An algebraic approach to parameter optimization in biomolecular bistable systems

2016 ◽  
Author(s):  
Vahid Mardanlou ◽  
Elisa Franco
Keyword(s):  
Parameter Optimization ◽  
Biological Networks ◽  
Optimization Problem ◽  
Biological Network ◽  
Algebraic Approach ◽  
Reaction Rates ◽  
Toggle Switch ◽  
Switching Speed ◽  
Bistable Systems ◽  
Total Concentrations

AbstractIn a synthetic biological network it may often be desirable to maximize or minimize parameters such as reaction rates, fluxes and total concentrations of reagents, while preserving a given dynamic behavior. We consider the problem of parameter optimization in biomolecular bistable circuits. We show that, under some assumptions often satisfied by bistable biological networks, it is possible to derive algebraic conditions on the parameters that determine when bistability occurs. These (global) algebraic conditions can be included as nonlinear constraints in a parameter optimization problem. We derive bistability conditions using Sturm's theorem for Gardner and Collins toggle switch. Then we optimize its nominal parameters to improve switching speed and robustness to a subset of uncertain parameters.

An improved sparrow search algorithm based on levy flight and opposition-based learning

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Danni Chen ◽  
JianDong Zhao ◽  
Peng Huang ◽  
Xiongna Deng ◽  
Tingting Lu
Keyword(s):  
Parameter Optimization ◽  
Optimization Problem ◽  
Heuristic Algorithms ◽  
Search Algorithm ◽  
Convergence Speed ◽  
Support Vector ◽  
Lévy Flight ◽  
Levy Flight ◽  
Content Type ◽  
Opposition Based Learning

Purpose Sparrow search algorithm (SSA) is a novel global optimization method, but it is easy to fall into local optimization, which leads to its poor search accuracy and stability. The purpose of this study is to propose an improved SSA algorithm, called levy flight and opposition-based learning (LOSSA), based on LOSSA strategy. The LOSSA shows better search accuracy, faster convergence speed and stronger stability. Design/methodology/approach To further enhance the optimization performance of the algorithm, The Levy flight operation is introduced into the producers search process of the original SSA to enhance the ability of the algorithm to jump out of the local optimum. The opposition-based learning strategy generates better solutions for SSA, which is beneficial to accelerate the convergence speed of the algorithm. On the one hand, the performance of the LOSSA is evaluated by a set of numerical experiments based on classical benchmark functions. On the other hand, the hyper-parameter optimization problem of the Support Vector Machine (SVM) is also used to test the ability of LOSSA to solve practical problems. Findings First of all, the effectiveness of the two improved methods is verified by Wilcoxon signed rank test. Second, the statistical results of the numerical experiment show the significant improvement of the LOSSA compared with the original algorithm and other natural heuristic algorithms. Finally, the feasibility and effectiveness of the LOSSA in solving the hyper-parameter optimization problem of machine learning algorithms are demonstrated. Originality/value An improved SSA based on LOSSA is proposed in this paper. The experimental results show that the overall performance of the LOSSA is satisfactory. Compared with the SSA and other natural heuristic algorithms, the LOSSA shows better search accuracy, faster convergence speed and stronger stability. Moreover, the LOSSA also showed great optimization performance in the hyper-parameter optimization of the SVM model.

scholarly journals Evaluation Method of Multiobjective Functions’ Combination and Its Application in Hydrological Model Evaluation

2020 ◽  
Vol 2020 ◽  
pp. 1-23 ◽  
Author(s):  
Jiuyuan Huo ◽  
Liqun Liu
Keyword(s):  
Objective Function ◽  
Parameter Optimization ◽  
Optimization Problem ◽  
Hydrological Model ◽  
Pareto Optimal ◽  
Pareto Optimal Solutions ◽  
Optimal Solutions ◽  
Objective Functions ◽  
Hydrological Forecasting ◽  
Model Parameter Optimization

