Predicting the short-term success of human influenza virus variants with machine learning.
Ontology highlight
ABSTRACT:
SUBMITTER: Hayati M
PROVIDER: S-EPMC7209065 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:After creation of a new arteriovenous fistula (AVF), assessment of readiness for use is an important clinical task. Accurate prediction of successful use is challenging, and augmentation of the physical exam with ultrasound has become routine. Herein, we propose a point-of-care tool based on machine learning to enhance prediction of successful unassisted radiocephalic arteriovenous fistula (AVF) use. Our analysis includes pooled patient-level data from 704 patients undergoing new radiocephalic AVF creation, eligible for hemodialysis, and enrolled in the 2014-2019 international multicenter PATENCY-1 or PATENCY-2 randomized controlled trials. The primary outcome being predicted is successful unassisted AVF use within 1-year, defined as 2-needle cannulation for hemodialysis for ≥90 days without preceding intervention. Logistic, penalized logistic (lasso and elastic net), decision tree, random forest, and boosted tree classification models were built with a training, tuning, and testing paradigm using a combination of baseline clinical characteristics and 4-6 week ultrasound parameters. Performance assessment includes receiver operating characteristic curves, precision-recall curves, calibration plots, and decision curves. All modeling approaches except the decision tree have similar discrimination performance and comparable net-benefit (area under the ROC curve 0.78-0.81, accuracy 69.1-73.6%). Model performance is superior to Kidney Disease Outcome Quality Initiative and University of Alabama at Birmingham ultrasound threshold criteria. The lasso model is presented as the final model due to its parsimony, retaining only 3 covariates: larger outflow vein diameter, higher flow volume, and absence of >50% luminal stenosis. A point-of-care online calculator is deployed to facilitate AVF assessment in the clinic.
| S-EPMC9592575 | biostudies-literature
Project description:BackgroundPrognostic prediction and the identification of prognostic factors are critical during the early period of atrial-fibrillation (AF)-related strokes as AF is associated with poor outcomes in stroke patients.MethodsTwo independent datasets, namely, the Korean Atrial Fibrillation Evaluation Registry in Ischemic Stroke Patients (K-ATTENTION) and the Korea University Stroke Registry (KUSR), were used for internal and external validation, respectively. These datasets include common variables such as demographic, laboratory, and imaging findings during early hospitalization. Outcomes were unfavorable functional status with modified Rankin scores of 3 or higher and mortality at 3 months. We developed two machine learning models, namely, a tree-based model and a multi-layer perceptron (MLP), along with a baseline logistic regression model. The area under the receiver operating characteristic curve (AUROC) was used as the outcome metric. The Shapley additive explanation (SHAP) method was used to evaluate the contributions of variables.ResultsMachine learning models outperformed logistic regression in predicting both outcomes. For 3-month unfavorable outcomes, MLP exhibited significantly higher AUROC values of 0.890 and 0.859 in internal and external validation sets, respectively, than those of logistic regression. For 3-month mortality, both machine learning models exhibited significantly higher AUROC values than the logistic regression for internal validation but not for external validation. The most significant predictor for both outcomes was the initial National Institute of Health and Stroke Scale.ConclusionThe explainable machine learning model can reliably predict short-term outcomes and identify high-risk patients with AF-related strokes.
| S-EPMC10663332 | biostudies-literature
Project description:Predicting time series has significant practical applications over different disciplines. Here, we propose an Anticipated Learning Machine (ALM) to achieve precise future-state predictions based on short-term but high-dimensional data. From non-linear dynamical systems theory, we show that ALM can transform recent correlation/spatial information of high-dimensional variables into future dynamical/temporal information of any target variable, thereby overcoming the small-sample problem and achieving multistep-ahead predictions. Since the training samples generated from high-dimensional data also include information of the unknown future values of the target variable, it is called anticipated learning. Extensive experiments on real-world data demonstrate significantly superior performances of ALM over all of the existing 12 methods. In contrast to traditional statistics-based machine learning, ALM is based on non-linear dynamics, thus opening a new way for dynamics-based machine learning.
