Using Machine Learning Techniques for Modelling and Simulation of Metabolic Networks

2011 ◽  
Author(s):  
Marenglen Biba ◽  
Fatos Xhafa ◽  
Floriana Esposito ◽  
Stefano Ferilli
Keyword(s):  
Machine Learning ◽  
Metabolic Networks ◽  
Modelling And Simulation ◽  
Machine Learning Techniques ◽  
Learning Techniques

scholarly journals Uncertainty Reduction in Biochemical Kinetic Models: Enforcing Desired Model Properties

2018 ◽  
Author(s):  
Ljubisa Miskovic ◽  
Jonas Béal ◽  
Michael Moret ◽  
Vassily Hatzimanikatis
Keyword(s):  
Machine Learning ◽  
Monte Carlo ◽  
Kinetic Parameters ◽  
Kinetic Models ◽  
Large Scale ◽  
Metabolic Networks ◽  
Sampling Methods ◽  
Machine Learning Techniques ◽  
Control Analysis ◽  
Learning Techniques

AbstractA persistent obstacle for constructing kinetic models of metabolism is uncertainty in the kinetic properties of enzymes. Currently, available methods for building kinetic models can cope indirectly with uncertainties by integrating data from different biological levels and origins into models. In this study, we use the recently proposed computational approach iSCHRUNK (in Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models), which combines Monte Carlo parameter sampling methods and machine learning techniques, in the context of Bayesian inference. Monte Carlo parameter sampling methods allow us to exploit synergies between different data sources and generate a population of kinetic models that are consistent with the available data and physicochemical laws. The machine learning allows us to data-mine the a priori generated kinetic parameters together with the integrated datasets and derive posterior distributions of kinetic parameters consistent with the observed physiology. In this work, we used iSCHRUNK to address a design question: can we identify which are the kinetic parameters and what are their values that give rise to a desired metabolic behavior? Such information is important for a wide variety of studies ranging from biotechnology to medicine. To illustrate the proposed methodology, we performed Metabolic Control Analysis, computed the flux control coefficients of the xylose uptake (XTR), and identified parameters that ensure a rate improvement of XTR in a glucose-xylose co-utilizing S. cerevisiae strain. Our results indicate that only three kinetic parameters need to be accurately characterized to describe the studied physiology, and ultimately to design and control the desired responses of the metabolism. This framework paves the way for a new generation of methods that will systematically integrate the wealth of available omics data and efficiently extract the information necessary for metabolic engineering and synthetic biology decisions.Author SummaryKinetic models are the most promising tool for understanding the complex dynamic behavior of living cells. The primary goal of kinetic models is to capture the properties of the metabolic networks as a whole, and thus we need large-scale models for dependable in silico analyses of metabolism. However, uncertainty in kinetic parameters impedes the development of kinetic models, and uncertainty levels increase with the model size. Tools that will address the issues with parameter uncertainty and that will be able to reduce the uncertainty propagation through the system are therefore needed. In this work, we applied a method called iSCHRUNK that combines parameter sampling and machine learning techniques to characterize the uncertainties and uncover intricate relationships between the parameters of kinetic models and the responses of the metabolic network. The proposed method allowed us to identify a small number of parameters that determine the responses in the network regardless of the values of other parameters. As a consequence, in future studies of metabolism, it will be sufficient to explore a reduced kinetic space, and more comprehensive analyses of large-scale and genome-scale metabolic networks will be computationally tractable.

Using machine learning techniques to reduce data annotation time

2006 ◽  
Author(s):  
Christopher Schreiner ◽  
Kari Torkkola ◽  
Mike Gardner ◽  
Keshu Zhang
Keyword(s):  
Machine Learning ◽  
Machine Learning Techniques ◽  
Data Annotation ◽  
Learning Techniques

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.

389-P: Ability for Detecting or Predicting Hypoglycemia with the Aid of Machine Learning Techniques: A Meta-analysis

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 389-P
Author(s):  
SATORU KODAMA ◽  
MAYUKO H. YAMADA ◽  
YUTA YAGUCHI ◽  
MASARU KITAZAWA ◽  
MASANORI KANEKO ◽  
...  
Keyword(s):  
Machine Learning ◽  
Meta Analysis ◽  
Machine Learning Techniques ◽  
Learning Techniques

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.

A Brief Survey on Text Classification Using Various Machine Learning Techniques

2018 ◽  
Vol 8 (1) ◽  
pp. 14
Author(s):  
Padmavathi .S ◽  
M. Chidambaram
Keyword(s):  
Machine Learning ◽  
Text Classification ◽  
Fixed Number ◽  
Machine Learning Techniques ◽  
Online Information ◽  
Rule Based ◽  
Learning Techniques ◽  
Machine Learning Approach ◽  
Rule Based Approach

Text classification has grown into more significant in managing and organizing the text data due to tremendous growth of online information. It does classification of documents in to fixed number of predefined categories. Rule based approach and Machine learning approach are the two ways of text classification. In rule based approach, classification of documents is done based on manually defined rules. In Machine learning based approach, classification rules or classifier are defined automatically using example documents. It has higher recall and quick process. This paper shows an investigation on text classification utilizing different machine learning techniques.

A Literature Review Study of Software Defect Prediction using Machine Learning Techniques

2018 ◽  
Vol 6 (6) ◽  
pp. 300 ◽  
Author(s):  
Feidu Akmel ◽  
Ermiyas Birihanu ◽  
Bahir Siraj
Keyword(s):  
Machine Learning ◽  
Software Metrics ◽  
Quality Standard ◽  
Machine Learning Techniques ◽  
Software Systems ◽  
Health Care Insurance ◽  
Software Defect ◽  
Learning Techniques ◽  
Software Product

Software systems are any software product or applications that support business domains such as Manufacturing,Aviation, Health care, insurance and so on.Software quality is a means of measuring how software is designed and how well the software conforms to that design. Some of the variables that we are looking for software quality are Correctness, Product quality, Scalability, Completeness and Absence of bugs, However the quality standard that was used from one organization is different from other for this reason it is better to apply the software metrics to measure the quality of software. Attributes that we gathered from source code through software metrics can be an input for software defect predictor. Software defect are an error that are introduced by software developer and stakeholders. Finally, in this study we discovered the application of machine learning on software defect that we gathered from the previous research works.

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