BioMedInformatics最新文献

{"title":"Overall Survival Time Estimation for Epithelioid Peritoneal Mesothelioma Patients from Whole-Slide Images","authors":"Kleanthis Marios Papadopoulos, P. Barmpoutis, Tania Stathaki, V. Kepenekian, Peggy Dartigues, S. Valmary-Degano, Claire Illac-Vauquelin, G. Avérous, A. Chevallier, M. Lavérriere, L. Villeneuve, Olivier Glehen, Sylvie Isaac, J. Hommell-Fontaine, Francois Ng Kee Kwong, N. Benzerdjeb","doi":"10.3390/biomedinformatics4010046","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010046","url":null,"abstract":"Background: The advent of Deep Learning initiated a new era in which neural networks relying solely on Whole-Slide Images can estimate the survival time of cancer patients. Remarkably, despite deep learning’s potential in this domain, no prior research has been conducted on image-based survival analysis specifically for peritoneal mesothelioma. Prior studies performed statistical analysis to identify disease factors impacting patients’ survival time. Methods: Therefore, we introduce MPeMSupervisedSurv, a Convolutional Neural Network designed to predict the survival time of patients diagnosed with this disease. We subsequently perform patient stratification based on factors such as their Peritoneal Cancer Index and on whether patients received chemotherapy treatment. Results: MPeMSupervisedSurv demonstrates improvements over comparable methods. Using our proposed model, we performed patient stratification to assess the impact of clinical variables on survival time. Notably, the inclusion of information regarding adjuvant chemotherapy significantly enhances the model’s predictive prowess. Conversely, repeating the process for other factors did not yield significant performance improvements. Conclusions: Overall, MPeMSupervisedSurv is an effective neural network which can predict the survival time of peritoneal mesothelioma patients. Our findings also indicate that treatment by adjuvant chemotherapy could be a factor affecting survival time.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"1 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140247976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effect of Data Missingness on Machine Learning Predictions of Uncontrolled Diabetes Using All of Us Data","authors":"Zain Jabbar, Peter Washington","doi":"10.3390/biomedinformatics4010043","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010043","url":null,"abstract":"Electronic Health Records (EHR) provide a vast amount of patient data that are relevant to predicting clinical outcomes. The inherent presence of missing values poses challenges to building performant machine learning models. This paper aims to investigate the effect of various imputation methods on the National Institutes of Health’s All of Us dataset, a dataset containing a high degree of data missingness. We apply several imputation techniques such as mean substitution, constant filling, and multiple imputation on the same dataset for the task of diabetes prediction. We find that imputing values causes heteroskedastic performance for machine learning models with increased data missingness. That is, the more missing values a patient has for their tests, the higher variance there is on a diabetes model AUROC, F1, precision, recall, and accuracy scores. This highlights a critical challenge in using EHR data for predictive modeling. This work highlights the need for future research to develop methodologies to mitigate the effects of missing data and heteroskedasticity in EHR-based predictive models.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140261449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine Learning Models and Technologies for Evidence-Based Telehealth and Smart Care: A Review","authors":"Stella C. Christopoulou","doi":"10.3390/biomedinformatics4010042","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010042","url":null,"abstract":"Background: Over the past few years, clinical studies have utilized machine learning in telehealth and smart care for disease management, self-management, and managing health issues like pulmonary diseases, heart failure, diabetes screening, and intraoperative risks. However, a systematic review of machine learning’s use in evidence-based telehealth and smart care is lacking, as evidence-based practice aims to eliminate biases and subjective opinions. Methods: The author conducted a mixed methods review to explore machine learning applications in evidence-based telehealth and smart care. A systematic search of the literature was performed during 16 June 2023–27 June 2023 in Google Scholar, PubMed, and the clinical registry platform ClinicalTrials.gov. The author included articles in the review if they were implemented by evidence-based health informatics and concerned with telehealth and smart care technologies. Results: The author identifies 18 key studies (17 clinical trials) from 175 citations found in internet databases and categorizes them using problem-specific groupings, medical/health domains, machine learning models, algorithms, and techniques. Conclusions: Machine learning combined with the application of evidence-based practices in healthcare can enhance telehealth and smart care strategies by improving quality of personalized care, early detection of health-related problems, patient quality of life, patient-physician communication, resource efficiency and cost-effectiveness. However, this requires interdisciplinary expertise and collaboration among stakeholders, including clinicians, informaticians, and policymakers. Therefore, further research using clinicall studies, systematic reviews, analyses, and meta-analyses is required to fully exploit the potential of machine learning in this area.