| S-EPMC8288952 | biostudies-literature
Project description:IntroductionSeasonal influenza A H3N2 viruses are constantly changing, reducing the effectiveness of existing vaccines. As a result, the World Health Organization (WHO) needs to frequently update the vaccine strains to match the antigenicity of emerged H3N2 variants. Traditional assessments of antigenicity rely on serological methods, which are both labor-intensive and time-consuming. Although numerous computational models aim to simplify antigenicity determination, they either lack a robust quantitative linkage between antigenicity and viral sequences or focus restrictively on selected features.MethodsHere, we propose a novel computational method to predict antigenic distances using multiple features, including not only viral sequence attributes but also integrating four distinct categories of features that significantly affect viral antigenicity in sequences.ResultsThis method exhibits low error in virus antigenicity prediction and achieves superior accuracy in discerning antigenic drift. Utilizing this method, we investigated the evolution process of the H3N2 influenza viruses and identified a total of 21 major antigenic clusters from 1968 to 2022.DiscussionInterestingly, our predicted antigenic map aligns closely with the antigenic map generated with serological data. Thus, our method is a promising tool for detecting antigenic variants and guiding the selection of vaccine candidates.
| S-EPMC10834737 | biostudies-literature
Project description:Background: Preoperative prediction of short-term postoperative outcomes in spinal tumor patients can lead to more precise patient care plans that reduce the likelihood of negative outcomes. With this study, we aimed to develop machine learning algorithms for predicting short-term postoperative outcomes and implement these models in an open-source web application. Methods: Patients who underwent surgical resection of spinal tumors were identified using the American College of Surgeons, National Surgical Quality Improvement Program. Three outcomes were predicted: prolonged length of stay (LOS), nonhome discharges, and major complications. Four machine learning algorithms were developed and integrated into an open access web application to predict these outcomes. Results: A total of 3073 patients that underwent spinal tumor resection were included in the analysis. The most accurately predicted outcomes in terms of the area under the receiver operating characteristic curve (AUROC) was the prolonged LOS with a mean AUROC of 0.745 The most accurately predicting algorithm in terms of AUROC was random forest, with a mean AUROC of 0.743. An open access web application was developed for getting predictions for individual patients based on their characteristics and this web application can be accessed here: huggingface.co/spaces/MSHS-Neurosurgery-Research/NSQIP-ST. Conclusion: Machine learning approaches carry significant potential for the purpose of predicting postoperative outcomes following spinal tumor resections. Development of predictive models as clinically useful decision-making tools may considerably enhance risk assessment and prognosis as the amount of data in spinal tumor surgery continues to rise.
| S-EPMC9913622 | biostudies-literature
Project description:Each influenza pandemic was caused at least partly by avian- and/or swine-origin influenza A viruses (IAVs). The timing of and the potential IAVs involved in the next pandemic are currently unpredictable. We aim to build machine learning (ML) models to predict human-adaptive IAV nucleotide composition. A total of 217,549 IAV full-length coding sequences of the PB2 (polymerase basic protein-2), PB1, PA (polymerase acidic protein), HA (hemagglutinin), NP (nucleoprotein), and NA (neuraminidase) segments were decomposed for their codon position-based mononucleotides (12 nts) and dinucleotides (48 dnts). A total of 68,742 human sequences and 68,739 avian sequences (1:1) were resampled to characterize the human adaptation-associated (d)nts with principal component analysis (PCA) and other ML models. Then, the human adaptation of IAV sequences was predicted based on the characterized (d)nts. Respectively, 9, 12, 11, 13, 10 and 9 human-adaptive (d)nts were optimized for the six segments. PCA and hierarchical clustering analysis revealed the linear separability of the optimized (d)nts between the human-adaptive and avian-adaptive sets. The results of the confusion matrix and the area under the receiver operating characteristic curve indicated a high performance of the ML models to predict human adaptation of IAVs. Our model performed well in predicting the human adaptation of the swine/avian IAVs before and after the 2009 H1N1 pandemic. In conclusion, we identified the human adaptation-associated genomic composition of IAV segments. ML models for IAV human adaptation prediction using large IAV genomic data sets can facilitate the identification of key viral factors that affect virus transmission/pathogenicity. Most importantly, it allows the prediction of pandemic influenza.
