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Background: Salvage radiation therapy (sRT) is often the sole curative option in patients with biochemical recurrence after radical prostatectomy. After sRT, we developed and validated a nomogram to predict freedom from biochemical failure., Objective: This study aims to evaluate prostate-specific membrane antigen-positron emission tomography (PSMA-PET)-based sRT efficacy for postprostatectomy prostate-specific antigen (PSA) persistence or recurrence. Objectives include developing a random survival forest (RSF) model for predicting biochemical failure, comparing it with a Cox model, and assessing predictive accuracy over time. Multinational cohort data will validate the model's performance, aiming to improve clinical management of recurrent prostate cancer., Methods: This multicenter retrospective study collected data from 13 medical facilities across 5 countries: Germany, Cyprus, Australia, Italy, and Switzerland. A total of 1029 patients who underwent sRT following PSMA-PET-based assessment for PSA persistence or recurrence were included. Patients were treated between July 2013 and June 2020, with clinical decisions guided by PSMA-PET results and contemporary standards. The primary end point was freedom from biochemical failure, defined as 2 consecutive PSA rises >0.2 ng/mL after treatment. Data were divided into training (708 patients), testing (271 patients), and external validation (50 patients) sets for machine learning algorithm development and validation. RSF models were used, with 1000 trees per model, optimizing predictive performance using the Harrell concordance index and Brier score. Statistical analysis used R Statistical Software (R Foundation for Statistical Computing), and ethical approval was obtained from participating institutions., Results: Baseline characteristics of 1029 patients undergoing sRT PSMA-PET-based assessment were analyzed. The median age at sRT was 70 (IQR 64-74) years. PSMA-PET scans revealed local recurrences in 43.9% (430/979) and nodal recurrences in 27.2% (266/979) of patients. Treatment included dose-escalated sRT to pelvic lymphatics in 35.6% (349/979) of cases. The external outlier validation set showed distinct features, including higher rates of positive lymph nodes (47/50, 94% vs 266/979, 27.2% in the learning cohort) and lower delivered sRT doses (<66 Gy in 57/979, 5.8% vs 46/50, 92% of patients; P<.001). The RSF model, validated internally and externally, demonstrated robust predictive performance (Harrell C-index range: 0.54-0.91) across training and validation datasets, outperforming a previously published nomogram., Conclusions: The developed RSF model demonstrates enhanced predictive accuracy, potentially improving patient outcomes and assisting clinicians in making treatment decisions., (©Ali Janbain, Andrea Farolfi, Armelle Guenegou-Arnoux, Louis Romengas, Sophia Scharl, Stefano Fanti, Francesca Serani, Jan C Peeken, Sandrine Katsahian, Iosif Strouthos, Konstantinos Ferentinos, Stefan A Koerber, Marco E Vogel, Stephanie E Combs, Alexis Vrachimis, Alessio Giuseppe Morganti, Simon KB Spohn, Anca-Ligia Grosu, Francesco Ceci, Christoph Henkenberens, Stephanie GC Kroeze, Matthias Guckenberger, Claus Belka, Peter Bartenstein, George Hruby, Louise Emmett, Ali Afshar Omerieh, Nina-Sophie Schmidt-Hegemann, Lucas Mose, Daniel M Aebersold, Constantinos Zamboglou, Thomas Wiegel, Mohamed Shelan. Originally published in JMIR Cancer (https://cancer.jmir.org), 20.09.2024.)

Background: Bipolar disorder (BD) is associated with increased morbidity/mortality. Adverse outcome prediction might help with the management of patients with BD., Methods: We systematically reviewed the performance of machine learning (ML) studies in predicting adverse outcomes (relapse or recurrence, hospital admission, and suicide-related events) in patients with BD. Demographic, clinical, and neuroimaging-related poor outcome predictors were also reviewed. Three databases (PubMed, Scopus, and Web of Science) were explored from inception to July 2023., Results: Eighteen studies, accounting for >30,000 patients, were included. Support vector machine, decision trees, random forest, and logistic regression were the most frequently used ML algorithms. ML models' area under the receiver operating characteristic (ROC) curve (AUC), sensitivity, and specificity ranged from 0.71 to 0.98, 72.7-92.8 %, and 59.0-95.2 % for relapse/recurrence prediction (4 studies (3 on relapses and 1 on recurrences). The corresponding values were 0.78-0.88, 21.4-100 %, and 77.0-99.7 % for hospital admissions (3 studies, 21,266 patients), and 0.71-0.99, 44.4-97.9 %, and 38.9-95.0 % for suicide-related events (10 studies, 5558 patients). Also, one study addressed a combination of the interest outcomes. Adverse outcome predictors included early onset BD, BD type I, comorbid psychiatric or substance use disorder, circadian rhythm disruption, hospitalization characteristics, and neuroimaging parameters, including increased dynamic amplitude of low-frequency fluctuation, decreased frontolimbic functional connectivity and aberrant dynamic functional connectivity in corticostriatal circuitry., Conclusions: ML models can predict adverse outcomes of BD with relatively acceptable performance measures. Future studies with larger samples and nested cross-validation validation should be conducted to reach more reliable results., Competing Interests: Declaration of competing interest There are no financial/personal relationships with any people or organizations that could inappropriately influence this study. There are no potential competing interests including employment, consultancies, stock ownership, honoraria, paid expert testimony, patent applications/registrations, and grants or other funding., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Regional Wall Motion Abnormality (RWMA) serves as an early indicator of myocardial infarction (MI), the global leader in mortality. Accurate and early detection of RWMA is vital for the successful treatment of MI. Current automated echocardiography analyses typically concentrate on peak values from left ventricular (LV) displacement curves, based on LV contour annotations or key frames during the heart's systolic or diastolic phases within a single echocardiographic cycle. This approach may overlook the rich motion field features available in multi-cycle cardiac data, which could enhance RWMA detection., Methods: In this research, we put forward an innovative approach to detect RWMA by harnessing motion information across multiple echocardiographic cycles and multi-views. Our methodology synergizes U-Net-based segmentation with optical flow algorithms for detailed cardiac structure delineation, and Temporal Convolutional Networks (ConvNet) to extract nuanced motion features. We utilize a variety of machine learning and deep learning classifiers on both A2C and A4C views echocardiograms to enhance detection accuracy. A three-phase algorithm-originating from the HMC-QU dataset-incorporates U-Net for segmentation, followed by optical flow for cardiac wall motion field features. Temporal ConvNet, inspired by the Temporal Segment Network (TSN), is then applied to interpret these motion field features, independent of traditional cardiac parameter curves or specific key phase frame inputs., Results: Employing five-fold cross-validation, our SVM classifier demonstrated high performance, with a sensitivity of 93.13%, specificity of 83.61%, precision of 88.52%, and an F1 score of 90.39%. When compared with other studies using the HMC-QU datasets, these Fig s stand out, underlining our method's effectiveness. The classifier also attained an overall accuracy of 89.25% and Area Under the Curve (AUC) of 95%, reinforcing its potential for reliable RWMA detection in echocardiographic analysis., Conclusions: This research not only demonstrates a novel technique but also contributes a more comprehensive and precise tool for early myocardial infarction diagnosis., Competing Interests: NO authors have competing interests., (Copyright: © 2024 Kasim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: The incidence and mortality rates of cardiovascular disease worldwide are a major concern in the healthcare industry. Precise prediction of cardiovascular disease is essential, and the use of machine learning and deep learning can aid in decision-making and enhance predictive abilities., Objective: The goal of this paper is to introduce a model for precise cardiovascular disease prediction by combining machine learning and deep learning., Method: Two public heart disease classification datasets with 70,000 and 1190 records besides a locally collected dataset with 600 records were used in our experiments. Then, a model which makes use of both machine learning and deep learning was proposed in this paper. The proposed model employed CNN and LSTM, as the representatives of deep learning models, besides KNN and XGB, as the representatives of machine learning models. As each classifier defined the output classes, majority voting was then used as an ensemble learner to predict the final output class., Result: The proposed model obtained the highest classification performance based on all evaluation metrics on all datasets, demonstrating its suitability and reliability in forecasting the probability of cardiovascular disease., (© 2024. The Author(s).)

