scholarly journals OutbreakFlow: Model-based Bayesian inference of disease outbreak dynamics with invertible neural networks and its application to the COVID-19 pandemics in Germany

2021 ◽  
Vol 17 (10) ◽  
pp. e1009472
Author(s):  
Stefan T. Radev ◽  
Frederik Graw ◽  
Simiao Chen ◽  
Nico T. Mutters ◽  
Vanessa M. Eichel ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Full Range ◽  
Real Data ◽  
Optimization Methods ◽  
Global Knowledge ◽  
Moderate Amount ◽  
Epidemiological Modeling ◽  
Trained Neural Network ◽  
Expensive Optimization

Mathematical models in epidemiology are an indispensable tool to determine the dynamics and important characteristics of infectious diseases. Apart from their scientific merit, these models are often used to inform political decisions and interventional measures during an ongoing outbreak. However, reliably inferring the epidemical dynamics by connecting complex models to real data is still hard and requires either laborious manual parameter fitting or expensive optimization methods which have to be repeated from scratch for every application of a given model. In this work, we address this problem with a novel combination of epidemiological modeling with specialized neural networks. Our approach entails two computational phases: In an initial training phase, a mathematical model describing the epidemic is used as a coach for a neural network, which acquires global knowledge about the full range of possible disease dynamics. In the subsequent inference phase, the trained neural network processes the observed data of an actual outbreak and infers the parameters of the model in order to realistically reproduce the observed dynamics and reliably predict future progression. With its flexible framework, our simulation-based approach is applicable to a variety of epidemiological models. Moreover, since our method is fully Bayesian, it is designed to incorporate all available prior knowledge about plausible parameter values and returns complete joint posterior distributions over these parameters. Application of our method to the early Covid-19 outbreak phase in Germany demonstrates that we are able to obtain reliable probabilistic estimates for important disease characteristics, such as generation time, fraction of undetected infections, likelihood of transmission before symptom onset, and reporting delays using a very moderate amount of real-world observations.

Application of various optimization methods in calculating the error of a neural network for diagnosing parasitological diseases of the gastrointestinal tract

2021 ◽  
Author(s):  
N.T. Abdullaev ◽  
U.N. Musevi ◽  
K.S. Pashaeva
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Gastrointestinal Tract ◽  
Optimization Methods ◽  
Optimization Method ◽  
Medical Diagnostics ◽  
The Body ◽  
Conjugate Gradients ◽  
Practical Significance ◽  
Parasitic Diseases

Formulation of the problem. This work is devoted to the use of artificial neural networks for diagnosing the functional state of the gastrointestinal tract caused by the influence of parasites in the body. For the experiment, 24 symptoms were selected, the number of which can be increased, and 9 most common diseases. The coincidence of neural network diagnostics with classical medical diagnostics for a specific disease is shown. The purpose of the work is to compare the neural networks in terms of their performance after describing the methods of preprocessing, isolating symptoms and classifying parasitic diseases of the gastrointestinal tract. Computer implementation of the experiment was carried out in the NeuroPro 0.25 software environment and optimization methods were chosen for training the network: "gradient descent" modified by Par Tan, "conjugate gradients", BFGS. Results. The results of forecasting using a multilayer perceptron using the above optimization methods are presented. To compare optimization methods, we used the values of the minimum and maximum network errors. Comparison of optimization methods using network errors makes it possible to draw the correct conclusion that for the task at hand, the best results were obtained when using the "conjugate gradients" optimization method. Practical significance. The proposed approach facilitates the work of the experimenter-doctor in choosing the optimization method when working with neural networks for the problem of diagnosing parasitic diseases of the gastrointestinal tract from the point of view of assessing the network error.

scholarly journals Massive computational acceleration by using neural networks to emulate mechanism-based biological models

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shangying Wang ◽  
Kai Fan ◽  
Nan Luo ◽  
Yangxiaolu Cao ◽  
Feilun Wu ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Mechanistic Model ◽  
Time Frame ◽  
Biological Applications ◽  
Biological Models ◽  
Parametric Space ◽  
Trained Neural Network ◽  
Short Time