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"98 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140079600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Forecasting Survival Rates in Metastatic Colorectal Cancer Patients Undergoing Bevacizumab-Based Chemotherapy: A Machine Learning Approach","authors":"Sergio Sánchez-Herrero, Abtin Tondar, E. Pérez-Bernabeu, Laura Calvet, Angel A. Juan","doi":"10.3390/biomedinformatics4010041","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010041","url":null,"abstract":"Background: Antibiotics can play a pivotal role in the treatment of colorectal cancer (CRC) at various stages of the disease, both directly and indirectly. Identifying novel patterns of antibiotic effects or responses in CRC within extensive medical data poses a significant challenge that can be addressed through algorithmic approaches. Machine Learning (ML) emerges as a promising solution for predicting clinical outcomes using clinical and heterogeneous cancer data. In the pursuit of our objective, we employed ML techniques for predicting CRC mortality and antibiotic influence. Methods: We utilized a dataset to examine the accuracy of death prediction in metastatic colorectal cancer. In addition, we analyzed the association between antibiotic exposure and mortality in metastatic colorectal cancer. The dataset comprised 147 patients, nineteen independent variables, and one dependent variable. Our analysis involved testing different classification-supervised ML, including an oversampling pool for classification models, Logistic Regression, Decision Trees, Naive Bayes, Support Vector Machine, Random Forest, XGBboost Classifier, a consensus of all models, and a consensus of top models (meta models). Results: The consensus of the top models’ classifier exhibited the highest accuracy among the algorithms tested (93%). This model met the standards for good accuracy, surpassing the 90% threshold considered useful in ML applications. Consistent with the accuracy results, other metrics are also good, including precision (0.96), recall (0.93), F-Beta (0.94), and AUC (0.93). Hazard ratio analysis suggests that there is no discernible difference between patients who received antibiotics and those who did not. Conclusions: Our modelling approach provides an alternative for analyzing and predicting the relationship between antibiotics and mortality in metastatic colorectal cancer patients treated with bevacizumab, complementing classic statistical methods. This methodology lays the groundwork for future use of datasets in cancer treatment research and highlights the advantages of meta models.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"35 47","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140081693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive Analysis of Endoscope Demand in Otolaryngology Outpatient Settings","authors":"David Lanier, Cristie Roush, Gwendolyn Young, Sara Masoud","doi":"10.3390/biomedinformatics4010040","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010040","url":null,"abstract":"Background: There has been a trend to transit reprocessing of flexible endoscopes from a high-level disinfectant (HLD) centralized manner to sterilization performed by nursing staff in some Ear, Nose, and Throat (ENT) clinics. In doing so, the clinic nursing staff are responsible for predicting and managing clinical demand for flexible endoscopes. The HLD disinfection process is time-consuming and requires specialized training and competency to be performed safely. Solely depending on human expertise for predicting the flexible endoscope demands is unreliable and produced a concern of an inadequate supply of devices available for diagnostic purposes. Method: The demand for flexible endoscopes for future patient visits has not been well studied but can be modeled based on patients’ historical information, provider, and other visit-related factors. Such factors are available to the clinic before the visit. Binary classifiers can be used to help inform the sterile processing department of reprocessing needs days or weeks earlier for each patient. Results: Among all our trained models, Logistic Regression reports an average AUC ROC score of 89% and accuracy of 80%. Conclusion: The proposed framework not only significantly reduces the reprocessing efforts in terms of time spent on communication, cleaning, scheduling, and transferring scopes, but also helps to improve patient safety by reducing the exposure risk to potential infections.