UNASSIGNED: The identification of microbe-drug associations can greatly facilitate drug research and development. Traditional methods for screening microbe-drug associations are time-consuming, manpower-intensive, and costly to conduct, so computational methods are a good alternative. However, most of them ignore the combination of abundant sequence, structural information, and microbe-drug network topology.
UNASSIGNED: In this study, we developed a computational framework based on a modified graph attention variational autoencoder (MGAVAEMDA) to infer potential microbedrug associations by combining biological information with the variational autoencoder. In MGAVAEMDA, we first used multiple databases, which include microbial sequences, drug structures, and microbe-drug association databases, to establish two comprehensive feature matrices of microbes and drugs after multiple similarity computations, fusion, smoothing, and thresholding. Then, we employed a combination of variational autoencoder and graph attention to extract low-dimensional feature representations of microbes and drugs. Finally, the lowdimensional feature representation and graphical adjacency matrix were input into the random forest classifier to obtain the microbe-drug association score to identify the potential microbe-drug association. Moreover, in order to correct the model complexity and redundant calculation to improve efficiency, we introduced a modified graph convolutional neural network embedded into the variational autoencoder for computing low dimensional features.
UNASSIGNED: The experiment results demonstrate that the prediction performance of MGAVAEMDA is better than the five state-of-the-art methods. For the major measurements (AUC =0.9357, AUPR =0.9378), the relative improvements of MGAVAEMDA compared to the suboptimal methods are 1.76 and 1.47%, respectively.
UNASSIGNED: We conducted case studies on two drugs and found that more than 85% of the predicted associations have been reported in PubMed. The comprehensive experimental results validated the reliability of our models in accurately inferring potential microbe-drug associations.

BACKGROUND: Health care-associated infections due to multidrug-resistant organisms (MDROs), such as methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile (CDI), place a significant burden on our health care infrastructure.
OBJECTIVE: Screening for MDROs is an important mechanism for preventing spread but is resource intensive. The objective of this study was to develop automated tools that can predict colonization or infection risk using electronic health record (EHR) data, provide useful information to aid infection control, and guide empiric antibiotic coverage.
METHODS: We retrospectively developed a machine learning model to detect MRSA colonization and infection in undifferentiated patients at the time of sample collection from hospitalized patients at the University of Virginia Hospital. We used clinical and nonclinical features derived from on-admission and throughout-stay information from the patient\'s EHR data to build the model. In addition, we used a class of features derived from contact networks in EHR data; these network features can capture patients\' contacts with providers and other patients, improving model interpretability and accuracy for predicting the outcome of surveillance tests for MRSA. Finally, we explored heterogeneous models for different patient subpopulations, for example, those admitted to an intensive care unit or emergency department or those with specific testing histories, which perform better.
RESULTS: We found that the penalized logistic regression performs better than other methods, and this model\'s performance measured in terms of its receiver operating characteristics-area under the curve score improves by nearly 11% when we use polynomial (second-degree) transformation of the features. Some significant features in predicting MDRO risk include antibiotic use, surgery, use of devices, dialysis, patient\'s comorbidity conditions, and network features. Among these, network features add the most value and improve the model\'s performance by at least 15%. The penalized logistic regression model with the same transformation of features also performs better than other models for specific patient subpopulations.
CONCLUSIONS: Our study shows that MRSA risk prediction can be conducted quite effectively by machine learning methods using clinical and nonclinical features derived from EHR data. Network features are the most predictive and provide significant improvement over prior methods. Furthermore, heterogeneous prediction models for different patient subpopulations enhance the model\'s performance.

The bicipital groove is an important anatomical feature of the proximal humerus that needs to be identified during surgical planning for procedures such as shoulder arthroplasty and proximal humeral fracture reconstruction. Current algorithms for automatic identification prove ineffective in arthritic humeri due to the presence of osteophytes, reducing their usefulness for total shoulder arthroplasty. Our methodology involves the use of a Random Forest Classifier (RFC) to automatically detect the bicipital groove on segmented computed tomography scans of humeri. We evaluated our model on two distinct test datasets: one comprising non-arthritic humeri and another with arthritic humeri characterized by significant osteophytes. Our model detected the bicipital groove with a mean absolute error of less than 1mm on arthritic humeri, demonstrating a significant improvement over the previous gold standard approach. Successful identification of the bicipital groove with a high degree of accuracy even in arthritic humeri was accomplished. This model is open source and included in the python package shoulder.