Data acquisition for transcriptomic studies used to be the bottleneck in the transcriptomic analytical pipeline. However, recent developments in transcriptome profiling technologies have increased researchers' ability to obtain data, resulting in a shift in focus to data analysis. Incorporating machine learning to traditional analytical methods allows the possibility of handling larger volumes of complex data more efficiently. Many bioinformaticians, especially those unfamiliar with ML in the study of human transcriptomics and complex biological systems, face a significant barrier stemming from their limited awareness of the current landscape of ML utilisation in this field. To address this gap, this review endeavours to introduce those individuals to the general types of ML, followed by a comprehensive range of more specific techniques, demonstrated through examples of their incorporation into analytical pipelines for human transcriptome investigations. Important computational aspects such as data pre-processing, task formulation, results (performance of ML models), and validation methods are encompassed. In hope of better practical relevance, there is a strong focus on studies published within the last five years, almost exclusively examining human transcriptomes, with outcomes compared with standard non-ML tools., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

In computational proteomics, machine learning (ML) has emerged as a vital tool for enhancing data analysis. Despite significant advancements, the diversity of ML model architectures and the complexity of proteomics data present substantial challenges in the effective development and evaluation of these tools. Here, we highlight the necessity for high-quality, comprehensive data sets to train ML models and advocate for the standardization of data to support robust model development. We emphasize the instrumental role of key data sets like ProteomeTools and MassIVE-KB in advancing ML applications in proteomics and discuss the implications of data set size on model performance, highlighting that larger data sets typically yield more accurate models. To address data scarcity, we explore algorithmic strategies such as self-supervised pretraining and multitask learning. Ultimately, we hope that this discussion can serve as a call to action for the proteomics community to collaborate on data standardization and collection efforts, which are crucial for the sustainable advancement and refinement of ML methodologies in the field.

Surface-enhanced Raman spectroscopy (SERS) has been well explored as a highly effective characterization technique that is capable of chemical pollutant detection and identification at very low concentrations. Machine learning has been previously used to identify compounds based on SERS spectral data. However, utilization of SERS to quantify concentrations, with or without machine learning, has been difficult due to the spectral intensity being sensitive to confounding factors such as the substrate parameters, orientation of the analyte, and sample preparation technique. Here, we demonstrate an approach for predicting the concentration of sample pollutants from SERS spectra using machine learning. Frequency domain transform methods, including the Fourier and Walsh-Hadamard transforms, are applied to spectral data sets of three analytes (rhodamine 6G, chlorpyrifos, and triclosan), which are then used to train machine learning algorithms. Using standard machine learning models, the concentration of the sample pollutants is predicted with >80% cross-validation accuracy from raw SERS data. A cross-validation accuracy of 85% was achieved using deep learning for a moderately sized data set (∼100 spectra), and 70-80% was achieved for small data sets (∼50 spectra). Performance can be maintained within this range even when combining various sample preparation techniques and environmental media interference. Additionally, as a spectral pretreatment, the Fourier and Hadamard transforms are shown to consistently improve prediction accuracy across multiple data sets. Finally, standard models were shown to accurately identify characteristic peaks of compounds via analysis of their importance scores, further verifying their predictive value.

Background: Machine learning algorithms as a research tool, including traditional machine learning and deep learning, are increasingly applied to the field of urodynamics. However, no studies have evaluated how to select appropriate algorithm models for different urodynamic research tasks., Methods: We undertook a narrative review evaluating how the published literature reports the applications of machine learning in urodynamics. We searched PubMed up to December 2023, limited to the English language. We selected the following search terms: artificial intelligence, machine learning, deep learning, urodynamics, and lower urinary tract symptoms. We identified three domains for assessment in advance of commencing the review. These were the applications of urodynamic studies examination, applications of diagnoses of dysfunction related to urodynamics, and applications of prognosis prediction., Results: The machine learning algorithm applied in the field of urodynamics can be mainly divided into three aspects, which are urodynamic examination, diagnosis of urinary tract dysfunction and prediction of the efficacy of various treatment methods. Most of these studies were single-center retrospective studies, lacking external validation, requiring further validation of model generalization ability, and insufficient sample size. The relevant research in this field is still in the preliminary exploration stage; there are few high-quality multi-center clinical studies, and the performance of various models still needs to be further optimized, and there is still a distance from clinical application., Conclusions: At present, there is no research to summarize and analyze the machine learning algorithms applied in the field of urodynamics. The purpose of this review is to summarize and classify the machine learning algorithms applied in this field and to guide researchers to select the appropriate algorithm model for different task requirements to achieve the best results., (© 2024 Wiley Periodicals LLC.)

Machine learning (ML) has led to significant advances in dentistry, easing the workload of professionals and improving the performance of various medical processes. The fields of periodontology and implantology can profit from these advances for tasks such as determining periodontally compromised teeth, assisting doctors in the implant planning process, determining types of implants, or predicting the occurrence of peri-implantitis. The current paper provides an overview of recent ML techniques applied in periodontology and implantology, aiming to identify popular models for different medical tasks, to assess the impact of the training data on the success of the automatic algorithms and to highlight advantages and disadvantages of various approaches. 48 original research papers, published between 2016 and 2023, were selected and divided into four classes: periodontology, implant planning, implant brands and types, and success of dental implants. These papers were analyzed in terms of aim, technical details, characteristics of training and testing data, results, and medical observations. The purpose of this paper is not to provide an exhaustive survey, but to show representative methods from recent literature that highlight the advantages and disadvantages of various approaches, as well as the potential of applying machine learning in dentistry., (© 2024. The Author(s).)

Examining the relationship between streetscape features and road traffic accidents is pivotal for enhancing roadway safety. While previous studies have primarily focused on the influence of street design characteristics, sociodemographic features, and land use features on crash occurrence, the impact of streetscape features on pedestrian crashes has not been thoroughly investigated. Furthermore, while machine learning models demonstrate high accuracy in prediction and are increasingly utilized in traffic safety research, understanding the prediction results poses challenges. To address these gaps, this study extracts streetscape environment characteristics from street view images (SVIs) using a combination of semantic segmentation and object detection deep learning networks. These characteristics are then incorporated into the eXtreme Gradient Boosting (XGBoost) algorithm, along with a set of control variables, to model the occurrence of pedestrian crashes at intersections. Subsequently, the SHapley Additive exPlanations (SHAP) method is integrated with XGBoost to establish an interpretable framework for exploring the association between pedestrian crash occurrence and the surrounding streetscape built environment. The results are interpreted from global, local, and regional perspectives. The findings indicate that, from a global perspective, traffic volume and commercial land use are significant contributors to pedestrian-vehicle collisions at intersections, while road, person, and vehicle elements extracted from SVIs are associated with higher risks of pedestrian crash onset. At a local level, the XGBoost-SHAP framework enables quantification of features' local contributions for individual intersections, revealing spatial heterogeneity in factors influencing pedestrian crashes. From a regional perspective, similar intersections can be grouped to define geographical regions, facilitating the formulation of spatially responsive strategies for distinct regions to reduce traffic accidents. This approach can potentially enhance the quality and accuracy of local policy making. These findings underscore the underlying relationship between streetscape-level environmental characteristics and vehicle-pedestrian crashes. The integration of SVIs and deep learning techniques offers a visually descriptive portrayal of the streetscape environment at locations where traffic crashes occur at eye level. The proposed framework not only achieves excellent prediction performance but also enhances understanding of traffic crash occurrences, offering guidance for optimizing traffic accident prevention and treatment programs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

In the last decade, artificial intelligence (AI) has significantly impacted ophthalmology, particularly in managing corneal diseases, a major reversible cause of blindness. This review explores AI's transformative role in the corneal subspecialty, which has adopted advanced technology for superior clinical judgment, early diagnosis, and personalized therapy. While AI's role in anterior segment diseases is less documented compared to glaucoma and retinal pathologies, this review highlights its integration into corneal diagnostics through imaging techniques like slit-lamp biomicroscopy, anterior segment optical coherence tomography (AS-OCT), and in vivo confocal biomicroscopy. AI has been pivotal in refining decision-making and prognosis for conditions such as keratoconus, infectious keratitis, and dystrophies. Multi-disease deep learning neural networks (MDDNs) have shown diagnostic ability in classifying corneal diseases using AS-OCT images, achieving notable metrics like an AUC of 0.910. AI's progress over two decades has significantly improved the accuracy of diagnosing conditions like keratoconus and microbial keratitis. For instance, AI has achieved a 90.7% accuracy rate in classifying bacterial and fungal keratitis and an AUC of 0.910 in differentiating various corneal diseases. Convolutional neural networks (CNNs) have enhanced the analysis of color-coded corneal maps, yielding up to 99.3% diagnostic accuracy for keratoconus. Deep learning algorithms have also shown robust performance in detecting fungal hyphae on in vivo confocal microscopy, with precise quantification of hyphal density. AI models combining tomography scans and visual acuity have demonstrated up to 97% accuracy in keratoconus staging according to the Amsler-Krumeich classification. However, the review acknowledges the limitations of current AI models, including their reliance on binary classification, which may not capture the complexity of real-world clinical presentations with multiple coexisting disorders. Challenges also include dependency on data quality, diverse imaging protocols, and integrating multimodal images for a generalized AI diagnosis. The need for interpretability in AI models is emphasized to foster trust and applicability in clinical settings. Looking ahead, AI has the potential to unravel the intricate mechanisms behind corneal pathologies, reduce healthcare's carbon footprint, and revolutionize diagnostic and management paradigms. Ethical and regulatory considerations will accompany AI's clinical adoption, marking an era where AI not only assists but augments ophthalmic care., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