Parameter optimization of a hydrological model is intrinsically a high dimensional, nonlinear, multivariable, combinatorial optimization problem which involves a set of different objectives. Currently, the assessment of optimization results for the hydrological model is usually made through calculations and comparisons of objective function values of simulated and observed variables. Thus, the proper selection of objective functions’ combination for model parameter optimization has an important impact on the hydrological forecasting. There exist various objective functions, and how to analyze and evaluate the objective function combinations for selecting the optimal parameters has not been studied in depth. Therefore, to select the proper objective function combination which can balance the trade-off among various design objectives and achieve the overall best benefit, a simple and convenient framework for the comparison of the influence of different objective function combinations on the optimization results is urgently needed. In this paper, various objective functions related to parameters optimization of hydrological models were collected from the literature and constructed to nine combinations. Then, a selection and evaluation framework of objective functions is proposed for hydrological model parameter optimization, in which a multiobjective artificial bee colony algorithm named RMOABC is employed to optimize the hydrological model and obtain the Pareto optimal solutions. The parameter optimization problem of the Xinanjiang hydrological model was taken as the application case for long-term runoff prediction in the Heihe River basin. Finally, the technique for order preference by similarity to ideal solution (TOPSIS) based on the entropy theory is adapted to sort the Pareto optimal solutions to compare these combinations of objective functions and obtain the comprehensive optimal objective functions’ combination. The experiments results demonstrate that the combination 2 of objective functions can provide more comprehensive and reliable dominant options (i.e., parameter sets) for practical hydrological forecasting in the study area. The entropy-based method has been proved that it is effective to analyze and evaluate the performance of different combinations of objective functions and can provide more comprehensive and impersonal decision support for hydrological forecasting.

scholarly journals Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Reagon Karki ◽  
Alpha Tom Kodamullil ◽  
Charles Tapley Hoyt ◽  
Martin Hofmann-Apitius
Keyword(s):  
Biological Networks ◽  
Molecular Mechanisms ◽  
Biological Network ◽  
Expression Patterns ◽  
Cell Types ◽  
Brain Regions ◽  
Heat Diffusion ◽  
Disease Etiology ◽  
The Individual ◽  
Biological Entities

Abstract Background Literature derived knowledge assemblies have been used as an effective way of representing biological phenomenon and understanding disease etiology in systems biology. These include canonical pathway databases such as KEGG, Reactome and WikiPathways and disease specific network inventories such as causal biological networks database, PD map and NeuroMMSig. The represented knowledge in these resources delineates qualitative information focusing mainly on the causal relationships between biological entities. Genes, the major constituents of knowledge representations, tend to express differentially in different conditions such as cell types, brain regions and disease stages. A classical approach of interpreting a knowledge assembly is to explore gene expression patterns of the individual genes. However, an approach that enables quantification of the overall impact of differentially expressed genes in the corresponding network is still lacking. Results Using the concept of heat diffusion, we have devised an algorithm that is able to calculate the magnitude of regulation of a biological network using expression datasets. We have demonstrated that molecular mechanisms specific to Alzheimer (AD) and Parkinson Disease (PD) regulate with different intensities across spatial and temporal resolutions. Our approach depicts that the mitochondrial dysfunction in PD is severe in cortex and advanced stages of PD patients. Similarly, we have shown that the intensity of aggregation of neurofibrillary tangles (NFTs) in AD increases as the disease progresses. This finding is in concordance with previous studies that explain the burden of NFTs in stages of AD. Conclusions This study is one of the first attempts that enable quantification of mechanisms represented as biological networks. We have been able to quantify the magnitude of regulation of a biological network and illustrate that the magnitudes are different across spatial and temporal resolution.

scholarly journals An Improved Method for Completely Uncertain Biological Network Alignment

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Bin Shen ◽  
Muwei Zhao ◽  
Wei Zhong ◽  
Jieyue He
Keyword(s):  
Biological Networks ◽  
Biological Network ◽  
Evaluation Criteria ◽  
Network Alignment ◽  
Global Network ◽  
Uncertain Information ◽  
Improved Method ◽  
Network Comparison ◽  
Probabilistic Network ◽  
Alignment Problem

