scholarly journals MDITRE: scalable and interpretable machine learning for predicting host status from temporal microbiome dynamics

2021 ◽  
Author(s):  
Venkata Suhas Maringanti ◽  
Vanni Bucci ◽  
Georg K Gerber

Longitudinal microbiome datasets are being generated with increasing regularity, and there is broad recognition that these studies are critical for unlocking the mechanisms through which the microbiome impacts human health and disease. Yet, there is a dearth of computational tools for analyzing microbiome time-series data. To address this gap, we developed an open-source software package, MDITRE, which implements a new highly efficient method leveraging deep-learning technologies to derive human-interpretable rules that predict host status from longitudinal microbiome data. Using semi-synthetic and a large compendium of publicly available 16S rRNA amplicon and metagenomics sequencing datasets, we demonstrate that in almost all cases, MDITRE performs on par or better than popular uninterpretable machine learning methods, and orders-of-magnitude faster than the prior interpretable technique. MDITRE also provides a graphical user interface, which we show through use cases can readily derive biologically meaningful interpretations linking patterns of microbiome changes over time with host phenotypes.

2018 ◽  
Author(s):  
Elijah Bogart ◽  
Richard Creswell ◽  
Georg K. Gerber

AbstractLongitudinal studies are crucial for discovering casual relationships between the microbiome and human disease. We present Microbiome Interpretable Temporal Rule Engine (MITRE), the first machine learning method specifically designed for predicting host status from microbiome time-series data. Our method maintains interpretability by learning predictive rules over automatically inferred time-periods and phylogenetically related microbes. We validate MITRE’s performance on semi-synthetic data, and five real datasets measuring microbiome composition over time in infant and adult cohorts. Our results demonstrate that MITRE performs on par or outperforms “black box” machine learning approaches, providing a powerful new tool enabling discovery of biologically interpretable relationships between microbiome and human host.


2021 ◽  
Author(s):  
Dhairya Vyas

In terms of Machine Learning, the majority of the data can be grouped into four categories: numerical data, category data, time-series data, and text. We use different classifiers for different data properties, such as the Supervised; Unsupervised; and Reinforcement. Each Categorises has classifier we have tested almost all machine learning methods and make analysis among them.


2021 ◽  
Author(s):  
Dhairya Vyas

In terms of Machine Learning, the majority of the data can be grouped into four categories: numerical data, category data, time-series data, and text. We use different classifiers for different data properties, such as the Supervised; Unsupervised; and Reinforcement. Each Categorises has classifier we have tested almost all machine learning methods and make analysis among them.


Author(s):  
Bharathi N. Gopalsamy ◽  
Brindha G. R. ◽  
B. Santhi

Machine learning (ML) is prevalent across the globe and applied in almost all domains. This chapter focuses on implementation of ML with real-time use cases. Day-to-day activities are automated to ease the task and increase the quality of decision. ML is the backbone of the perfect decision support system with a plethora of applications. The use case described in this chapter is ML & Security, which is implemented in R Script. Adversaries took advantages of ML to avoid detection and evade defenses. Network intrusion detection system (IDS) is the major issue nowadays. Its primary task is to collect relevant features from the computer network. These selected features can be fed into the ML algorithms to predict the label. The challenge in this use case is what type of feature to consider for intrusion and anomaly detection (AD). This chapter focuses on end-to-end process to get insight into the stream of data from the network connection with priority given to forecasting mechanism and prediction of the future. Forecasting is applied to the time series data to get sensible decisions.


2020 ◽  
Author(s):  
Hsiao-Ko Chang ◽  
Hui-Chih Wang ◽  
Chih-Fen Huang ◽  
Feipei Lai

