scholarly journals Comparison of Co-temporal Modeling Algorithms on Sparse Experimental Time Series Data Sets

2010 ◽  
Author(s):  
Edward E. Allen ◽  
James L. Norris ◽  
David J. John ◽  
Stan J. Thomas ◽  
William H. Turkett Jr. ◽  
...  
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Series Data ◽  
Data Sets ◽  
Temporal Modeling ◽  
Experimental Time ◽  
Experimental Time Series

scholarly journals Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis

2013 ◽  
Vol 10 (80) ◽  
pp. 20120935 ◽  
Author(s):  
Abdullah Hamadeh ◽  
Brian Ingalls ◽  
Eduardo Sontag
Keyword(s):  
Time Series ◽  
Change Detection ◽  
Rhodobacter Sphaeroides ◽  
Time Series Data ◽  
Series Data ◽  
Transient Dynamic ◽  
Experimental Time ◽  
Theoretical Assumptions ◽  
Experimental Time Series ◽  
Fold Change Detection

The chemotaxis pathway of the bacterium Rhodobacter sphaeroides shares many similarities with that of Escherichia coli . It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent theoretical results have correctly predicted that the E. coli output behaviour is unchanged under scaling of its ligand input signal; this property is known as fold-change detection (FCD). In the light of recent experimental results suggesting that R. sphaeroides may also show FCD, we present theoretical assumptions on the R. sphaeroides chemosensory dynamics that can be shown to yield FCD behaviour. Furthermore, it is shown that these assumptions make FCD a property of this system that is robust to structural and parametric variations in the chemotaxis pathway, in agreement with experimental results. We construct and examine models of the full chemotaxis pathway that satisfy these assumptions and reproduce experimental time-series data from earlier studies. We then propose experiments in which models satisfying our theoretical assumptions predict robust FCD behaviour where earlier models do not. In this way, we illustrate how transient dynamic phenotypes such as FCD can be used for the purposes of discriminating between models that reproduce the same experimental time-series data.

Finding Unstable Fixed Points From Time Series Data

2003 ◽  
Author(s):  
Takaaki Maehara ◽  
Mikio Nakai
Keyword(s):  
Time Series ◽  
Fixed Points ◽  
Time Series Data ◽  
Piecewise Linear ◽  
Duffing Oscillator ◽  
Conley Index ◽  
Series Data ◽  
Experimental Time ◽  
Index Pairs ◽  
Experimental Time Series

This study employs topological methods to extract unstable fixed points in phase space from both numerical and experimental time series data. Conley index of an isolated invariant subset and the R-B method can determine unstable fixed points contained in strange attractor from numerical time series data. For experimental time series data, the theorem for the relationship between index pairs and Conley index enables one to predict them with acceptable accuracy. As a corollary, some results for Duffing oscillator and piecewise linear system are shown.

Measurement of Chaotic Behavior of Operator Stabilizing an Inverted Pendulum and Its Fuzzy Identification from Time Series Data

2001 ◽  
Vol 13 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Yoshihiko Kawazoe ◽  
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Fuzzy Inference ◽  
Fuzzy Controller ◽  
Chaotic Behavior ◽  
Series Data ◽  
Experimental Time ◽  
Experimental Time Series ◽  
Simulated Time ◽  
Simulated Time Series

This paper investigates the identification of the chaotic characteristics of human operation with individual difference and the skill difference from the experimental time series data by utilizing fuzzy inference. It shows how to construct rules automatically for a fuzzy controller from experimental time series data of each trial of each operator to identify a controller from human-generated decision-making data. The characteristics of each operator trial were identified fairly well from experimental time series data by utilizing fuzzy reasoning. It was shown that the estimated maximum Lyapunov exponents of simulated time series data using an identified fuzzy controller were positive against embedding dimensions, which means a chaotic phenomenon. It was also recognized that the simulated human behavior have a large amount of disorder according to the result of estimated entropy from the simulated time, series data.

scholarly journals Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems

2017 ◽  
Author(s):  
Anthony Szedlak ◽  
Spencer Sims ◽  
Nicholas Smith ◽  
Giovanni Paternostro ◽  
Carlo Piermarocchi
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Cell Cycle ◽  
Time Series ◽  
Time Series Data ◽  
Series Data ◽  
Data Sets ◽  
Expression Data ◽  
Time Series Gene Expression ◽  
Human Cervical Cancer

