scholarly journals Associations between the gut microbiome and metabolome in early life

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Quang P. Nguyen ◽  
Margaret R. Karagas ◽  
Juliette C. Madan ◽  
Erika Dade ◽  
Thomas J. Palys ◽  
...  
Keyword(s):  
Machine Learning ◽  
Early Life ◽  
Procrustes Analysis ◽  
Metabolic Phenotype ◽  
Support Vector ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Unifrac Distance ◽  
Metabolite Concentrations ◽  
Function Relationship

Abstract Background The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationship within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life. Results Stool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 158) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg: − 5.06% -- 6 weeks; − 3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg: 0.344–6 weeks; 0.265–12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations. Conclusions Our results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.

scholarly journals Multi-omic Characterization of the Taxa-function Relationship in Infant Gut Microbiomes

2020 ◽  
Author(s):  
Quang P Nguyen ◽  
Margaret R. Karagas ◽  
Juliette C. Madan ◽  
Erika Dade ◽  
Tom J. Palys ◽  
...  
Keyword(s):  
Machine Learning ◽  
Early Life ◽  
Procrustes Analysis ◽  
Metabolic Phenotype ◽  
Support Vector ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Unifrac Distance ◽  
Metabolite Concentrations ◽  
Function Relationship

Abstract BackgroundThe infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationships within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life.ResultsStool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 168) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis of sample distances (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg. R2: -5.06% -- 6 weeks; -3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg. correlation: 0.344 – 6 weeks; 0.265 – 12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations. ConclusionsOur results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.

scholarly journals Obesity Measures and Dietary Parameters as Predictors of Gut Microbiota Phyla in Healthy Individuals

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2695 ◽  
Author(s):  
Katja Bezek ◽  
Ana Petelin ◽  
Jure Pražnikar ◽  
Esther Nova ◽  
Noemi Redondo ◽  
...  
Keyword(s):  
Machine Learning ◽  
Gut Microbiota ◽  
Clustering Algorithm ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Healthy Individuals ◽  
Data Set ◽  
Bacterial Phyla

The dynamics and diversity of human gut microbiota that can remarkably influence the wellbeing and health of the host are constantly changing through the host’s lifetime in response to various factors. The aim of the present study was to determine a set of parameters that could have a major impact on classifying subjects into a single cluster regarding gut bacteria composition. Therefore, a set of demographical, environmental, and clinical data of healthy adults aged 25–50 years (117 female and 83 men) was collected. Fecal microbiota composition was characterized using Illumina MiSeq 16S rRNA gene amplicon sequencing. Hierarchical clustering was performed to analyze the microbiota data set, and a supervised machine learning model (SVM; Support Vector Machines) was applied for classification. Seventy variables from collected data were included in machine learning analysis. The agglomerative clustering algorithm suggested the presence of four distinct community types of most abundant bacterial phyla. Each cluster harbored a statistically significant different proportion of bacterial phyla. Regarding prediction, the most important features classifying subjects into clusters were measures of obesity (waist to hip ratio, BMI, and visceral fat index), total body water, blood pressure, energy intake, total fat, olive oil intake, total fiber intake, and water intake. In conclusion, the SVM model was shown as a valuable tool to classify healthy individuals based on their gut microbiota composition.

scholarly journals Urine-Based Metabolomics and Machine Learning Reveals Metabolites Associated with Renal Cell Carcinoma Stage

Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6253
Author(s):  
Olatomiwa O. Bifarin ◽  
David A. Gaul ◽  
Samyukta Sah ◽  
Rebecca S. Arnold ◽  
Kenneth Ogan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Tumor Size ◽  
Renal Cell ◽  
Metabolic Phenotype ◽  
Support Vector ◽  
Size Estimation ◽  
Urine Metabolites ◽  
Adaptive Boosting

Urine metabolomics profiling has potential for non-invasive RCC staging, in addition to providing metabolic insights into disease progression. In this study, we utilized liquid chromatography-mass spectrometry (LC-MS), nuclear magnetic resonance (NMR), and machine learning (ML) for the discovery of urine metabolites associated with RCC progression. Two machine learning questions were posed in the study: Binary classification into early RCC (stage I and II) and advanced RCC stages (stage III and IV), and RCC tumor size estimation through regression analysis. A total of 82 RCC patients with known tumor size and metabolomic measurements were used for the regression task, and 70 RCC patients with complete tumor-nodes-metastasis (TNM) staging information were used for the classification tasks under ten-fold cross-validation conditions. A voting ensemble regression model consisting of elastic net, ridge, and support vector regressor predicted RCC tumor size with a R2 value of 0.58. A voting classifier model consisting of random forest, support vector machines, logistic regression, and adaptive boosting yielded an AUC of 0.96 and an accuracy of 87%. Some identified metabolites associated with renal cell carcinoma progression included 4-guanidinobutanoic acid, 7-aminomethyl-7-carbaguanine, 3-hydroxyanthranilic acid, lysyl-glycine, glycine, citrate, and pyruvate. Overall, we identified a urine metabolic phenotype associated with renal cell carcinoma stage, exploring the promise of a urine-based metabolomic assay for staging this disease.

