated cardiomyopathy (Bonferroni p

Biomedical data analysis is essential in current diagnosis, treatment, and patient condition monitoring. The large volumes of data that characterize this area require simple but accurate and fast methods of intellectual analysis to improve the level of medical services. Existing machine learning (ML) methods require many resources (time, memory, energy) when processing large datasets. Or they demonstrate a level of accuracy that is insufficient for solving a specific application task. In this paper, we developed a new ensemble model of increased accuracy for solving approximation problems of large biomedical data sets. The model is based on cascading of the ML methods and response surface linearization principles. In addition, we used Ito decomposition as a means of nonlinearly expanding the inputs at each level of the model. As weak learners, Support Vector Regression (SVR) with linear kernel was used due to many significant advantages demonstrated by this method among the existing ones. The training and application procedures of the developed SVR-based cascade model are described, and a flow chart of its implementation is presented. The modeling was carried out on a real-world tabular set of biomedical data of a large volume. The task of predicting the heart rate of individuals was solved, which provides the possibility of determining the level of human stress, and is an essential indicator in various applied fields. The optimal parameters of the SVR-based cascade model operating were selected experimentally. The authors shown that the developed model provides more than 20 times higher accuracy (according to Mean Squared Error (MSE)), as well as a significant reduction in the duration of the training procedure compared to the existing method, which provided the highest accuracy of work among those considered.

This paper proposes a novel deep-learning framework for super-resolution ultrasound images and videos in terms of spatial resolution and line reconstruction. To this end, we up-sample the acquired low-resolution image through a vision-based interpolation method; then, we train a learning-based model to improve the quality of the up-sampling. We qualitatively and quantitatively test our model on different anatomical districts (e.g., cardiac, obstetric) images and with different up-sampling resolutions (i.e., 2X, 4X). Our method improves the PSNR median value with respect to SOTA methods of 1.7 % on obstetric 2X raw images, 6.1 % on cardiac 2X raw images, and 4.4 % on abdominal raw 4X images; it also improves the number of pixels with a low prediction error of 9.0 % on obstetric 4X raw images, 5.2 % on cardiac 4X raw images, and 6.2 % on abdominal 4X raw images. The proposed method is then applied to the spatial super-resolution of 2D videos, by optimising the sampling of lines acquired by the probe in terms of the acquisition frequency. Our method specialises trained networks to predict the high-resolution target through the design of the network architecture and the loss function, taking into account the anatomical district and the up-sampling factor and exploiting a large ultrasound data set. The use of deep learning on large data sets overcomes the limitations of vision-based algorithms that are general and do not encode the characteristics of the data. Furthermore, the data set can be enriched with images selected by medical experts to further specialise the individual networks. Through learning and high-performance computing, the proposed super-resolution is specialised to different anatomical districts by training multiple networks. Furthermore, the computational demand is shifted to centralised hardware resources with a real-time execution of the network's prediction on local devices. [ABSTRACT FROM AUTHOR]

Recent breakthroughs are making a significant contribution to big data in biomedicine which are anticipated to assist in disease diagnosis and patient care management. To obtain relevant information from this data, effective administration and analysis are required. One of the major challenges associated with biomedical data analysis is the so-called "curse of dimensionality". For this issue, a new version of Binary Sand Cat Swarm Optimization (called PILC-BSCSO), incorporating a pinhole-imaging-based learning strategy and crossover operator, is presented for selecting the most informative features. First, the crossover operator is used to strengthen the search capability of BSCSO. Second, the pinhole-imaging learning strategy is utilized to effectively increase exploration capacity while avoiding premature convergence. The Support Vector Machine (SVM) classifier with a linear kernel is used to assess classification accuracy. The experimental results show that the PILC-BSCSO algorithm beats 11 cutting-edge techniques in terms of classification accuracy and the number of selected features using three public medical datasets. Moreover, PILC-BSCSO achieves a classification accuracy of 100% for colon cancer, which is difficult to classify accurately, based on just 10 genes. A real Liver Hepatocellular Carcinoma (TCGA-HCC) data set was also used to further evaluate the effectiveness of the PILC-BSCSO approach. PILC-BSCSO identifies a subset of five marker genes, including prognostic biomarkers HMMR, CHST4, and COL15A1, that have excellent predictive potential for liver cancer using TCGA data. [ABSTRACT FROM AUTHOR]