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"17 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140081989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Naturalize Revolution: Unprecedented AI-Driven Precision in Skin Cancer Classification Using Deep Learning","authors":"Mohamad Abou Ali, F. Dornaika, I. Arganda-Carreras, Hussein Ali, Malak Karaouni","doi":"10.3390/biomedinformatics4010035","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010035","url":null,"abstract":"Background: In response to the escalating global concerns surrounding skin cancer, this study aims to address the imperative for precise and efficient diagnostic methodologies. Focusing on the intricate task of eight-class skin cancer classification, the research delves into the limitations of conventional diagnostic approaches, often hindered by subjectivity and resource constraints. The transformative potential of Artificial Intelligence (AI) in revolutionizing diagnostic paradigms is underscored, emphasizing significant improvements in accuracy and accessibility. Methods: Utilizing cutting-edge deep learning models on the ISIC2019 dataset, a comprehensive analysis is conducted, employing a diverse array of pre-trained ImageNet architectures and Vision Transformer models. To counteract the inherent class imbalance in skin cancer datasets, a pioneering “Naturalize” augmentation technique is introduced. This technique leads to the creation of two indispensable datasets—the Naturalized 2.4K ISIC2019 and groundbreaking Naturalized 7.2K ISIC2019 datasets—catalyzing advancements in classification accuracy. The “Naturalize” augmentation technique involves the segmentation of skin cancer images using the Segment Anything Model (SAM) and the systematic addition of segmented cancer images to a background image to generate new composite images. Results: The research showcases the pivotal role of AI in mitigating the risks of misdiagnosis and under-diagnosis in skin cancer. The proficiency of AI in analyzing vast datasets and discerning subtle patterns significantly augments the diagnostic prowess of dermatologists. Quantitative measures such as confusion matrices, classification reports, and visual analyses using Score-CAM across diverse dataset variations are meticulously evaluated. The culmination of these endeavors resulted in an unprecedented achievement—100% average accuracy, precision, recall, and F1-score—within the groundbreaking Naturalized 7.2K ISIC2019 dataset. Conclusion: This groundbreaking exploration highlights the transformative capabilities of AI-driven methodologies in reshaping the landscape of skin cancer diagnosis and patient care. The research represents a pivotal stride towards redefining dermatological diagnosis, showcasing the remarkable impact of AI-powered solutions in surmounting the challenges inherent in skin cancer diagnosis. The attainment of 100% across crucial metrics within the Naturalized 7.2K ISIC2019 dataset serves as a testament to the transformative capabilities of AI-driven approaches in reshaping the trajectory of skin cancer diagnosis and patient care. This pioneering work paves the way for a new era in dermatological diagnostics, heralding the dawn of unprecedented precision and efficacy in the identification and classification of skin cancers.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"63 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140085542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reliability and Agreement of Free Web-Based 3D Software for Computing Facial Area and Volume Measurements","authors":"Oguzhan Topsakal, Philip Sawyer, T. Akinci, Elif Topsakal, M. Celikoyar","doi":"10.3390/biomedinformatics4010038","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010038","url":null,"abstract":"Background: Facial surgeries require meticulous planning and outcome assessments, where facial analysis plays a critical role. This study introduces a new approach by utilizing three-dimensional (3D) imaging techniques, which are known for their ability to measure facial areas and volumes accurately. The purpose of this study is to introduce and evaluate a free web-based software application designed to take area and volume measurements on 3D models of patient faces. Methods: This study employed the online facial analysis software to conduct ten measurements on 3D models of subjects, including five measurements of area and five measurements of volume. These measurements were then compared with those obtained from the established 3D modeling software called Blender (version 3.2) using the Bland–Altman plot. To ensure accuracy, the intra-rater and inter-rater reliabilities of the web-based software were evaluated using the Intraclass Correlation Coefficient (ICC) method. Additionally, statistical assumptions such as normality and homoscedasticity were rigorously verified before analysis. Results: This study found that the web-based facial analysis software showed high agreement with the 3D software Blender within 95% confidence limits. Moreover, the online application demonstrated excellent intra-rater and inter-rater reliability in most analyses, as indicated by the ICC test. Conclusion: The findings suggest that the free online 3D software is reliable for facial analysis, particularly in measuring areas and volumes. This indicates its potential utility in enhancing surgical planning and evaluation in facial surgeries. This study underscores the software’s capability to improve surgical outcomes by integrating precise area and volume measurements into facial surgery planning and assessment processes.