scholarly journals Development of Childhood Asthma Prediction Models using Machine Learning Approaches

2021 ◽  
Author(s):  
Dilini M Kothalawala ◽  
Clare Murray ◽  
Angela Simpson ◽  
Adnan Custovic ◽  
William J Tapper ◽  
...  
Keyword(s):  
Machine Learning ◽  
Childhood Asthma ◽  
Early Life ◽  
Prediction Models ◽  
Predictive Performance ◽  
Preschool Age ◽  
Receiver Operating Curve ◽  
Support Vector ◽  
School Age ◽  
Learning Approaches

Background: Wheeze is common in early life and often transient. It is difficult to identify which children will experience persistent symptoms and subsequently develop asthma. Machine learning approaches have the potential for better predictive performance and generalisability over existing childhood asthma prediction models. Objective: To apply machine learning approaches for predicting school-age asthma (age 10) in early life (Childhood Asthma Prediction in Early life, CAPE model) and at preschool age (Childhood Asthma Prediction at Preschool age, CAPP model). Methods: Data on clinical symptoms and environmental exposures were collected from children enrolled in the Isle of Wight Birth Cohort (N=1368, ~15% asthma prevalence). Recursive Feature Elimination (RFE) identified the optimal subset of features predictive of school-age asthma for each model. Seven state-of-the-art machine learning classification algorithms were used to develop the models and the results were compared. To optimize the models, training was performed by applying 5-fold cross-validation, imputation and resampling. Predictive performances were evaluated on the test set and externally validated in the Manchester Asthma and Allergy Study (MAAS) cohort. Results: RFE identified eight and 12 predictors for the CAPE and CAPP models, respectively. The best predictive performance was demonstrated by a Support Vector Machine (SVM) algorithm for both the CAPE model (area under the receiver operating curve, AUC=0.71) and CAPP model (AUC=0.82). Both models demonstrated good generalisability in MAAS (CAPE 8YR=0.71, 11YR=0.71, CAPP 8YR=0.83, 11YR=0.79). Conclusion: Using machine learning approaches improved upon the predictive performance of existing regression-based models, with good generalisability and ability to rule in asthma.

Using Machine Learning Algorithms on Prediction of Stock Price

2020 ◽  
Vol 12 (2) ◽  
pp. 84-99
Author(s):  
Li-Pang Chen
Keyword(s):  
Machine Learning ◽  
Stock Price ◽  
Short Term Memory ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Short Term ◽  
Learning Techniques ◽  
Historical Database ◽  
Long Short Term Memory

In this paper, we investigate analysis and prediction of the time-dependent data. We focus our attention on four different stocks are selected from Yahoo Finance historical database. To build up models and predict the future stock price, we consider three different machine learning techniques including Long Short-Term Memory (LSTM), Convolutional Neural Networks (CNN) and Support Vector Regression (SVR). By treating close price, open price, daily low, daily high, adjusted close price, and volume of trades as predictors in machine learning methods, it can be shown that the prediction accuracy is improved.

A Comparative Study of Different Machine Learning Algorithms for Disease Prediction

2017 ◽  
Vol 7 (7) ◽  
pp. 172
Author(s):  
Anantvir Singh Romana
Keyword(s):  
Machine Learning ◽  
Subsequent Treatment ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Disease Prediction ◽  
Classification Problems ◽  
Learning Techniques ◽  
Neural Network Classifiers ◽  
Diagnostic Detection

Accurate diagnostic detection of the disease in a patient is critical and may alter the subsequent treatment and increase the chances of survival rate. Machine learning techniques have been instrumental in disease detection and are currently being used in various classification problems due to their accurate prediction performance. Various techniques may provide different desired accuracies and it is therefore imperative to use the most suitable method which provides the best desired results. This research seeks to provide comparative analysis of Support Vector Machine, Naïve bayes, J48 Decision Tree and neural network classifiers breast cancer and diabetes datsets.

Structure-Based Virtual Screening of Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) as Endocrine Disruptors of Androgen Receptor Activity Using Molecular Docking and Machine Learning

2020 ◽  
Author(s):  
Azhagiya Singam Ettayapuram Ramaprasad ◽  
Phum Tachachartvanich ◽  
Denis Fourches ◽  
Anatoly Soshilov ◽  
Jennifer C.Y. Hsieh ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Docking ◽  
Androgen Receptor ◽  
Endocrine Disruptors ◽  
Hormone Receptors ◽  
Steroid Hormone Receptors ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Polyfluoroalkyl Substances ◽  
Perfluoroalkyl And Polyfluoroalkyl Substances

Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) pose a substantial threat as endocrine disruptors, and thus early identification of those that may interact with steroid hormone receptors, such as the androgen receptor (AR), is critical. In this study we screened 5,206 PFASs from the CompTox database against the different binding sites on the AR using both molecular docking and machine learning techniques. We developed support vector machine models trained on Tox21 data to classify the active and inactive PFASs for AR using different chemical fingerprints as features. The maximum accuracy was 95.01% and Matthew’s correlation coefficient (MCC) was 0.76 respectively, based on MACCS fingerprints (MACCSFP). The combination of docking-based screening and machine learning models identified 29 PFASs that have strong potential for activity against the AR and should be considered priority chemicals for biological toxicity testing.