The ICU is a specialized hospital department that offers critical care to patients at high risk. The massive burden of ICU-requiring care requires accurate and timely ICU outcome predictions for alleviating the economic and healthcare burdens imposed by critical care needs. Existing research faces challenges such as feature extraction difficulties, low accuracy, and resource-intensive features. Some studies have explored deep learning models that utilize raw clinical inputs. However, these models are considered non-interpretable black boxes, which prevents their wide application. The objective of the study is to develop a new method using stochastic signal analysis and machine learning techniques to effectively extract features with strong predictive power from ICU patients' real-time time series of vital signs for accurate and timely ICU outcome prediction. The results show the proposed method extracted meaningful features and outperforms baseline methods, including APACHE IV (AUC = 0.750), deep learning-based models (AUC = 0.732, 0.712, 0.698, 0.722), and statistical feature classification methods (AUC = 0.765) by a large margin (AUC = 0.869). The proposed method has clinical, management, and administrative implications since it enables healthcare professionals to identify deviations from prognostications timely and accurately and, therefore, to conduct proper interventions.

Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many diseases. The recent breakthrough in artificial intelligence has made it possible to predict protein-protein interactions and model their structures. Unfortunately, detecting antigen-binding sites associated with a specific antibody is still a challenging problem. To tackle this challenge, we implemented a deep learning model to characterize interaction patterns between antibodies and their corresponding antigens. With high accuracy, our model can distinguish between antibody-antigen complexes and other types of protein-protein complexes. More intriguingly, we can identify antigens from other common protein binding regions with an accuracy of higher than 70% even if we only have the epitope information. This indicates that antigens have distinct features on their surface that antibodies can recognize. Additionally, our model was unable to predict the partnerships between antibodies and their particular antigens. This result suggests that one antigen may be targeted by more than one antibody and that antibodies may bind to previously unidentified proteins. Taken together, our results support the precision of antibody-antigen interactions while also suggesting positive future progress in the prediction of specific pairing., Competing Interests: Declaration of competing interest The authors declare no conflict of interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data. In recent years, both multi-omics and ML have assisted in the escalation of CBM. Condition-specific omics data, such as transcriptomics and proteomics, helped contextualize the model prediction while analyzing a particular phenotypic signature. At the same time, the advanced ML tools have eased the model reconstruction and analysis to increase the accuracy and prediction power. However, the development of these multi-disciplinary methodological frameworks mainly occurs independently, which limits the concatenation of biological knowledge from different domains. Hence, we have reviewed the potential of integrating multi-disciplinary tools and strategies from various fields, such as synthetic biology, CBM, omics, and ML, to explore the biochemical phenomenon beyond the conventional biological dogma. How the integrative knowledge of these intersected domains has improved bioengineering and biomedical applications has also been highlighted. We categorically explained the conventional genome-scale metabolic model (GEM) reconstruction tools and their improvement strategies through ML paradigms. Further, the crucial role of ML and DL in omics data restructuring for GEM development has also been briefly discussed. Finally, the case-study-based assessment of the state-of-the-art method for improving biomedical and metabolic engineering strategies has been elaborated. Therefore, this review demonstrates how integrating experimental and in silico strategies can help map the ever-expanding knowledge of biological systems driven by condition-specific cellular information. This multiview approach will elevate the application of ML-based CBM in the biomedical and bioengineering fields for the betterment of society and the environment., Competing Interests: Declaration of competing interest The authors reported no potential conflict of interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Optical continuous glucose monitoring (CGM) systems are emerging for personalized glucose management owing to their lower cost and prolonged durability compared to conventional electrochemical CGMs. Here, we report a computational CGM system, which integrates a biocompatible phosphorescence-based insertable biosensor and a custom-designed phosphorescence lifetime imager (PLI). This compact and cost-effective PLI is designed to capture phosphorescence lifetime images of an insertable sensor through the skin, where the lifetime of the emitted phosphorescence signal is modulated by the local concentration of glucose. Because this phosphorescence signal has a very long lifetime compared to tissue autofluorescence or excitation leakage processes, it completely bypasses these noise sources by measuring the sensor emission over several tens of microseconds after the excitation light is turned off. The lifetime images acquired through the skin are processed by neural network-based models for misalignment-tolerant inference of glucose levels, accurately revealing normal, low (hypoglycemia) and high (hyperglycemia) concentration ranges. Using a 1 mm thick skin phantom mimicking the optical properties of human skin, we performed in vitro testing of the PLI using glucose-spiked samples, yielding 88.8% inference accuracy, also showing resilience to random and unknown misalignments within a lateral distance of ∼4.7 mm with respect to the position of the insertable sensor underneath the skin phantom. Furthermore, the PLI accurately identified larger lateral misalignments beyond 5 mm, prompting user intervention for realignment. The misalignment-resilient glucose concentration inference capability of this compact and cost-effective PLI makes it an appealing wearable diagnostics tool for real-time tracking of glucose and other biomarkers.

Molecular Property Prediction (MPP) is vital for drug discovery, crop protection, and environmental science. Over the last decades, diverse computational techniques have been developed, from using simple physical and chemical properties and molecular fingerprints in statistical models and classical machine learning to advanced deep learning approaches. In this review, we aim to distill insights from current research on employing transformer models for MPP. We analyze the currently available models and explore key questions that arise when training and fine-tuning a transformer model for MPP. These questions encompass the choice and scale of the pretraining data, optimal architecture selections, and promising pretraining objectives. Our analysis highlights areas not yet covered in current research, inviting further exploration to enhance the field's understanding. Additionally, we address the challenges in comparing different models, emphasizing the need for standardized data splitting and robust statistical analysis.

Background: Mental stress and its consequent mental health disorders (MDs) constitute a significant public health issue. With the advent of machine learning (ML), there is potential to harness computational techniques for better understanding and addressing mental stress and MDs. This comprehensive review seeks to elucidate the current ML methodologies used in this domain to pave the way for enhanced detection, prediction, and analysis of mental stress and its subsequent MDs., Objective: This review aims to investigate the scope of ML methodologies used in the detection, prediction, and analysis of mental stress and its consequent MDs., Methods: Using a rigorous scoping review process with PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines, this investigation delves into the latest ML algorithms, preprocessing techniques, and data types used in the context of stress and stress-related MDs., Results: A total of 98 peer-reviewed publications were examined for this review. The findings highlight that support vector machine, neural network, and random forest models consistently exhibited superior accuracy and robustness among all ML algorithms examined. Physiological parameters such as heart rate measurements and skin response are prevalently used as stress predictors due to their rich explanatory information concerning stress and stress-related MDs, as well as the relative ease of data acquisition. The application of dimensionality reduction techniques, including mappings, feature selection, filtering, and noise reduction, is frequently observed as a crucial step preceding the training of ML algorithms., Conclusions: The synthesis of this review identified significant research gaps and outlines future directions for the field. These encompass areas such as model interpretability, model personalization, the incorporation of naturalistic settings, and real-time processing capabilities for the detection and prediction of stress and stress-related MDs., (©Moein Razavi, Samira Ziyadidegan, Ahmadreza Mahmoudzadeh, Saber Kazeminasab, Elaheh Baharlouei, Vahid Janfaza, Reza Jahromi, Farzan Sasangohar. Originally published in JMIR Mental Health (https://mental.jmir.org), 21.08.2024.)

