PTOMSM: A modified version of Topological Overlap Measure used for predicting Protein-Protein Interaction Network

A variety of methods are developed to integrating diverse biological data to predict novel interaction relationship between proteins. However, traditional integration can only generate protein interaction pairs within existing relationships. Therefore, we propose a modified version of Topological Overlap Measure to identify not only extant direct PPIs links, but also novel protein interactions that can be indirectly inferred from various relationships between proteins. Our method is more powerful than a naïve Bayesian-network-based integration in PPI prediction, and could generate more reliable candidate PPIs. Furthermore, we examined the influence of the sizes of training and test datasets on prediction, and further demonstrated the effectiveness of PTOMSM in predicting PPI. More importantly, this method can be extended naturally to predict other types of biological networks, and may be combined with Bayesian method to further improve the prediction

A fourier pseudospectral method for some computational aeroacoustics problems

A Fourier pseudospectral time-domain method is applied to wave propagation problems pertinent to computational aeroacoustics. The original algorithm of the Fourier pseudospectral time-domain method works for periodical problems without the interaction with physical boundaries. In this paper we develop a slip wall boundary condition, combined with buffer zone technique to solve some non-periodical problems. For a linear sound propagation problem whose governing equations could be transferred to ordinary differential equations in pseudospectral space, a new algorithm only requiring time stepping is developed and tested. For other wave propagation problems, the original algorithm has to be employed, and the developed slip wall boundary condition still works. The accuracy of the presented numerical algorithm is validated by benchmark problems, and the efficiency is assessed by comparing with high-order finite difference methods. It is indicated that the Fourier pseudospectral time-domain method, time stepping method, slip wall and absorbing boundary conditions combine together to form a fully-fledged computational algorithm

A Linear-Quadratic Optimal Control Problem for Mean-Field Stochastic Differential Equations in Infinite Horizon

A linear-quadratic (LQ, for short) optimal control problem is considered for mean-field stochastic differential equations with constant coefficients in an infinite horizon. The stabilizability of the control system is studied followed by the discussion of the well-posedness of the LQ problem. The optimal control can be expressed as a linear state feedback involving the state and its mean, through the solutions of two algebraic Riccati equations. The solvability of such kind of Riccati equations is investigated by means of semi-definite programming method.Comment: 40 page

Necessary Condition for Near Optimal Control of Linear Forward-backward Stochastic Differential Equations

This paper investigates the near optimal control for a kind of linear stochastic control systems governed by the forward backward stochastic differential equations, where both the drift and diffusion terms are allowed to depend on controls and the control domain is not assumed to be convex. In the previous work (Theorem 3.1) of the second and third authors [\textit{% Automatica} \textbf{46} (2010) 397-404], some problem of near optimal control with the control dependent diffusion is addressed and our current paper can be viewed as some direct response to it. The necessary condition of the near-optimality is established within the framework of optimality variational principle developed by Yong [\textit{SIAM J. Control Optim.} \textbf{48} (2010) 4119--4156] and obtained by the convergence technique to treat the optimal control of FBSDEs in unbounded control domains by Wu [% \textit{Automatica} \textbf{49} (2013) 1473--1480]. Some new estimates are given here to handle the near optimality. In addition, an illustrating example is discussed as well.Comment: To appear in International Journal of Contro