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Ma B, Fang M, Jiao X. Inference of gene regulatory networks based on nonlinear ordinary differential equations. Bioinformatics 2020; 36:4885-4893. [DOI: 10.1093/bioinformatics/btaa032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/30/2019] [Accepted: 01/15/2020] [Indexed: 01/05/2023] Open
Abstract
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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Affiliation(s)
- Baoshan Ma
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Mingkun Fang
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Xiangtian Jiao
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
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Decentralized Event-Triggered Exponential Stability for Uncertain Delayed Genetic Regulatory Networks with Markov Jump Parameters and Distributed Delays. Neural Process Lett 2017. [DOI: 10.1007/s11063-017-9695-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Senthilraj S, Raja R, Zhu Q, Samidurai R, Zhou H. Delay-dependent asymptotic stability criteria for genetic regulatory networks with impulsive perturbations. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2016.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cakır T, Khatibipour MJ. Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. Front Bioeng Biotechnol 2014; 2:62. [PMID: 25520953 PMCID: PMC4253960 DOI: 10.3389/fbioe.2014.00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/14/2014] [Indexed: 11/13/2022] Open
Abstract
The primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts from genome-scale metabolic networks, which cover all possible reactions known to occur in the related organism in a condition-independent manner, and applies methods such as the optimization-based Flux-Balance Analysis to elucidate the active network. The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization-based methods to extract information content of the data such that the active network is inferred. These approaches, termed bottom-up and top-down, respectively, are currently employed independently. However, considering that both approaches have the same goal, they can both benefit from each other paving the way for the novel integrative analysis methods of metabolome data- and flux-analysis approaches in the post-genomic era. This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two approaches to shed better light on how the metabolism functions.
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Affiliation(s)
- Tunahan Cakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University (formerly known as Gebze Institute of Technology) , Gebze , Turkey
| | - Mohammad Jafar Khatibipour
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University (formerly known as Gebze Institute of Technology) , Gebze , Turkey ; Department of Chemical Engineering, Gebze Technical University (formerly known as Gebze Institute of Technology) , Gebze , Turkey
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Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BIOMED RESEARCH INTERNATIONAL 2014; 2014:863298. [PMID: 25025072 PMCID: PMC4082904 DOI: 10.1155/2014/863298] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/07/2014] [Accepted: 05/18/2014] [Indexed: 11/18/2022]
Abstract
The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of
high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.
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Chai LE, Loh SK, Low ST, Mohamad MS, Deris S, Zakaria Z. A review on the computational approaches for gene regulatory network construction. Comput Biol Med 2014; 48:55-65. [PMID: 24637147 DOI: 10.1016/j.compbiomed.2014.02.011] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 01/08/2023]
Abstract
Many biological research areas such as drug design require gene regulatory networks to provide clear insight and understanding of the cellular process in living cells. This is because interactions among the genes and their products play an important role in many molecular processes. A gene regulatory network can act as a blueprint for the researchers to observe the relationships among genes. Due to its importance, several computational approaches have been proposed to infer gene regulatory networks from gene expression data. In this review, six inference approaches are discussed: Boolean network, probabilistic Boolean network, ordinary differential equation, neural network, Bayesian network, and dynamic Bayesian network. These approaches are discussed in terms of introduction, methodology and recent applications of these approaches in gene regulatory network construction. These approaches are also compared in the discussion section. Furthermore, the strengths and weaknesses of these computational approaches are described.
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Affiliation(s)
- Lian En Chai
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Swee Kuan Loh
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Swee Thing Low
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Mohd Saberi Mohamad
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia.
| | - Safaai Deris
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Zalmiyah Zakaria
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
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8
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Using gene expression programming to infer gene regulatory networks from time-series data. Comput Biol Chem 2013; 47:198-206. [DOI: 10.1016/j.compbiolchem.2013.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 09/19/2013] [Accepted: 09/21/2013] [Indexed: 11/22/2022]
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Wu SJ, Wu CT. Computational optimization for S-type biological systems: Cockroach genetic algorithm. Math Biosci 2013; 245:299-313. [DOI: 10.1016/j.mbs.2013.07.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 11/16/2022]
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Abstract
Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools that facilitate the analysis of dynamic biological systems. This paper depicts major developments in BST up to the current state of the art in 2012. It discusses its rationale, describes the typical strategies and methods of designing, diagnosing, analyzing, and utilizing BST models, and reviews areas of application. The paper is intended as a guide for investigators entering the fascinating field of biological systems analysis and as a resource for practitioners and experts.