Abstract For many biological applications, exploration of the massive parametric space of a mechanism-based model can impose a prohibitive computational demand. To overcome this limitation, we present a framework to improve computational efficiency by orders of magnitude. The key concept is to train a neural network using a limited number of simulations generated by a mechanistic model. This number is small enough such that the simulations can be completed in a short time frame but large enough to enable reliable training. The trained neural network can then be used to explore a much larger parametric space. We demonstrate this notion by training neural networks to predict pattern formation and stochastic gene expression. We further demonstrate that using an ensemble of neural networks enables the self-contained evaluation of the quality of each prediction. Our work can be a platform for fast parametric space screening of biological models with user defined objectives.

scholarly journals Obtaining the Correspondence Between Bayesian and Neural Networks

1998 ◽  
Vol 12 (07) ◽  
pp. 901-920 ◽  
Author(s):  
A. Stassopoulou ◽  
M. Petrou
Keyword(s):  
Neural Network ◽  
Bayesian Network ◽  
Full Range ◽  
Closed Form Solution ◽  
Real Data ◽  
Form Solution ◽  
Least Square ◽  
Novel Method ◽  
Probability Matrices ◽  
Desertification Assessment

We present in this paper a novel method for eliciting the conditional probability matrices needed for a Bayesian network with the help of a neural network. We demonstrate how we can obtain a correspondence between the two networks by deriving a closed-form solution so that the outputs of the two networks are similar in the least square error sense, not only when determining the discriminant function, but for the full range of their outputs. For this purpose we take into consideration the probability density functions of the independent variables of the problem when we compute the least square error approximation. Our methodoloy is demonstrated with the help of some real data concerning the problem of risk of desertification assessment for some burned forests in Attica, Greece where the parameters of the Bayesian network constructed for this task are successfully estimated given a neural network trained with a set of data.

scholarly journals Neural Networks for Postprocessing Ensemble Weather Forecasts

2018 ◽  
Vol 146 (11) ◽  
pp. 3885-3900 ◽  
Author(s):  
Stephan Rasp ◽  
Sebastian Lerch
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Predictive Distribution ◽  
Predictor Variables ◽  
Specific Information ◽  
Observation Data ◽  
Neural Network Approach ◽  
Weather Forecasts ◽  
Probabilistic Forecasts ◽  
Trained Neural Network

Abstract Ensemble weather predictions require statistical postprocessing of systematic errors to obtain reliable and accurate probabilistic forecasts. Traditionally, this is accomplished with distributional regression models in which the parameters of a predictive distribution are estimated from a training period. We propose a flexible alternative based on neural networks that can incorporate nonlinear relationships between arbitrary predictor variables and forecast distribution parameters that are automatically learned in a data-driven way rather than requiring prespecified link functions. In a case study of 2-m temperature forecasts at surface stations in Germany, the neural network approach significantly outperforms benchmark postprocessing methods while being computationally more affordable. Key components to this improvement are the use of auxiliary predictor variables and station-specific information with the help of embeddings. Furthermore, the trained neural network can be used to gain insight into the importance of meteorological variables, thereby challenging the notion of neural networks as uninterpretable black boxes. Our approach can easily be extended to other statistical postprocessing and forecasting problems. We anticipate that recent advances in deep learning combined with the ever-increasing amounts of model and observation data will transform the postprocessing of numerical weather forecasts in the coming decade.

scholarly journals Use of a Multilayer Perceptron to Automate Terrain Assessment for the Needs of the Armed Forces

2018 ◽  
Vol 7 (11) ◽  
pp. 430 ◽  
Author(s):  
Krzysztof Pokonieczny
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Multilayer Perceptron ◽  
Learning Algorithm ◽  
Armed Forces ◽  
Shuttle Radar Topography Mission ◽  
Terrain Classification ◽  
The Neural Network ◽  
Data Configuration ◽  
Trained Neural Network

The classification of terrain in terms of passability plays a significant role in the process of military terrain assessment. It involves classifying selected terrain to specific classes (GO, SLOW-GO, NO-GO). In this article, the problem of terrain classification to the respective category of passability was solved by applying artificial neural networks (multilayer perceptron) to generate a continuous Index of Passability (IOP). The neural networks defined this factor for primary fields in two sizes (1000 × 1000 m and 100 × 100 m) based on the land cover elements obtained from Vector Smart Map (VMap) Level 2 and Shuttle Radar Topography Mission (SRTM). The work used a feedforward neural network consisting of three layers. The paper presents a comprehensive analysis of the reliability of the neural network parameters, taking into account the number of neurons, learning algorithm, activation functions and input data configuration. The studies and tests carried out have shown that a well-trained neural network can automate the process of terrain classification in terms of passability conditions.