This article provides a comprehensive overview of the importance of selecting the right statistical method for data analysis in biomedical research. It explains the differences between parametric and non-parametric methods and highlights the need to consider the purpose of the study, the type of data, and the measurements when choosing a statistical test. The article offers a range of parametric and non-parametric approaches for comparing means, proportions, and other statistical techniques. It also discusses the benefits and drawbacks of non-parametric methods, emphasizing their usefulness when data does not meet the assumptions of parametric tests. The article stresses the significance of sample size and the p-value in determining statistical significance and concludes by emphasizing the importance of researchers having a basic understanding of statistics to select the appropriate statistical methods for their research. [Extracted from the article]

Artificial intelligence (AI)-based solutions have revolutionized our world, using extensive datasets and computational resources to create automatic tools for complex tasks that, until now, have been performed by humans. Massive data is a fundamental aspect of the most powerful AI-based algorithms. However, for AI-based healthcare solutions, there are several socioeconomic, technical/infrastructural, and most importantly, legal restrictions, which limit the large collection and access of biomedical data, especially medical imaging. To overcome this important limitation, several alternative solutions have been suggested, including transfer learning approaches, generation of artificial data, adoption of blockchain technology, and creation of an infrastructure composed of anonymous and abstract data. However, none of these strategies is currently able to completely solve this challenge. The need to build large datasets that can be used to develop healthcare solutions deserves special attention from the scientific community, clinicians, all the healthcare players, engineers, ethicists, legislators, and society in general. This paper offers an overview of the data limitation in medical predictive models; its impact on the development of healthcare solutions; benefits and barriers of sharing data; and finally, suggests future directions to overcome data limitations in the medical field and enable AI to enhance healthcare. This perspective is dedicated to the technical requirements of the learning models, and it explains the limitation that comes from poor and small datasets in the medical domain and the technical options that try or can solve the problem related to the lack of massive healthcare data.

Purpose: Retinal vein occlusion (RVO) is the second leading cause of visual loss due to retinal disease. Retinal vein occlusion increases the risk of cardiovascular mortality and the risk of stroke. This article describes the data contained within the INSIGHT eye health data set for RVO and cardiovascular disease. Design: Data set descriptor for routinely collected eye and systemic disease data. Participants: All people who had suffered an RVO aged ≥ 18 years old, attending the Ophthalmology Clinic at Queen Elizabeth Hospital, University Hospitals Birmingham (UHB) National Health Service (NHS) Trust were included. Methods: The INSIGHT Health Data Research Hub for Eye Health is an NHS-led ophthalmic bioresource. It provides researchers with safe access to anonymized routinely collected data from contributing NHS hospitals to advance research for patient benefit. This report describes the INSIGHT UHB RVO and major adverse cardiovascular events data set, a data set of ophthalmology and systemic data derived from the United Kingdom’s largest acute care trust. Main Outcome Measures: This data set consists of routinely collected data from the hospital’s electronic patient records. The data set primarily includes structured data (relating to their hospital eye care and any cardiovascular data held for the individual) and OCT ocular images. Further details regarding the available data points are available in the supplementary information. Results: At the time point of this analysis (September 30, 2022) the data set was composed of clinical data from 1521 patients, from Medisoft records inception. The data set includes 2196 occurrences of RVO affecting 2026 eyes, longitudinal eye follow-up clinical parameters, over 6217 eye-related procedures, and 982 encountered complications. The data set contains information on 2534 major adverse cardiovascular event occurrences, their subtype, number experienced per patient, and chronological relation to RVO event. Longitudinal follow-up data including laboratory results, regular medications, and all-cause mortality are also available within the data set. Conclusions: This data set descriptor article summarizes the data set contents, the process of its curation, and potential uses. The data set is available through the structured application process that ensures research studies are for patient benefit. Further information regarding the data repository and contact details can be found at https://www.insight.hdrhub.org/. Financial Disclosure(s): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Purpose: Diabetic retinopathy (DR) is the most common microvascular complication associated with diabetes mellitus (DM), affecting approximately 40% of this patient population. Early detection of DR is vital to ensure monitoring of disease progression and prompt sight saving treatments as required. This article describes the data contained within the INSIGHT Birmingham, Solihull, and Black Country Diabetic Retinopathy Dataset. Design: Dataset descriptor for routinely collected eye screening data. Participants: All diabetic patients aged 12 years and older, attending annual digital retinal photography-based screening within the Birmingham, Solihull, and Black Country Eye Screening Programme. Methods: The INSIGHT Health Data Research Hub for Eye Health is a National Health Service (NHS)–led ophthalmic bioresource that provides researchers with safe access to anonymized, routinely collected data from contributing NHS hospitals to advance research for patient benefit. This report describes the INSIGHT Birmingham, Solihull, and Black Country DR Screening Dataset, a dataset of anonymized images and linked screening data derived from the United Kingdom’s largest regional DR screening program. Main Outcome Measures: This dataset consists of routinely collected data from the eye screening program. The data primarily include retinal photographs with the associated DR grading data. Additional data such as corresponding demographic details, information regarding patients’ diabetic status, and visual acuity data are also available. Further details regarding available data points are available in the supplementary information, in addition to the INSIGHT webpage included below. Results: At the time point of this analysis (December 31, 2019), the dataset comprised 6 202 161 images from 246 180 patients, with a dataset inception date of January 1, 2007. The dataset includes 1 360 547 grading episodes between R0M0 and R3M1. Conclusions: This dataset descriptor article summarizes the content of the dataset, how it has been curated, and what its potential uses are. Data are available through a structured application process for research studies that support discovery, clinical evidence analyses, and innovation in artificial intelligence technologies for patient benefit. Further information regarding the data repository and contact details can be found at https://www.insight.hdrhub.org/. Financial Disclosure(s): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Cross-border data transmission in the biomedical area is on the rise, which brings potential risks and management challenges to data security, biosafety, and national security. Focusing on cross-border data security assessment and risk management, many countries have successively issued relevant laws, regulations, and assessment guidelines. This study aims to provide an index system model and management application reference for the risk assessment of the cross-border data movement. From the perspective of a single organization, the relevant risk assessment standards of several countries are integrated to guide the identification and determination of risk factors. Then, the risk assessment index system of cross-border data flow is constructed. A case study of risk assessment in 358 biomedical organizations is carried out, and the suggestions for data management are offered. This study is condusive to improving security monitoring and the early warning of the cross-border data flow, thereby realizing the safe and orderly global flow of biomedical data.