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Sun J, Garibaldi JM, Hodgman C. Parameter estimation using meta-heuristics in systems biology: a comprehensive review. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:185-202. [PMID: 21464505 DOI: 10.1109/tcbb.2011.63] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
This paper gives a comprehensive review of the application of meta-heuristics to optimization problems in systems biology, mainly focussing on the parameter estimation problem (also called the inverse problem or model calibration). It is intended for either the system biologist who wishes to learn more about the various optimization techniques available and/or the meta-heuristic optimizer who is interested in applying such techniques to problems in systems biology. First, the parameter estimation problems emerging from different areas of systems biology are described from the point of view of machine learning. Brief descriptions of various meta-heuristics developed for these problems follow, along with outlines of their advantages and disadvantages. Several important issues in applying meta-heuristics to the systems biology modelling problem are addressed, including the reliability and identifiability of model parameters, optimal design of experiments, and so on. Finally, we highlight some possible future research directions in this field.
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Mitra S, Das R, Hayashi Y. Genetic networks and soft computing. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:94-107. [PMID: 21071800 DOI: 10.1109/tcbb.2009.39] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The analysis of gene regulatory networks provides enormous information on various fundamental cellular processes involving growth, development, hormone secretion, and cellular communication. Their extraction from available gene expression profiles is a challenging problem. Such reverse engineering of genetic networks offers insight into cellular activity toward prediction of adverse effects of new drugs or possible identification of new drug targets. Tasks such as classification, clustering, and feature selection enable efficient mining of knowledge about gene interactions in the form of networks. It is known that biological data is prone to different kinds of noise and ambiguity. Soft computing tools, such as fuzzy sets, evolutionary strategies, and neurocomputing, have been found to be helpful in providing low-cost, acceptable solutions in the presence of various types of uncertainties. In this paper, we survey the role of these soft methodologies and their hybridizations, for the purpose of generating genetic networks.
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Affiliation(s)
- Sushmita Mitra
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India.
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14
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Wu H, Liao X, Feng W, Guo S, Zhang W. Robust stability for uncertain genetic regulatory networks with interval time-varying delays. Inf Sci (N Y) 2010. [DOI: 10.1016/j.ins.2010.05.032] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Zhang SQ, Ching WK, Chen X, Tsing NK. Generating probabilistic Boolean networks from a prescribed stationary distribution. Inf Sci (N Y) 2010. [DOI: 10.1016/j.ins.2010.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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A clustering-based approach for inferring recurrent neural networks as gene regulatory networks. Neurocomputing 2008. [DOI: 10.1016/j.neucom.2007.07.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bernhardt K. Finding alternatives and reduced formulations for process-based models. EVOLUTIONARY COMPUTATION 2008; 16:63-88. [PMID: 18386996 DOI: 10.1162/evco.2008.16.1.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This paper addresses the problem of model complexity commonly arising in constructing and using process-based models with intricate interactions. Apart from complex process details the dynamic behavior of such systems is often limited to a discrete number of typical states. Thus, models reproducing the system's processes in all details are often too complex and over-parameterized. In order to reduce simulation times and to get a better impression of the important mechanisms, simplified formulations are desirable. In this work a data adaptive model reduction scheme that automatically builds simple models from complex ones is proposed. The method can be applied to the transformation and reduction of systems of ordinary differential equations. It consists of a multistep approach using a low dimensional projection of the model data followed by a Genetic Programming/Genetic Algorithm hybrid to evolve new model systems. As the resulting models again consist of differential equations, their process-based interpretation in terms of new state variables becomes possible. Transformations of two simple models with oscillatory dynamics, simulating a mathematical pendulum and predator-prey interactions respectively, serve as introductory examples of the method's application. The resulting equations of force indicate the predator-prey system's equivalence to a nonlinear oscillator. In contrast to the simple pendulum it contains driving and damping forces that produce a stable limit cycle.
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Affiliation(s)
- Knut Bernhardt
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, P.O. Box 2503, 26111 Oldenburg, Germany.
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Ponzoni I, Azuaje F, Augusto J, Glass D. Inferring adaptive regulation thresholds and association rules from gene expression data through combinatorial optimization learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2007; 4:624-634. [PMID: 17975273 DOI: 10.1109/tcbb.2007.1049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
There is a need to design computational methods to support the prediction of gene regulatory networks. Such models should offer both biologically-meaningful and computationally-accurate predictions, which in combination with other techniques may improve large-scale, integrative studies. This paper presents a new machine learning method for the prediction of putative regulatory associations from expression data, which exhibit properties never or only partially addressed by other techniques recently published. The method was tested on a Saccharomyces cerevisiae gene expression dataset. The results were statistically validated and compared with the relationships inferred by two machine learning approaches to gene regulatory network prediction. Furthermore, the resulting predictions were assessed using domain knowledge. The proposed algorithm may be able to accurately predict relevant biological associations between genes. One of the most relevant features of this new method is the prediction of adaptive regulation thresholds for the discretization of gene expression values, which is required prior to the rule association learning process. Moreover, an important advantage consists of its low computational cost to infer association rules. The proposed system may significantly support exploratory, large-scale studies of automated identification of potentially-relevant gene expression associations.