Background: Electronic health records (EHRs) contain patients' health information over time, including possible early indicators of disease. However, the increasing amount of data hinders clinicians from using them. There is accumulating evidence suggesting that machine learning (ML) and deep learning (DL) can assist clinicians in analyzing these large-scale EHRs, as algorithms thrive on high volumes of data. Although ML has become well developed, studies mainly focus on engineering but lack medical outcomes., Objective: This study aims for a scoping review of the evidence on how the use of ML on longitudinal EHRs can support the early detection and prevention of disease. The medical insights and clinical benefits that have been generated were investigated by reviewing applications in a variety of diseases., Methods: This study was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. A literature search was performed in 2022 in collaboration with a medical information specialist in the following databases: PubMed, Embase, Web of Science Core Collection (Clarivate Analytics), and IEEE Xplore Digital Library and computer science bibliography. Studies were eligible when longitudinal EHRs were used that aimed for the early detection of disease via ML in a prevention context. Studies with a technical focus or using imaging or hospital admission data were beyond the scope of this review. Study screening and selection and data extraction were performed independently by 2 researchers., Results: In total, 20 studies were included, mainly published between 2018 and 2022. They showed that a variety of diseases could be detected or predicted, particularly diabetes; kidney diseases; diseases of the circulatory system; and mental, behavioral, and neurodevelopmental disorders. Demographics, symptoms, procedures, laboratory test results, diagnoses, medications, and BMI were frequently used EHR data in basic recurrent neural network or long short-term memory techniques. By developing and comparing ML and DL models, medical insights such as a high diagnostic performance, an earlier detection, the most important predictors, and additional health indicators were obtained. A clinical benefit that has been evaluated positively was preliminary screening. If these models are applied in practice, patients might also benefit from personalized health care and prevention, with practical benefits such as workload reduction and policy insights., Conclusions: Longitudinal EHRs proved to be helpful for support in health care. Current ML models on EHRs can support the detection of diseases in terms of accuracy and offer preliminary screening benefits. Regarding the prevention of diseases, ML and specifically DL models can accurately predict or detect diseases earlier than current clinical diagnoses. Adding personally responsible factors allows targeted prevention interventions. While ML models based on textual EHRs are still in the developmental stage, they have high potential to support clinicians and the health care system and improve patient outcomes., (©Laura Swinckels, Frank C Bennis, Kirsten A Ziesemer, Janneke F M Scheerman, Harmen Bijwaard, Ander de Keijzer, Josef Jan Bruers. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 20.08.2024.)

Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results. Feature selection and feature extraction are two pivotal techniques employed to address these challenges by reducing the dimensionality of the data, thereby enhancing model performance, interpretability, and computational efficiency. Feature selection and feature extraction can be categorized into statistical and machine learning methods. The present study conducts a comprehensive and comparative review of various statistical, machine learning, and deep learning-based feature selection and extraction techniques specifically tailored for NGS and microarray data interpretation of humankind. A thorough literature search was performed to gather information on these techniques, focusing on array-based and NGS data analysis. Various techniques, including deep learning architectures, machine learning algorithms, and statistical methods, have been explored for microarray, bulk RNA-Seq, and single-cell, single-cell RNA-Seq (scRNA-Seq) technology-based datasets surveyed here. The study provides an overview of these techniques, highlighting their applications, advantages, and limitations in the context of high-dimensional NGS data. This review provides better insights for readers to apply feature selection and feature extraction techniques to enhance the performance of predictive models, uncover underlying biological patterns, and gain deeper insights into massive and complex NGS and microarray data., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

TB/HIV coinfection poses a complex public health challenge. Accurate forecasting of future trends is essential for efficient resource allocation and intervention strategy development. This study compares classical statistical and machine learning models to predict TB/HIV coinfection cases stratified by gender and the general populations. We analyzed time series data using exponential smoothing and ARIMA to establish the baseline trend and seasonality. Subsequently, machine learning models (SVR, XGBoost, LSTM, CNN, GRU, CNN-GRU, and CNN-LSTM) were employed to capture the complex dynamics and inherent non-linearities of TB/HIV coinfection data. Performance metrics (MSE, MAE, sMAPE) and the Diebold-Mariano test were used to evaluate the model performance. Results revealed that Deep Learning models, particularly Bidirectional LSTM and CNN-LSTM, significantly outperformed classical methods. This demonstrates the effectiveness of Deep Learning for modeling TB/HIV coinfection time series and generating more accurate forecasts., (© 2024. The Author(s).)

The concept of 'brain age', derived from neuroimaging data, serves as a crucial biomarker reflecting cognitive vitality and neurodegenerative trajectories. In the past decade, machine learning (ML) and deep learning (DL) integration has transformed the field, providing advanced models for brain age estimation. However, achieving precise brain age prediction across all ages remains a significant analytical challenge. This comprehensive review scrutinizes advancements in ML- and DL-based brain age prediction, analyzing 52 peer-reviewed studies from 2020 to 2024. It assesses various model architectures, highlighting their effectiveness and nuances in lifespan brain age studies. By comparing ML and DL, strengths in forecasting and methodological limitations are revealed. Finally, key findings from the reviewed articles are summarized and a number of major issues related to ML/DL-based lifespan brain age prediction are discussed. Through this study, we aim at the synthesis of the current state of brain age prediction, emphasizing both advancements and persistent challenges, guiding future research, technological advancements, and improving early intervention strategies for neurodegenerative diseases.

Parkinson's disease (PD) exhibits heterogeneity in terms of symptoms and prognosis, likely due to diverse neuroanatomical alterations. This study employs a contrastive deep learning approach to analyze Magnetic Resonance Imaging (MRI) data from 932 PD patients and 366 controls, aiming to disentangle PD-specific neuroanatomical alterations. The results reveal that these neuroanatomical alterations in PD are correlated with individual differences in dopamine transporter binding deficit, neurodegeneration biomarkers, and clinical severity and progression. The correlation with clinical severity is verified in an external cohort. Notably, certain proteins in the cerebrospinal fluid are strongly associated with PD-specific features, particularly those involved in the immune function. The most notable neuroanatomical alterations are observed in both subcortical and temporal regions. Our findings provide deeper insights into the patterns of brain atrophy in PD and potential underlying molecular mechanisms, paving the way for earlier patient stratification and the development of treatments to slow down neurodegeneration., (© 2024. The Author(s).)

Introduction: Intraoperative Hypotension (IOH) poses a substantial risk during surgical procedures. The integration of Artificial Intelligence (AI) in predicting IOH holds promise for enhancing detection capabilities, providing an opportunity to improve patient outcomes. This systematic review and meta analysis explores the intersection of AI and IOH prediction, addressing the crucial need for effective monitoring in surgical settings., Method: A search of Pubmed, Scopus, Web of Science, and Embase was conducted. Screening involved two-phase assessments by independent reviewers, ensuring adherence to predefined PICOS criteria. Included studies focused on AI models predicting IOH in any type of surgery. Due to the high number of studies evaluating the hypotension prediction index (HPI), we conducted two sets of meta-analyses: one involving the HPI studies and one including non-HPI studies. In the HPI studies the following outcomes were analyzed: cumulative duration of IOH per patient, time weighted average of mean arterial pressure < 65 (TWA-MAP < 65), area under the threshold of mean arterial pressure (AUT-MAP), and area under the receiver operating characteristics curve (AUROC). In the non-HPI studies, we examined the pooled AUROC of all AI models other than HPI., Results: 43 studies were included in this review. Studies showed significant reduction in IOH duration, TWA-MAP < 65 mmHg, and AUT-MAP < 65 mmHg in groups where HPI was used. AUROC for HPI algorithms demonstrated strong predictive performance (AUROC = 0.89, 95CI). Non-HPI models had a pooled AUROC of 0.79 (95CI: 0.74, 0.83)., Conclusion: HPI demonstrated excellent ability to predict hypotensive episodes and hence reduce the duration of hypotension. Other AI models, particularly those based on deep learning methods, also indicated a great ability to predict IOH, while their capacity to reduce IOH-related indices such as duration remains unclear., (© 2024. The Author(s).)

Atrial fibrillation (AF) prediction and screening are of important clinical interest because of the potential to prevent serious adverse events. Devices capable of detecting short episodes of arrhythmia are now widely available. Although it has recently been suggested that some high-risk patients with AF detected on implantable devices may benefit from anticoagulation, long-term management remains challenging in lower-risk patients and in those with AF detected on monitors or wearable devices as the development of clinically meaningful arrhythmia burden in this group remains unknown. Identification and prediction of clinically relevant AF is therefore of unprecedented importance to the cardiologic community. Family history and underlying genetic markers are important risk factors for AF. Recent studies suggest a good predictive ability of polygenic risk scores, with a possible additive value to clinical AF prediction scores. Artificial intelligence, enabled by the exponentially increasing computing power and digital data sets, has gained traction in the past decade and is of increasing interest in AF prediction using a single or multiple lead sinus rhythm electrocardiogram. Integrating these novel approaches could help predict AF substrate severity, thereby potentially improving the effectiveness of AF screening and personalizing the management of patients presenting with conditions such as embolic stroke of undetermined source or subclinical AF. This review presents current evidence surrounding deep learning and polygenic risk scores in the prediction of incident AF and provides a futuristic outlook on possible ways of implementing these modalities into clinical practice, while considering current limitations and required areas of improvement., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Cardiology.)