Background and Objectives: Heart failure (HF) is a prevalent and debilitating condition that imposes a significant burden on healthcare systems and adversely affects the quality of life of patients worldwide. Comorbidities such as chronic kidney disease (CKD), arterial hypertension, and diabetes mellitus (DM) are common among HF patients, as they share similar risk factors. This study aimed to identify the prognostic significance of multiple factors and their correlation with disease prognosis and outcomes in a Jordanian cohort. Materials and Methods: Data from the Jordanian Heart Failure Registry (JoHFR) were analyzed, encompassing medical records from acute and chronic HF patients attending public and private cardiology clinics and hospitals across Jordan. An online form was utilized for data collection, focusing on three kidney function tests, estimated glomerular filtration rate (eGFR), blood urea nitrogen (BUN), and creatinine levels, with the eGFR calculated using the Cockcroft-Gault formula. We also built six machine learning models to predict mortality in our cohort. Results: From the JoHFR, 2151 HF patients were included, with 644, 1799, and 1927 records analyzed for eGFR, BUN, and creatinine levels, respectively. Age negatively impacted all measures (p ≤ 0.001), while smokers surprisingly showed better results than non-smokers (p ≤ 0.001). Males had more normal eGFR levels compared to females (p = 0.002). Comorbidities such as hypertension, diabetes, arrhythmias, and implanted devices were inversely related to eGFR (all with p-values <0.05). Higher BUN levels were associated with chronic HF, dyslipidemia, and ASCVD (p ≤ 0.001). Higher creatinine levels were linked to hypertension, diabetes, dyslipidemia, arrhythmias, and previous HF history (all with p-values <0.05). Low eGFR levels were associated with increased mechanical ventilation needs (p = 0.049) and mortality (p ≤ 0.001), while BUN levels did not significantly affect these outcomes. Machine learning analysis employing the Random Forest Classifier revealed that length of hospital stay and creatinine >115 were the most significant predictors of mortality. The classifier achieved an accuracy of 90.02% with an AUC of 80.51%, indicating its efficacy in predictive modeling. Conclusions: This study reveals the intricate relationship among kidney function tests, comorbidities, and clinical outcomes in HF patients in Jordan, highlighting the importance of kidney function as a predictive tool. Integrating machine learning models into clinical practice may enhance the predictive accuracy of patient outcomes, thereby supporting a more personalized approach to managing HF and related kidney dysfunction. Further research is necessary to validate these findings and to develop innovative treatment strategies for the CKD population within the HF cohort.

The leading cause of cancer-related deaths worldwide is skin cancer. Effective therapy depends on the early diagnosis of skin cancer through the precise classification of skin lesions. However, dermatologists may find it difficult and time-consuming to accurately classify skin lesions. The use of transfer learning to boost skin cancer classification model precision is a promising strategy. In this work, we proposed a hybrid CNN with a transfer learning model and a random forest classifier for skin cancer disease detection. To evaluate the efficacy of the proposed model, it was verified over two datasets of benign skin moles and malignant skin moles. The proposed model is able to classify images with an accuracy of up to 90.11%. The empirical results and analysis assure the feasibility and effectiveness of the proposed model for skin cancer classification.

Background: Although acute kidney injury (AKI) is a common complication in patients undergoing hematopoietic stem cell transplantation (HSCT), its prophylaxis remains a clinical challenge. Attempts at prevention or early diagnosis focus on various methods for the identification of factors influencing the incidence of AKI. Our aim was to test the artificial intelligence (AI) potential in the construction of a model defining parameters predicting AKI development. Methods: The analysis covered the clinical data of children followed up for 6 months after HSCT. Kidney function was assessed before conditioning therapy, 24 h after HSCT, 1, 2, 3, 4, and 8 weeks after transplantation, and, finally, 3 and 6 months post-transplant. The type of donor, conditioning protocol, and complications were incorporated into the model. Results: A random forest classifier (RFC) labeled the 93 patients according to presence or absence of AKI. The RFC model revealed that the values of the estimated glomerular filtration rate (eGFR) before and just after HSCT, as well as methotrexate use, acute graft versus host disease (GvHD), and viral infection occurrence, were the major determinants of AKI incidence within the 6-month post-transplant observation period. Conclusions: Artificial intelligence seems a promising tool in predicting the potential risk of developing AKI, even before HSCT or just after the procedure.