Acquisition of medical data such as blood pressure, ECG, pulse, and other values is currently often carried out in doctor’s offices by physicians or medical staff. This requires valuable time of patients as well as of practices’ personel and can deliver specific data only of the time of the visit. In this paper we describe a different approach. Patients measure their biomedical vital data at home. Therefore a technical infrastructure together with a workflow were developed and applied within a current project with patients in a rural area. Vital data is transferred via smartphone apps to a cloud environment where doctors can easily access and assess the data.

Autism spectrum disorder (ASD) is regarded as a neurological disorder well-defined by a specific set of problems associated with social skills, recurrent conduct, and communication. Identifying ASD as soon as possible is favourable due to prior identification of ASD permits prompt interferences in children with ASD. Recognition of ASD related to objective pathogenicmutation screening is the initial step against prior intervention and efficient treatment of children who were affected. Nowadays, healthcare and machine learning (ML) industries are combined for determining the existence of various diseases. This article devises a Jellyfish Search Optimization with Deep Learning Driven ASD Detection and Classification (JSODL-ASDDC) model. The goal of the JSODL-ASDDC algorithm is to identify the different stages of ASD with the help of biomedical data. The proposed JSODLASDDC model initially performs min-max data normalization approach to scale the data into uniform range. In addition, the JSODL-ASDDC model involves JSO based feature selection (JFSO-FS) process to choose optimal feature subsets. Moreover, Gated Recurrent Unit (GRU) based classification model is utilized for the recognition and classification of ASD. Furthermore, the Bacterial Foraging Optimization (BFO) assisted parameter tuning process gets executed to enhance the efficacy of the GRU system. The experimental assessment of the JSODL-ASDDC model is investigated against distinct datasets. The experimental outcomes highlighted the enhanced performances of the JSODL-ASDDC algorithm over recent approaches. [ABSTRACT FROM AUTHOR]

In this article, an attempt is made to propose a novel method of lifetime distributions with maximum flexibility using a popular T–X approach together with an exponential distribution, which is known as the New Generalized Logarithmic-X Family (NGLog–X for short) of distributions. Additionally, the generalized form of the Weibull distribution was derived by using the NGLog–X family, known as the New Generalized Logarithmic Weibull (NGLog–Weib) distribution. For the proposed method, some statistical properties, including the moments, moment generating function (MGF), residual and reverse residual life, identifiability, order statistics, and quantile functions, were derived. The estimation of the model parameters was derived by using the well-known method of maximum likelihood estimation (MLE). A comprehensive Monte Carlo simulation study (MCSS) was carried out to evaluate the performance of these estimators by computing the biases and mean square errors. Finally, the NGLog–Weib distribution was implemented on four real biomedical datasets and compared with some other distributions, such as the Alpha Power Transformed Weibull distribution, Marshal Olkin Weibull distribution, New Exponent Power Weibull distribution, Flexible Reduced Logarithmic Weibull distribution, and Kumaraswamy Weibull distribution. The analysis results demonstrate that the new proposed model performs as a better fit than the other competitive distributions. [ABSTRACT FROM AUTHOR]