This review presents a comprehensive history of Artificial Intelligence (AI) in the context of the revolutionary application of machine learning (ML) to medical research and clinical utilization, particularly for the benefit of researchers interested in the application of ML in otology. To this end, we discuss the key components of ML-input, output, and algorithms. In particular, some representation algorithms commonly used in medical research are discussed. Subsequently, we review ML applications in otology research, including diagnosis, influential identification, and surgical outcome prediction. In the context of surgical outcome prediction, specific surgical treatments, including cochlear implantation, active middle ear implantation, tympanoplasty, and vestibular schwannoma resection, are considered. Finally, we highlight the obstacles and challenges that need to be overcome in future research., Competing Interests: Declaration of competing interest The author has no conflict of interest to disclose regarding this article., (Copyright © 2024. Published by Elsevier B.V.)

Nuclear magnetic resonance (NMR) crystallography is one of the main methods in structural biology for analyzing protein stereochemistry and structure. The chemical shift of the resonance frequency reflects the effect of the protons in a molecule producing distinct NMR signals in different chemical environments. Apprehending chemical shifts from NMR signals can be challenging since having an NMR structure does not necessarily provide all the required chemical shift information, making predictive models essential for accurately deducing chemical shifts, either from protein structures or, more ideally, directly from amino acid sequences. Here, we present EFG-CS, a web server that specializes in chemical shift prediction. EFG-CS employs a machine learning-based transfer prediction model for backbone atom chemical shift prediction, using ESMFold-predicted protein structures. Additionally, ESG-CS incorporates a graph neural network-based model to provide comprehensive side-chain atom chemical shift predictions. Our method demonstrated reliable performance in backbone atom prediction, achieving comparable accuracy levels with root mean square errors (RMSE) of 0.30 ppm for H, 0.22 ppm for Hα, 0.89 ppm for C, 0.89 ppm for Cα, 0.84 ppm for Cβ, and 1.69 ppm for N. Moreover, our approach also showed predictive capabilities in side-chain atom chemical shift prediction achieving RMSE values of 0.71 ppm for Hβ, 0.74-1.15 ppm for Hδ, and 0.58-0.94 ppm for Hγ, solely utilizing amino acid sequences without homology or feature curation. This work shows for the first time that generative AI protein models can predict NMR shifts nearly comparable to experimental models. This web server is freely available at https://biosig.lab.uq.edu.au/efg&#95;cs, and the chemical shift prediction results can be downloaded in tabular format and visualized in 3D format., (© 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

The National Cancer Institute and the Department of Energy strategic partnership applies advanced computing and predictive machine learning and deep learning models to automate the capture of information from unstructured clinical text for inclusion in cancer registries. Applications include extraction of key data elements from pathology reports, determination of whether a pathology or radiology report is related to cancer, extraction of relevant biomarker information, and identification of recurrence. With the growing complexity of cancer diagnosis and treatment, capturing essential information with purely manual methods is increasingly difficult. These new methods for applying advanced computational capabilities to automate data extraction represent an opportunity to close critical information gaps and create a nimble, flexible platform on which new information sources, such as genomics, can be added. This will ultimately provide a deeper understanding of the drivers of cancer and outcomes in the population and increase the timeliness of reporting. These advances will enable better understanding of how real-world patients are treated and the outcomes associated with those treatments in the context of our complex medical and social environment., (Published by Oxford University Press 2024.)

Providing a model that achieves a strong predictive performance and is simultaneously interpretable by humans is one of the most difficult challenges in machine learning research due to the conflicting nature of these two objectives. To address this challenge, we propose a modification of the radial basis function neural network model by equipping its Gaussian kernel with a learnable precision matrix. We show that precious information is contained in the spectrum of the precision matrix that can be extracted once the training of the model is completed. In particular, the eigenvectors explain the directions of maximum sensitivity of the model revealing the active subspace and suggesting potential applications for supervised dimensionality reduction. At the same time, the eigenvectors highlight the relationship in terms of absolute variation between the input and the latent variables, thereby allowing us to extract a ranking of the input variables based on their importance to the prediction task enhancing the model interpretability. We conducted numerical experiments for regression, classification, and feature selection tasks, comparing our model against popular machine learning models, the state-of-the-art deep learning-based embedding feature selection techniques, and a transformer model for tabular data. Our results demonstrate that the proposed model does not only yield an attractive prediction performance compared to the competitors but also provides meaningful and interpretable results that potentially could assist the decision-making process in real-world applications. A PyTorch implementation of the model is available on GitHub at the following link. 1 ., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Objective: To construct a risk prediction model for assisted diagnosis of Diabetic Nephropathy (DN) using machine learning algorithms, and to validate it internally and externally., Methods: Firstly, the data was cleaned and enhanced, and was divided into training and test sets according to the 7:3 ratio. Then, the metrics related to DN were filtered by difference analysis, Least Absolute Shrinkage and Selection Operator (LASSO), Recursive Feature Elimination (RFE), and Max-relevance and Min-redundancy (MRMR) algorithms. Ten machine learning models were constructed based on the key variables. The best model was filtered by Receiver Operating Characteristic (ROC), Precision-Recall (PR), Accuracy, Matthews Correlation Coefficient (MCC), and Kappa, and was internally and externally validated. Based on the best model, an online platform had been constructed., Results: 15 key variables were selected, and among the 10 machine learning models, the Random Forest model achieved the best predictive performance. In the test set, the area under the ROC curve was 0.912, and in two external validation cohorts, the area under the ROC curve was 0.828 and 0.863, indicating excellent predictive and generalization abilities., Conclusion: The model has a good predictive value and is expected to help in the early diagnosis and screening of clinical DN., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The two main things needed to fulfill the world's impending need for water in the face of the widespread water crisis are collecting water and recycling. To do this, the present study has placed a greater focus on water management strategies used in a variety of contexts areas. To distribute water effectively, save it, and satisfy water quality requirements for a variety of uses, it is imperative to apply intelligent water management mechanisms while keeping in mind the population density index. The present review unveiled the latest trends in water and wastewater recycling, utilizing several Artificial Intelligence (AI) and machine learning (ML) techniques for distribution, rainfall collection, and control of irrigation models. The data collected for these purposes are unique and comes in different forms. An efficient water management system could be developed with the use of AI, Deep Learning (DL), and the Internet of Things (IoT) structure. This study has investigated several water management methodologies using AI, DL and IoT with case studies and sample statistical assessment, to provide an efficient framework for water management., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Machine learning (ML) is changing the way health care is practiced and recent applications of these novel statistical techniques have started to impact orthopaedic sports medicine. Machine learning enables the analysis of large volumes of data to establish complex relationships between "input" and "output" variables. These relationships may be more complex than could be established through traditional statistical analysis and can lead to the ability to predict the "output" with high levels of accuracy. Supervised learning is the most common ML approach for healthcare data and recent studies have developed algorithms to predict patient-specific outcome after surgical procedures such as hip arthroscopy and anterior cruciate ligament reconstruction. Deep learning is a higher-level ML approach that facilitates the processing and interpretation of complex datasets through artificial neural networks that are inspired by the way the human brain processes information. In orthopaedic sports medicine, deep learning has primarily been used for automatic image (computer vision) and text (natural language processing) interpretation. While applications in orthopaedic sports medicine have been increasing exponentially, one significant barrier to widespread adoption of ML remains clinician unfamiliarity with the associated methods and concepts. The goal of this review is to introduce these concepts, review current machine learning models in orthopaedic sport medicine, and discuss future opportunities for innovation within the specialty., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Introduction: Predicting postoperative incontinence beforehand is crucial for intensified and personalized rehabilitation after robot-assisted radical prostatectomy. Although nomograms exist, their retrospective limitations highlight artificial intelligence (AI)'s potential. This study seeks to develop a machine learning algorithm using robot-assisted radical prostatectomy (RARP) data to predict postoperative incontinence, advancing personalized care. Materials and Methods: In this propsective observational study, patients with localized prostate cancer undergoing RARP between April 2022 and January 2023 were assessed. Preoperative variables included age, body mass index, prostate-specific antigen (PSA) levels, digital rectal examination (DRE) results, Gleason score, International Society of Urological Pathology grade, and continence and potency questionnaires responses. Intraoperative factors, postoperative outcomes, and pathological variables were recorded. Urinary continence was evaluated using the Expanded Prostate cancer Index Composite questionnaire, and machine learning models (XGBoost, Random Forest, Logistic Regression) were explored to predict incontinence risk. The chosen model's SHAP values elucidated variables impacting predictions. Results: A dataset of 227 patients undergoing RARP was considered for the study. Post-RARP complications were predominantly low grade, and urinary continence rates were 74.2%, 80.7%, and 91.4% at 7, 13, and 90 days after catheter removal, respectively. Employing machine learning, XGBoost proved the most effective in predicting postoperative incontinence risk. Significant variables identified by the algorithm included nerve-sparing approach, age, DRE, and total PSA. The model's threshold of 0.67 categorized patients into high or low risk, offering personalized predictions about the risk of incontinence after surgery. Conclusions: Predicting postoperative incontinence is crucial for tailoring rehabilitation after RARP. Machine learning algorithm, particularly XGBoost, can effectively identify those variables more heavily, impacting the outcome of postoperative continence, allowing to build an AI-driven model addressing the current challenges in post-RARP rehabilitation.

