Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

Non-compressive wideband spectrum sensing with sub-Nyquist sampling rates

In this paper, we propose a low complexity and reliable wideband spectrum sensing technique that operates at sub-Nyquist sampling rates. Unlike the majority of other sub-Nyquist spectrum sensing algorithms that rely on the Compressive Sensing (CS) methodology, the introduced method does not entail solving an optimisation problem. It is characterised by simplicity and low computational complexity without compromising the system performance and yet delivers substantial reductions on the operational sampling rates. The reliability guidelines of the devised non-compressive sensing approach are provided and simulations are presented to illustrate its superior performance. © 2013 IEEE.

Convex approaches to model wavelet sparsity patterns

Statistical dependencies among wavelet coefficients are commonly represented by graphical models such as hidden Markov trees (HMTs). However, in linear inverse problems such as deconvolution, tomography, and compressed sensing, the presence of a sensing or observation matrix produces a linear mixing of the simple Markovian dependency structure. This leads to reconstruction problems that are non-convex optimizations. Past work has dealt with this issue by resorting to greedy or suboptimal iterative reconstruction methods. In this paper, we propose new modeling approaches based on group-sparsity penalties that leads to convex optimizations that can be solved exactly and efficiently. We show that the methods we develop perform significantly better in de-convolution and compressed sensing applications, while being as computationally efficient as standard coefficient-wise approaches such as lasso. © 2011 IEEE.

High-resolution strain sensing on steel by Silicon-On-Insulator flexural resonators fabricated with chip-level vacuum packaging

This paper reports on the fabrication and characterization of high-resolution strain sensors for steel based on Silicon On Insulator flexural resonators manufactured with chip-level LPCVD vacuum packaging. The sensors present high sensitivity (120 Hz/μ), very high resolution (4 n), low drift, and near-perfect reversibility in bending tests performed in both tensile and compressive strain regimes. © 2013 IEEE.

Integration of holographic sensors into microfluidics for the real-time pH sensing of L. casei metabolism

We describe developments in the integration of analyte specific holographic sensors into PDMS-based microfluidic devices for the purpose of continuous, low-impact monitoring of extra-cellular change in micro-bioreactors. Holographic sensors respond to analyte concentration via volume change, which makes their reduction in size and integration into spatially confined fluidics difficult. Through design and process modification many of these constraints have been addressed, and a microfluidics-based device capable of real-time monitoring of the pH change caused by Lactobacillus casei fermentation is presented as a general proof-of-concept for a wide array of possible devices.