Predicting Food Safety Compliance for Informed Food Outlet Inspections: A Machine Learning Approach.
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ABSTRACT:
SUBMITTER: Oldroyd RA
PROVIDER: S-EPMC8656817 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background and purposeResearchers have not disaggregated neighbourhood exposure to takeaway ('fast-') food outlets by cuisine type sold, which would otherwise permit examination of differential impacts on diet, obesity and related disease. This is partly due to the substantial resource challenge of manual classification of unclassified takeaway outlets at scale. We describe the development of a new model to automatically classify takeaway food outlets, by 10 major cuisine types, based on business name alone.Material and methodsWe used machine (deep) learning, and specifically a Long Short Term Memory variant of a Recurrent Neural Network, to develop a predictive model trained on labelled outlets (n = 14,145), from an online takeaway food ordering platform. We validated the accuracy of predictions on unseen labelled outlets (n = 4,000) from the same source.ResultsAlthough accuracy of prediction varied by cuisine type, overall the model (or 'classifier') made a correct prediction approximately three out of four times. We demonstrated the potential of the classifier to public health researchers and for surveillance to support decision-making, through using it to characterise nearly 55,000 takeaway food outlets in England by cuisine type, for the first time.ConclusionsAlthough imperfect, we successfully developed a model to classify takeaway food outlets, by 10 major cuisine types, from business name alone, using innovative data science methods. We have made the model available for use elsewhere by others, including in other contexts and to characterise other types of food outlets, and for further development.
| S-EPMC8700226 | biostudies-literature
Project description:Quantifying sequence-specific protein-ligand interactions is critical for understanding and exploiting numerous cellular processes, including gene expression regulation and signal transduction. Given their importance, next-generation sequencing (NGS) based assays that characterize such recognition with high-throughput are increasingly being used to profile a range of protein classes and interactions. However, these methods do not measure the biophysical parameters that have long been used to uncover the quantitative rules underlying sequence recognition. We developed a highly flexible machine learning framework, called ProBound, to quantify sequence recognition in terms of biophysical parameters based on NGS data. ProBound quantifies transcription factor (TF) behavior with models that accurately predict binding affinity over a range exceeding that of previous resources, captures the impact of DNA modifications and conformational flexibility of multi-TF complexes, and infers specificity directly from \textit{in vivo} data such as ChIP-seq without peak calling. When coupled with a new assay called Kd-seq, it quantifies the absolute affinity of protein-ligand interactions. Its applicability extends beyond thermodynamic equilibrium binding, to the kinetics of kinase-substrate interactions. Altogether, ProBound provides a versatile algorithmic framework for understanding sequence recognition in a wide variety of biological contexts.
2021-06-02 | GSE175942 | GEO
Project description:INTRODUCTION:Developing cross-validated multi-biomarker models for the prediction of the rate of cognitive decline in Alzheimer's disease (AD) is a critical yet unmet clinical challenge. METHODS:We applied support vector regression to AD biomarkers derived from cerebrospinal fluid, structural magnetic resonance imaging (MRI), amyloid-PET and fluorodeoxyglucose positron-emission tomography (FDG-PET) to predict rates of cognitive decline. Prediction models were trained in autosomal-dominant Alzheimer's disease (ADAD, n = 121) and subsequently cross-validated in sporadic prodromal AD (n = 216). The sample size needed to detect treatment effects when using model-based risk enrichment was estimated. RESULTS:A model combining all biomarker modalities and established in ADAD predicted the 4-year rate of decline in global cognition (R2 = 24%) and memory (R2 = 25%) in sporadic AD. Model-based risk-enrichment reduced the sample size required for detecting simulated intervention effects by 50%-75%. DISCUSSION:Our independently validated machine-learning model predicted cognitive decline in sporadic prodromal AD and may substantially reduce sample size needed in clinical trials in AD.
