scholarly journals Improving forecasting accuracy of river flow using gene expression programming based on wavelet decomposition and de-noising

2017 ◽  
Vol 49 (3) ◽  
pp. 711-723 ◽  
Author(s):  
Xiaorong Lu ◽  
Xuelei Wang ◽  
Liang Zhang ◽  
Ting Zhang ◽  
Chao Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Wavelet Decomposition ◽  
Water Resource Management ◽  
River Flow ◽  
Time Series Data ◽  
Gene Expression Programming ◽  
Stationary Time Series ◽  
Series Data ◽  
Effective Measure

Abstract Due to the effects of anthropogenic activities and natural climate change, streamflows of rivers have gradually decreased. In order to maintain reliable water supplies, reservoir operation and water resource management, accurate streamflow forecasts are very important. Based on monthly flow data from five hydrological stations in the middle and lower parts of the Hanjiang River Basin, between 1989 and 2009, we consider an efficient approach of adopting the gene expression programming model based on wavelet decomposition and de-noising (WDDGEP) to forecast river flow. Original flow time series data are initially decomposed into one sub-signal approximation and seven sub-signal details using the dmey wavelet. A wavelet threshold de-noising method is also applied in this study. Data that have been de-noised after decomposition are then adopted as inputs for WDDGEP models. Finally, the forecasted sub-signal results are summed to formulate an ensemble forecast for the original monthly flow series. A comparison of the prediction accuracy between the two models is based on three performance evaluation measures. Results show that the new WDDGEP models can effectively enhance accuracy in forecasting streamflow, and the proposed wavelet-based de-noising of the observed non-stationary time series is an effective measure to improve simulation accuracy.

scholarly journals An improved framework to predict river flow time series data

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7183 ◽  
Author(s):  
Hafiza Mamona Nazir ◽  
Ijaz Hussain ◽  
Ishfaq Ahmad ◽  
Muhammad Faisal ◽  
Ibrahim M. Almanjahie
Keyword(s):  
Time Series ◽  
Water Resource Management ◽  
River Flow ◽  
Time Series Data ◽  
Flow Time ◽  
Indus Basin ◽  
Series Data ◽  
Percentage Error ◽  
Empirical Bayesian ◽  
Noise Characteristics

Due to non-stationary and noise characteristics of river flow time series data, some pre-processing methods are adopted to address the multi-scale and noise complexity. In this paper, we proposed an improved framework comprising Complete Ensemble Empirical Mode Decomposition with Adaptive Noise-Empirical Bayesian Threshold (CEEMDAN-EBT). The CEEMDAN-EBT is employed to decompose non-stationary river flow time series data into Intrinsic Mode Functions (IMFs). The derived IMFs are divided into two parts; noise-dominant IMFs and noise-free IMFs. Firstly, the noise-dominant IMFs are denoised using empirical Bayesian threshold to integrate the noises and sparsities of IMFs. Secondly, the denoised IMF’s and noise free IMF’s are further used as inputs in data-driven and simple stochastic models respectively to predict the river flow time series data. Finally, the predicted IMF’s are aggregated to get the final prediction. The proposed framework is illustrated by using four rivers of the Indus Basin System. The prediction performance is compared with Mean Square Error, Mean Absolute Error (MAE) and Mean Absolute Percentage Error (MAPE). Our proposed method, CEEMDAN-EBT-MM, produced the smallest MAPE for all four case studies as compared with other methods. This suggests that our proposed hybrid model can be used as an efficient tool for providing the reliable prediction of non-stationary and noisy time series data to policymakers such as for planning power generation and water resource management.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

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.

Inference of gene regulatory networks based on nonlinear ordinary differential equations

2020 ◽  
Vol 36 (19) ◽  
pp. 4885-4893 ◽  
Author(s):  
Baoshan Ma ◽  
Mingkun Fang ◽  
Xiangtian Jiao
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Steady State ◽  
Differential Equations ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Time Series Data ◽  
Series Data ◽  
State Data ◽  
Gene Regulatory

Abstract Motivation Gene regulatory networks (GRNs) capture the regulatory interactions between genes, resulting from the fundamental biological process of transcription and translation. In some cases, the topology of GRNs is not known, and has to be inferred from gene expression data. Most of the existing GRNs reconstruction algorithms are either applied to time-series data or steady-state data. Although time-series data include more information about the system dynamics, steady-state data imply stability of the underlying regulatory networks. Results In this article, we propose a method for inferring GRNs from time-series and steady-state data jointly. We make use of a non-linear ordinary differential equations framework to model dynamic gene regulation and an importance measurement strategy to infer all putative regulatory links efficiently. The proposed method is evaluated extensively on the artificial DREAM4 dataset and two real gene expression datasets of yeast and Escherichia coli. Based on public benchmark datasets, the proposed method outperforms other popular inference algorithms in terms of overall score. By comparing the performance on the datasets with different scales, the results show that our method still keeps good robustness and accuracy at a low computational complexity. Availability and implementation The proposed method is written in the Python language, and is available at: https://github.com/lab319/GRNs_nonlinear_ODEs Supplementary information Supplementary data are available at Bioinformatics online.

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