scholarly journals Neural network aided approximation and parameter inference of non-Markovian models of gene expression

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qingchao Jiang ◽  
Xiaoming Fu ◽  
Shifu Yan ◽  
Runlai Li ◽  
Wenli Du ◽  
...  
Keyword(s):  
Neural Network ◽  
Stochastic Dynamics ◽  
Stochastic Simulations ◽  
Parameter Inference ◽  
Biochemical Processes ◽  
Markovian Models ◽  
The Neural Network ◽  
Large Numbers ◽  
Small Set ◽  
Noisy Measurements

AbstractNon-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the system’s history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markovian models by the solutions of much simpler time-inhomogeneous Markovian models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markovian model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markovian models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.

scholarly journals Neural network aided approximation and parameter inference of stochastic models of gene expression

2020 ◽  
Author(s):  
Qingchao Jiang ◽  
Xiaoming Fu ◽  
Shifu Yan ◽  
Runlai Li ◽  
Wenli Du ◽  
...  
Keyword(s):  
Neural Network ◽  
Stochastic Dynamics ◽  
Markov Models ◽  
Stochastic Simulations ◽  
Parameter Inference ◽  
Biochemical Processes ◽  
The Neural Network ◽  
Large Numbers ◽  
Small Set ◽  
Noisy Measurements

Non-Markov models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the system's history. Here we use an artificial neural network to approximate the time dependent distributions of non-Markov models by the solutions of much simpler time-inhomogeneous Markov models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markov model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markov models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.

scholarly journals Use of neural networks in ground-based aerosol retrievals from multi-angle spectropolarimetric observations

2014 ◽  
Vol 7 (9) ◽  
pp. 9047-9094 ◽  
Author(s):  
A. Di Noia ◽  
O. P. Hasekamp ◽  
G. van Harten ◽  
J. H. H. Rietjens ◽  
J. M. Smit ◽  
...  
Keyword(s):  
Neural Network ◽  
Complex Refractive Index ◽  
Effective Radius ◽  
The Other ◽  
Look Up Table ◽  
The Neural Network ◽  
Retrieval Scheme ◽  
Small Set ◽  
Neural Network Algorithm ◽  
Aerosol Properties

Abstract. In this paper, the use of a neural network algorithm for the retrieval of the aerosol properties from ground-based spectropolarimetric measurements is discussed. The neural network is able to retrieve the aerosol properties with an accuracy that is almost comparable to that of an iterative retrieval. By using the outcome of the neural network as a first guess of the iterative retrieval scheme, the accuracy of the fine and coarse mode optical thickness are further improved while for the other parameters the improvement is small or absent. The resulting scheme (neural network + iterative retrieval) is compared to the original one (look-up table + iterative retrieval) on a set of simulated ground-based measurements, and on a small set of real observations carried out by an accurate ground-based spectropolarimeter. The results show that the use of a neural network based first guess leads to an increase in the number of converging retrievals, and possibly to more accurate estimates of the aerosol effective radius and complex refractive index.

scholarly journals Combining Gene Ontology with Deep Neural Networks to Enhance the Clustering of Single Cell RNA-Seq Data

2018 ◽  
Author(s):  
Jiajie Peng ◽  
Xiaoyu Wang ◽  
Xuequn Shang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Neural Networks ◽  
Gene Ontology ◽  
Single Cell ◽  
Cell Function ◽  
Rna Seq ◽  
The Neural Network ◽  
Large Numbers ◽  
The Individual

AbstractBackgroundSingle cell RNA sequencing (scRNA-seq) is applied to assay the individual transcriptomes of large numbers of cells. The gene expression at single-cell level provides an opportunity for better understanding of cell function and new discoveries in biomedical areas. To ensure that the single-cell based gene expression data are interpreted appropriately, it is crucial to develop new computational methods.ResultsIn this article, we try to construct the structure of neural networks based on the prior knowledge of Gene Ontology (GO). By integrating GO with both unsupervised and supervised models, two novel methods are proposed, named GOAE (Gene Ontology AutoEncoder) and GONN (Gene Ontology Neural Network) respectively, for clustering of scRNA-seq data.ConclusionsThe evaluation results show that the proposed models outperform some state-of-the-art approaches. Furthermore, incorporating with GO, we provide an opportunity to interpret the underlying biological mechanism behind the neural network-based model.