BACKGROUND In most of Taiwan’s medical institutions, congestion is a serious problem for emergency departments. Due to a lack of beds, patients spend more time in emergency retention zones, which make it difficult to detect cardiac arrest (CA). OBJECTIVE We seek to develop a Drug Early Warning System Model (DEWSM), it included drug injections and vital signs as this research important features. We use it to predict cardiac arrest in emergency departments via drug classification and medical expert suggestion. METHODS We propose this new model for detecting cardiac arrest via drug classification and by using a sliding window; we apply learning-based algorithms to time-series data for a DEWSM. By treating drug features as a dynamic time-series factor for cardiopulmonary resuscitation (CPR) patients, we increase sensitivity, reduce false alarm rates and mortality, and increase the model’s accuracy. To evaluate the proposed model, we use the area under the receiver operating characteristic curve (AUROC). RESULTS Four important findings are as follows: (1) We identify the most important drug predictors: bits (intravenous therapy), and replenishers and regulators of water and electrolytes (fluid and electrolyte supplement). The best AUROC of bits is 85%, it means the medical expert suggest the drug features: bits, it will affect the vital signs, and then the evaluate this model correctly classified patients with CPR reach 85%; that of replenishers and regulators of water and electrolytes is 86%. These two features are the most influential of the drug features in the task. (2) We verify feature selection, in which accounting for drugs improve the accuracy: In Task 1, the best AUROC of vital signs is 77%, and that of all features is 86%. In Task 2, the best AUROC of all features is 85%, which demonstrates that thus accounting for the drugs significantly affects prediction. (3) We use a better model: For traditional machine learning, this study adds a new AI technology: the long short-term memory (LSTM) model with the best time-series accuracy, comparable to the traditional random forest (RF) model; the two AUROC measures are 85%. It can be seen that the use of new AI technology will achieve better results, currently comparable to the accuracy of traditional common RF, and the LSTM model can be adjusted in the future to obtain better results. (4) We determine whether the event can be predicted beforehand: The best classifier is still an RF model, in which the observational starting time is 4 hours before the CPR event. Although the accuracy is impaired, the predictive accuracy still reaches 70%. Therefore, we believe that CPR events can be predicted four hours before the event. CONCLUSIONS This paper uses a sliding window to account for dynamic time-series data consisting of the patient’s vital signs and drug injections. The National Early Warning Score (NEWS) only focuses on the score of vital signs, and does not include factors related to drug injections. In this study, the experimental results of adding the drug injections are better than only vital signs. In a comparison with NEWS, we improve predictive accuracy via feature selection, which includes drugs as features. In addition, we use traditional machine learning methods and deep learning (using LSTM method as the main processing time series data) as the basis for comparison of this research. The proposed DEWSM, which offers 4-hour predictions, is better than the NEWS in the literature. This also confirms that the doctor’s heuristic rules are consistent with the results found by machine learning algorithms.


2021 ◽  
Vol 13 (3) ◽  
pp. 67
Author(s):  
Eric Hitimana ◽  
Gaurav Bajpai ◽  
Richard Musabe ◽  
Louis Sibomana ◽  
Jayavel Kayalvizhi

Many countries worldwide face challenges in controlling building incidence prevention measures for fire disasters. The most critical issues are the localization, identification, detection of the room occupant. Internet of Things (IoT) along with machine learning proved the increase of the smartness of the building by providing real-time data acquisition using sensors and actuators for prediction mechanisms. This paper proposes the implementation of an IoT framework to capture indoor environmental parameters for occupancy multivariate time-series data. The application of the Long Short Term Memory (LSTM) Deep Learning algorithm is used to infer the knowledge of the presence of human beings. An experiment is conducted in an office room using multivariate time-series as predictors in the regression forecasting problem. The results obtained demonstrate that with the developed system it is possible to obtain, process, and store environmental information. The information collected was applied to the LSTM algorithm and compared with other machine learning algorithms. The compared algorithms are Support Vector Machine, Naïve Bayes Network, and Multilayer Perceptron Feed-Forward Network. The outcomes based on the parametric calibrations demonstrate that LSTM performs better in the context of the proposed application.


Author(s):  
Gudipally Chandrashakar

In this article, we used historical time series data up to the current day gold price. In this study of predicting gold price, we consider few correlating factors like silver price, copper price, standard, and poor’s 500 value, dollar-rupee exchange rate, Dow Jones Industrial Average Value. Considering the prices of every correlating factor and gold price data where dates ranging from 2008 January to 2021 February. Few algorithms of machine learning are used to analyze the time-series data are Random Forest Regression, Support Vector Regressor, Linear Regressor, ExtraTrees Regressor and Gradient boosting Regression. While seeing the results the Extra Tree Regressor algorithm gives the predicted value of gold prices more accurately.


The aim of this research is to do risk modelling after analysis of twitter posts based on certain sentiment analysis. In this research we analyze posts of several users or a particular user to check whether they can be cause of concern to the society or not. Every sentiment like happy, sad, anger and other emotions are going to provide scaling of severity in the conclusion of final table on which machine learning algorithm is applied. The data which is put under the machine learning algorithms are been monitored over a period of time and it is related to a particular topic in an area


Sign in / Sign up

Export Citation Format

Share Document