| S-EPMC7222030 | biostudies-literature
Project description:BackgroundVaccine safety surveillance is important because it is related to vaccine hesitancy, which affects vaccination rate. To increase confidence in vaccination, the active monitoring of vaccine adverse events is important. For effective active surveillance, we developed and verified a machine learning-based active surveillance system using national claim data.MethodsWe used two databases, one from the Korea Disease Control and Prevention Agency, which contains flu vaccination records for the elderly, and another from the National Health Insurance Service, which contains the claim data of vaccinated people. We developed a case-crossover design based machine learning model to predict the health outcome of interest events (anaphylaxis and agranulocytosis) using a random forest. Feature importance values were evaluated to determine candidate associations with each outcome. We investigated the relationship of the features to each event via a literature review, comparison with the Side Effect Resource, and using the Local Interpretable Model-agnostic Explanation method.ResultsThe trained model predicted each health outcome of interest with a high accuracy (approximately 70%). We found literature supporting our results, and most of the important drug-related features were listed in the Side Effect Resource database as inducing the health outcome of interest. For anaphylaxis, flu vaccination ranked high in our feature importance analysis and had a positive association in Local Interpretable Model-Agnostic Explanation analysis. Although the feature importance of vaccination was lower for agranulocytosis, it also had a positive relationship in the Local Interpretable Model-Agnostic Explanation analysis.ConclusionWe developed a machine learning-based active surveillance system for detecting possible factors that can induce adverse events using health claim and vaccination databases. The results of the study demonstrated a potentially useful application of two linked national health record databases. Our model can contribute to the establishment of a system for conducting active surveillance on vaccination.
| S-EPMC8352788 | biostudies-literature
Project description:BackgroundEfforts to identify important risk factors for cognitive impairment and dementia have to date mostly relied on meta-analytic strategies. A comprehensive empirical evaluation of these risk factors within a single study is currently lacking.ObjectiveWe used a combined methodology of machine learning and semi-parametric survival analysis to estimate the relative importance of 52 predictors in forecasting cognitive impairment and dementia in a large, population-representative sample of older adults.MethodsParticipants from the Health and Retirement Study (N = 9,979; aged 50-98 years) were followed for up to 10 years (M = 6.85 for cognitive impairment; M = 7.67 for dementia). Using a split-sample methodology, we first estimated the relative importance of predictors using machine learning (random forest survival analysis), and we then used semi-parametric survival analysis (Cox proportional hazards) to estimate effect sizes for the most important variables.ResultsAfrican Americans and individuals who scored high on emotional distress were at relatively highest risk for developing cognitive impairment and dementia. Sociodemographic (lower education, Hispanic ethnicity) and health variables (worse subjective health, increasing BMI) were comparatively strong predictors for cognitive impairment. Cardiovascular factors (e.g., smoking, physical inactivity) and polygenic scores (with and without APOEɛ4) appeared less important than expected. Post-hoc sensitivity analyses underscored the robustness of these results.ConclusionsHigher-order factors (e.g., emotional distress, subjective health), which reflect complex interactions between various aspects of an individual, were more important than narrowly defined factors (e.g., clinical and behavioral indicators) when evaluated concurrently to predict cognitive impairment and dementia.
