reverse engineering time discrete finite dynamical systems a feasible undertaking逆向工程时间有限离散动力系统可行的事业.pdfVIP

Reverse Engineering Time Discrete Finite Dynamical Systems: A Feasible Undertaking? Edgar Delgado-Eckert1,2¤* ¨ ¨ 1 Centre for Mathematical Sciences, Technische Universitat Munchen, Garching, Germany, 2 Pathology Department, Tufts University, Boston, Massachusetts, United States of America Abstract With the advent of high-throughput profiling methods, interest in reverse engineering the structure and dynamics of biochemical networks is high. Recently an algorithm for reverse engineering of biochemical networks was developed by Laubenbacher and Stigler. It is a top-down approach using time discrete dynamical systems. One of its key steps includes ¨ the choice of a term order, a technicality imposed by the use of Grobner-bases calculations. The aim of this paper is to identify minimal requirements on data sets to be used with this algorithm and to characterize optimal data sets. We found minimal requirements on a data set based on how many terms the functions to be reverse engineered display. Furthermore, we identified optimal data sets, which we characterized using a geometric property called ‘‘general position’’. Moreover, we developed a constructive method to generate optimal data sets, provided a codimensional condition is fulfilled. In addition, we present a generalization of their algorithm that does not depend on the choice of a term order. For this method we derived a formula for the probability of finding the correct model, provided the data set used is optimal. We analyzed the asymptotic behavior of the probability formula for a growing number of variables n (i.e. interacting chemicals). Unfortunately, this formula converges to zero as fast as rðqn Þ, where q[N