With the continuous development of biological experiment technology, more and more data related to uncertain biological networks needs to be analyzed. However, most of current alignment methods are designed for the deterministic biological network. Only a few can solve the probabilistic network alignment problem. However, these approaches only use the part of probabilistic data in the original networks allowing only one of the two networks to be probabilistic. To overcome the weakness of current approaches, an improved method called completely probabilistic biological network comparison alignment (C_PBNA) is proposed in this paper. This new method is designed for complete probabilistic biological network alignment based on probabilistic biological network alignment (PBNA) in order to take full advantage of the uncertain information of biological network. The degree of consistency (agreement) indicates that C_PBNA can find the results neglected by PBNA algorithm. Furthermore, the GO consistency (GOC) and global network alignment score (GNAS) have been selected as evaluation criteria, and all of them proved that C_PBNA can obtain more biologically significant results than those of PBNA algorithm.

HiSCF: leveraging higher-order structures for clustering analysis in biological networks

2020 ◽  
Author(s):  
Lun Hu ◽  
Jun Zhang ◽  
Xiangyu Pan ◽  
Hong Yan ◽  
Zhu-Hong You
Keyword(s):  
Biological Networks ◽  
Clustering Analysis ◽  
Biological Network ◽  
Higher Order ◽  
Supplementary Information ◽  
Network Motifs ◽  
Functional Modules ◽  
Connectivity Patterns ◽  
Biological Entities ◽  
Insight Into

Abstract Motivation Clustering analysis in a biological network is to group biological entities into functional modules, thus providing valuable insight into the understanding of complex biological systems. Existing clustering techniques make use of lower-order connectivity patterns at the level of individual biological entities and their connections, but few of them can take into account of higher-order connectivity patterns at the level of small network motifs. Results Here, we present a novel clustering framework, namely HiSCF, to identify functional modules based on the higher-order structure information available in a biological network. Taking advantage of higher-order Markov stochastic process, HiSCF is able to perform the clustering analysis by exploiting a variety of network motifs. When compared with several state-of-the-art clustering models, HiSCF yields the best performance for two practical clustering applications, i.e. protein complex identification and gene co-expression module detection, in terms of accuracy. The promising performance of HiSCF demonstrates that the consideration of higher-order network motifs gains new insight into the analysis of biological networks, such as the identification of overlapping protein complexes and the inference of new signaling pathways, and also reveals the rich higher-order organizational structures presented in biological networks. Availability and implementation HiSCF is available at https://github.com/allenv5/HiSCF. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Biological network analysis with deep learning

2020 ◽  
Author(s):  
Giulia Muzio ◽  
Leslie O’Bray ◽  
Karsten Borgwardt
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Biological Networks ◽  
Protein Function ◽  
Regulatory Networks ◽  
Biological Network ◽  
Gene Interaction ◽  
Disease Diagnosis ◽  
Interaction Prediction ◽  
Graph Neural Networks

Abstract Recent advancements in experimental high-throughput technologies have expanded the availability and quantity of molecular data in biology. Given the importance of interactions in biological processes, such as the interactions between proteins or the bonds within a chemical compound, this data is often represented in the form of a biological network. The rise of this data has created a need for new computational tools to analyze networks. One major trend in the field is to use deep learning for this goal and, more specifically, to use methods that work with networks, the so-called graph neural networks (GNNs). In this article, we describe biological networks and review the principles and underlying algorithms of GNNs. We then discuss domains in bioinformatics in which graph neural networks are frequently being applied at the moment, such as protein function prediction, protein–protein interaction prediction and in silico drug discovery and development. Finally, we highlight application areas such as gene regulatory networks and disease diagnosis where deep learning is emerging as a new tool to answer classic questions like gene interaction prediction and automatic disease prediction from data.

