scholarly journals Inferring causality in biological oscillators

2021 ◽  
Author(s):  
Jonathan Tyler ◽  
Daniel Forger ◽  
JaeKyoung Kim
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Supplementary Information ◽  
Series Data ◽  
Biological Study ◽  
Oscillatory Systems ◽  
Model Based ◽  
Model Free ◽  
Oscillatory Networks ◽  
Inference Methods

Abstract Motivation Fundamental to biological study is identifying regulatory interactions. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulations computationally. However, when components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test the reproducibility of time series given a specific model but require inefficient simulations and have limited applicability. Results We develop an inference method based on a general model of molecular, neuronal, and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability, and usability. Our method successfully infers the positive and negative regulations within various oscillatory networks, e.g., the repressilator and a network of cofactors at the pS2 promoter, outperforming popular inference methods. Availability We provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to uncover the mechanisms by which diverse systems generate oscillations. Accompanying MATLAB code under a BSD-style license and examples are available at ttps://github.com/Mathbiomed/ION. Additionally, the code is available under a CC-BY 4.0 License at https://doi.org/10.6084/m9.figshare.16431408.v1. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Inferring causality in biological oscillators

2021 ◽  
Author(s):  
Jonathan Tyler ◽  
Daniel Forger ◽  
Jae Kyoung Kim
Keyword(s):  
Time Series ◽  
Regulatory Networks ◽  
Time Series Data ◽  
Series Data ◽  
Biological Study ◽  
Oscillatory Systems ◽  
Model Based ◽  
Model Free ◽  
Oscillatory Networks ◽  
Inference Methods

A fundamental goal of biological study is to identify regulatory interactions among components. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulatory networks computationally. However, when the components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test whether time series are reproducible with a specific model but require inefficient simulations and have limited applicability. Here, we develop an inference method based on a general model of molecular, neuronal, and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability, and usability. Our method successfully infers the positive and negative regulations of various oscillatory networks, including the repressilator and a network of cofactors of pS2 promoter, outperforming popular inference methods. We also provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to decipher the mechanisms by which diverse systems generate oscillations.

scholarly journals Benchmarking time-series data discretization on inference methods

2019 ◽  
Vol 35 (17) ◽  
pp. 3102-3109 ◽  
Author(s):  
Yuezhe Li ◽  
Tiffany Jann ◽  
Paola Vera-Licona
Keyword(s):  
Time Series ◽  
Reverse Engineering ◽  
Time Series Data ◽  
Supplementary Information ◽  
Series Data ◽  
Discretization Method ◽  
Discretization Methods ◽  
Inference Methods ◽  
Data Discretization ◽  
The Impact

AbstractSummaryThe rapid development in quantitatively measuring DNA, RNA and protein has generated a great interest in the development of reverse-engineering methods, that is, data-driven approaches to infer the network structure or dynamical model of the system. Many reverse-engineering methods require discrete quantitative data as input, while many experimental data are continuous. Some studies have started to reveal the impact that the choice of data discretization has on the performance of reverse-engineering methods. However, more comprehensive studies are still greatly needed to systematically and quantitatively understand the impact that discretization methods have on inference methods. Furthermore, there is an urgent need for systematic comparative methods that can help select between discretization methods. In this work, we consider four published intracellular networks inferred with their respective time-series datasets. We discretized the data using different discretization methods. Across all datasets, changing the data discretization to a more appropriate one improved the reverse-engineering methods’ performance. We observed no universal best discretization method across different time-series datasets. Thus, we propose DiscreeTest, a two-step evaluation metric for ranking discretization methods for time-series data. The underlying assumption of DiscreeTest is that an optimal discretization method should preserve the dynamic patterns observed in the original data across all variables. We used the same datasets and networks to show that DiscreeTest is able to identify an appropriate discretization among several candidate methods. To our knowledge, this is the first time that a method for benchmarking and selecting an appropriate discretization method for time-series data has been proposed.Availability and implementationAll the datasets, reverse-engineering methods and source code used in this paper are available in Vera-Licona’s lab Github repository: https://github.com/VeraLiconaResearchGroup/Benchmarking_TSDiscretizations.Supplementary informationSupplementary data are available at Bioinformatics online.