Biomedical data classification has become a hot research topic in recent years, thanks to the latest technological advancements made in healthcare. Biomedical data is usually examined by physicians for decision making process in patient treatment. Since manual diagnosis is a tedious and time consuming task, numerous automated models, using Artificial Intelligence (AI) techniques, have been presented so far. With this motivation, the current research work presents a novel Biomedical Data Classification using Cat and Mouse Based Optimizer with AI (BDC-CMBOAI) technique. The aim of the proposed BDC-CMBOAI technique is to determine the occurrence of diseases using biomedical data. Besides, the proposed BDC-CMBOAI technique involves the design of Cat and Mouse Optimizer-based Feature Selection (CMBO-FS) technique to derive a useful subset of features. In addition, Ridge Regression (RR) model is also utilized as a classifier to identify the existence of disease. The novelty of the current work is its designing of CMBO-FS model for data classification. Moreover, CMBO-FS technique is used to get rid of unwanted features and boosts the classification accuracy. The results of the experimental analysis accomplished by BDCCMBOAI technique on benchmark medical dataset established the supremacy of the proposed technique under different evaluation measures. [ABSTRACT FROM AUTHOR]

Living in the era of Big Data, one may advocate that the additional synthetic generation of data is redundant. However, to be able to truly say whether it is valid or not, one needs to focus more on the meaning and quality of data than on the quantity. In some domains, such as biomedical and translational sciences, data privacy still holds a higher importance than data sharing. This by default limits access to valuable research data. Intensive discussion, agreements, and conventions among different medical research players, as well as effective techniques and regulations for data anonymization, already made a big step toward simplification of data sharing. However, the situation with the availability of data about rare diseases or outcomes of novel treatments still requires costly and risky clinical trials and, thus, would greatly benefit from smart data generation. Clinical trials and tests on animals initiate a cyclic procedure that may involve multiple redesigns and retesting, which typically takes two or three years for medical devices and up to eight years for novel medicines, and costs between 10 and 20 million euros. The US Food and Drug Administration (FDA) acknowledges that for many novel devices, practical limitations require alternative approaches, such as computer modeling and engineering tests, to conduct large, randomized studies. In this article, we give an overview of global initiatives advocating for computer simulations in support of the 3R principles (Replacement, Reduction, and Refinement) in humane experimentation. We also present several research works that have developed methodologies of smart and comprehensive generation of synthetic biomedical data, such as virtual cohorts of patients, in support of In Silico Clinical Trials (ISCT) and discuss their common ground.

Biomedical datasets distill many mechanisms of human diseases, linking diseases to genes and phenotypes (signs and symptoms of disease), genetic mutations to altered protein structures, and altered proteins to changes in molecular functions and biological processes. It is desirable to gain new insights from these data, especially with regard to the uncovering of hierarchical structures relating disease variants. However, analysis to this end has proven difficult due to the complexity of the connections between multi-categorical symbolic data. This article proposes symbolic tree adaptive resonance theory (START), with additional supervised, dual-vigilance (DV-START), and distributed dual-vigilance (DDV-START) formulations, for the clustering of multi-categorical symbolic data from biomedical datasets by demonstrating its utility in clustering variants of Charcot–Marie–Tooth disease using genomic, phenotypic, and proteomic data.

Biomedical datasets are usually large and complex, containing biological information about a disease. Computational analytics and the interactive visualisation of such data are essential decision-making tools for disease diagnosis and treatment. Oncology data models were observed in a virtual reality environment to analyse gene expression and clinical data from a cohort of cancer patients. The technology enables a new way to view information from the outside in (exocentric view) and the inside out (egocentric view), which is otherwise not possible on ordinary displays. This paper presents a usability study on the exocentric and egocentric views of biomedical data visualisation in virtual reality and their impact on usability on human behaviour and perception. Our study revealed that the performance time was faster in the exocentric view than in the egocentric view. The exocentric view also received higher ease-of-use scores than the egocentric view. However, the influence of usability on time performance was only evident in the egocentric view. The findings of this study could be used to guide future development and refinement of visualisation tools in virtual reality.