| S-EPMC7934087 | biostudies-literature
Project description:BackgroundThe Centers for Medicare and Medicaid Services projects that health care costs will continue to grow over the next few years. Rising readmission costs contribute significantly to increasing health care costs. Multiple areas of health care, including readmissions, have benefited from the application of various machine learning algorithms in several ways.ObjectiveWe aimed to identify suitable models for predicting readmission charges billed by hospitals. Our literature review revealed that this application of machine learning is underexplored. We used various predictive methods, ranging from glass-box models (such as regularization techniques) to black-box models (such as deep learning-based models).MethodsWe defined readmissions as readmission with the same major diagnostic category (RSDC) and all-cause readmission category (RADC). For these readmission categories, 576,701 and 1,091,580 individuals, respectively, were identified from the Nationwide Readmission Database of the Healthcare Cost and Utilization Project by the Agency for Healthcare Research and Quality for 2013. Linear regression, lasso regression, elastic net, ridge regression, eXtreme gradient boosting (XGBoost), and a deep learning model based on multilayer perceptron (MLP) were the 6 machine learning algorithms we tested for RSDC and RADC through 10-fold cross-validation.ResultsOur preliminary analysis using a data-driven approach revealed that within RADC, the subsequent readmission charge billed per patient was higher than the previous charge for 541,090 individuals, and this number was 319,233 for RSDC. The top 3 major diagnostic categories (MDCs) for such instances were the same for RADC and RSDC. The average readmission charge billed was higher than the previous charge for 21 of the MDCs in the case of RSDC, whereas it was only for 13 of the MDCs in RADC. We recommend XGBoost and the deep learning model based on MLP for predicting readmission charges. The following performance metrics were obtained for XGBoost: (1) RADC (mean absolute percentage error [MAPE]=3.121%; root mean squared error [RMSE]=0.414; mean absolute error [MAE]=0.317; root relative squared error [RRSE]=0.410; relative absolute error [RAE]=0.399; normalized RMSE [NRMSE]=0.040; mean absolute deviation [MAD]=0.031) and (2) RSDC (MAPE=3.171%; RMSE=0.421; MAE=0.321; RRSE=0.407; RAE=0.393; NRMSE=0.041; MAD=0.031). The performance obtained for MLP-based deep neural networks are as follows: (1) RADC (MAPE=3.103%; RMSE=0.413; MAE=0.316; RRSE=0.410; RAE=0.397; NRMSE=0.040; MAD=0.031) and (2) RSDC (MAPE=3.202%; RMSE=0.427; MAE=0.326; RRSE=0.413; RAE=0.399; NRMSE=0.041; MAD=0.032). Repeated measures ANOVA revealed that the mean RMSE differed significantly across models with P<.001. Post hoc tests using the Bonferroni correction method indicated that the mean RMSE of the deep learning/XGBoost models was statistically significantly (P<.001) lower than that of all other models, namely linear regression/elastic net/lasso/ridge regression.ConclusionsModels built using XGBoost and MLP are suitable for predicting readmission charges billed by hospitals. The MDCs allow models to accurately predict hospital readmission charges.
| S-EPMC9472041 | biostudies-literature
Project description:AIMS:Most cigarette smokers want to quit smoking and more than half make an attempt every year, but less than 10% remain abstinent for at least 6 months. Evidence-based tobacco use treatment improves the likelihood of quitting, but more than two-thirds of individuals relapse when provided even the most robust treatments. Identifying for whom treatment is effective will improve the success of our treatments and perhaps identify strategies for improving current approaches. METHODS:Two cohorts (training: N = 90, validation: N = 71) of cigarette smokers enrolled in group cognitive-behavioral therapy (CBT). Generalized estimating equations were used to identify baseline predictors of outcome, as defined by breath carbon monoxide and urine cotinine. Significant measures were entered as candidate variables to predict quit status. The resulting decision trees were used to predict cessation outcomes in a validation cohort. RESULTS:In the training cohort, the decision trees significantly improved on chance classification of smoking status following treatment and at 6-month follow-up. The first split of all decision trees, which was delay discounting, significantly improved on chance classification rates in both the training and validation cohort. Delay discounting emerged as the single best predictor of group CBT treatment response with an average baseline discount rate of ln(k) = -7.1, correctly predicting smoking status of 80% of participants at posttreatment and 81% of participants at follow-up. CONCLUSIONS:This study provides a first step toward personalized care for smoking cessation though future work is needed to identify individuals that are likely to be successful in treatments beyond group CBT. IMPLICATIONS:This study provides a first step toward personalized care for smoking cessation. Using a novel machine-learning approach, baseline measures of clinical and executive functioning are used to predict smoking cessation outcomes following group CBT. A decision point is recommended for the single best predictor of treatment outcomes, delay discounting, to inform future research or clinical practice in an effort to better allocate patients to treatments that are likely to work.
