Computer methods and programs in biomedicine update最新文献

{"title":"Towards automatization of organoid analysis: A deep learning approach to localize and quantify organoid images","authors":"Asmaa Haja ,&nbsp;José M. Horcas-Nieto ,&nbsp;Barbara M. Bakker ,&nbsp;Lambert Schomaker","doi":"10.1016/j.cmpbup.2023.100101","DOIUrl":"10.1016/j.cmpbup.2023.100101","url":null,"abstract":"<div><p>The interest in the use of organoids in the biomedical field has increased exponentially in the past years. Organoids, or three-dimensional “mini-organs”, have the ability to proliferate and self-organize <em>in-vitro</em>, while displaying varying morphologies. When in culture, these structures can overlap with each other making the quantification and morphological characterization a challenging task. Quick and reliable analysis of organoid images could help in precisely modeling disease phenotypes as well as provide information on organ development. Therefore, automatization of the quantification and measurements is an important step towards an easier, faster, and less biased workflow.</p><p>In order to accomplish this, a free e-Science service (OrganelX) has been developed for localization and quantification of organoid size based on deep learning methods. The ability of the system was tested on murine liver organoids, and the data are made publicly available. The OrganelX e-Science free service is available at <span>https://organelx.hpc.rug.nl/organoid/</span><svg><path></path></svg>.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"3 ","pages":"Article 100101"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42429858","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":"Improving SVM performance for type II diabetes prediction with an improved non-linear kernel: Insights from the PIMA dataset","authors":"Md.Shamim Reza ,&nbsp;Umme Hafsha ,&nbsp;Ruhul Amin ,&nbsp;Rubia Yasmin ,&nbsp;Sabba Ruhi","doi":"10.1016/j.cmpbup.2023.100118","DOIUrl":"10.1016/j.cmpbup.2023.100118","url":null,"abstract":"<div><p>Type 2 diabetes is a chronic metabolic disease that affects a significant portion of the worldwide people. Prediction of this disease using different machine learning (ML) based algorithms has gained substantial attention due to its potential for early detection and effective intervention. One of the most powerful ML algorithm support vector machines (SVM) has proven to be effective in a variety of classification tasks, including diabetes prediction. However, the kernel function chosen has a substantial effect on the performance of SVM classifiers. This paper proposes an improved non-linear kernel for the SVM model to enhance Type 2 diabetes classification. The new kernel uses radial basis function (RBF) and RBF city block kernels that enable SVM to learn complex decision boundaries and adapt to the intricacies of the PIMA dataset. The PIMA dataset contains various clinical and demographic features of individuals. To address missing values and outliers, we impute them using the median, ensuring the integrity of the dataset. We tackle the class imbalance issue by leveraging a robust synthetic-based over-sampling approach.</p><p>A comparative analysis is performed against several existing kernel functions to show that the proposed approach is superior in terms of various prediction evaluation matrices. Our recommended integrated kernel model also showed improved performance (ACC = 85.5, Recall = 87.0, Precision = 83.4, F1 score = 85.2, and AUC = 85.5) when compared to other approaches in the literature. The results of this study indicate that the proposed non-linear kernel in SVM outperforms existing kernel functions for predicting Type 2 diabetes using the PIMA dataset. Furthermore, a simulation study is carried out to robustify the proposed kernel in SVM and perform well. The improved accuracy and robustness of the model suggest its potential utility in clinical settings, aiding in the early identification and management of individuals at risk for developing diabetes.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"4 ","pages":"Article 100118"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46853720","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":"A comparative approach to alleviating the prevalence of diabetes mellitus using machine learning","authors":"Md. Rifatul Islam ,&nbsp;Semonti Banik ,&nbsp;Kazi Naimur Rahman ,&nbsp;Mohammad Mizanur Rahman","doi":"10.1016/j.cmpbup.2023.100113","DOIUrl":"10.1016/j.cmpbup.2023.100113","url":null,"abstract":"<div><p>Diabetes mellitus, a metabolic disease with elevated blood sugar levels, is a significant global public health concern. Identification of diabetes at its very early stage can reduce the prevalence of cases. This work focuses on developing a machine learning-based system that will have a significant impact on diabetic patient identification. To develop such a system we utilized a dataset made up by acquiring direct questionnaires from Sylhet Diabetic Hospital patients. The dataset contains information about the signs and symptoms of patients who are new or likely to have diabetes. We applied 14 different machine-learning techniques where the Gradient Boosting Machine (GBM) outperformed other algorithms with the highest F1 and ROC scores of 99.37%, and 99.92% respectively. We also employed various ensemble-based approaches that show competitive performance to the individual model’s performance.