scholarly journals Use of neural networks in ground-based aerosol retrievals from multi-angle spectropolarimetric observations

2015 ◽  
Vol 8 (1) ◽  
pp. 281-299 ◽  
Author(s):  
A. Di Noia ◽  
O. P. Hasekamp ◽  
G. van Harten ◽  
J. H. H. Rietjens ◽  
J. M. Smit ◽  
...  
Keyword(s):  
Neural Network ◽  
Complex Refractive Index ◽  
Effective Radius ◽  
The Other ◽  
Look Up Table ◽  
The Neural Network ◽  
Retrieval Scheme ◽  
Small Set ◽  
Neural Network Algorithm ◽  
Aerosol Properties

Abstract. In this paper, the use of a neural network algorithm for the retrieval of the aerosol properties from ground-based spectropolarimetric measurements is discussed. The neural network is able to retrieve the aerosol properties with an accuracy that is almost comparable to that of an iterative retrieval. By using the outcome of the neural network as first guess in the iterative retrieval scheme, the accuracy of the retrieved fine- and coarse-mode optical thickness is further improved, while for the other parameters the improvement is small or absent. The resulting scheme (neural network + iterative retrieval) is compared to the original one (look-up table + iterative retrieval) on a set of simulated ground-based measurements, and on a small set of real observations carried out by an accurate ground-based spectropolarimeter. The results show that the use of a neural-network-based first guess leads to an increase in the number of converging retrievals, and possibly to more accurate estimates of the aerosol effective radius and complex refractive index.

Constructive Neural Networks and Their Application to Ship Multidisciplinary Design Optimization

2007 ◽  
Vol 51 (04) ◽  
pp. 297-312
Author(s):  
Eric Besnard ◽  
Adeline Schmitz ◽  
Hamid Hefazi ◽  
Rahul Shinde
Keyword(s):  
Neural Network ◽  
Data Sets ◽  
Mathematical Function ◽  
Training Set ◽  
The Neural Network ◽  
Development Cycle ◽  
Cascade Correlation ◽  
Small Set ◽  
Validation Set ◽  
The Cost

This paper presents a neural network-based response surface method for reducing the cost of computer-intensive optimizations for applications in ship design. In the approach, complex or costly analyses are replaced by a neural network, which is used to instantaneously estimate the value of the function(s) of interest. The cost of the optimization is shifted to the generation of (smaller) data sets used for training the network. The focus of the paper is on the use and analysis of constructive networks, as opposed to networks of fixed size, for treating problems with a large number of variables, say around 30. The advantages offered by constructive networks are emphasized, leading to the selection and discussion of the cascade correlation algorithm. This topology allows for efficient neural network determination when dealing with function representation over large design spaces without requiring prior experience from the user. During training, the network grows until the error on a small set (validation set), different from that used in the training itself (training set), starts increasing. The method is validated for a mathematical function for dimensions ranging from 5 to 30, and the importance of analyzing the error on a set other than the training set is emphasized. The approach is then applied to the automated computational fluid dynamics-based shape optimization of a fast ship configuration known as the twin H-body. The classical approach yields a design improvement of 26%, whereas the neural network-based method allows reaching a 34% improvement at one fifth of the cost of the former. Based on the analysis of the results, areas for future improvements and research are outlined. The results demonstrate the potential of the method in saving valuable development cycle time and increasing the performance of future ship designs.