scholarly journals Elements of an algorithm for optimizing a parameter-structural neural network

2016 ◽  
Vol 101 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Maria Mrówczyńska
Keyword(s):  
Neural Network ◽  
Artificial Intelligence ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Optimization Methods ◽  
Group Method ◽  
Data Handling ◽  
Training Process ◽  
Measurement Results ◽  
Processing Information

Abstract The field of processing information provided by measurement results is one of the most important components of geodetic technologies. The dynamic development of this field improves classic algorithms for numerical calculations in the aspect of analytical solutions that are difficult to achieve. Algorithms based on artificial intelligence in the form of artificial neural networks, including the topology of connections between neurons have become an important instrument connected to the problem of processing and modelling processes. This concept results from the integration of neural networks and parameter optimization methods and makes it possible to avoid the necessity to arbitrarily define the structure of a network. This kind of extension of the training process is exemplified by the algorithm called the Group Method of Data Handling (GMDH), which belongs to the class of evolutionary algorithms. The article presents a GMDH type network, used for modelling deformations of the geometrical axis of a steel chimney during its operation.

scholarly journals Sample-efficient Optimization Using Neural Networks

2021 ◽  
Author(s):  
◽  
Mashall Aryan
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Monte Carlo ◽  
Gaussian Process ◽  
Optimization Methods ◽  
Optimization Method ◽  
Monte Carlo Sampling ◽  
Bayesian Optimization ◽  
Expected Improvement ◽  
Bayesian Neural Network

<p>The solution to many science and engineering problems includes identifying the minimum or maximum of an unknown continuous function whose evaluation inflicts non-negligible costs in terms of resources such as money, time, human attention or computational processing. In such a case, the choice of new points to evaluate is critical. A successful approach has been to choose these points by considering a distribution over plausible surfaces, conditioned on all previous points and their evaluations. In this sequential bi-step strategy, also known as Bayesian Optimization, first a prior is defined over possible functions and updated to a posterior in the light of available observations. Then using this posterior, namely the surrogate model, an infill criterion is formed and utilized to find the next location to sample from. By far the most common prior distribution and infill criterion are Gaussian Process and Expected Improvement, respectively.    The popularity of Gaussian Processes in Bayesian optimization is partially due to their ability to represent the posterior in closed form. Nevertheless, the Gaussian Process is afflicted with several shortcomings that directly affect its performance. For example, inference scales poorly with the amount of data, numerical stability degrades with the number of data points, and strong assumptions about the observation model are required, which might not be consistent with reality. These drawbacks encourage us to seek better alternatives. This thesis studies the application of Neural Networks to enhance Bayesian Optimization. It proposes several Bayesian optimization methods that use neural networks either as their surrogates or in the infill criterion.    This thesis introduces a novel Bayesian Optimization method in which Bayesian Neural Networks are used as a surrogate. This has reduced the computational complexity of inference in surrogate from cubic (on the number of observation) in GP to linear. Different variations of Bayesian Neural Networks (BNN) are put into practice and inferred using a Monte Carlo sampling. The results show that Monte Carlo Bayesian Neural Network surrogate could performed better than, or at least comparably to the Gaussian Process-based Bayesian optimization methods on a set of benchmark problems.  This work develops a fast Bayesian Optimization method with an efficient surrogate building process. This new Bayesian Optimization algorithm utilizes Bayesian Random-Vector Functional Link Networks as surrogate. In this family of models the inference is only performed on a small subset of the entire model parameters and the rest are randomly drawn from a prior. The proposed methods are tested on a set of benchmark continuous functions and hyperparameter optimization problems and the results show the proposed methods are competitive with state-of-the-art Bayesian Optimization methods.  This study proposes a novel Neural network-based infill criterion. In this method locations to sample from are found by minimizing the joint conditional likelihood of the new point and parameters of a neural network. The results show that in Bayesian Optimization methods with Bayesian Neural Network surrogates, this new infill criterion outperforms the expected improvement.   Finally, this thesis presents order-preserving generative models and uses it in a variational Bayesian context to infer Implicit Variational Bayesian Neural Network (IVBNN) surrogates for a new Bayesian Optimization. This new inference mechanism is more efficient and scalable than Monte Carlo sampling. The results show that IVBNN could outperform Monte Carlo BNN in Bayesian optimization of hyperparameters of machine learning models.</p>

scholarly journals Using Domain-specific Fingerprints Generated Through Neural Networks to Enhance Ligand-based Virtual Screening.

