scholarly journals Predicting COVID-19 (Coronavirus Disease) Outbreak Dynamics Using SIR-based Models: Comparative Analysis of SIRD and Weibull-SIRD

2020 ◽  
Author(s):  
Ahmad Sedaghat ◽  
Amir Mosavi
Keyword(s):  
Dynamic Systems ◽  
Optimization Methods ◽  
Initial Guess ◽  
Biological Data ◽  
Data Sets ◽  
Mathematical Methods ◽  
Ode Model ◽  
Initial Value ◽  
Novel Method ◽  
Insight Into

AbstractThe SIR type models are built by a set of ordinary differential equations (ODE), which are strongly initial value dependant. To fit multiple biological data with SIR type equations requires fitting coefficients of these equations by an initial guess and applying optimization methods. These coefficients are also extremely initial value-dependent. In the vast publication of these types, we hardly see, among simple to highly complicated SIR type methods, that these methods presented more than a maximum of two biological data sets. We propose a novel method that integrates an analytical solution of the infectious population using Weibull distribution function into any SIR type models. The Weibull-SIRD method has easily fitted 4 set of COVID-19 biological data simultaneously. It is demonstrated that the Weibull-SIRD method predictions for susceptible, infected, recovered, and deceased populations from COVID-19 in Kuwait and UAE are superior compared with SIRD original ODE model. The proposed method here opens doors for new deeper studying of biological dynamic systems with realistic biological data trends than providing some complicated, cumbersome mathematical methods with little insight into biological data’s real physics.

scholarly journals Predicting COVID-19 (Coronavirus Disease) Outbreak Dynamics Using SIR-based Models: Comparative Analysis of SIRD and Weibull-SIRD

2020 ◽  
Author(s):  
Ahmad Sedaghat ◽  
Amir Mosavi
Keyword(s):  
Dynamic Systems ◽  
Optimization Methods ◽  
Initial Guess ◽  
Biological Data ◽  
Data Sets ◽  
Mathematical Methods ◽  
Ode Model ◽  
Initial Value ◽  
Novel Method ◽  
Insight Into

The SIR type models are built by a set of ordinary differential equations (ODE), which are strongly initial value dependant. To fit multiple biological data with SIR type equations requires fitting coefficients of these equations by an initial guess and applying optimization methods. These coefficients are also extremely initial value-dependent. In the vast publication of these types, we hardly see, among simple to highly complicated SIR type methods, that these methods presented more than a maximum of two biological data sets. We propose a novel method that integrates an analytical solution of the infectious population using Weibull distribution function into any SIR type models. The Weibull-SIRD method has easily fitted 4 set of COVID-19 biological data simultaneously. It is demonstrated that the Weibull-SIRD method predictions for susceptible, infected, recovered, and deceased populations from COVID-19 in Kuwait and UAE are superior compared with SIRD original ODE model. The proposed method here opens doors for new deeper studying of biological dynamic systems with realistic biological data trends than providing some complicated, cumbersome mathematical methods with little insight into biological data's real physics.

scholarly journals Understanding large and complex biological data sets using visualization

2021 ◽  
Author(s):  
Stephen Taylor
Keyword(s):  
Large Data ◽  
Physical Structure ◽  
Biological Data ◽  
Large Data Sets ◽  
Data Driven ◽  
Data Sets ◽  
Epigenetic Changes ◽  
Mass Cytometry ◽  
High Level ◽  
Insight Into

Molecular biology experiments are generating an unprecedented amount of information from a variety of different experimental modalities. DNA sequencing machines, proteomics mass cytometry and microscopes generate huge amounts of data every day. Not only is the data large, but it is also multidimensional. Understanding trends and getting actionable insights from these data requires techniques that allow comprehension at a high level but also insight into what underlies these trends. Lots of small errors or poor summarization can lead to false results and reproducibility issues in large data sets. Hence it is essential we do not cherry-pick results to suit a hypothesis but instead examine all data and publish accurate insights in a data-driven way. This article will give an overview of some of the problems faced by the researcher in understanding epigenetic changes (which are related to changes in the physical structure of DNA) when presented with raw analysis results using visualization methods. We will also discuss the new challenges faced by using machine learning which can be helped by visualization.