IMPLEMENTASI SUPPORT VECTOR MACHINE PADA PREDIKSI HARGA SAHAM GABUNGAN (IHSG)

2020 ◽  
Vol 25 (1) ◽  
pp. 24-38
Author(s):  
Eka Patriya
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Support Vector Regression ◽  
Support Vector

Saham adalah instrumen pasar keuangan yang banyak dipilih oleh investor sebagai alternatif sumber keuangan, akan tetapi saham yang diperjual belikan di pasar keuangan sering mengalami fluktuasi harga (naik dan turun) yang tinggi. Para investor berpeluang tidak hanya mendapat keuntungan, tetapi juga dapat mengalami kerugian di masa mendatang. Salah satu indikator yang perlu diperhatikan oleh investor dalam berinvestasi saham adalah pergerakan Indeks Harga Saham Gabungan (IHSG). Tindakan dalam menganalisa IHSG merupakan hal yang penting dilakukan oleh investor dengan tujuan untuk menemukan suatu trend atau pola yang mungkin berulang dari pergerakan harga saham masa lalu, sehingga dapat digunakan untuk memprediksi pergerakan harga saham di masa mendatang. Salah satu metode yang dapat digunakan untuk memprediksi pergerakan harga saham secara akurat adalah machine learning. Pada penelitian ini dibuat sebuah model prediksi harga penutupan IHSG menggunakan algoritma Support Vector Regression (SVR) yang menghasilkan kemampuan prediksi dan generalisasi yang baik dengan nilai RMSE training dan testing sebesar 14.334 dan 20.281, serta MAPE training dan testing sebesar 0.211% dan 0.251%. Hasil penelitian ini diharapkan dapat membantu para investor dalam mengambil keputusan untuk menyusun strategi investasi saham.

Binary Spectrum Feature for Improved Classifier Performance

2020 ◽  
Author(s):  
Nalika Ulapane ◽  
Karthick Thiyagarajan ◽  
sarath kodagoda
Keyword(s):  
Machine Learning ◽  
Classification Performance ◽  
Feature Reduction ◽  
Sensor Data ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Svm Classifier ◽  
Monitoring Task ◽  
Classifier Performance ◽  
Spectrum Feature

<div>Classification has become a vital task in modern machine learning and Artificial Intelligence applications, including smart sensing. Numerous machine learning techniques are available to perform classification. Similarly, numerous practices, such as feature selection (i.e., selection of a subset of descriptor variables that optimally describe the output), are available to improve classifier performance. In this paper, we consider the case of a given supervised learning classification task that has to be performed making use of continuous-valued features. It is assumed that an optimal subset of features has already been selected. Therefore, no further feature reduction, or feature addition, is to be carried out. Then, we attempt to improve the classification performance by passing the given feature set through a transformation that produces a new feature set which we have named the “Binary Spectrum”. Via a case study example done on some Pulsed Eddy Current sensor data captured from an infrastructure monitoring task, we demonstrate how the classification accuracy of a Support Vector Machine (SVM) classifier increases through the use of this Binary Spectrum feature, indicating the feature transformation’s potential for broader usage.</div><div><br></div>

In silico Prediction of Inhibitory Constant of Thrombin Inhibitors Using Machine Learning

2019 ◽  
Vol 21 (9) ◽  
pp. 662-669 ◽  
Author(s):  
Junnan Zhao ◽  
Lu Zhu ◽  
Weineng Zhou ◽  
Lingfeng Yin ◽  
Yuchen Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Regression Tree ◽  
Large Data ◽  
Thrombin Inhibitors ◽  
Coagulation Cascade ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Descriptor Selection

Background: Thrombin is the central protease of the vertebrate blood coagulation cascade, which is closely related to cardiovascular diseases. The inhibitory constant Ki is the most significant property of thrombin inhibitors. Method: This study was carried out to predict Ki values of thrombin inhibitors based on a large data set by using machine learning methods. Taking advantage of finding non-intuitive regularities on high-dimensional datasets, machine learning can be used to build effective predictive models. A total of 6554 descriptors for each compound were collected and an efficient descriptor selection method was chosen to find the appropriate descriptors. Four different methods including multiple linear regression (MLR), K Nearest Neighbors (KNN), Gradient Boosting Regression Tree (GBRT) and Support Vector Machine (SVM) were implemented to build prediction models with these selected descriptors. Results: The SVM model was the best one among these methods with R2=0.84, MSE=0.55 for the training set and R2=0.83, MSE=0.56 for the test set. Several validation methods such as yrandomization test and applicability domain evaluation, were adopted to assess the robustness and generalization ability of the model. The final model shows excellent stability and predictive ability and can be employed for rapid estimation of the inhibitory constant, which is full of help for designing novel thrombin inhibitors.

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