2020 ◽  
Author(s):  
Janosch Menke ◽  
Oliver Koch
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Virtual Screening ◽  
Molecular Fingerprint ◽  
Molecular Fingerprints ◽  
Domain Specific ◽  
Trained Neural Network ◽  
Hidden Layer ◽  
Graph Neural Networks ◽  
Combine Information

Molecular fingerprints are essential for different cheminformatics approaches like similarity-based virtual screening. In this work, the concept of neural (network) fingerprints in the context of similarity search is introduced in which the activation of the last hidden layer of a trained neural network represents the molecular fingerprint. The neural fingerprint performance of five different neural network architectures was analyzed and compared to the well-established Extended Connectivity Fingerprint (ECFP) and an autoencoder-based fingerprint. This is done using a published compound dataset with known bioactivity on 160 different kinase targets. We expect neural networks to combine information about the molecular space of<br>already known bioactive compounds together with the information on the molecular structure of the query and by doing so enrich the fingerprint. The results show that indeed neural fingerprints can greatly improve the performance of similarity searches. Most importantly, it could be shown that the neural fingerprint performs well even for kinase targets that were not included in the training. Surprisingly, while Graph Neural Networks (GNNs) are thought to offer an advantageous alternative, the best performing neural fingerprints were based on traditional fully connected layers using the ECFP4 as input. The best performing kinase-specific neural fingerprint will be provided for public use.

Neural networks for modelling the energy consumption of metro trains

2019 ◽  
Vol 234 (7) ◽  
pp. 722-733 ◽  
Author(s):  
Pablo Martínez Fernández ◽  
Pablo Salvador Zuriaga ◽  
Ignacio Villalba Sanchís ◽  
Ricardo Insa Franco
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Energy Consumption ◽  
Mean Square Error ◽  
Mean Square ◽  
The Neural Network ◽  
Train Speed ◽  
Input Variables ◽  
Trained Neural Network ◽  
Traction Power

This paper presents the application of machine learning systems based on neural networks to model the energy consumption of electric metro trains, as a first step in a research project that aims to optimise the energy consumed for traction in the Metro Network of Valencia (Spain). An experimental dataset was gathered and used for training. Four input variables (train speed and acceleration, track slope and curvature) and one output variable (traction power) were considered. The fully trained neural network shows good agreement with the target data, with relative mean square error around 21%. Additional tests with independent datasets also give good results (relative mean square error = 16%). The neural network has been applied to five simple case studies to assess its performance – and has proven to correctly model basic consumption trends (e.g. the influence of the slope) – and to properly reproduce acceleration, holding and braking, although it tends to slightly underestimate the energy regenerated during braking. Overall, the neural network provides a consistent estimation of traction power and the global energy consumption of metro trains, and thus may be used as a modelling tool during further stages of research.

Forecasting Emerging Market Indexes with Neural Networks

2011 ◽  
pp. 80-101 ◽  
Author(s):  
Steven Walczah
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Time Series ◽  
Global Knowledge ◽  
Index Change ◽  
Market Index ◽  
The Neural Network ◽  
Neural Network System ◽  
Homogeneous Models ◽  
Using Data

Forecasting financial time series with neural networks is problematic. Multiple decisions, each of which affects the performance of the neural network forecasting model, must be made, including which data to use and the size and architecture of the neural network system. While most previous research with neural networks has focused on homogenous models, that is, only using data from the single time series to be forecast, the ever more global nature of the world’s financial markets necessitates the inclusion of more global knowledge into neural network design. This chapter demonstrates how specific markets are at least partially dependent on other global markets and that inclusion of heterogeneous market information will improve neural network forecasting performance over similar homogeneous models by as much as 12 percent (i.e., moving from a near 51% prediction accuracy for the direction of the market index change to a 63% accuracy of predicting the direction of the market index change).

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