Robust network reconstruction in polynomial time

This paper presents an efficient algorithm for robust network reconstruction of Linear Time-Invariant (LTI) systems in the presence of noise, estimation errors and unmodelled nonlinearities. The method here builds on previous work [1] on robust reconstruction to provide a practical implementation with polynomial computational complexity. Following the same experimental protocol, the algorithm obtains a set of structurally-related candidate solutions spanning every level of sparsity. We prove the existence of a magnitude bound on the noise, which if satisfied, guarantees that one of these structures is the correct solution. A problem-specific model-selection procedure then selects a single solution from this set and provides a measure of confidence in that solution. Extensive simulations quantify the expected performance for different levels of noise and show that significantly more noise can be tolerated in comparison to the original method. © 2012 IEEE.

Network reconstruction using knock-out and over-expression data

This paper outlines necessary and sufficient conditions for network reconstruction of linear, time-invariant systems using data from either knock-out or over-expression experiments. These structural system perturbations, which are common in biological experiments, can be formulated as unknown system inputs, allowing the network topology and dynamics to be found. We assume that only partial state measurements are available and propose an algorithm that can reconstruct the network at the level of the measured states using either time-series or steady-state data. A simulated example illustrates how the algorithm successfully reconstructs a network from data. © 2013 EUCA.

Numerical study on hydrate bearing sediments during gas production

The fully coupled methane hydrate model developed in Cambridge was adopted in this numerical study on gas production trial at the Eastern Nankai Trough, Japan 2013. Based on the latest experimental data of hydrate soil core samples, the clay parameters at Eastern Nankai site were successfully calibrated. With updated clay parameters and site geometry, a 50 days gas production trail was numerically simulated in FLAC2D. The geomechanical behaviour of hydrate bearing sediments under 3 different depressurization strategies were explored and discussed. The results from both axisymmetrical and plane-strain models suggest, the slope of the seabed only affects mechanical properties while no significant impact on the dissociation, temperature and pore pressure. For mechanical deformation after PT recovery, there are large settlements above the perforation zone and small uplift underneath the production zone. To validate the fully coupled model, numerical simulation with finer mesh in the hydrate production zone was carried out. The simulation results suggest good agreement between our model and JOE's results on history matching of gas and water production during trial. Parameter sensitivity of gas production is also investigated and concluded the sea water salinity is a dominant factor for gas production.