BioMedInformatics, Volume 3, Issue 3 (September 2023) – 18 articles

A consumer’s decision-making process regarding the purchase of chicken meat is a multifaceted one, influenced by various food-related, personal, and environmental factors that interact with one another. The mediating effect of food lifestyle that bridges the gap between consumer food values and the environment, further shapes consumer behavior towards meat purchase and consumption. This research introduces the concept of Food-Related Lifestyle (FRL) and aims to identify and explain the factors associated with chicken meat consumption in Northern Greece using a machine learning pipeline. To achieve this, the Boruta algorithm and four widely recognized classifiers were employed, achieving a binary classification accuracy of up to 78.26%. The study primarily focuses on determining the items from the FRL tool that carry significant weight in the classification output, thereby providing valuable insights. Additionally, the research aims to interpret the significance of these selected factors in the decision-making process using the SHAP model. Specifically, it turns out that the freshness, safety, and nutritional value of chicken meat are essential considerations for consumers in their eating habits. Additionally, external factors like health crises and price fluctuations can have a significant impact on consumer choices related to chicken meat consumption. The findings contribute to a more nuanced understanding of consumer preferences, enabling the food industry to align its offerings and marketing efforts with consumer needs and desires. Ultimately, this work demonstrates the potential of AI in shaping the future of the food industry and informs strategies for effective decision-making. Full article

CT scans are currently the most common imaging modality used for suspected stroke patients due to their short acquisition time and wide availability. However, MRI offers superior tissue contrast and image quality. In this study, eight deep learning models are developed, trained, and tested using a dataset of 181 CT/MR pairs from stroke patients. The resultant synthetic MRIs generated by these models are compared through a variety of qualitative and quantitative methods. The synthetic MRIs generated by a 3D UNet model consistently demonstrated superior performance across all methods of evaluation. Overall, the generation of synthetic MRIs from CT scans using the methods described in this paper produces realistic MRIs that can guide the registration of CT scans to MRI atlases. The synthetic MRIs enable the segmentation of white matter, grey matter, and cerebrospinal fluid by using algorithms designed for MRIs, exhibiting a high degree of similarity to true MRIs. Full article

The anesthetic dosing procedure is a key element of safe surgical practice, where it is paramount to ensure sufficient dosing of the anesthetic agent to the patient in order to reach the desired depth of sedation for the necessary procedure. One means of monitoring the depth of anesthesia (DoA) involves the use of the bispectral index (BIS), which decodes electroencephalography (EEG) signals acquired from the frontal cortex in a continuous fashion. The shortcomings of this include the complexity of the decoding of EEG signals, insensitivity to certain anesthetic agents, and the costly nature of the technology, which limits its adoption in resource-constrained settings. In this paper, we investigate an alternative source of physiological measurement modalities that can track DoA sufficiently while being much more affordable. Thus, we investigate this notion with the use of the University of Queensland database, which comprises EEG-EMG-ECG physiological data from patients going through a variety of surgical procedures. As part of this, select patient datasets were utilized in addition to a variety of signal decomposition and machine learning models—which totaled around 200 simulations—in order to investigate the most optimal combination of algorithms to track DoA using different physiological measurement modalities. The results showed that under certain algorithmic combinations and modeling processes, the ECG measurement (a ubiquitous monitor in anesthetic practice) can rival and occasionally surpass the accuracy of the EEG for DoA monitoring. In addition to this, we also propose a 2-phase modeling process that involves an algorithmic selection stage followed by a model deployment stage. Subsequent work in this area is advised to involve the acquisition of more physiological data from a broader mix of patients in order to further validate the consistency of the findings made in this study. Full article