| S-EPMC7297111 | biostudies-literature
Project description:Objective: The brain age gap estimate (BrainAGE) is the difference between the estimated age and the individual chronological age. BrainAGE was studied primarily using MRI techniques. EEG signals in combination with machine learning (ML) approaches were not commonly used for the human age prediction, and BrainAGE. We investigated whether age-related changes are affecting brain EEG signals, and whether we can predict the chronological age and obtain BrainAGE estimates using a rigorous ML framework with a novel and extensive EEG features extraction. Methods: EEG data were obtained from 468 healthy, mood/anxiety, eating and substance use disorder participants (297 females) from the Tulsa-1000, a naturalistic longitudinal study based on Research Domain Criteria framework. Five sets of preprocessed EEG features across channels and frequency bands were used with different ML methods to predict age. Using a nested-cross-validation (NCV) approach and stack-ensemble learning from EEG features, the predicted age was estimated. The important features and their spatial distributions were deduced. Results: The stack-ensemble age prediction model achieved R2 = 0.37 (0.06), Mean Absolute Error (MAE) = 6.87(0.69) and RMSE = 8.46(0.59) in years. The age and predicted age correlation was r = 0.6. The feature importance revealed that age predictors are spread out across different feature types. The NCV approach produced a reliable age estimation, with features consistent behavior across different folds. Conclusion: Our rigorous ML framework and extensive EEG signal features allow a reliable estimation of chronological age, and BrainAGE. This general framework can be extended to test EEG association with and to predict/study other physiological relevant responses.
| S-EPMC6036180 | biostudies-literature
Project description:Background and objectiveSpirometry patterns can suggest that a patient has a restrictive ventilatory impairment; however, lung volume measurements such as total lung capacity (TLC) are required to confirm the diagnosis. The aim of the study was to train a supervised machine learning model that can accurately estimate TLC values from spirometry and subsequently identify which patients would most benefit from undergoing a complete pulmonary function test.MethodsWe trained three tree-based machine learning models on 51,761 spirometry data points with corresponding TLC measurements. We then compared model performance using an independent test set consisting of 1,402 patients. The best-performing model was used to retrospectively identify restrictive ventilatory impairment in the same test set. The algorithm was compared against different spirometry patterns commonly used to predict restriction.ResultsThe prevalence of restrictive ventilatory impairment in the test set is 16.7% (234/1402). CatBoost was the best-performing machine learning model. It predicted TLC with a mean squared error (MSE) of 560.1 mL. The sensitivity, specificity, and F1-score of the optimal algorithm for predicting restrictive ventilatory impairment was 83, 92, and 75%, respectively.ConclusionA machine learning model trained on spirometry data can estimate TLC to a high degree of accuracy. This approach could be used to develop future smart home-based spirometry solutions, which could aid decision making and self-monitoring in patients with restrictive lung diseases.
| S-EPMC10238228 | biostudies-literature
Project description:BackgroundWe present a machine learning approach to the problem of protein ligand interaction prediction. We focus on a set of binding data obtained from 113 different protein kinases and 20 inhibitors. It was attained through ATP site-dependent binding competition assays and constitutes the first available dataset of this kind. We extract information about the investigated molecules from various data sources to obtain an informative set of features.ResultsA Support Vector Machine (SVM) as well as a decision tree algorithm (C5/See5) is used to learn models based on the available features which in turn can be used for the classification of new kinase-inhibitor pair test instances. We evaluate our approach using different feature sets and parameter settings for the employed classifiers. Moreover, the paper introduces a new way of evaluating predictions in such a setting, where different amounts of information about the binding partners can be assumed to be available for training. Results on an external test set are also provided.ConclusionsIn most of the cases, the presented approach clearly outperforms the baseline methods used for comparison. Experimental results indicate that the applied machine learning methods are able to detect a signal in the data and predict binding affinity to some extent. For SVMs, the binding prediction can be improved significantly by using features that describe the active site of a kinase. For C5, besides diversity in the feature set, alignment scores of conserved regions turned out to be very useful.
| S-EPMC3151211 | biostudies-literature