Neural Network for Automatic Analysis of Motility Data

1994 ◽  
Vol 33 (01) ◽  
pp. 157-160 ◽  
Author(s):  
S. Kruse-Andersen ◽  
J. Kolberg ◽  
E. Jakobsen
Keyword(s):  
Neural Network ◽  
Muscular Activity ◽  
Recording System ◽  
Automatic Analysis ◽  
Biologically Relevant ◽  
System A ◽  
The Neural Network ◽  
Valuable Method ◽  
Motor Abnormalities ◽  
Trained Network

Abstract:Continuous recording of intraluminal pressures for extended periods of time is currently regarded as a valuable method for detection of esophageal motor abnormalities. A subsequent automatic analysis of the resulting motility data relies on strict mathematical criteria for recognition of pressure events. Due to great variation in events, this method often fails to detect biologically relevant pressure variations. We have tried to develop a new concept for recognition of pressure events based on a neural network. Pressures were recorded for over 23 hours in 29 normal volunteers by means of a portable data recording system. A number of pressure events and non-events were selected from 9 recordings and used for training the network. The performance of the trained network was then verified on recordings from the remaining 20 volunteers. The accuracy and sensitivity of the two systems were comparable. However, the neural network recognized pressure peaks clearly generated by muscular activity that had escaped detection by the conventional program. In conclusion, we believe that neu-rocomputing has potential advantages for automatic analysis of gastrointestinal motility data.

Decision Support for Psychiatric Diagnosis Based on a Simple Questionnaire

1997 ◽  
Vol 36 (04/05) ◽  
pp. 349-351
Author(s):  
H. Mizuta ◽  
K. Kawachi ◽  
H. Yoshida ◽  
K. Iida ◽  
Y. Okubo ◽  
...  
Keyword(s):  
Neural Network ◽  
Decision Support ◽  
Psychiatric Diagnosis ◽  
Psychiatric Patients ◽  
Bayesian Classifier ◽  
Neural Network Classifier ◽  
Correct Decision ◽  
Neurotic Disorders ◽  
The Neural Network

Abstract:This paper compares two classifiers: Pseudo Bayesian and Neural Network for assisting in making diagnoses of psychiatric patients based on a simple yes/no questionnaire which is provided at the outpatient’s first visit to the hospital. The classifiers categorize patients into three most commonly seen ICD classes, i.e. schizophrenic, emotional and neurotic disorders. One hundred completed questionnaires were utilized for constructing and evaluating the classifiers. Average correct decision rates were 73.3% for the Pseudo Bayesian Classifier and 77.3% for the Neural Network classifier. These rates were higher than the rate which an experienced psychiatrist achieved based on the same restricted data as the classifiers utilized. These classifiers may be effectively utilized for assisting psychiatrists in making their final diagnoses.

SCORING MODELING BASED ON NEURAL NETWORKS FOR DETERMINING A BANK BORROWER'S RATING

2020 ◽  
Vol 2020 (10) ◽  
pp. 54-62
Author(s):  
Oleksii VASYLIEV ◽  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Architecture ◽  
Statistical Data ◽  
Activation Function ◽  
Decision Making Process ◽  
Neural Network Architecture ◽  
Acceptable Accuracy ◽  
The Neural Network ◽  
Sigmoid Activation Function

The problem of applying neural networks to calculate ratings used in banking in the decision-making process on granting or not granting loans to borrowers is considered. The task is to determine the rating function of the borrower based on a set of statistical data on the effectiveness of loans provided by the bank. When constructing a regression model to calculate the rating function, it is necessary to know its general form. If so, the task is to calculate the parameters that are included in the expression for the rating function. In contrast to this approach, in the case of using neural networks, there is no need to specify the general form for the rating function. Instead, certain neural network architecture is chosen and parameters are calculated for it on the basis of statistical data. Importantly, the same neural network architecture can be used to process different sets of statistical data. The disadvantages of using neural networks include the need to calculate a large number of parameters. There is also no universal algorithm that would determine the optimal neural network architecture. As an example of the use of neural networks to determine the borrower's rating, a model system is considered, in which the borrower's rating is determined by a known non-analytical rating function. A neural network with two inner layers, which contain, respectively, three and two neurons and have a sigmoid activation function, is used for modeling. It is shown that the use of the neural network allows restoring the borrower's rating function with quite acceptable accuracy.

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