| S-EPMC7086167 | biostudies-literature
Project description:AimsFrailty may be found in heart failure patients especially in the elderly and is associated with a poor prognosis. However, assessment of frailty status is time-consuming, and the electronic frailty indices developed using health records have served as useful surrogates. We hypothesized that an electronic frailty index developed using machine learning can improve short-term mortality prediction in patients with heart failure.Methods and resultsThis was a retrospective observational study that included patients admitted to nine public hospitals for heart failure from Hong Kong between 2013 and 2017. Age, sex, variables in the modified frailty index, Deyo's Charlson co-morbidity index (≥2), neutrophil-to-lymphocyte ratio (NLR), and prognostic nutritional index at baseline were analysed. Gradient boosting, which is a supervised sequential ensemble learning algorithm with weak prediction submodels (typically decision trees), was applied to predict mortality. Variables were ranked in the order of importance with a total score of 100 and used to build the frailty models. Comparisons were made with decision tree and multivariable logistic regression. A total of 8893 patients (median: age 81, Q1-Q3: 71-87 years old) were included, in whom 9% had 30 day mortality and 17% had 90 day mortality. Prognostic nutritional index, age, and NLR were the most important variables predicting 30 day mortality (importance score: 37.4, 32.1, and 20.5, respectively) and 90 day mortality (importance score: 35.3, 36.3, and 14.6, respectively). Gradient boosting significantly outperformed decision tree and multivariable logistic regression. The area under the curve from a five-fold cross validation was 0.90 for gradient boosting and 0.87 and 0.86 for decision tree and logistic regression in predicting 30 day mortality. For the prediction of 90 day mortality, the area under the curve was 0.92, 0.89, and 0.86 for gradient boosting, decision tree, and logistic regression, respectively.ConclusionsThe electronic frailty index based on co-morbidities, inflammation, and nutrition information can readily predict mortality outcomes. Their predictive performances were significantly improved by gradient boosting techniques.
| S-EPMC8318426 | biostudies-literature
Project description:Antimicrobial-resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know whether the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole-genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single-copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict whether the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial taxa, including Campylobacter, Escherichia coli and Salmonella, and has a taxon agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as a standalone tool and via a web interface.
| S-EPMC8743549 | biostudies-literature
Project description:Whereas transcatheter aortic valve implantation (TAVI) has become the gold standard for aortic valve stenosis treatment in high-risk patients, it has recently been extended to include intermediate risk patients. However, the mortality rate at 5 years is still elevated. The aim of the present study was to develop a novel machine learning (ML) approach able to identify the best predictors of 5-year mortality after TAVI among several clinical and echocardiographic variables, which may improve the long-term prognosis. We retrospectively enrolled 471 patients undergoing TAVI. More than 80 pre-TAVI variables were collected and analyzed through different feature selection processes, which allowed for the identification of several variables with the highest predictive value of mortality. Different ML models were compared. Multilayer perceptron resulted in the best performance in predicting mortality at 5 years after TAVI, with an area under the curve, positive predictive value, and sensitivity of 0.79, 0.73, and 0.71, respectively. We presented an ML approach for the assessment of risk factors for long-term mortality after TAVI to improve clinical prognosis. Fourteen potential predictors were identified with the organic mitral regurgitation (myxomatous or calcific degeneration of the leaflets and/or annulus) which showed the highest impact on 5 years mortality.
| S-EPMC8072967 | biostudies-literature
Project description:BackgroundMobile technology offers unique opportunities for monitoring short-term suicide risk in daily life. In this study of suicidal adolescent inpatients, theoretically informed risk factors were assessed daily following discharge to predict near-term suicidal ideation and inform decision algorithms for identifying elevations in daily level risk, with implications for real-time suicide-focused interventions.MethodsAdolescents (N = 78; 67.9% female) completed brief surveys texted daily for 4 weeks after discharge (n = 1621 observations). Using multi-level classification and regression trees (CARTSs) with repeated 5-fold cross-validation, we tested (a) a simple prediction model incorporating previous-day scores for each of 10 risk factors, and (b) a more complex model incorporating, for each of these factors, a time-varying person-specific mean over prior days together with deviation from that mean. Models also incorporated missingness and contextual (study week, day of the week) indicators. The outcome was the presence/absence of next-day suicidal ideation.ResultsThe best-performing model (cross-validated AUC = 0.86) was a complex model that included ideation duration, hopelessness, burdensomeness, and self-efficacy to refrain from suicidal action. An equivalent model that excluded ideation duration had acceptable overall performance (cross-validated AUC = 0.78). Models incorporating only previous-day scores, with and without ideation duration (cross-validated AUC of 0.82 and 0.75, respectively), showed relatively weaker performance.ConclusionsResults suggest that specific combinations of dynamic risk factors assessed in adolescents' daily life have promising utility in predicting next-day suicidal thoughts. Findings represent an important step in the development of decision tools identifying short-term risk as well as guiding timely interventions sensitive to proximal elevations in suicide risk in daily life.
| S-EPMC9814182 | biostudies-literature