981 research outputs found
Neural Networks: Training and Application to Nonlinear System Identification and Control
This dissertation investigates training neural networks for system identification and classification. The research contains two main contributions as follow:1. Reducing number of hidden layer nodes using a feedforward componentThis research reduces the number of hidden layer nodes and training time of neural networks to make them more suited to online identification and control applications by adding a parallel feedforward component. Implementing the feedforward component with a wavelet neural network and an echo state network provides good models for nonlinear systems.The wavelet neural network with feedforward component along with model predictive controller can reliably identify and control a seismically isolated structure during earthquake. The network model provides the predictions for model predictive control. Simulations of a 5-story seismically isolated structure with conventional lead-rubber bearings showed significant reductions of all response amplitudes for both near-field (pulse) and far-field ground motions, including reduced deformations along with corresponding reduction in acceleration response. The controller effectively regulated the apparent stiffness at the isolation level. The approach is also applied to the online identification and control of an unmanned vehicle. Lyapunov theory is used to prove the stability of the wavelet neural network and the model predictive controller. 2. Training neural networks using trajectory based optimization approachesTraining neural networks is a nonlinear non-convex optimization problem to determine the weights of the neural network. Traditional training algorithms can be inefficient and can get trapped in local minima. Two global optimization approaches are adapted to train neural networks and avoid the local minima problem. Lyapunov theory is used to prove the stability of the proposed methodology and its convergence in the presence of measurement errors. The first approach transforms the constraint satisfaction problem into unconstrained optimization. The constraints define a quotient gradient system (QGS) whose stable equilibrium points are local minima of the unconstrained optimization. The QGS is integrated to determine local minima and the local minimum with the best generalization performance is chosen as the optimal solution. The second approach uses the QGS together with a projected gradient system (PGS). The PGS is a nonlinear dynamical system, defined based on the optimization problem that searches the components of the feasible region for solutions. Lyapunov theory is used to prove the stability of PGS and QGS and their stability under presence of measurement noise
In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum
The Maurer’s clefts (MCs) are very important for the survival of Plasmodium falciparum within an infected cell as they are induced by the parasite itself in the erythrocyte for protein trafficking. The MCs form an interesting part of the parasite’s biology as they shed more light on how the parasite remodels the erythrocyte leading to host pathogenesis and death. Here, we predicted and analyzed the genetic regulatory network of genes identified to belong to the MCs using regularized graphical Gaussian model. Our network shows four major activators, their corresponding target genes, and predicted binding sites. One of these master activators is the serine repeat antigen 5 (SERA5), predominantly expressed among the SERA multigene family of P. falciparum, which is one of the blood-stage malaria vaccine candidates. Our results provide more details about functional interactions and the regulation of the genes in the MCs’ pathway of P. falciparum
In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum
The Maurer’s clefts (MCs) are very important for the survival of Plasmodium falciparum within an infected cell as they are induced by the parasite itself in the erythrocyte for protein trafficking. The MCs form an interesting part of the parasite’s biology as they shed more light on how the parasite remodels the erythrocyte leading to host pathogenesis and death. Here, we predicted and analyzed the genetic regulatory network of genes identified to belong to the MCs using regularized graphical Gaussian model. Our network shows four major activators, their corresponding target genes, and predicted binding sites. One of these master activators is the serine repeat antigen 5 (SERA5), predominantly expressed among the SERA multigene family of P. falciparum, which is one of the blood-stage malaria vaccine candidates. Our results provide more details about functional interactions and the regulation of the genes in the MCs’ pathway of P. falciparum
Artificial Neural Network Inference (ANNI): A Study on Gene-Gene Interaction for Biomarkers in Childhood Sarcomas
Objective: To model the potential interaction between previously identified biomarkers in children sarcomas using artificial neural network inference (ANNI).
Method: To concisely demonstrate the biological interactions between correlated genes in an interaction network map, only 2 types of sarcomas in the children small round blue cell tumors (SRBCTs) dataset are discussed in this paper. A backpropagation neural network was used to model the potential interaction between genes. The prediction weights and signal directions were used to model the strengths of the interaction signals and the direction of the interaction link between genes. The ANN model was validated using Monte Carlo cross-validation to minimize the risk of over-fitting and to optimize generalization ability of the model.
Results: Strong connection links on certain genes (TNNT1 and FNDC5 in rhabdomyosarcoma (RMS); FCGRT and OLFM1 in Ewing’s sarcoma (EWS)) suggested their potency as central hubs in the interconnection of genes with different functionalities. The results showed that the RMS patients in this dataset are likely to be congenital and at low risk of cardiomyopathy development. The EWS patients are likely to be complicated by EWS-FLI fusion and deficiency in various signaling pathways, including Wnt, Fas/Rho and intracellular oxygen.
Conclusions: The ANN network inference approach and the examination of identified genes in the published literature within the context of the disease highlights the substantial influence of certain genes in sarcomas
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach
9 páginas, 6 figuras.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution LicenseMotivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters.
Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cellsD.H., J.R.B. and J.S.R. acknowledge funding from the EU FP7 projects
‘NICHE’ (ITN Grant number 289384) and ‘BioPreDyn’ (KBBE grant number
289434). J.R.B. also acknowledges funding from the Spanish Ministerio de
EconomÃa y Competitividad (and the FEDER) through the project
MultiScales (DPI2011-28112-C04-03).Peer reviewe
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimisation approach
Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters.Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells.D.H., J.R.B. and J.S.R. acknowledge funding from the EU FP7 projects 'NICHE' (ITN Grant number 289384) and 'BioPreDyn' (KBBE grant number 289434). J.R.B. also acknowledges funding from the Spanish Ministerio de Economia y Competitividad (and the FEDER) through the project MultiScales (DPI2011-28112-C04-03)
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