AbstractModern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of time series data sets in the near future, we use the Hopfield model, a recurrent neural network based on spin glasses, to model the dynamics of cell cycle in HeLa (human cervical cancer) and S. cerevisiae cells. We study some of the rich dynamical properties of these cyclic Hopfield systems, including the ability of populations of simulated cells to recreate experimental expression data and the effects of noise on the dynamics. Next, we use a genetic algorithm to identify sets of genes which, when selectively inhibited by local external fields representing gene silencing compounds such as kinase inhibitors, disrupt the encoded cell cycle. We find, for example, that inhibiting the set of four kinases BRD4, MAPK1, NEK7, and YES1 in HeLa cells causes simulated cells to accumulate in the M phase. Finally, we suggest possible improvements and extensions to our model.Author SummaryCell cycle – the process in which a parent cell replicates its DNA and divides into two daughter cells – is an upregulated process in many forms of cancer. Identifying gene inhibition targets to regulate cell cycle is important to the development of effective therapies. Although modern high throughput techniques offer unprecedented resolution of the molecular details of biological processes like cell cycle, analyzing the vast quantities of the resulting experimental data and extracting actionable information remains a formidable task. Here, we create a dynamical model of the process of cell cycle using the Hopfield model (a type of recurrent neural network) and gene expression data from human cervical cancer cells and yeast cells. We find that the model recreates the oscillations observed in experimental data. Tuning the level of noise (representing the inherent randomness in gene expression and regulation) to the “edge of chaos” is crucial for the proper behavior of the system. We then use this model to identify potential gene targets for disrupting the process of cell cycle. This method could be applied to other time series data sets and used to predict the effects of untested targeted perturbations.

An Efficient Method for Forecasting Using Fuzzy Time Series

2017 ◽  
pp. 287-304 ◽  
Author(s):  
Pritpal Singh
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Weather Forecasting ◽  
Small Error ◽  
Fuzzy Time Series ◽  
Series Data ◽  
Data Sets ◽  
Proposed Model ◽  
Temperature Forecasting ◽  
The University

Forecasting using fuzzy time series has been applied in several areas including forecasting university enrollments, sales, road accidents, financial forecasting, weather forecasting, etc. Recently, many researchers have paid attention to apply fuzzy time series in time series forecasting problems. In this paper, we present a new model to forecast the enrollments in the University of Alabama and the daily average temperature in Taipei, based on one-factor fuzzy time series. In this model, a new frequency based clustering technique is employed for partitioning the time series data sets into different intervals. For defuzzification function, two new principles are also incorporated in this model. In case of enrollments as well daily temperature forecasting, proposed model exhibits very small error rate.

scholarly journals AstroCatR: a mechanism and tool for efficient time series reconstruction of large-scale astronomical catalogues

2020 ◽  
Vol 496 (1) ◽  
pp. 629-637
Author(s):  
Ce Yu ◽  
Kun Li ◽  
Shanjiang Tang ◽  
Chao Sun ◽  
Bin Ma ◽  
...  
Keyword(s):  
Time Series ◽  
High Performance ◽  
Large Scale ◽  
Extrasolar Planets ◽  
Time Series Data ◽  
Series Data ◽  
Data Sets ◽  
Observation Data ◽  
Data Volume ◽  
And Performance

ABSTRACT Time series data of celestial objects are commonly used to study valuable and unexpected objects such as extrasolar planets and supernova in time domain astronomy. Due to the rapid growth of data volume, traditional manual methods are becoming extremely hard and infeasible for continuously analysing accumulated observation data. To meet such demands, we designed and implemented a special tool named AstroCatR that can efficiently and flexibly reconstruct time series data from large-scale astronomical catalogues. AstroCatR can load original catalogue data from Flexible Image Transport System (FITS) files or data bases, match each item to determine which object it belongs to, and finally produce time series data sets. To support the high-performance parallel processing of large-scale data sets, AstroCatR uses the extract-transform-load (ETL) pre-processing module to create sky zone files and balance the workload. The matching module uses the overlapped indexing method and an in-memory reference table to improve accuracy and performance. The output of AstroCatR can be stored in CSV files or be transformed other into formats as needed. Simultaneously, the module-based software architecture ensures the flexibility and scalability of AstroCatR. We evaluated AstroCatR with actual observation data from The three Antarctic Survey Telescopes (AST3). The experiments demonstrate that AstroCatR can efficiently and flexibly reconstruct all time series data by setting relevant parameters and configuration files. Furthermore, the tool is approximately 3× faster than methods using relational data base management systems at matching massive catalogues.

FRACTAL ANALYSIS OF DIFFERENT EASTERN AND WESTERN MUSICAL INSTRUMENTS

Fractals ◽  
2006 ◽  
Vol 14 (03) ◽  
pp. 165-170 ◽  
Author(s):  
ATIN DAS ◽  
PRITHA DAS
Keyword(s):  
Time Series ◽  
Spectral Analysis ◽  
Fractal Dimension ◽  
Time Series Data ◽  
Musical Instruments ◽  
Series Data ◽  
Data Sets ◽  
Different Types ◽  
Frequency Regime ◽  
Musical Sounds

In this paper, we attempt musical analysis by measuring fractal dimension (D) of musical pieces played by several musical instruments. We collected solo performances of popular instruments of Western and Eastern origin as samples. We attempted usual spectral analysis of the selected clips to observe peaks of fundamental and harmonics in frequency regime. After appropriate processing, we converted them into time series data sets and computed their fractal dimension. Based on our results, we conclude that instrumental musical sounds may have higher Ds than those computed from vocal performances of different types of Indian songs.

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