Dualities, Dialectics, and Paradoxes in Organizational Life

2018 ◽  
Keyword(s):  
Dynamic Systems ◽  
Empirical Studies ◽  
Organizational Studies ◽  
Organizational Life ◽  
Organizational Processes ◽  
Organization Studies ◽  
Process Studies ◽  
Convergence And Divergence ◽  
Insight Into ◽  
Over Time

Organizational contradictions and process studies offer interwoven and complementary insights. Studies of dialectics, paradox, and dualities depict organizational contradictions that are oppositional as well as interrelated such that they persistently morph and shift over time. Studies of process often examine how contradictions fuel emergent, dynamic systems and stimulate novelty, adaptation, and transformation. Drawing from rich conversations at the Eighth International Symposium on Process Organization Studies, the contributors to this volume unpack these relationships in more depth. The chapters explore three main, connected themes through both conceptual and empirical studies, including (1) offering insight into how process theorizing advances understandings of organizational contradictions; (2) shedding light on how dialectics, paradoxes, and dualities fuel organizational processes that affect persistence and transformation; and (3) exploring the convergence and divergence of dialectics, paradox, and dualities lenses. Taken together, this book offers key insights in order to inform persistent, contradictory dynamics in organizations and organizational studies.

scholarly journals Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

2020 ◽  
Vol 21 (S18) ◽  
Author(s):  
Sudipta Acharya ◽  
Laizhong Cui ◽  
Yi Pan
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Selection ◽  
Marker Gene ◽  
Biological Data ◽  
Protein Interaction Data ◽  
Marker Genes ◽  
Data Sets ◽  
Gene Markers ◽  
Multi Objective

Abstract Background In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting knowledge from multiple potential biological resources may be an effective way to understand the spectrum of cancer or other diseases with applications in specific epidemiology for a particular population. Results In the current article, we design the feature selection and marker gene detection as a multi-view multi-objective clustering problem. Regarding that, we propose an Unsupervised Multi-View Multi-Objective clustering-based gene selection approach called UMVMO-select. Three important resources of biological data (gene ontology, protein interaction data, protein sequence) along with gene expression values are collectively utilized to design two different views. UMVMO-select aims to reduce gene space without/minimally compromising the sample classification efficiency and determines relevant and non-redundant gene markers from three cancer gene expression benchmark data sets. Conclusion A thorough comparative analysis has been performed with five clustering and nine existing feature selection methods with respect to several internal and external validity metrics. Obtained results reveal the supremacy of the proposed method. Reported results are also validated through a proper biological significance test and heatmap plotting.

scholarly journals Suspended Sediment Modeling Using a Heuristic Regression Method Hybridized with Kmeans Clustering

2021 ◽  
Vol 13 (9) ◽  
pp. 4648
Author(s):  
Rana Muhammad Adnan ◽  
Kulwinder Singh Parmar ◽  
Salim Heddam ◽  
Shamsuddin Shahid ◽  
Ozgur Kisi
Keyword(s):  
Clustering Algorithm ◽  
Suspended Sediments ◽  
Ecological Impacts ◽  
Accurate Estimation ◽  
Data Sets ◽  
The Novel ◽  
Neuro Fuzzy ◽  
Adaptive Regression ◽  
Novel Method ◽  
Model Training

The accurate estimation of suspended sediments (SSs) carries significance in determining the volume of dam storage, river carrying capacity, pollution susceptibility, soil erosion potential, aquatic ecological impacts, and the design and operation of hydraulic structures. The presented study proposes a new method for accurately estimating daily SSs using antecedent discharge and sediment information. The novel method is developed by hybridizing the multivariate adaptive regression spline (MARS) and the Kmeans clustering algorithm (MARS–KM). The proposed method’s efficacy is established by comparing its performance with the adaptive neuro-fuzzy system (ANFIS), MARS, and M5 tree (M5Tree) models in predicting SSs at two stations situated on the Yangtze River of China, according to the three assessment measurements, RMSE, MAE, and NSE. Two modeling scenarios are employed; data are divided into 50–50% for model training and testing in the first scenario, and the training and test data sets are swapped in the second scenario. In Guangyuan Station, the MARS–KM showed a performance improvement compared to ANFIS, MARS, and M5Tree methods in term of RMSE by 39%, 30%, and 18% in the first scenario and by 24%, 22%, and 8% in the second scenario, respectively, while the improvement in RMSE of ANFIS, MARS, and M5Tree was 34%, 26%, and 27% in the first scenario and 7%, 16%, and 6% in the second scenario, respectively, at Beibei Station. Additionally, the MARS–KM models provided much more satisfactory estimates using only discharge values as inputs.

Nondegenerate Piecewise Linear Systems: A Finite Newton Algorithm and Applications in Machine Learning

2012 ◽  
Vol 24 (4) ◽  
pp. 1047-1084 ◽  
Author(s):  
Xiao-Tong Yuan ◽  
Shuicheng Yan
Keyword(s):  
Linear Systems ◽  
Optimization Problems ◽  
Piecewise Linear ◽  
Optimization Methods ◽  
Coefficient Matrix ◽  
Learning Problems ◽  
Support Vector ◽  
Data Sets ◽  
Piecewise Linear Systems ◽  
Vector Machines