Chest X-ray image contains sufficient information that finds wide-spread applications in diverse disease diagnosis and decision making to assist the medical experts. This paper has proposed an intelligent approach to detect Covid-19 from the chest X-ray image using the hybridization of deep convolutional neural network (CNN) and discrete wavelet transform (DWT) features. At first, the X-ray image is enhanced and segmented through preprocessing tasks, and then deep CNN and DWT features are extracted. The optimum features are extracted from these hybridized features through minimum redundancy and maximum relevance (mRMR) along with recursive feature elimination (RFE). Finally, the random forest-based bagging approach is used for doing the detection task. An extensive experiment is performed, and the results confirm that our approach gives satisfactory performance compare to the existing methods with an overall accuracy of more than 98.5%.

The human gut microbiota relies on complex carbohydrates (glycans) for energy and growth, primarily dietary fiber and host-derived mucins. We introduce a mathematical model of a glycan generalist and a mucin specialist in a two-compartment chemostat model of the human colon. Our objective is to characterize the influence of dietary fiber and mucin supply on the abundance of mucin-degrading species within the gut ecosystem. Current mathematical gut reactor models that include the enzymatic degradation of glycans do not differentiate between glycan types and their degraders. The model we present distinguishes between a generalist that can degrade both dietary fiber and mucin, and a specialist species that can only degrade mucin. The integrity of the colonic mucus barrier is essential for overall human health and well-being, with the mucin specialist Akkermanisa muciniphila being associated with a healthy mucus layer. Competition, particularly between the specialist and generalists like Bacteroides thetaiotaomicron, may lead to mucus layer erosion, especially during periods of dietary fiber deprivation. Our model treats the colon as a gut reactor system, dividing it into two compartments that represent the lumen and the mucus of the gut, resulting in a complex system of ordinary differential equations with a large and uncertain parameter space. To understand the influence of model parameters on long-term behavior, we employ a random forest classifier, a supervised machine learning method. Additionally, a variance-based sensitivity analysis is utilized to determine the sensitivity of steady-state values to changes in model parameter inputs. By constructing this model, we can investigate the underlying mechanisms that control gut microbiota composition and function, free from confounding factors.

Forest canopy cover (FCC) is essential in forest assessment and management, affecting ecosystem services such as carbon sequestration, wildlife habitat, and water regulation. Ongoing advancements in techniques for accurately and efficiently mapping and extracting FCC information require a thorough evaluation of their validity and reliability. The primary objectives of this study are to: (1) create a large-scale forest FCC dataset with a 1-meter spatial resolution, (2) assess the regional spatial distribution of FCC at a regional scale, and (3) investigate differences in FCC areas among the Global Forest Change (Hansen et al., 2013) and U.S. Forest Service Tree Canopy Cover products at various spatial scales in Arkansas (i.e., county and city levels). This study utilized high-resolution aerial imagery and a machine learning algorithm processed and analyzed using the Google Earth Engine cloud computing platform to produce the FCC dataset. The accuracy of this dataset was validated using one-third of the reference locations obtained from the Global Forest Change (Hansen et al., 2013) dataset and the National Agriculture Imagery Program (NAIP) aerial imagery with a 0.6-m spatial resolution. The results showed that the dataset successfully identified FCC at a 1-m resolution in the study area, with overall accuracy ranging between 83.31% and 94.35% per county. Spatial comparison results between the produced FCC dataset and the Hansen et al., 2013 and USFS products indicated a strong positive correlation, with R2 values ranging between 0.94 and 0.98 for county and city levels. This dataset provides valuable information for monitoring, forecasting, and managing forest resources in Arkansas and beyond. The methodology followed in this study enhances efficiency, cost-effectiveness, and scalability, as it enables the processing of large-scale datasets with high computational demands in a cloud-based environment. It also demonstrates that machine learning and cloud computing technologies can generate high-resolution forest cover datasets, which might be helpful in other regions of the world.

The rapid, low cost, and efficient detection of SARS-CoV-2 virus infection, especially in clinical samples, remains a major challenge. A promising solution to this problem is the combination of a spectroscopic technique: surface-enhanced Raman spectroscopy (SERS) with advanced chemometrics based on machine learning (ML) algorithms. In the present study, we conducted SERS investigations of saliva and nasopharyngeal swabs taken from a cohort of patients (saliva: 175; nasopharyngeal swabs: 114). Obtained SERS spectra were analyzed using a range of classifiers in which random forest (RF) achieved the best results, e.g., for saliva, the precision and recall equals 94.0% and 88.9%, respectively. The results demonstrate that even with a relatively small number of clinical samples, the combination of SERS and shallow machine learning can be used to identify SARS-CoV-2 virus in clinical practice.