Rules for biological regulation based on error minimization

The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control). What determines the choice of mode of control for each gene? This study proposes rules for gene regulation based on the assumption that free regulatory sites are exposed to nonspecific binding errors, whereas sites bound to their cognate regulators are protected from errors. Hence, the selected mechanisms keep the sites bound to their designated regulators for most of the time, thus minimizing fitness-reducing errors. This offers an explanation of the empirically demonstrated Savageau demand rule: Genes that are needed often in the natural environment tend to be regulated by activators, and rarely needed genes tend to be regulated by repressors; in both cases, sites are bound for most of the time, and errors are minimized. The fitness advantage of error minimization appears to be readily selectable. The present approach can also generate rules for multi-regulator systems. The error-minimization framework raises several experimentally testable hypotheses. It may also apply to other biological regulation systems, such as those involving protein-protein interactions.Comment: biological physics, complex networks, systems biology, transcriptional regulation http://www.weizmann.ac.il/complex/tlusty/papers/PNAS2006.pdf http://www.pnas.org/content/103/11/3999.ful

A novel approach to error function minimization for feedforward neural networks

Feedforward neural networks with error backpropagation (FFBP) are widely applied to pattern recognition. One general problem encountered with this type of neural networks is the uncertainty, whether the minimization procedure has converged to a global minimum of the cost function. To overcome this problem a novel approach to minimize the error function is presented. It allows to monitor the approach to the global minimum and as an outcome several ambiguities related to the choice of free parameters of the minimization procedure are removed.Comment: 11 pages, latex, 3 figures appended as uuencoded fil

Noisy Signal Recovery via Iterative Reweighted L1-Minimization

Compressed sensing has shown that it is possible to reconstruct sparse high dimensional signals from few linear measurements. In many cases, the solution can be obtained by solving an L1-minimization problem, and this method is accurate even in the presence of noise. Recent a modified version of this method, reweighted L1-minimization, has been suggested. Although no provable results have yet been attained, empirical studies have suggested the reweighted version outperforms the standard method. Here we analyze the reweighted L1-minimization method in the noisy case, and provide provable results showing an improvement in the error bound over the standard bounds

Robust Sum MSE Optimization for Downlink Multiuser MIMO Systems with Arbitrary Power Constraint: Generalized Duality Approach

This paper considers linear minimum meansquare- error (MMSE) transceiver design problems for downlink multiuser multiple-input multiple-output (MIMO) systems where imperfect channel state information is available at the base station (BS) and mobile stations (MSs). We examine robust sum mean-square-error (MSE) minimization problems. The problems are examined for the generalized scenario where the power constraint is per BS, per BS antenna, per user or per symbol, and the noise vector of each MS is a zero-mean circularly symmetric complex Gaussian random variable with arbitrary covariance matrix. For each of these problems, we propose a novel duality based iterative solution. Each of these problems is solved as follows. First, we establish a novel sum average meansquare- error (AMSE) duality. Second, we formulate the power allocation part of the problem in the downlink channel as a Geometric Program (GP). Third, using the duality result and the solution of GP, we utilize alternating optimization technique to solve the original downlink problem. To solve robust sum MSE minimization constrained with per BS antenna and per BS power problems, we have established novel downlink-uplink duality. On the other hand, to solve robust sum MSE minimization constrained with per user and per symbol power problems, we have established novel downlink-interference duality. For the total BS power constrained robust sum MSE minimization problem, the current duality is established by modifying the constraint function of the dual uplink channel problem. And, for the robust sum MSE minimization with per BS antenna and per user (symbol) power constraint problems, our duality are established by formulating the noise covariance matrices of the uplink and interference channels as fixed point functions, respectively.Comment: IEEE TSP Journa