One of the most remarkable techniques recently introduced into the field of bioprocess engineering is machine learning. Bioprocess engineering has drawn much attention due to its vast application in different domains like biopharmaceuticals, fossil fuel alternatives, environmental remediation, and food and beverage industry, etc. However, due to their unpredictable mechanisms, they are very often challenging to optimize. Furthermore, biological systems are extremely complicated; hence, machine learning algorithms could potentially be utilized to improve and build new biotechnological processes. Gaining insight into the fundamental mathematical understanding of commonly used machine learning algorithms, including Support Vector Machine, Principal Component Analysis, Partial Least Squares and Reinforcement Learning, the present study aims to discuss various case studies related to the application of machine learning in bioprocess engineering. Recent advancements as well as challenges posed in this area along with their potential solutions are also presented., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Introduction: This systematic review aims to evaluate the use of machine learning and artificial intelligence in hernia surgery., Methods: The PRISMA guidelines were followed throughout this systematic review. The ROBINS-I and Rob 2 tools were used to perform qualitative assessment of all studies included in this review. Recommendations were then summarized for the following pre-defined key items: protocol, research question, search strategy, study eligibility, data extraction, study design, risk of bias, publication bias, and statistical analysis., Results: A total of 13 articles were ultimately included for this review, describing the use of machine learning and deep learning for hernia surgery. All studies were published from 2020 to 2023. Articles varied regarding the population studied, type of machine learning or Deep Learning Model (DLM) used, and hernia type. Of the thirteen included studies, all included either inguinal, ventral, or incisional hernias. Four studies evaluated recognition of surgical steps during inguinal hernia repair videos. Two studies predicted outcomes using image-based DMLs. Seven studies developed and validated deep learning algorithms to predict outcomes and identify factors associated with postoperative complications., Conclusion: The use of ML for abdominal wall reconstruction has been shown to be a promising tool for predicting outcomes and identifying factors that could lead to postoperative complications., (© 2024. The Author(s), under exclusive licence to Springer-Verlag France SAS, part of Springer Nature.)

The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such a major viral outbreak demands early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. Due to the continued evolution of the SARS-CoV-2 pandemic, researchers worldwide are working to mitigate, suppress its spread, and better understand it by deploying deep learning and machine learning approaches. In a general computational context for biomedical data analysis, DNA sequence classification is a crucial challenge. Several machine and deep learning techniques have been used in recent years to complete this task with some success. The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art deep learning-based models are proposed using two DNA sequence conversion methods. We also proposed a novel multi-transformer deep learning model and pairwise features fusion technique for DNA sequence classification. Furthermore, deep features are extracted from the last layer of the multi-transformer and used in machine-learning models for DNA sequence classification. The k-mer and one-hot encoding sequence conversion techniques have been presented. The proposed multi-transformer achieved the highest performance in COVID DNA sequence classification. Automatic identification and classification of viruses are essential to avoid an outbreak like COVID-19. It also helps in detecting the effect of viruses and drug design., Competing Interests: Declaration of competing interest All authors declared that they have no conflict of interest in this work., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background and Purpose: Intracranial hemorrhage (ICH) in leukemia patients progresses rapidly with high mortality. Limited data are available on imaging studies in this population. The study aims to develop prediction models for 7-day and short-term mortality risk based on the non-contrast computed tomography (NCCT) image features., Methods: The NCCT image features of ICH in 135 leukemia patients between 2007-2023 were retrospectively extracted using manual assessment and radiomics methods. After multiple imputation of missing laboratory data, univariate logistic regression and least absolute shrinkage and selection operator (LASSO) were used for feature selection. Random forest models were built with comprehensive evaluation and ranking of feature importance., Result: 135 and 129 patients were included in the studies for 7-day and short-term prognostic models, respectively. The median age of all enrolled patients was 35 years, and there were 86 male patients (63.7 %). Clinical models (validation: AUC [area under the curve] = 0.78, AUPRC [area under the precision-recall curve] = 0.73; AUC = 0.84, AUPRC = 0.86), radiomics models (validation: AUC = 0.82, AUPRC = 0.78; AUC = 0.75, AUPRC = 0.77), and the combined models (validation: AUC = 0.84, AUPRC = 0.83; AUC = 0.87, AUPRC = 0.89) predicted 7-day and short-term mortality with good predictive efficacy. Clinical decision curve analysis showed that the combined models predicted 7-day and 30-day risk of death would be more beneficial than other models. Shape features contributed significantly more than semantic features in both radiomics models and combined models (93.3 %, 52.1 %, as well as 85.2 %,37.4 %, respectively) for 7-day and 30-day mortality., Conclusions: Combined models constructed based on NCCT perform well in predicting the risk of 7-day and short-term mortality in ICH patients with leukemia. Shape features extracted by radiomics are important markers for modeling the prognosis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Objectives: The surge in patient portal messages (PPMs) with increasing needs and workloads for efficient PPM triage in healthcare settings has spurred the exploration of AI-driven solutions to streamline the healthcare workflow processes, ensuring timely responses to patients to satisfy their healthcare needs. However, there has been less focus on isolating and understanding patient primary concerns in PPMs-a practice which holds the potential to yield more nuanced insights and enhances the quality of healthcare delivery and patient-centered care., Materials and Methods: We propose a fusion framework to leverage pretrained language models (LMs) with different language advantages via a Convolution Neural Network for precise identification of patient primary concerns via multi-class classification. We examined 3 traditional machine learning models, 9 BERT-based language models, 6 fusion models, and 2 ensemble models., Results: The outcomes of our experimentation underscore the superior performance achieved by BERT-based models in comparison to traditional machine learning models. Remarkably, our fusion model emerges as the top-performing solution, delivering a notably improved accuracy score of 77.67 ± 2.74% and an F1 score of 74.37 ± 3.70% in macro-average., Discussion: This study highlights the feasibility and effectiveness of multi-class classification for patient primary concern detection and the proposed fusion framework for enhancing primary concern detection., Conclusions: The use of multi-class classification enhanced by a fusion of multiple pretrained LMs not only improves the accuracy and efficiency of patient primary concern identification in PPMs but also aids in managing the rising volume of PPMs in healthcare, ensuring critical patient communications are addressed promptly and accurately., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