NMDB: NETWORK MOTIF DATABASE ENVISAGED AND EXPLICATED FROM HUMAN DISEASE SPECIFIC PATHWAYS

2014 ◽  
Vol 22 (01) ◽  
pp. 89-100 ◽  
Author(s):  
ABHAY PRATAP ◽  
SETU TALIYAN ◽  
TIRATHA RAJ SINGH
Keyword(s):  
Biological Networks ◽  
Human Disease ◽  
Biological Network ◽  
Metabolic Diseases ◽  
Network Motif ◽  
Network Motifs ◽  
Efficient Detection ◽  
Single Input ◽  
Motif Database ◽  
Disease Specific

The study of network motifs for large number of networks can aid us to resolve the functions of complex biological networks. In biology, network motifs that reappear within a network more often than expected in random networks include negative autoregulation, positive autoregulation, single-input modules, feedforward loops, dense overlapping regulons and feedback loops. These network motifs have their different dynamical functions. In this study, our main objective is to examine the enrichment of network motifs in different biological networks of human disease specific pathways. We characterize biological network motifs as biologically significant sub-graphs. We used computational and statistical criteria for efficient detection of biological network motifs, and introduced several estimation measures. Pathways of cardiovascular, cancer, infectious, repair, endocrine and metabolic diseases, were used for identifying and interlinking the relation between nodes. 3–8 sub-graph size network motifs were generated. Network Motif Database was then developed using PHP and MySQL. Results showed that there is an abundance of autoregulation, feedforward loops, single-input modules, dense overlapping regulons and other putative regulatory motifs in all the diseases included in this study. It is believed that the database will assist molecular and system biologists, biotechnologists, and other scientific community to encounter biologically meaningful information. Network Motif Database is freely available for academic and research purpose at: http://www.bioinfoindia.org/nmdb .

Thermal morphing anisogrid smart space structures part 2: Ranking of geometric parameter importance, trust region optimization, and performance evaluation

2017 ◽  
Vol 24 (13) ◽  
pp. 2873-2893 ◽  
Author(s):  
Austin A Phoenix ◽  
Jeff Borggaard ◽  
Pablo A Tarazaga
Keyword(s):  
Parameter Optimization ◽  
Optimization Problem ◽  
Optimal Allocation ◽  
Search Algorithm ◽  
Thermal Strain ◽  
Computational Cost ◽  
Trust Region ◽  
Minimum Cost ◽  
Space Mission ◽  
Model Parameters

As future space mission structures are required to achieve more with scarcer resources, new structural configurations and modeling capabilities will be needed to meet the next generation space structural challenges. A paradigm shift is required away from the current structures that are static, heavy, and stiff, to innovative lightweight structures that meet requirements by intelligently adapting to the environment. As the complexity of these intelligent structures increases, the computational cost of the modeling and optimization efforts become increasingly demanding. Novel methods that identify and reduce the number of parameters to only those most critical considerably reduce these complex problems, allowing highly iterative evaluations and in-depth optimization efforts to be computationally feasible. This parameter ranking methodology will be demonstrated on the optimization of the thermal morphing anisogrid boom. The proposed novel morphing structure provides high precision morphing through the use of thermal strain as the sole actuation mechanism. The morphing concept uses the helical members in the anisogrid structure to provide complex constrained actuations that can achieve the six degree of freedom morphing capability. This structure provides a unique potential to develop an integrated structural morphing system, where the adaptive morphing capability is integrated directly into the primary structure. To identify parameters of interest, the Q-DEIM model reduction algorithm is implemented to rank the model parameters based on their impact on the morphing performance. This parameter ranking method provides insight into the system and enables the optimal allocation of computational and engineering resources to the most critical areas of the system for optimization. The methodology, in conjunction with a singular value decomposition (SVD), provides a ranking and identifies parameters of relative importance. The SVD is used to truncate the nine parameters problem at two locations, generating a five parameter optimization problem and a three parameter optimization problem. To evaluate the ranking, a parameter sweep in conjunction with a simple minimum cost function search algorithm will compare all 120 five parameter ranking orders to the Q-DEIM ranking. This reduced parameter set significantly reduces the parameter complexity and the computational cost of the model optimization. This paper will present the methodology to define the resulting performance of the optimal thermal morphing anisogrid structure, minimum morphing control, and the systems frequency response capability as a function of available power.

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