Approximate parameter inference in systems biology using gradient matching: a comparative evaluation

Background: A challenging problem in current systems biology is that of parameter inference in biological pathways expressed as coupled ordinary differential equations (ODEs). Conventional methods that repeatedly numerically solve the ODEs have large associated computational costs. Aimed at reducing this cost, new concepts using gradient matching have been proposed, which bypass the need for numerical integration. This paper presents a recently established adaptive gradient matching approach, using Gaussian processes, combined with a parallel tempering scheme, and conducts a comparative evaluation with current state of the art methods used for parameter inference in ODEs. Among these contemporary methods is a technique based on reproducing kernel Hilbert spaces (RKHS). This has previously shown promising results for parameter estimation, but under lax experimental settings. We look at a range of scenarios to test the robustness of this method. We also change the approach of inferring the penalty parameter from AIC to cross validation to improve the stability of the method. Methodology: Methodology for the recently proposed adaptive gradient matching method using Gaussian processes, upon which we build our new method, is provided. Details of a competing method using reproducing kernel Hilbert spaces are also described here. Results: We conduct a comparative analysis for the methods described in this paper, using two benchmark ODE systems. The analyses are repeated under different experimental settings, to observe the sensitivity of the techniques. Conclusions: Our study reveals that for known noise variance, our proposed method based on Gaussian processes and parallel tempering achieves overall the best performance. When the noise variance is unknown, the RKHS method proves to be more robust

PinMe: Tracking a Smartphone User around the World

With the pervasive use of smartphones that sense, collect, and process valuable information about the environment, ensuring location privacy has become one of the most important concerns in the modern age. A few recent research studies discuss the feasibility of processing data gathered by a smartphone to locate the phone's owner, even when the user does not intend to share his location information, e.g., when the Global Positioning System (GPS) is off. Previous research efforts rely on at least one of the two following fundamental requirements, which significantly limit the ability of the adversary: (i) the attacker must accurately know either the user's initial location or the set of routes through which the user travels and/or (ii) the attacker must measure a set of features, e.g., the device's acceleration, for potential routes in advance and construct a training dataset. In this paper, we demonstrate that neither of the above-mentioned requirements is essential for compromising the user's location privacy. We describe PinMe, a novel user-location mechanism that exploits non-sensory/sensory data stored on the smartphone, e.g., the environment's air pressure, along with publicly-available auxiliary information, e.g., elevation maps, to estimate the user's location when all location services, e.g., GPS, are turned off.Comment: This is the preprint version: the paper has been published in IEEE Trans. Multi-Scale Computing Systems, DOI: 0.1109/TMSCS.2017.275146

Data based identification and prediction of nonlinear and complex dynamical systems

We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin