Dataset Information

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

ABSTRACT: The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from the reference database. Here we present the machine learning based approach PaPrBaG (Pathogenicity Prediction for Bacterial Genomes). PaPrBaG overcomes genetic divergence by training on a wide range of species with known pathogenicity phenotype. To that end we compiled a comprehensive list of pathogenic and non-pathogenic bacteria with human host, using various genome metadata in conjunction with a rule-based protocol. A detailed comparative study reveals that PaPrBaG has several advantages over sequence similarity approaches. Most importantly, it always provides a prediction whereas other approaches discard a large number of sequencing reads with low similarity to currently known reference genomes. Furthermore, PaPrBaG remains reliable even at very low genomic coverages. CombiningPaPrBaG with existing approaches further improves prediction results.

SUBMITTER: Deneke C

PROVIDER: S-EPMC5209729 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

Deneke Carlus C Rentzsch Robert R Renard Bernhard Y BY

Scientific reports 20170104

The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from the reference database. Here we present the machine learning based approach PaPrBaG (Pathogenicity Prediction for Bacterial Genomes). PaPrBaG overcomes genetic divergence by training on a wide range of ...[more]

PMID: 28051068

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Project description:The main cause of stroke is the unexpected blockage of blood flow to the brain. The brain cells die if blood is not supplied to them, resulting in body disability. The timely identification of medical conditions ensures patients receive the necessary treatments and assistance. This early diagnosis plays a crucial role in managing symptoms effectively and enhancing the overall quality of life for individuals affected by the stroke. The research proposed an ensemble machine learning (ML) model that predicts brain stroke while reducing parameters and computational complexity. The dataset was obtained from an open-source website Kaggle and the total number of participants is 3,254. However, this dataset needs a significant class imbalance problem. To address this issue, we utilized Synthetic Minority Over-sampling Technique (SMOTE) and Adaptive Synthetic Sampling (ADAYSN), a technique for oversampling issues. The primary focus of this study centers around developing a stacking and voting approach that exhibits exceptional performance. We propose a stacking ensemble classifier that is more accurate and effective in predicting stroke disease in order to improve the classifier's performance and minimize overfitting problems. To create a final stronger classifier, the study used three tree-based ML classifiers. Hyperparameters are used to train and fine-tune the random forest (RF), decision tree (DT), and extra tree classifier (ETC), after which they were combined using a stacking classifier and a k-fold cross-validation technique. The effectiveness of this method is verified through the utilization of metrics such as accuracy, precision, recall, and F1-score. In addition, we utilized nine ML classifiers with Hyper-parameter tuning to predict the stroke and compare the effectiveness of Proposed approach with these classifiers. The experimental outcomes demonstrated the superior performance of the stacking classification method compared to other approaches. The stacking method achieved a remarkable accuracy of 100% as well as exceptional F1-score, precision, and recall score. The proposed approach demonstrates a higher rate of accurate predictions compared to previous techniques.

Project description:BackgroundPerioperative quantitative monitoring of neuromuscular function in patients receiving neuromuscular blockers has become internationally recognized as an absolute and core necessity in modern anesthesia care. Because of their kinetic nature, artifactual recordings of acceleromyography-based neuromuscular monitoring devices are not unusual. These generate a great deal of cynicism among anesthesiologists, constituting an obstacle toward their widespread adoption. Through outlier analysis techniques, monitoring devices can learn to detect and flag signal abnormalities. Outlier analysis (or anomaly detection) refers to the problem of finding patterns in data that do not conform to expected behavior.ObjectiveThis study was motivated by the development of a smartphone app intended for neuromuscular monitoring based on combined accelerometric and angular hand movement data. During the paired comparison stage of this app against existing acceleromyography monitoring devices, it was noted that the results from both devices did not always concur. This study aims to engineer a set of features that enable the detection of outliers in the form of erroneous train-of-four (TOF) measurements from an acceleromyographic-based device. These features are tested for their potential in the detection of erroneous TOF measurements by developing an outlier detection algorithm.MethodsA data set encompassing 533 high-sensitivity TOF measurements from 35 patients was created based on a multicentric open label trial of a purpose-built accelero- and gyroscopic-based neuromuscular monitoring app. A basic set of features was extracted based on raw data while a second set of features was purpose engineered based on TOF pattern characteristics. Two cost-sensitive logistic regression (CSLR) models were deployed to evaluate the performance of these features. The final output of the developed models was a binary classification, indicating if a TOF measurement was an outlier or not.ResultsA total of 7 basic features were extracted based on raw data, while another 8 features were engineered based on TOF pattern characteristics. The model training and testing were based on separate data sets: one with 319 measurements (18 outliers) and a second with 214 measurements (12 outliers). The F1 score (95% CI) was 0.86 (0.48-0.97) for the CSLR model with engineered features, significantly larger than the CSLR model with the basic features (0.29 [0.17-0.53]; P<.001).ConclusionsThe set of engineered features and their corresponding incorporation in an outlier detection algorithm have the potential to increase overall neuromuscular monitoring data consistency. Integrating outlier flagging algorithms within neuromuscular monitors could potentially reduce overall acceleromyography-based reliability issues.Trial registrationClinicalTrials.gov NCT03605225; https://clinicaltrials.gov/ct2/show/NCT03605225.

Dataset Information

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

Publications

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

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