Growing Seed Genes from Time Series Data and Thresholded Boolean Networks with Perturbation

2013 ◽  
Vol 10 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Carlos H. A. Higa ◽  
Tales P. Andrade ◽  
Ronaldo F. Hashimoto
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Boolean Networks ◽  
Series Data

Improved Fuzzy Cognitive Maps for Gene Regulatory Networks Inference Based on Time Series Data

2021 ◽  
Author(s):  
Marzieh Emadi ◽  
Farsad Zamani Boroujeni ◽  
jamshid Pirgazi
Keyword(s):  
Time Series ◽  
Compressed Sensing ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Time Series Data ◽  
Cognitive Maps ◽  
Boolean Networks ◽  
Fuzzy Cognitive Maps ◽  
Series Data ◽  
Gene Regulatory

Abstract Recently with the advancement of high-throughput sequencing, gene regulatory network inference has turned into an interesting subject in bioinformatics and system biology. But there are many challenges in the field such as noisy data, uncertainty, time-series data with numerous gene numbers and low data, time complexity and so on. In recent years, many research works have been conducted to tackle these challenges, resulting in different methods in gene regulatory networks inference. A number of models have been used in modeling of the gene regulatory networks including Boolean networks, Bayesian networks, Markov model, relational networks, state space model, differential equations model, artificial neural networks and so on. In this paper, the fuzzy cognitive maps are used to model gene regulatory networks because of their dynamic nature and learning capabilities for handling non-linearity and inherent uncertainty. Fuzzy cognitive maps belong to the family of recurrent networks and are well-suited for gene regulatory networks. In this research study, the Kalman filtered compressed sensing is used to infer the fuzzy cognitive map for the gene regulatory networks. This approach, using the advantages of compressed sensing and Kalman filters, allows robustness to noise and learning of sparse gene regulatory networks from data with high gene number and low samples. In the proposed method, stream data and previous knowledge can be used in the inference process. Furthermore, compressed sensing finds likely edges and Kalman filter estimates their weights. The proposed approach uses a novel method to decrease the noise of data. The proposed method is compared to CSFCM, LASSOFCM, KFRegular, ABC, RCGA, ICLA, and CMI2NI. The results show that the proposed approach is superior to the other approaches in fuzzy cognitive maps learning. This behavior is related to the stability against noise and offers a proper balance between data error and network structure.

scholarly journals Constraint-based analysis of gene interactions using restricted boolean networks and time-series data

2011 ◽  
Vol 5 (Suppl 2) ◽  
pp. S5 ◽  
Author(s):  
Carlos HA Higa ◽  
Vitor HP Louzada ◽  
Tales P Andrade ◽  
Ronaldo F Hashimoto
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Boolean Networks ◽  
Series Data ◽  
Gene Interactions

Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data

2018 ◽  
pp. 59-74 ◽  
Author(s):  
Misbah Razzaq ◽  
Roland Kaminski ◽  
Javier Romero ◽  
Torsten Schaub ◽  
Jeremie Bourdon ◽  
...  
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Boolean Networks ◽  
Series Data

scholarly journals A Novel Algorithm for the Maximal Fit Problem in Boolean Networks

2016 ◽  
Author(s):  
Guy Karlebach
Keyword(s):  
Time Series ◽  
Regulatory Networks ◽  
Time Series Data ◽  
Boolean Networks ◽  
Large Datasets ◽  
Series Data ◽  
Np Complete ◽  
Regulation Functions ◽  
Regulatory Controls ◽  
Novel Algorithm

AbstractGene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one another. Boolean networks are a common modeling choice since they balance between detail and ease of analysis. However, even for Boolean networks the problem of fitting a given network model to an expression dataset is NP-Complete. Previous methods have addressed this issue heuristically or by focusing on acyclic networks and specific classes of regulation functions. In this paper we introduce a novel algorithm for this problem that makes use of sampling in order to handle large datasets. Our algorithm can handle time series data for any network type and steady state data for acyclic networks. Using in-silico time series data we demonstrate good performance on large datasets with a significant level of noise.

scholarly journals ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics

2019 ◽  
Author(s):  
Ning Shi ◽  
Zexuan Zhu ◽  
Ke Tang ◽  
David Parker ◽  
Shan He
Keyword(s):  
Time Series ◽  
Network Topology ◽  
Regulatory Networks ◽  
Boolean Network ◽  
Target Gene ◽  
Time Series Data ◽  
Boolean Networks ◽  
Series Data ◽  
Prime Implicants ◽  
Cell Life

Abstract Motivation Inferring gene regulatory networks from gene expression time series data is important for gaining insights into the complex processes of cell life. A popular approach is to infer Boolean networks. However, it is still a pressing open problem to infer accurate Boolean networks from experimental data that are typically short and noisy. Results To address the problem, we propose a Boolean network inference algorithm which is able to infer accurate Boolean network topology and dynamics from short and noisy time series data. The main idea is that, for each target gene, we use an And/Or tree ensemble algorithm to select prime implicants of which each is a conjunction of a set of input genes. The selected prime implicants are important features for predicting the states of the target gene. Using these important features we then infer the Boolean function of the target gene. Finally, the Boolean functions of all target genes are combined as a Boolean network. Using the data generated from artificial and real-world gene regulatory networks, we show that our algorithm can infer more accurate Boolean network topology and dynamics from short and noisy time series data than other algorithms. Our algorithm enables us to gain better insights into complex regulatory mechanisms of cell life. Availability and implementation Package ATEN is freely available at https://github.com/ningshi/ATEN. Supplementary information Supplementary data are available at Bioinformatics online.

Graphical Exploratory Data Analysis for Categorical Longitudinal and Time Series Data

2013 ◽  
Author(s):  
Stephen J. Tueller ◽  
Richard A. Van Dorn ◽  
Georgiy Bobashev ◽  
Barry Eggleston
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Exploratory Data Analysis ◽  
Time Series Data ◽  
Series Data ◽  
Exploratory Data
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