Artificial intelligence is gaining interest among clinicians, but its results are difficult to be interpreted, especially when dealing with survival outcomes and censored observations. Explainable machine learning (XAI) has been recently extended to this context to improve explainability, interpretability and transparency for modeling results. A cohort of 231 patients undergoing an allogeneic bone marrow transplantation was analyzed by XAI for survival by two different uni- and multi-variate survival models, proportional hazard regression and random survival forest, having as the main outcome the overall survival (OS) and its main determinants, using the survex package for R. Both models’ performances were investigated using the integrated Brier score, the integrated Cumulative/Dynamic AUC and the concordance C-index. Global explanation for the whole cohort was performed using the time-dependent variable importance and the partial dependence survival plot. The local explanation for each single patient was obtained via the SurvSHAP(t) and SurvLIME plots and the ceteris paribus survival profile. The survex package common interface ensured a good feasibility of XAI for survival, and the advanced graphical options allowed us to easily explore, explain and compare OS results coming from the two survival models. Before the modeling results to be suitable for clinical use, understandability, clinical relevance and computational efficiency were the most important criteria ensured by this XAI for survival approach, in adherence to clinical XAI guidelines. Full article

Tuberculosis (TB) is one of the leading infectious causes of death worldwide. The effective management and public health control of this disease depends on early detection and careful treatment monitoring. For many years, the microscopy-based analysis of sputum smears has been the most common method to detect and quantify Mycobacterium tuberculosis (Mtb) bacteria. Nonetheless, this form of analysis is a challenging procedure since sputum examination can only be reliably performed by trained personnel with rigorous quality control systems in place. Additionally, it is affected by subjective judgement. Furthermore, although fluorescence-based sample staining methods have made the procedure easier in recent years, the microscopic examination of sputum is a time-consuming operation. Over the past two decades, attempts have been made to automate this practice. Most approaches have focused on establishing an automated method of diagnosis, while others have centred on measuring the bacterial load or detecting and localising Mtb cells for further research on the phenotypic characteristics of their morphology. The literature has incorporated machine learning (ML) and computer vision approaches as part of the methodology to achieve these goals. In this review, we first gathered publicly available TB sputum smear microscopy image sets and analysed the disparities in these datasets. Thereafter, we analysed the most common evaluation metrics used to assess the efficacy of each method in its particular field. Finally, we generated comprehensive summaries of prior work on ML and deep learning (DL) methods for automated TB detection, including a review of their limitations. Full article

Minimal joint space width (mJSW) is a radiographic measurement used in the diagnosis of hip osteoarthritis. A large variance when measuring mJSW highlights the need for a supporting diagnostic tool. This study aimed to estimate the reliability of a deep learning algorithm designed to measure the mJSW in pelvic radiographs and to estimate agreement between the algorithm and orthopedic surgeons, radiologists, and a reporting radiographer. The algorithm was highly consistent when measuring mJSW with a mean difference at 0.00. Human readers, however, were subject to variance with a repeatability coefficient of up to 1.31. Statistically, although not clinically significant, differences were found between the algorithm’s and all readers’ measurements with mean measured differences ranging from −0.78 to −0.36 mm. In conclusion, the algorithm was highly reliable, and the mean measured difference between the human readers combined and the algorithm was low, i.e., −0.5 mm bilaterally. Given the consistency of the algorithm, it may be a useful tool for monitoring hip osteoarthritis. Full article

Since December 2019, a novel coronavirus disease (COVID-19) has infected millions of individuals. This paper conducts a thorough study of the use of deep learning (DL) and federated learning (FL) approaches to COVID-19 screening. To begin, an evaluation of research articles published between 1 January 2020 and 28 June 2023 is presented, considering the preferred reporting items of systematic reviews and meta-analysis (PRISMA) guidelines. The review compares various datasets on medical imaging, including X-ray, computed tomography (CT) scans, and ultrasound images, in terms of the number of images, COVID-19 samples, and classes in the datasets. Following that, a description of existing DL algorithms applied to various datasets is offered. Additionally, a summary of recent work on FL for COVID-19 screening is provided. Efforts to improve the quality of FL models are comprehensively reviewed and objectively evaluated. Full article