We investigate Newton-type optimization methods for solving piecewise linear systems (PLSs) with nondegenerate coefficient matrix. Such systems arise, for example, from the numerical solution of linear complementarity problem, which is useful to model several learning and optimization problems. In this letter, we propose an effective damped Newton method, PLS-DN, to find the exact (up to machine precision) solution of nondegenerate PLSs. PLS-DN exhibits provable semiiterative property, that is, the algorithm converges globally to the exact solution in a finite number of iterations. The rate of convergence is shown to be at least linear before termination. We emphasize the applications of our method in modeling, from a novel perspective of PLSs, some statistical learning problems such as box-constrained least squares, elitist Lasso (Kowalski & Torreesani, 2008 ), and support vector machines (Cortes & Vapnik, 1995 ). Numerical results on synthetic and benchmark data sets are presented to demonstrate the effectiveness and efficiency of PLS-DN on these problems.

scholarly journals BioNetLink - An Architecture for Working with Network Data

2014 ◽  
Vol 11 (2) ◽  
pp. 68-79
Author(s):  
Matthias Klapperstück ◽  
Falk Schreiber
Keyword(s):  
Experimental Data ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Large Data ◽  
Biological Data ◽  
Network Data ◽  
Data Sets ◽  
Dynamic Views ◽  
Gene Regulatory ◽  
Multiple Network

Summary The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

Migration‐based traveltime waveform inversion of 2-D simple structures: A synthetic example

Geophysics ◽  
2001 ◽  
Vol 66 (3) ◽  
pp. 845-860 ◽  
Author(s):  
François Clément ◽  
Guy Chavent ◽  
Susana Gómez
Keyword(s):  
Least Squares ◽  
Waveform Inversion ◽  
Domain Of Attraction ◽  
Optimization Methods ◽  
Data Sets ◽  
Seismic Reflection Data ◽  
Prestack Migration ◽  
Reflection Data ◽  
Full Wave ◽  
The Time Domain

Migration‐based traveltime (MBTT) formulation provides algorithms for automatically determining background velocities from full‐waveform surface seismic reflection data using local optimization methods. In particular, it addresses the difficulty of the nonconvexity of the least‐squares data misfit function. The method consists of parameterizing the reflectivity in the time domain through a migration step and providing a multiscale representation for the smooth background velocity. We present an implementation of the MBTT approach for a 2-D finite‐difference (FD) full‐wave acoustic model. Numerical analysis on a 2-D synthetic example shows the ability of the method to find much more reliable estimates of both long and short wavelengths of the velocity than the classical least‐squares approach, even when starting from very poor initial guesses. This enlargement of the domain of attraction for the global minima of the least‐squares misfit has a price: each evaluation of the new objective function requires, besides the usual FD full‐wave forward modeling, an additional full‐wave prestack migration. Hence, the FD implementation of the MBTT approach presented in this paper is expected to provide a useful tool for the inversion of data sets of moderate size.

Advanced Geodynamics

2021 ◽  
Author(s):  
David T. Sandwell
Keyword(s):  
Plate Tectonics ◽  
Driving Forces ◽  
Data Sets ◽  
Earthquake Cycle ◽  
Mathematical Methods ◽  
Graduate Course ◽  
Field Development ◽  
Linear Partial Differential Equations ◽  
Global Data Sets ◽  
Global Data

David Sandwell developed this advanced textbook over a period of nearly 30 years for his graduate course at Scripps Institution of Oceanography. The book augments the classic textbook Geodynamics by Don Turcotte and Jerry Schubert, presenting more complex and foundational mathematical methods and approaches to geodynamics. The main new tool developed in the book is the multi-dimensional Fourier transform for solving linear partial differential equations. The book comprises nineteen chapters, including: the latest global data sets; quantitative plate tectonics; plate driving forces associated with lithospheric heat transfer and subduction; the physics of the earthquake cycle; postglacial rebound; and six chapters on gravity field development and interpretation. Each chapter has a set of student exercises that make use of the higher-level mathematical and numerical methods developed in the book. Solutions to the exercises are available online for course instructors, on request.

A WEIGHTED COMBINER OF STACKING BASED METHODS

2012 ◽  
Vol 21 (06) ◽  
pp. 1250040
Author(s):  
NIALL ROONEY
Keyword(s):  
Empirical Analysis ◽  
Data Sets ◽  
Computational Overhead ◽  
Novel Method ◽  
Regression Problems ◽  
Weighted Combination

In this paper we present a novel method that forms a weighted combination of a range of Stacking based methods for regression problems, without adding any major computational overhead in comparison to stacking itself. The intention of the technique is to benefit from the variation in performance of individual Stacking methods as demonstrated with different data sets, in order to provide a more robust technique overall. We detail an empirical analysis of the technique referred to as weighted Meta–Combiner (wMetaComb) and compare its performance to its underlying techniques.

Sign in / Sign up

Export Citation Format

Share Document