A Novel Approach to Time Series Forecasting Using Model-Free Adaptive Control Framework

2020 ◽  
Author(s):  
Meenakshi Narayan ◽  
Ann Majewicz Fey
Keyword(s):  
Time Series ◽  
Adaptive Control ◽  
Real Time ◽  
Time Series Data ◽  
Mean Squared Error ◽  
Force Sensor ◽  
Sensor Data ◽  
Series Data ◽  
Model Free ◽  
Control Framework

Abstract Sensor data predictions could significantly improve the accuracy and effectiveness of modern control systems; however, existing machine learning and advanced statistical techniques to forecast time series data require significant computational resources which is not ideal for real-time applications. In this paper, we propose a novel forecasting technique called Compact Form Dynamic Linearization Model-Free Prediction (CFDL-MFP) which is derived from the existing model-free adaptive control framework. This approach enables near real-time forecasts of seconds-worth of time-series data due to its basis as an optimal control problem. The performance of the CFDL-MFP algorithm was evaluated using four real datasets including: force sensor readings from surgical needle, ECG measurements for heart rate, and atmospheric temperature and Nile water level recordings. On average, the forecast accuracy of CFDL-MFP was 28% better than the benchmark Autoregressive Integrated Moving Average (ARIMA) algorithm. The maximum computation time of CFDL-MFP was 49.1ms which was 170 times faster than ARIMA. Forecasts were best for deterministic data patterns, such as the ECG data, with a minimum average root mean squared error of (0.2±0.2).

scholarly journals Pengujian Efek Fisher:Pengaruh Ekspektasi Inflasi Dan Kegiatan Ekonomi Terhadap Tingkat Bunga Nominal Di Indonesia

2019 ◽  
Author(s):  
Dian Pratiwi
Keyword(s):  
Time Series ◽  
Economic Activity ◽  
Time Series Data ◽  
Series Data ◽  
Fisher Effect ◽  
Model Based ◽  
Expected Inflation ◽  
Effect Theory ◽  
Nominal Rate

The purpose of this paper is to investigate the effect of inflation and economic activity to nominal rate. A model based on Fisher Effect and used time series data for the period of 2010-2012. The finding suggests that expected inflation and economic activity have significant effect on the nominal rate as dependent variable. As the limitation, the data used in this paper are limited to three years time series data. A more detail analysis would use data more completely. The findings of the study clearly demonstrate the Fisher Effect theory. Keywords: Fisher Effect, Expected Inflation, Economic Activity, Nominal Rate

scholarly journals Research on Combined Model Based on Multi-Objective Optimization and Application in Wind Speed Forecast

2019 ◽  
Vol 9 (3) ◽  
pp. 423 ◽  
Author(s):  
Shenghui Zhang ◽  
Yuewei Liu ◽  
Jianzhou Wang ◽  
Chen Wang
Keyword(s):  
Time Series ◽  
Wind Speed ◽  
Linear Models ◽  
Time Series Data ◽  
Mean Absolute Percentage Error ◽  
Series Data ◽  
Percentage Error ◽  
Combined Model ◽  
Absolute Percentage Error ◽  
Model Based

Wind power is an important part of a power system, and its use has been rapidly increasing as compared with fossil energy. However, due to the intermittence and randomness of wind speed, system operators and researchers urgently need to find more reliable wind-speed prediction methods. It was found that the time series of wind speed not only has linear characteristics, but also nonlinear. In addition, most methods only consider one criterion or rule (stability or accuracy), or one objective function, which can lead to poor forecasting results. So, wind-speed forecasting is still a difficult and challenging problem. The existing forecasting models based on combination-model theory can adapt to some time-series data and overcome the shortcomings of the single model, which achieves poor accuracy and instability. In this paper, a combined forecasting model based on data preprocessing, a nondominated sorting genetic algorithm (NSGA-III) with three objective functions and four models (two hybrid nonlinear models and two linear models) is proposed and was successfully applied to forecasting wind speed, which not only overcomes the issue of forecasting accuracy, but also solves the difficulties of forecasting stability. The experimental results show that the stability and accuracy of the proposed combined model are better than the single models, improving the mean absolute percentage error (MAPE) range from 0.007% to 2.31%, and the standard deviation mean absolute percentage error (STDMAPE) range from 0.0044 to 0.3497.

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