Human immunoglobulin allotypes are allelic antigenic determinants (or “markers”) determined serologically, classically by hemagglutination inhibition, on the human immunoglobulin (IG) or antibody heavy and light chains. The allotypes have been identified on the gamma1, gamma2, gamma3, and alpha2 heavy chains (designated as G1m, G2m, G3m, and A2m allotypes, respectively) and on the kappa light chain (Km allotypes). Gm and Am allotypes have been one of the most powerful tools in population genetics, as they are inherited in fixed combinations, or Gm–Am haplotypes, owing to the linkage of the human IGHC genes in the IGH locus on chromosome 14. They have been very instrumental in molecular characterization of the human IGHC genes (gene polymorphisms or alleles, and IG heavy-chain structure in domains) and of the IGH locus (IGHC gene order, gene conversion, and copy number variation (CNV)). They represent a major system for understanding immunogenicity of the polymorphic IG chains in relation to amino acid and conformational changes. The WHO/IMGT allotype nomenclature and the IMGT unique numbering for constant (C) domain bridge Gm–Am and Km alleles to IGHC and IGKC gene alleles and structures and, by definition, to IG chain immunogenicity, opening the way for immunoinformatics of personalized therapeutic antibodies and engineered variants. Full article

Clinical laboratories frequently conduct method verification studies to ensure that the process meets quality standards for its intended use, such as patient testing. They play a pivotal role in healthcare, but issues such as accurate statistical assessment and reporting of verification data often make these studies challenging. Missteps can lead to false conclusions about method performance, risking patient safety or leading to incorrect diagnoses. Despite a requirement for accredited labs to document method performance, existing solutions are often expensive and complex. Addressing these issues, we present Method Verification-Graphical User Interface (MV-GUI), a software package designed for ease of use. It is platform-independent, capable of statistical analysis, and generates accreditation-ready reports swiftly and efficiently. Users can input patient data from one or more .CSV files, and MV-GUI will produce comprehensive reports, including statistical comparison tables, regression plots, and Bland–Altman plots. While method validation, which establishes the performance of new diagnostic tools, remains a crucial concern for manufacturers, MV-GUI primarily streamlines the method verification process. The software aids both medical practitioners and researchers and is designed to be user-friendly, even for non-experienced users. Requiring no internet connection, MV-GUI can operate in restricted IT environments, making method verification widely accessible and efficient. Full article

Breast cancer is among the most common cancers found in women, causing cancer-related deaths and making it a severe public health issue. Early prediction of breast cancer can increase the chances of survival and promote early medical treatment. Moreover, the accurate classification of benign cases can prevent cancer patients from undergoing unnecessary treatments. Therefore, the accurate and early diagnosis of breast cancer and the classification into benign or malignant classes are much-needed research topics. This paper presents an effective feature engineering method to extract and modify features from data and the effects on different classifiers using the Wisconsin Breast Cancer Diagnosis Dataset. We then use the feature to compare six popular machine-learning models for classification. The models compared were Logistic Regression, Random Forest, Decision Tree, K-Neighbors, Multi-Layer Perception (MLP), and XGBoost. The results showed that the Decision Tree model, when applied to the proposed feature engineering, was the best performing, achieving an average accuracy of 98.64%. Full article

Marginalized populations often experience health disparities due to the significant obstacles to care associated with social, economic, and environmental inequities. When compared with advantaged social groups, these populations frequently experience increased risks, poorer health outcomes, and reduced quality of life (QoL). This research examines the clinical and demographic characteristics—age, gender, and race—related to patients with varying stages of type 2 diabetes mellitus (T2DM), comparing the utilization of telemedicine (TM) with traditional healthcare face-to-face (F2F) appointments in an urban medically underserved population area (UMUPA). A logistic regression model, was used to analyze retrospective electronic patient health records (EHRs) from 1 January 2019 to 30 June 2021 of 265 patients with T2DM who had 3357 healthcare appointments. The overall percentage of healthcare provider appointments using TM was 46.7%, in comparison with 53.3% traditional F2F visits. Compared to patients with prediabetes, those with uncontrolled diabetes were more likely to utilize the TM mode of care rather than the traditional F2F mode (adjusted odds ratio (AoR), 1.33; confidence interval (CI), 1.07 to 1.64) after controlling for the other covariates in the model. Compared to patients in the age group 20–49 years, those in the age groups 50–64 years and ≥65 years had significantly lower odds (AoR, 0.78; CI, 0.65 to 0.94 and AoR, 0.71; CI, 0.58 to 0.88, respectively) of utilization of TM than the traditional F2F mode of care. White patients had significantly higher odds of using telemedicine rather than the traditional F2F mode (AoR, 1.25; CI, 1.07 to 1.47) when compared to the Black patients. Gender differences did not exist in the care utilization mode. As healthcare and public health continue to strive for health equity by eliminating health disparities within marginalized populations, it is essential that the mode of care for patients, such as those with T2DM, must evolve and adapt to the needs and resources of the patients. Multisectoral partners have the opportunity to employ a systems thinking approach to improve the technological elements related to the global health disparities crisis. An essential goal is to to create a user-friendly interface that prioritizes easy navigation, affordability, and accessiblity for populations in medically underserved regions to improve overall population health outcomes. Full article