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"112 45","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140088664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Classification and Explanation of Iron Deficiency Anemia from Complete Blood Count Data Using Machine Learning","authors":"Siddartha Pullakhandam, S. McRoy","doi":"10.3390/biomedinformatics4010036","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010036","url":null,"abstract":"Background: Currently, discriminating Iron Deficiency Anemia (IDA) from other anemia requires an expensive test (serum ferritin). Complete Blood Count (CBC) tests are less costly and more widely available. Machine learning models have not yet been applied to discriminating IDA but do well for similar tasks. Methods: We constructed multiple machine learning methods to classify IDA from CBC data using a US NHANES dataset of over 19,000 instances, calculating accuracy, precision, recall, and precision AUC (PR AUC). We validated the results using an unseen dataset from Kenya, using the same model. We calculated ranked feature importance to explain the global behavior of the model. Results: Our model classifies IDA with a PR AUC of 0.87 and recall/sensitivity of 0.98 and 0.89 for the original dataset and an unseen Kenya dataset, respectively. The explanations indicate that low blood level of hemoglobin, higher age, and higher Red Blood Cell distribution width were most critical. We also found that optimization made only minor changes to the explanations and that the features used remained consistent with professional practice. Conclusions: The overall high performance and consistency of the results suggest that the approach would be acceptable to health professionals and would support enhancements to current automated CBC analyzers.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"73 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140282323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revolutionizing Kidney Transplantation: Connecting Machine Learning and Artificial Intelligence with Next-Generation Healthcare—From Algorithms to Allografts","authors":"L. Ramalhete, Paula Almeida, Raquel Ferreira, Olga Abade, Cristiana Teixeira, Rúben Araújo","doi":"10.3390/biomedinformatics4010037","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010037","url":null,"abstract":"This review explores the integration of artificial intelligence (AI) and machine learning (ML) into kidney transplantation (KT), set against the backdrop of a significant donor organ shortage and the evolution of ‘Next-Generation Healthcare’. Its purpose is to evaluate how AI and ML can enhance the transplantation process, from donor selection to postoperative patient care. Our methodology involved a comprehensive review of current research, focusing on the application of AI and ML in various stages of KT. This included an analysis of donor–recipient matching, predictive modeling, and the improvement in postoperative care. The results indicated that AI and ML significantly improve the efficiency and success rates of KT. They aid in better donor–recipient matching, reduce organ rejection, and enhance postoperative monitoring and patient care. Predictive modeling, based on extensive data analysis, has been particularly effective in identifying suitable organ matches and anticipating postoperative complications. In conclusion, this review discusses the transformative impact of AI and ML in KT, offering more precise, personalized, and effective healthcare solutions. Their integration into this field addresses critical issues like organ shortages and post-transplant complications. However, the successful application of these technologies requires careful consideration of their ethical, privacy, and training aspects in healthcare settings.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"108 41","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140090081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Development and Usability Assessment of an Augmented Reality Decision Support System to Address Burn Patient Management","authors":"S. Veazey, Nicole Caldwell, David E. Luellen, Angela B. Samosorn, Allison McGlasson, P. Colston, C. Fenrich, Jose Salinas, Jared Mike, Jacob Rivera, M. Serio-Melvin","doi":"10.3390/biomedinformatics4010039","DOIUrl":"https://doi.org/10.3390/biomedinformatics4010039","url":null,"abstract":"Critical care injuries, such as burn trauma, require specialized skillsets and knowledge. A clinical decision support system to aid clinicians in providing burn patient management can increase proficiency and provide knowledge content for specific interventions. In austere environments, decision support tools can be used to aid in decision making and task guidance when skilled personnel or resources are limited. Therefore, we developed a novel software system that utilizes augmented reality (AR) capabilities to provide enhanced step-by-step instructions based on best practices for managing burn patients. To better understand how new technologies, such as AR, can be used for burn care management, we developed a burn care application for use on a heads-up display. We developed four sub-set applications for documenting and conducting burn wound mapping, fluid resuscitation, medication calculations, and an escharotomy. After development, we conducted a usability study utilizing the System Usability Scale, pre- and post- simulation surveys, and after-action reviews to evaluate the AR-based software application in a simulation scenario. Results of the study indicate that the decision support tool has generalized usability and subjects were able to use the software as intended. Here we present the first use case of a comprehensive burn management system utilizing augmented reality capabilities to deliver care.","PeriodicalId":72394,"journal":{"name":"BioMedInformatics","volume":"120 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140090361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}