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.

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.

Aberration correction for free space optical communications using rectangular zernike modal wavefront sensing

A time multiplexed rectangular Zernike modal wavefront sensor based on a nematic phase-only liquid crystal spatial light modulator and specially designed for a high power two-electrode tapered laser diode which is a compact and novel free space optical communication source is used in an adaptive beam steering free space optical communication system, enabling the system to have 1.25 GHz modulation bandwidth, 4.6° angular coverage and the capability of sensing aberrations within the system and caused by atmosphere turbulence up to absolute value of 0.15 waves amplitude and correcting them in one correction cycle. Closed-loop aberration correction algorithm can be implemented to provide convergence for larger and time varying aberrations. Improvement of the system signal-to-noise-ratio performance is achieved by aberration correction. To our knowledge, it is first time to use rectangular orthonormal Zernike polynomials to represent balanced aberrations for high power rectangular laser beam in practice. © 2014 IEEE.

Simulating dynamic covariance structures for testing the adaptive behavior of variable selection algorithms (Invited Paper)

Variable selection for regression is a classical statistical problem, motivated by concerns that too large a number of covariates may bring about overfitting and unnecessarily high measurement costs. Novel difficulties arise in streaming contexts, where the correlation structure of the process may be drifting, in which case it must be constantly tracked so that selections may be revised accordingly. A particularly interesting phenomenon is that non-selected covariates become missing variables, inducing bias on subsequent decisions. This raises an intricate exploration-exploitation tradeoff, whose dependence on the covariance tracking algorithm and the choice of variable selection scheme is too complex to be dealt with analytically. We hence capitalise on the strength of simulations to explore this problem, taking the opportunity to tackle the difficult task of simulating dynamic correlation structures. © 2008 IEEE.

Temporally adaptive estimation of logistic classifiers on data streams

Modern technology has allowed real-time data collection in a variety of domains, ranging from environmental monitoring to healthcare. Consequently, there is a growing need for algorithms capable of performing inferential tasks in an online manner, continuously revising their estimates to reflect the current status of the underlying process. In particular, we are interested in constructing online and temporally adaptive classifiers capable of handling the possibly drifting decision boundaries arising in streaming environments. We first make a quadratic approximation to the log-likelihood that yields a recursive algorithm for fitting logistic regression online. We then suggest a novel way of equipping this framework with self-tuning forgetting factors. The resulting scheme is capable of tracking changes in the underlying probability distribution, adapting the decision boundary appropriately and hence maintaining high classification accuracy in dynamic or unstable environments. We demonstrate the scheme's effectiveness in both real and simulated streaming environments. © Springer-Verlag 2009.

Streaming covariance selection with applications to adaptive querying in sensor networks

Sensor networks can be naturally represented as graphical models, where the edge set encodes the presence of sparsity in the correlation structure between sensors. Such graphical representations can be valuable for information mining purposes as well as for optimizing bandwidth and battery usage with minimal loss of estimation accuracy. We use a computationally efficient technique for estimating sparse graphical models which fits a sparse linear regression locally at each node of the graph via the Lasso estimator. Using a recently suggested online, temporally adaptive implementation of the Lasso, we propose an algorithm for streaming graphical model selection over sensor networks. With battery consumption minimization applications in mind, we use this algorithm as the basis of an adaptive querying scheme. We discuss implementation issues in the context of environmental monitoring using sensor networks, where the objective is short-term forecasting of local wind direction. The algorithm is tested against real UK weather data and conclusions are drawn about certain tradeoffs inherent in decentralized sensor networks data analysis. © 2010 The Author. Published by Oxford University Press on behalf of The British Computer Society. All rights reserved.

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.