Early disease detection using microarray data is vital for prompt and efficient treatment. However, the intricate nature of these data and the ongoing need for more precise interpretation techniques make it a persistently active research field. Numerous gene expression datasets are publicly available, containing microarray data that reflect the activation status of thousands of genes in patients who may have a specific disease. These datasets encompass a vast number of genes, resulting in high-dimensional feature vectors that present significant challenges for human analysis. Consequently, pinpointing the genes frequently associated with a particular disease becomes a crucial task. In this paper, we present a method capable of determining the frequency with which a gene (feature) is selected for the classification of a specific disease, by incorporating feature discretization and selection techniques into a machine learning pipeline. The experimental results demonstrate high accuracy and a low false negative rate, while significantly reducing the data’s dimensionality in the process. The resulting subsets of genes are manageable for clinical experts, enabling them to verify the presence of a given disease. Full article

Digital twins (DTs) are becoming increasingly popular in various industries, and their potential for healthcare in the metaverse continues to attract attention. The metaverse is a virtual world where individuals interact with digital replicas of themselves and the environment. This paper focuses on personalized and precise medicine and examines the current application of DTs in healthcare within the metaverse. Healthcare practitioners may use immersive virtual worlds to replicate medical scenarios, improve teaching experiences, and provide personalized care to patients. However, the integration of DTs in the metaverse poses technical, regulatory, and ethical challenges that need to be addressed, including data privacy, standards, and accessibility. Through this examination, we aim to provide insights into the transformative potential of DTs in healthcare within the metaverse and encourage further research and development in this exciting domain. Full article

Women that receive news that they have a malignancy of gynecologic origin can have questions about their diagnosis. These questions might be posed as voice queries to the virtual assistants Siri, Alexa, Google, and Cortana. Because our world has increasingly adopted smart phones and standalone voice query devices, this study focused on the accuracy of audible replies by the virtual assistants (VAs) Siri, Alexa, Google, and Cortana to voice queries related to gynecologic oncology. Twenty-one evaluators analyzed VA audible answers to select voice queries related to gynecologic oncology. Questions were posed in three different ways for each voice query in order to maximize the likelihood of acceptability to the VAs in a 24-question panel. For general queries that were not related to gynecologic oncology, Google provided the most correct audible replies (83.3% correct), followed by Alexa (66.7% correct), Siri (45.8% correct), and Cortana (20.8% correct). For gynecologic oncology-related queries, the accuracy of the VAs was considerably lower: Google provided the most correct audible replies (18.1%), followed by Alexa (6.5%), Siri (5.5%), and Cortana (2.3%). There was a considerable drop in the accuracy of audible replies to oral queries on topics in gynecologic oncology relative to general queries that were not related to gynecologic oncology. There is considerable room for improvement in VA performance, so that caution is advised when using VAs for medical queries in gynecologic oncology. Our specific findings related to gynecologic oncology extend the work of others with regard to the low usability of general medical information obtained from VAs, so that reliance on conversational assistants for actionable medical information represents a safety risk for patients and consumers. Full article