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Lin TC. A new adaptive center weighted median filter for suppressing impulsive noise in images. Inf Sci (N Y) 2007. [DOI: 10.1016/j.ins.2006.07.030] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cho DY, Cho KH, Zhang BT. Identification of biochemical networks by S-tree based genetic programming. Bioinformatics 2006; 22:1631-40. [PMID: 16585066 DOI: 10.1093/bioinformatics/btl122] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Most previous approaches to model biochemical networks have focused either on the characterization of a network structure with a number of components or on the estimation of kinetic parameters of a network with a relatively small number of components. For system-level understanding, however, we should examine both the interactions among the components and the dynamic behaviors of the components. A key obstacle to this simultaneous identification of the structure and parameters is the lack of data compared with the relatively large number of parameters to be estimated. Hence, there are many plausible networks for the given data, but most of them are not likely to exist in the real system. RESULTS We propose a new representation named S-trees for both the structural and dynamical modeling of a biochemical network within a unified scheme. We further present S-tree based genetic programming to identify the structure of a biochemical network and to estimate the corresponding parameter values at the same time. While other evolutionary algorithms require additional techniques for sparse structure identification, our approach can automatically assemble the sparse primitives of a biochemical network in an efficient way. We evaluate our algorithm on the dynamic profiles of an artificial genetic network. In 20 trials for four settings, we obtain the true structure and their relative squared errors are <5% regardless of releasing constraints about structural sparseness. In addition, we confirm that the proposed algorithm is robust within +/-10% noise ratio. Furthermore, the proposed approach ensures a reasonable estimate of a real yeast fermentation pathway. The comparatively less important connections with non-zero parameters can be detected even though their orders are below 10(-2). To demonstrate the usefulness of the proposed algorithm for real experimental biological data, we provide an additional example on the transcriptional network of SOS response to DNA damage in Escherichia coli. We confirm that the proposed algorithm can successfully identify the true structure except only one relation.
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Affiliation(s)
- Dong-Yeon Cho
- School of Computer Science and Engineering, Seoul National University Seoul 151-742, Korea
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Wu SJ, Wu CT, Lee TT. Computation intelligent for eukaryotic cell-cycle gene network. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2006; 2006:2017-2020. [PMID: 17945692 DOI: 10.1109/iembs.2006.260339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Computational intelligent approaches is adopted to construct the S-system of eukaryotic cell cycle for further analysis of genetic regulatory networks. A highly nonlinear power-law differential equation is constructed to describe the transcriptional regulation of gene network from the time-courses dataset. Global artificial algorithm, based on hybrid differential evolution, can achieve global optimization for the highly nonlinear differential gene network modeling. The constructed gene regulatory networks will be a reference for researchers to realize the inhibitory and activatory operator for genes synthesis and decomposition in Eukaryotic cell cycle.
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Affiliation(s)
- Shinq-Jen Wu
- Dept. of Electr. Eng., Da-Yeh Univ., Chang-Hwa, Taiwan, ROC.
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22
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Styczynski MP, Stephanopoulos G. Overview of computational methods for the inference of gene regulatory networks. Comput Chem Eng 2005. [DOI: 10.1016/j.compchemeng.2004.08.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sugimoto M, Kikuchi S, Tomita M. Reverse engineering of biochemical equations from time-course data by means of genetic programming. Biosystems 2004; 80:155-64. [PMID: 15823414 DOI: 10.1016/j.biosystems.2004.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Revised: 11/12/2004] [Accepted: 11/14/2004] [Indexed: 10/26/2022]
Abstract
Increased research aimed at simulating biological systems requires sophisticated parameter estimation methods. All current approaches, including genetic algorithms, need pre-existing equations to be functional. A generalized approach to predict not only parameters but also biochemical equations from only observable time-course information must be developed and a computational method to generate arbitrary equations without knowledge of biochemical reaction mechanisms must be developed. We present a technique to predict an equation using genetic programming. Our technique can search topology and numerical parameters of mathematical expression simultaneously. To improve the search ability of numeric constants, we added numeric mutation to the conventional procedure. As case studies, we predicted two equations of enzyme-catalyzed reactions regarding adenylate kinase and phosphofructokinase. Our numerical experimental results showed that our approach could obtain correct topology and parameters that were close to the originals. The mean errors between given and simulation-predicted time-courses were 1.6 x 10(-5)% and 2.0 x 10(-3)%, respectively. Our equation prediction approach can be applied to identify metabolic reactions from observable time-courses.
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Affiliation(s)
- Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata , Japan
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Crampin EJ, Schnell S, McSharry PE. Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2004; 86:77-112. [PMID: 15261526 DOI: 10.1016/j.pbiomolbio.2004.04.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Time series data can now be routinely collected for biochemical reaction pathways, and recently, several methods have been proposed to infer reaction mechanisms for metabolic pathways and networks. In this paper we provide a survey of mathematical techniques for determining reaction mechanisms for time series data on the concentration or abundance of different reacting components, with little prior information about the pathways involved.
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Affiliation(s)
- E J Crampin
- Centre for Mathematical Biology, Mathematical Institute, 24-29 St. Giles', Oxford OX 1 3LB, UK.
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