Background: Spinal cord injury (SCI) is a significant public health issue, leading to physical, psychological, and social complications. Machine learning (ML) algorithms have shown potential in diagnosing and predicting the functional and neurologic outcomes of subjects with SCI. ML algorithms can predict scores for SCI classification systems and accurately predict outcomes by analyzing large amounts of data. This systematic review aimed to examine the performance of ML algorithms for diagnosing and predicting the outcomes of subjects with SCI., Methods: The literature was comprehensively searched for the pertinent studies from inception to May 25, 2023. Therefore, electronic databases of PubMed, Embase, Scopus, and Web of Science were systematically searched with individual search syntax., Results: A total of 9424 individuals diagnosed with SCI across multiple studies were analyzed. Among the 21 studies included, 5 specifically aimed to evaluate diagnostic accuracy, while the remaining 16 focused on exploring prognostic factors or management strategies., Conclusions: ML and deep learning (DL) have shown great potential in various aspects of SCI. ML and DL algorithms have been employed multiple times in predicting and diagnosing patients with SCI. While there are studies on diagnosing acute SCI using DL algorithms, further research is required in this area., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: Alzheimer's disease (AD) is the most prevalent cause of dementia, characterized by a steady decline in mental, behavioral, and social abilities and impairs a person's capacity for independent functioning. It is a fatal neurodegenerative disease primarily affecting older adults., Objectives: The purpose of this literature review is to investigate various AD detection techniques, datasets, input modalities, algorithms, libraries, and performance evaluation metrics used to determine which model or strategy may provide superior performance., Method: The initial search yielded 807 papers, but only 100 research articles were chosen after applying the inclusion-exclusion criteria. This SLR analyzed research items published between January 2019 and December 2022. The ACM, Elsevier, IEEE Xplore Digital Library, PubMed, Springer and Taylor & Francis were systematically searched. The current study considers articles that used Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), APOe4 genotype, Diffusion Tensor Imaging (DTI) and Cerebrospinal Fluid (CSF) biomarkers. The study was performed following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines., Conclusion: According to the literature survey, most studies (n = 76) used the DL strategy. The datasets used by studies were primarily derived from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The majority of studies (n = 73) used single-modality neuroimaging data, while the remaining used multi-modal input data. In a multi-modality approach, the combination of MRI and PET scans is commonly preferred. Also, Regarding the algorithm used, Convolution Neural Network (CNN) showed the highest accuracy, 100 %, in classifying AD vs. CN subjects whereas the SVM was the most common ML algorithm, with a maximum accuracy of 99.82 %., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Skin cancer is a lethal disease, and its early detection plays a pivotal role in preventing its spread to other body organs and tissues. Artificial Intelligence (AI)-based automated methods can play a significant role in its early detection. This study presents an AI-based novel approach, termed 'DualAutoELM' for the effective identification of various types of skin cancers. The proposed method leverages a network of autoencoders, comprising two distinct autoencoders: the spatial autoencoder and the FFT (Fast Fourier Transform)-autoencoder. The spatial-autoencoder specializes in learning spatial features within input lesion images whereas the FFT-autoencoder learns to capture textural and distinguishing frequency patterns within transformed input skin lesion images through the reconstruction process. The use of attention modules at various levels within the encoder part of these autoencoders significantly improves their discriminative feature learning capabilities. An Extreme Learning Machine (ELM) with a single layer of feedforward is trained to classify skin malignancies using the characteristics that were recovered from the bottleneck layers of these autoencoders. The 'HAM10000' and 'ISIC-2017' are two publicly available datasets used to thoroughly assess the suggested approach. The experimental findings demonstrate the accuracy and robustness of the proposed technique, with AUC, precision, and accuracy values for the 'HAM10000' dataset being 0.98, 97.68% and 97.66%, and for the 'ISIC-2017' dataset being 0.95, 86.75% and 86.68%, respectively. This study highlights the possibility of the suggested approach for accurate detection of skin cancer., (© 2024. The Author(s).)

3D (Bio)printing is a highly effective method for fabricating tissue engineering scaffolds, renowned for their exceptional precision and control. Artificial intelligence (AI) has become a crucial technology in this field, capable of learning and replicating complex patterns that surpass human capabilities. However, the integration of AI in tissue engineering is often hampered by the lack of comprehensive and reliable data. This study addresses these challenges by providing one of the most extensive datasets on 3D-printed scaffolds. It provides the most comprehensive open-source dataset and employs various AI techniques, from unsupervised to supervised learning. This dataset includes detailed information on 1171 scaffolds, featuring a variety of biomaterials and concentrations-including 60 biomaterials such as natural and synthesized biomaterials, crosslinkers, enzymes, etc.-along with 49 cell lines, cell densities, and different printing conditions. We used over 40 machine learning and deep learning algorithms, tuning their hyperparameters to reveal hidden patterns and predict cell response, printability, and scaffold quality. The clustering analysis using KMeans identified five distinct ones. In classification tasks, algorithms such as XGBoost, Gradient Boosting, Extra Trees Classifier, Random Forest Classifier, and LightGBM demonstrated superior performance, achieving higher accuracy and F1 scores. A fully connected neural network with six hidden layers from scratch was developed, precisely tuning its hyperparameters for accurate predictions. The developed dataset and the associated code are publicly available onhttps://github.com/saeedrafieyan/MLATEto promote future research., (© 2024 IOP Publishing Ltd.)

Engineering enzyme-substrate binding pockets is the most efficient approach for modifying catalytic activity, but is limited if the substrate binding sites are indistinct. Here, we developed a 3D convolutional neural network for predicting protein-ligand binding sites. The network was integrated by DenseNet, UNet, and self-attention for extracting features and recovering sample size. We attempted to enlarge the dataset by data augmentation, and the model achieved success rates of 48.4%, 35.5%, and 43.6% at a precision of ≥50% and 52%, 47.6%, and 58.1%. The distance of predicted and real center is ≤4 Å, which is based on SC6K, COACH420, and BU48 validation datasets. The substrate binding sites of Klebsiella variicola acid phosphatase (KvAP) and Bacillus anthracis proline 4-hydroxylase (BaP4H) were predicted using DUnet, showing high competitive performance of 53.8% and 56% of the predicted binding sites that critically affected the catalysis of KvAP and BaP4H. Virtual saturation mutagenesis was applied based on the predicted binding sites of KvAP, and the top-ranked 10 single mutations contributed to stronger enzyme-substrate binding varied while the predicted sites were different. The advantage of DUnet for predicting key residues responsible for enzyme activity further promoted the success rate of virtual mutagenesis. This study highlighted the significance of correctly predicting key binding sites for enzyme engineering., (© The Author(s) 2024. Published by Oxford University Press.)

The causes of depression are complex, and the current diagnosis methods rely solely on psychiatric evaluations with no incorporation of laboratory biomarkers in clinical practices. We investigated the stability of blood DNA methylation depression signatures in six different populations using six public and two domestic cohorts (n = 1942) conducting mega-analysis and meta-analysis of the individual studies. We evaluated 12 machine learning and deep learning strategies for depression classification both in cross-validation (CV) and in hold-out tests using merged data from 8 separate batches, constructing models with both biased and unbiased feature selection. We found 1987 CpG sites related to depression in both mega- and meta-analysis at the nominal level, and the associated genes were nominally related to axon guidance and immune pathways based on enrichment analysis and eQTM data. Random forest classifiers achieved the highest performance (AUC 0.73 and 0.76) in CV and hold-out tests respectively on the batch-level processed data. In contrast, the methylation showed low predictive power (all AUCs < 0.57) for all classifiers in CV and no predictive power in hold-out tests when used with harmonized data. All models achieved significantly better performance (>14% gain in AUCs) with pre-selected features (selection bias), with some of the models (joint autoencoder-classifier) reaching AUCs of up to 0.91 in the final testing regardless of data preparation. Different algorithmic feature selection approaches may outperform limma, however, random forest models perform well regardless of the strategy. The results provide an overview over potential future biomarkers for depression and highlight many important methodological aspects for DNA methylation-based depression profiling including the use of machine learning strategies., (© 2024. The Author(s).)

Corneal infection is a major public health concern worldwide and the most common cause of unilateral corneal blindness. Toxic effects of different microorganisms, such as bacteria and fungi, worsen keratitis leading to corneal perforation even with optimal drug treatment. The cornea forms the main refractive surface of the eye. Diseases affecting the cornea can cause severe visual impairment. Therefore, it is crucial to analyze the risk of corneal perforation and visual impairment in corneal ulcer patients for making early treatment strategies. The modeling of a fully automated prognostic model system was performed in two parts. In the first part, the dataset contained 4973 slit lamp images of corneal ulcer patients in three centers. A deep learning model was developed and tested for segmenting and classifying five lesions (corneal ulcer, corneal scar, hypopyon, corneal descementocele, and corneal neovascularization) in the eyes of corneal ulcer patients. Further, hierarchical quantification was carried out based on policy rules. In the second part, the dataset included clinical data (name, gender, age, best corrected visual acuity, and type of corneal ulcer) of 240 patients with corneal ulcers and respective 1010 slit lamp images under two light sources (natural light and cobalt blue light). The slit lamp images were then quantified hierarchically according to the policy rules developed in the first part of the modeling. Combining the above clinical data, the features were used to build the final prognostic model system for corneal ulcer perforation outcome and visual impairment using machine learning algorithms such as XGBoost, LightGBM. The ROC curve area (AUC value) evaluated the model's performance. For segmentation of the five lesions, the accuracy rates of hypopyon, descemetocele, corneal ulcer under blue light, and corneal neovascularization were 96.86, 91.64, 90.51, and 93.97, respectively. For the corneal scar lesion classification, the accuracy rate of the final model was 69.76. The XGBoost model performed the best in predicting the 1-month prognosis of patients, with an AUC of 0.81 (95% CI 0.63-1.00) for ulcer perforation and an AUC of 0.77 (95% CI 0.63-0.91) for visual impairment. In predicting the 3-month prognosis of patients, the XGBoost model received the best AUC of 0.97 (95% CI 0.92-1.00) for ulcer perforation, while the LightGBM model achieved the best performance with an AUC of 0.98 (95% CI 0.94-1.00) for visual impairment., (© 2024. The Author(s).)