Neonatal jaundice is a prevalent condition among newborns, with potentially severe complications that can result in permanent brain damage if left untreated during its early stages. The existing approaches for jaundice detection involve invasive procedures such as blood sample collection, which can inflict pain and distress on the patient, and may give rise to additional complications. Alternatively, a non-invasive method using image-processing techniques and implementing kNN, Random Forest, and XGBoost machine learning algorithms as a classifier can be employed to diagnose jaundice, necessitating a comprehensive database of infant images to achieve a diagnosis with high accuracy. This data article presents the NJN collection, a repository of newborn images encompassing diverse birthweights and skin tones, spanning an age range of 2 to 8 days. The dataset is accompanied by an Excel sheet file in CSV format containing the RGB and YCrCb channel values, as well as the status of each sample. The dataset and associated resources are openly accessible at Zenodo website. Moreover, the Python code for data testing utilizing various AI techniques is provided. Consequently, this article offers an unparalleled resource for AI researchers, enabling them to train their AI systems and develop algorithms that can assist neonatal intensive care unit (NICU) healthcare specialists in monitoring neonates while facilitating the fast, real-time, non-invasive, and accurate diagnosis of jaundice. Full article

Some diseases are known to cause or coincide with volume changes of certain structures in the body. Since these changes can be used to identify diseases, in this paper, we aimed to discover such new correlations. To this end, we trained a machine learning model based on the TotalSegmentator model on computed tomography (CT) image data, to segment 104 anatomical structures, while trying to improve the accuracy of the model. We then used the model to segment CT scans of decedents who had at least one of 18 diseases. After correlating the structure volumes with disease occurrences, a possible new correlation between chronic artery failure and iliac artery volume was found and others were confirmed. However, due to the limitations of the model and the underlying data, further research is required. Full article

The Ann Arbor system is disadvantaged in utilizing information from additional prognostic factors. In this study, we applied the Ensemble Algorithm for Clustering Cancer Data (EACCD) to create a prognostic system for lymphoma that integrates additional prognostic factors. Hodgkin and non-Hodgkin lymphoma survival data were extracted from the Surveillance, Epidemiology, and End Results Program of the National Cancer Institute and divided into the training set (131,725 cases) and the validation set (15,683 cases). Five prognostic factors were studied: Ann Arbor stage, type, site, age, and sex. EACCD was applied to the training set to produce a prognostic system, called an EACCD system, for convenience. The EACCD system stratified patients into eight prognostic groups with well-separated survival curves. These eight prognostic groups had significantly higher accuracies in survival prediction than the 24 Ann Arbor substages. A higher-risk group in the EACCD system roughly corresponds to a higher Ann Arbor substage. The proposed system shows a good performance in risk stratification and survival prediction on both the training and the validation sets. The EACCD system expands the traditional Ann Arbor staging system by leveraging additional prognostic information and is expected to advance treatment management for lymphoma patients. Full article

Physicians often label anatomical structure sets in Digital Imaging and Communications in Medicine (DICOM) images with nonstandard random names. Hence, the standardization of these names for the Organs at Risk (OARs), Planning Target Volumes (PTVs), and ‘Other’ organs is a vital problem. This paper presents novel deep learning methods on structure sets by integrating multimodal data compiled from the radiotherapy centers of the US Veterans Health Administration (VHA) and Virginia Commonwealth University (VCU). These de-identified data comprise 16,290 prostate structures. Our method integrates the multimodal textual and imaging data with Convolutional Neural Network (CNN)-based deep learning approaches such as CNN, Visual Geometry Group (VGG) network, and Residual Network (ResNet) and shows improved results in prostate radiotherapy structure name standardization. Evaluation with macro-averaged F1 score shows that our model with single-modal textual data usually performs better than previous studies. The models perform well on textual data alone, while the addition of imaging data shows that deep neural networks achieve better performance using information present in other modalities. Additionally, using masked images and masked doses along with text leads to an overall performance improvement with the CNN-based architectures than using all the modalities together. Undersampling the majority class leads to further performance enhancement. The VGG network on the masked image-dose data combined with CNNs on the text data performs the best and presents the state-of-the-art in this domain. Full article