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"4 ","pages":"Article 100113"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48119339","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":"Development and validation of an electronic application (FoodEapp) to assess the dietary intake of adults in Karachi, Pakistan","authors":"Umber S Khan ,&nbsp;Maira Mubashir ,&nbsp;Tansheet Jawad ,&nbsp;Iqbal Azam ,&nbsp;Amna R Siddiqui ,&nbsp;Romaina Iqbal","doi":"10.1016/j.cmpbup.2023.100124","DOIUrl":"https://doi.org/10.1016/j.cmpbup.2023.100124","url":null,"abstract":"<div><h3>Background</h3><p>Under and over-nutrition-related health conditions are highly prevalent in Pakistan. Dietary data are required to understand the challenges of over and undernutrition in Pakistan.</p></div><div><h3>Objective</h3><p>The purpose of the study was to develop and validate a FoodEapp application (FoodEapp) for field staff with no formal education in nutrition (unskilled) to accurately collect 24-hour (24HR) dietary recall (DR) data to assess the dietary intake of adults in Karachi, Pakistan.</p></div><div><h3>Method</h3><p>We designed a novel FoodEapp application for unskilled data collectors to collect 24HR DR data. We validated the FoodEapp against the conventional 24HR DR method in rural and urban Karachi. We compared the mean intake of total energy (kcal), macronutrients, and micronutrients, reported through both methods using Pearson Correlation and Intraclass Correlation (ICC). We also used Bland Altman analysis to assess the agreement between the methods.</p></div><div><h3>Results</h3><p>We found a high correlation between the two methods for total energy (ρ = 0.88, <em>p</em>-value &lt; 0.001), protein (g) (ρ = 0.81, <em>p</em>-value &lt; 0.001), total lipids (g) (ρ = 0.74, <em>p</em>-value &lt; 0.001), and carbohydrates (g) (ρ = 0.68, <em>p</em>-value &lt; 0.001). Bland Altman's analysis showed good agreement in all the nutrients between the two methods.</p></div><div><h3>Conclusions</h3><p>FoodEapp has good validity and can be used to assess the dietary intake of the adult population in Karachi by non-nutritionists. This study may help overcome the limitation of dietary data collection and facilitate the researchers to conduct larger dietary surveys in Pakistan.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"4 ","pages":"Article 100124"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49727004","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":"Semi-supervised active transfer learning for fetal ECG arrhythmia detection","authors":"Mohammad Reza Mohebbian ,&nbsp;Hamid Reza Marateb ,&nbsp;Khan A. Wahid","doi":"10.1016/j.cmpbup.2023.100096","DOIUrl":"https://doi.org/10.1016/j.cmpbup.2023.100096","url":null,"abstract":"","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"3 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49780851","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":"Exploring the impact of digital health literacy on COVID-19 behaviors in New York state college students during the COVID-19 pandemic","authors":"Molly Hadley ,&nbsp;Uday Patil ,&nbsp;Kimberly F. Colvin ,&nbsp;Tetine Sentell ,&nbsp;Philip M. Massey ,&nbsp;Mary Gallant ,&nbsp;Jennifer A. Manganello","doi":"10.1016/j.cmpbup.2023.100126","DOIUrl":"https://doi.org/10.1016/j.cmpbup.2023.100126","url":null,"abstract":"<div><p>Early in 2020, the COVID-19 pandemic became a global public health concern. College students became dependent on the online environment for learning, but also to receive COVID-19 information. Understanding digital health literacy and subsequent prevention behaviors in a digitally connected population during a public health crisis is crucial to prepare for future pandemics. This study focused on college students in the United States and explored whether digital health literacy predicted their main source of pandemic information, adherence to public health guidelines, and intentions to receive a COVID-19 vaccine. During the summer of 2020, 254 New York State college students completed the survey. Digital health literacy was found to predict using ‘<em>Government agencies websites’</em> as a main source of information and adherence to public health guidelines. It was not found to predict vaccine intentions. The findings confirm the importance of digital health literacy interventions in younger populations, especially with the rise of health misinformation available on the Internet.