The need for intubation in methanol-poisoned patients, if not predicted in time, can lead to irreparable complications and even death. Artificial intelligence (AI) techniques like machine learning (ML) and deep learning (DL) greatly aid in accurately predicting intubation needs for methanol-poisoned patients. So, our study aims to assess Explainable Artificial Intelligence (XAI) for predicting intubation necessity in methanol-poisoned patients, comparing deep learning and machine learning models. This study analyzed a dataset of 897 patient records from Loghman Hakim Hospital in Tehran, Iran, encompassing cases of methanol poisoning, including those requiring intubation (202 cases) and those not requiring it (695 cases). Eight established ML (SVM, XGB, DT, RF) and DL (DNN, FNN, LSTM, CNN) models were used. Techniques such as tenfold cross-validation and hyperparameter tuning were applied to prevent overfitting. The study also focused on interpretability through SHAP and LIME methods. Model performance was evaluated based on accuracy, specificity, sensitivity, F1-score, and ROC curve metrics. Among DL models, LSTM showed superior performance in accuracy (94.0%), sensitivity (99.0%), specificity (94.0%), and F1-score (97.0%). CNN led in ROC with 78.0%. For ML models, RF excelled in accuracy (97.0%) and specificity (100%), followed by XGB with sensitivity (99.37%), F1-score (98.27%), and ROC (96.08%). Overall, RF and XGB outperformed other models, with accuracy (97.0%) and specificity (100%) for RF, and sensitivity (99.37%), F1-score (98.27%), and ROC (96.08%) for XGB. ML models surpassed DL models across all metrics, with accuracies from 93.0% to 97.0% for DL and 93.0% to 99.0% for ML. Sensitivities ranged from 98.0% to 99.37% for DL and 93.0% to 99.0% for ML. DL models achieved specificities from 78.0% to 94.0%, while ML models ranged from 93.0% to 100%. F1-scores for DL were between 93.0% and 97.0%, and for ML between 96.0% and 98.27%. DL models scored ROC between 68.0% and 78.0%, while ML models ranged from 84.0% to 96.08%. Key features for predicting intubation necessity include GCS at admission, ICU admission, age, longer folic acid therapy duration, elevated BUN and AST levels, VBG&#95;HCO3 at initial record, and hemodialysis presence. This study as the showcases XAI's effectiveness in predicting intubation necessity in methanol-poisoned patients. ML models, particularly RF and XGB, outperform DL counterparts, underscoring their potential for clinical decision-making., (© 2024. The Author(s).)

Brain stroke, or a cerebrovascular accident, is a devastating medical condition that disrupts the blood supply to the brain, depriving it of oxygen and nutrients. Each year, according to the World Health Organization, 15 million people worldwide experience a stroke. This results in approximately 5 million deaths and another 5 million individuals suffering permanent disabilities. The complex interplay of various risk factors highlights the urgent need for sophisticated analytical methods to more accurately predict stroke risks and manage their outcomes. Machine learning and deep learning technologies offer promising solutions by analyzing extensive datasets including patient demographics, health records, and lifestyle choices to uncover patterns and predictors not easily discernible by humans. These technologies enable advanced data processing, analysis, and fusion techniques for a comprehensive health assessment. We conducted a comprehensive review of 25 review papers published between 2020 and 2024 on machine learning and deep learning applications in brain stroke diagnosis, focusing on classification, segmentation, and object detection. Furthermore, all these reviews explore the performance evaluation and validation of advanced sensor systems in these areas, enhancing predictive health monitoring and personalized care recommendations. Moreover, we also provide a collection of the most relevant datasets used in brain stroke analysis. The selection of the papers was conducted according to PRISMA guidelines. Furthermore, this review critically examines each domain, identifies current challenges, and proposes future research directions, emphasizing the potential of AI methods in transforming health monitoring and patient care.

The United Nations (UN) emphasizes the pivotal role of sustainable agriculture in addressing persistent starvation and working towards zero hunger by 2030 through global development. Intensive agricultural practices have adversely impacted soil quality, necessitating soil nutrient analysis for enhancing farm productivity and environmental sustainability. Researchers increasingly turn to Artificial Intelligence (AI) techniques to improve crop yield estimation and optimize soil nutrition management. This study reviews 155 papers published from 2014 to 2024, assessing the use of machine learning (ML) and deep learning (DL) in predicting soil nutrients. It highlights the potential of hyperspectral and multispectral sensors, which enable precise nutrient identification through spectral analysis across multiple bands. The study underscores the importance of feature selection techniques to improve model performance by eliminating redundant spectral bands with weak correlations to targeted nutrients. Additionally, the use of spectral indices, derived from mathematical ratios of spectral bands based on absorption spectra, is examined for its effectiveness in accurately predicting soil nutrient levels. By evaluating various performance measures and datasets related to soil nutrient prediction, this paper offers comprehensive insights into the applicability of AI techniques in optimizing soil nutrition management. The insights gained from this review can inform future research and policy decisions to achieve global development goals and promote environmental sustainability., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Sleep disorders can have harmful consequences in both the short and long term. They can lead to attention deficits, as well as cardiac, neurological and behavioral repercussions. One of the most widely used methods for assessing sleep disorders is polysomnography (PSG). A major challenge associated with this method is all the cables needed to connect the recording devices, making the examination more intrusive and usually requiring a clinical environment. This can have potential consequences on the test results and their accuracy. One simple way to assess the state of the central nervous system (CNS), a well-known indicator of sleep disorder, could be the use of a portable medical device. With this in mind, we implemented a simple model using both the RR interval (RRI) and its second derivative to accurately predict the awake and napping states of a subject using a feature classification model. For training and validation, we used a database providing measurements from nine healthy young adults (six men and three women), in which heart rate variability (HRV) associated with light-on, light-off, sleep onset and sleep offset events. Results show that using a 30 min RRI time series window suffices for this lightweight model to accurately predict whether the patient was awake or napping.

Antimicrobial resistance (AMR) undermines the United Nations Sustainable Development Goals of good health and well-being. Antibiotics are known to exacerbate AMR, but nonantibiotic antimicrobials, such as quaternary ammonium compounds (QACs), are now emerging as another significant driver of AMR. However, assessing the AMR risks of QACs in complex environmental matrices remains challenging due to the ambiguity in their chemical structures and antibacterial activity. By machine learning prediction and high-resolution mass spectrometric analysis, a list of antibacterial QACs ( n = 856) from industrial chemical inventories is compiled, and it leads to the identification of 50 structurally diverse antibacterial QACs in sediments, including traditional hydrocarbon-based compounds and new subclasses that bear additional functional groups, such as choline, ester, betaine, aryl ether, and pyridine. Urban wastewater, aquaculture, and hospital discharges are the main factors influencing QAC distribution patterns in estuarine sediments. Toxic unit calculations and metagenomic analysis revealed that these QACs can influence antibiotic resistance genes (particularly sulfonamide resistance genes) through cross- and coresistances. The potential to influence the AMR is related to their environmental persistence. These results suggest that controlling the source, preventing the co-use of QACs and sulfonamides, and prioritizing control of highly persistent molecules will lead to global stewardship and sustainable use of QACs.

Introduction: This review explores the transformative impact of machine learning (ML) on carcinogenicity prediction within drug development. It discusses the historical context and recent advancements, emphasizing the significance of ML methodologies in overcoming challenges related to data interpretation, ethical considerations, and regulatory acceptance., Areas Covered: The review comprehensively examines the integration of ML, deep learning, and diverse artificial intelligence (AI) approaches in various aspects of drug development safety assessments. It explores applications ranging from early-phase compound screening to clinical trial optimization, highlighting the versatility of ML in enhancing predictive accuracy and efficiency., Expert Opinion: Through the analysis of traditional approaches such as in vivo rodent bioassays and in vitro assays, the review underscores the limitations and resource intensity associated with these methods. It provides expert insights into how ML offers innovative solutions to address these challenges, revolutionizing safety assessments in drug development.