Statistical Indicators of Collective Behavior and Functional Clusters in Gene Networks of Yeast

We analyze gene expression time-series data of yeast S. cerevisiae measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.Comment: 8 pages, 4 figure

Variable neural networks for adaptive control of nonlinear systems

This paper is concerned with the adaptive control of continuous-time nonlinear dynamical systems using neural networks. A novel neural network architecture, referred to as a variable neural network, is proposed and shown to be useful in approximating the unknown nonlinearities of dynamical systems. In the variable neural networks, the number of basis functions can be either increased or decreased with time, according to specified design strategies, so that the network will not overfit or underfit the data set. Based on the Gaussian radial basis function (GRBF) variable neural network, an adaptive control scheme is presented. The location of the centers and the determination of the widths of the GRBFs in the variable neural network are analyzed to make a compromise between orthogonality and smoothness. The weight-adaptive laws developed using the Lyapunov synthesis approach guarantee the stability of the overall control scheme, even in the presence of modeling error(s). The tracking errors converge to the required accuracy through the adaptive control algorithm derived by combining the variable neural network and Lyapunov synthesis techniques. The operation of an adaptive control scheme using the variable neural network is demonstrated using two simulated example

Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites

We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis approaches for uncovering biological insights. We determine the gene co-expression network of Bacillus subtilis using Affymetrix GeneChip time series data and show how the inferred network topology can be linked to sequence-level information hard-wired in the organism's genome. We propose a systematic way for determining the correlation threshold at which two genes are assessed to be co-expressed by using the clustering coefficient and we expand the scope of the gene co-expression network by proposing the slope ratio metric as a means for incorporating directionality on the edges. We show through specific examples for B. subtilis that by incorporating expression level information in addition to the temporal expression patterns, we can uncover sequence-level biological insights. In particular, we are able to identify a number of cases where (i) the co-expressed genes are part of a single transcriptional unit or operon and (ii) the inferred directionality arises due to the presence of intra-operon transcription termination sites.Comment: 7 pages, 8 figures, accepted in Bioinformatic

Digital IP Protection Using Threshold Voltage Control

This paper proposes a method to completely hide the functionality of a digital standard cell. This is accomplished by a differential threshold logic gate (TLG). A TLG with $n$ inputs implements a subset of Boolean functions of $n$ variables that are linear threshold functions. The output of such a gate is one if and only if an integer weighted linear arithmetic sum of the inputs equals or exceeds a given integer threshold. We present a novel architecture of a TLG that not only allows a single TLG to implement a large number of complex logic functions, which would require multiple levels of logic when implemented using conventional logic primitives, but also allows the selection of that subset of functions by assignment of the transistor threshold voltages to the input transistors. To obfuscate the functionality of the TLG, weights of some inputs are set to zero by setting their device threshold to be a high $V_t$. The threshold voltage of the remaining transistors is set to low $V_t$ to increase their transconductance. The function of a TLG is not determined by the cell itself but rather the signals that are connected to its inputs. This makes it possible to hide the support set of the function by essentially removing some variable from the support set of the function by selective assignment of high and low $V_t$ to the input transistors. We describe how a standard cell library of TLGs can be mixed with conventional standard cells to realize complex logic circuits, whose function can never be discovered by reverse engineering. A 32-bit Wallace tree multiplier and a 28-bit 4-tap filter were synthesized on an ST 65nm process, placed and routed, then simulated including extracted parastics with and without obfuscation. Both obfuscated designs had much lower area (25%) and much lower dynamic power (30%) than their nonobfuscated CMOS counterparts, operating at the same frequency