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"4 ","pages":"Article 100126"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666990023000344/pdfft?md5=048d105c4d91a9f611fcbfdcf043a9f2&pid=1-s2.0-S2666990023000344-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138390524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving assessment in kidney transplantation by multitask general path model","authors":"Qing Lan ,&nbsp;Xiaoyu Chen ,&nbsp;Murong Li ,&nbsp;John Robertson ,&nbsp;Yong Lei ,&nbsp;Ran Jin","doi":"10.1016/j.cmpbup.2023.100127","DOIUrl":"https://doi.org/10.1016/j.cmpbup.2023.100127","url":null,"abstract":"<div><h3>Background</h3><p>Kidney transplantation is a pivotal intervention for individuals suffering from end-stage renal diseases, offering them the potential for restored health and an enhanced quality of life. However, the successful outcome of these transplantation procedures relies significantly on the careful matching of donor kidneys with compatible recipients. Unfortunately, the current kidney-matching process overlooks viability changes during preservation. The objective of this study is to investigate the potential for forecasting heterogeneous kidney viability using historical datasets to enhance kidney-matching decision-making.</p></div><div><h3>Methods</h3><p>We present a multitask general path model designed for continuous forecasting of kidney viability during preservation. This model quantifies likely viability trajectories of donor kidneys based on pathologist-provided biopsy scores during preservation, explicitly addressing both inter-kidney similarities and individual differences. To validate our model, we conducted viability assessments on six recently procured porcine kidneys and needle biopsy insertion experiments on phantoms, utilizing a leave-one-kidney-out cross-validation approach.</p></div><div><h3>Results</h3><p>Our proposed model consistently exhibited the lowest forecasting error (averaged root mean squared error, RMSEbegin=0.61 at the beginning and RMSEend&lt;0.05 at the end of kidney preservation) when compared to widely-adopted benchmark models, including multitask learning (RMSEbegin=0.65, RMSEend=0.54), general path (RMSEbegin=0.58, RMSEend=0.49), and generalized linear models (RMSEbegin=0.59, RMSEend=0.56) in the kidney viability assessment study. Additionally, across all testing scenarios, the forecasting RMSE of our model rapidly diminished with minimal initial kidney samples during preservation. Similar patterns were observed from the needle biopsy insertion study.</p></div><div><h3>Conclusions</h3><p>In both validation studies, our model outperformed benchmark models and exhibited rapid learning with limited initial samples. This approach holds promise for enhancing kidney transplantation decision-making, including improving tissue extraction accuracy through needle biopsy data analysis. By implementing this model across various kidney assessment stages in transplantation, we aim to reduce kidney discards and benefit a larger number of patients.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"4 ","pages":"Article 100127"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666990023000356/pdfft?md5=946267e50461f174efd8003330cdeb27&pid=1-s2.0-S2666990023000356-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138430873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine and deep learning identified metabolites and clinical features associated with gallstone disease","authors":"Nourah M Salem ,&nbsp;Khadijah M Jack ,&nbsp;Haiwei Gu ,&nbsp;Ashok Kumar ,&nbsp;Marlene Garcia ,&nbsp;Ping Yang ,&nbsp;Valentin Dinu","doi":"10.1016/j.cmpbup.2023.100106","DOIUrl":"10.1016/j.cmpbup.2023.100106","url":null,"abstract":"<div><p>Machine Learning (ML) algorithms can be used to analyze metabolomic expression data to explore the association between metabolite expression and disease etiology. In this study, we used and compared the performance of ML algorithms to analyze polar aqueous and blood-based lipid-based metabolites to identify meaningful patterns correlated with the development of gallstone disease (GSD) while examining the sex disparity. We also developed ML approaches that used clinical risk factors for predicting GSD, including age, obesity, body mass index, hemoglobin A1c, dyslipidemia index cholesterol to high-density lipoprotein ratio (CHOL/HDL). A more powerful data fusion model that combines both metabolomic and clinical features achieved accuracy of 83% for accurate prediction of the presence of GSD.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"3 ","pages":"Article 100106"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42471739","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":"Fitness dependent optimizer with neural networks for COVID-19 patients","authors":"Maryam T. Abdulkhaleq ,&nbsp;Tarik A. Rashid ,&nbsp;Bryar A. Hassan ,&nbsp;Abeer Alsadoon ,&nbsp;Nebojsa Bacanin ,&nbsp;Amit Chhabra ,&nbsp;S. Vimal","doi":"10.1016/j.cmpbup.2022.100090","DOIUrl":"10.1016/j.cmpbup.2022.100090","url":null,"abstract":"<div><p>The Coronavirus, known as COVID-19, which appeared in 2019 in China, has significantly affected the global health and become a huge burden on health institutions all over the world. These effects are continuing today. One strategy for limiting the virus's transmission is to have an early diagnosis of suspected cases and take appropriate measures before the disease spreads further. This work aims to diagnose and show the probability of getting infected by the disease according to textual clinical data. In this work, we used five machine learning techniques (GWO_MLP, GWO_CMLP, MGWO_MLP, FDO_MLP, FDO_CMLP) all of which aim to classify Covid-19 patients into two categories (Positive and Negative). Experiments showed promising results for all used models. The applied methods showed very similar performance, typically in terms of accuracy. However, in each tested dataset, FDO_MLP and FDO_CMLP produced the best results with 100% accuracy. The other models' results varied from one experiment to the other. It is concluded that the models on which the FDO algorithm was used as a learning algorithm had the possibility of obtaining higher accuracy. However, it is found that FDO has the longest runtime compared to the other algorithms. The link to the Covid 19 models is found here: <span>https://github.com/Tarik4Rashid4/covid19models</span><svg><path></path></svg></p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"3 ","pages":"Article 100090"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9792427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9991364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an OpenMRS-OMOP ETL tool to support informatics research and collaboration in LMICs","authors":"Juan Espinoza ,&nbsp;Sab Sikder ,&nbsp;Armine Lulejian ,&nbsp;Barry Levine","doi":"10.1016/j.cmpbup.2023.100119","DOIUrl":"https://doi.org/10.1016/j.cmpbup.2023.100119","url":null,"abstract":"<div><h3>Background</h3><p>As more low and middle-income countries (LMICs) implement electronic health record systems (EHRs), informatics has become an important component of global health. OpenMRS is a popular open-source EHR that has been implemented in over 60 countries. As in high income countries, interoperability and research capabilities remain a challenge. The Observational Medical Outcomes Partnership (OMOP) is one of the most relevant common data models (CDM) to support EHR-based research and data sharing, but its adoption has been limited in LMICs. To address this gap, we developed an OpenMRS to OMOP extract, transform, and load (ETL) tool using Talend.</p></div><div><h3>Methods</h3><p>We built on existing documentation to develop a comprehensive concept map from OpenMRS to OMOP. The OMOP domains were reviewed for overlapping concepts in OpenMRS, and a core set of tables were selected for ETL development. Specific variables were then identified from OpenMRS tables which mapped to OMOP domain fields. Afterwards, the ETL tool was developed using MySQL Workbench, PostgreSQL, and Talend.</p></div><div><h3>Results</h3><p>Seven of 14 OMOP domains were selected for ETL pipeline development . The location, person, and provider domains required the least amount of Talend job components, which involved ≤2 tDBInputs, 1 tMap, and 1 tDBOutput. Care_site, observation_period, observation, and person_death all required additional Talend components to properly transform the respective data fields. It took 15 min to transform 9,932 OpenMRS observation records to OMOP.</p></div><div><h3>Conclusions</h3><p>It is feasible to develop a free, open-source ETL pipeline to transform clinical data in OpenMRS instances into OMOP. Processing large datasets is swift and scalable with potential for more improvement. Using this tool alongside OpenMRS can dramatically increase the potential for global health informatics collaborations and building local infrastructure and research capacity. Further testing and development will be required prior to widespread dissemination, along with appropriate documentation and training resources.</p></div>","PeriodicalId":72670,"journal":{"name":"Computer methods and programs in biomedicine update","volume":"4 ","pages":"Article 100119"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49726803","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}