The restriction mapping problem revisited

In computational molecular biology, the aim of restriction mapping is to locate the restriction sites of a given enzyme on a DNA molecule. Double digest and partial digest are two well-studied techniques for restriction mapping. While double digest is NP-complete, there is no known polynomial-time algorithm for partial digest. Another disadvantage of the above techniques is that there can be multiple solutions for reconstruction. In this paper, we study a simple technique called labeled partial digest for restriction mapping. We give a fast polynomial time (O(n(2) log n) worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. An important advantage of the algorithm is the unique reconstruction of the DNA molecule from the digest. The technique is also robust in handling errors in fragment lengths which arises in the laboratory. We give a robust O(n(4)) worst-case algorithm that can provably tolerate an absolute error of O(Delta/n) (where Delta is the minimum inter-site distance), while giving a unique reconstruction. We test our theoretical results by simulating the performance of the algorithm on a real DNA molecule. Motivated by the similarity to the labeled partial digest problem, we address a related problem of interest-the de novo peptide sequencing problem (ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000, pp. 389-398), which arises in the reconstruction of the peptide sequence of a protein molecule. We give a simple and efficient algorithm for the problem without using dynamic programming. The algorithm runs in time O(k log k), where k is the number of ions and is an improvement over the algorithm in Chen et al. (C) 2002 Elsevier Science (USA). All rights reserved.

Localisation of discrete change in a transformer winding: a network-function-loci approach

An entirely different approach for localisation of winding deformation based on terminal measurements is presented. Within the context of this study, winding deformation means, a discrete and specific change externally imposed at a particular position on the winding. The proposed method is based on pre-computing and plotting the complex network-function loci e.g. driving-point impedance (DPI)] at a selected frequency, for a meaningful range of values for each element (increasing and decreasing) of the ladder network which represents the winding. This loci diagram is called the nomogram. After introducing a discrete change, amplitude and phase of DPI are measured. By plotting this single measurement on the nomogram, it is possible to estimate the location and identify the extent of change. In contrast to the existing approach, the proposed method is fast, non-iterative and yields reasonably good localisation. Experimental results for actual transformer windings (interleaved and continuous disc) are presented.

PL due to Discrete Gap Levels in Some Chalcogenide Glasses- A Configurational Coordinate Diagram Illustration

Photoluminescence (PL) studies were carried out on a-Se and a few Ge20Se80−xBix and Ge20Se70−xBixTe10 bulk glassy semiconductors at 4.2 K with Ar+ laser as excitation source. While a-Se and samples with lesser at% of Bi show fine structured PL with a large Stokes shift, samples with higher at% of Bi did not show any detectable PL. The investigations show at least three radiative recombination transitions. Features extracted by deconvoluting the experimental spectra show that the discrete gap levels associated with the inherent coordination defects are involved in the PL transitions. Absence of PL in samples with higher Bi at% are explained on the basis of nonradiative transition mechanisms. Overall PL mechanism involving gap levels in chalcogenide glasses is illustrated with the help of a configurational coordinate diagram.

Uncertainty analysis of vibrational frequencies of an incompressible liquid in a rectangular tank with and without a baffle using polynomial chaos expansion

Polynomial chaos expansion (PCE) with Latin hypercube sampling (LHS) is employed for calculating the vibrational frequencies of an inviscid incompressible fluid partially filled in a rectangular tank with and without a baffle. Vibration frequencies of the coupled system are described through their projections on the PCE which uses orthogonal basis functions. PCE coefficients are evaluated using LHS. Convergence on the coefficient of variation is used to find the orthogonal polynomial basis function order which is employed in PCE. It is observed that the dispersion in the eigenvalues is more in the case of a rectangular tank with a baffle. The accuracy of the PCE method is verified with standard MCS results and is found to be more efficient.

Optimal local polynomial regression of noisy time varying signals

We address the problem of local-polynomial modeling of smooth time-varying signals with unknown functional form, in the presence of additive noise. The problem formulation is in the time domain and the polynomial coefficients are estimated in the pointwise minimum mean square error (PMMSE) sense. The choice of the window length for local modeling introduces a bias-variance tradeoff, which we solve optimally by using the intersection-of-confidence-intervals (ICI) technique. The combination of the local polynomial model and the ICI technique gives rise to an adaptive signal model equipped with a time-varying PMMSE-optimal window length whose performance is superior to that obtained by using a fixed window length. We also evaluate the sensitivity of the ICI technique with respect to the confidence interval width. Simulation results on electrocardiogram (ECG) signals show that at 0dB signal-to-noise ratio (SNR), one can achieve about 12dB improvement in SNR. Monte-Carlo performance analysis shows that the performance is comparable to the basic wavelet techniques. For 0 dB SNR, the adaptive window technique yields about 2-3dB higher SNR than wavelet regression techniques and for SNRs greater than 12dB, the wavelet techniques yield about 2dB higher SNR.

A Nash Bargaining Approach to Retention Enhancing Bid Optimization in Sponsored Search Auctions with Discrete Bids

Bid optimization is now becoming quite popular in sponsored search auctions on the Web. Given a keyword and the maximum willingness to pay of each advertiser interested in the keyword, the bid optimizer generates a profile of bids for the advertisers with the objective of maximizing customer retention without compromising the revenue of the search engine. In this paper, we present a bid optimization algorithm that is based on a Nash bargaining model where the first player is the search engine and the second player is a virtual agent representing all the bidders. We make the realistic assumption that each bidder specifies a maximum willingness to pay values and a discrete, finite set of bid values. We show that the Nash bargaining solution for this problem always lies on a certain edge of the convex hull such that one end point of the edge is the vector of maximum willingness to pay of all the bidders. We show that the other endpoint of this edge can be computed as a solution of a linear programming problem. We also show how the solution can be transformed to a bid profile of the advertisers.

Polynomial Coefficient Based Multi-Tone Testing of Analog Circuits

Abstract—A method of testing for parametric faults of analog circuits based on a polynomial representaion of fault-free function of the circuit is presented. The response of the circuit under test (CUT) is estimated as a polynomial in the applied input voltage at relevant frequencies apart from DC. Classification of CUT is based on a comparison of the estimated polynomial coefficients with those of the fault free circuit. The method needs very little augmentation of circuit to make it testable as only output parameters are used for classification. This procedure is shown to uncover several parametric faults causing smaller than 5 % deviations the nominal values. Fault diagnosis based upon sensitivity of polynomial coefficients at relevant frequencies is also proposed.

V-Transform: “An Enhanced Polynomial Coefficient Based DC Test for Non-linear Analog Circuits

Abstract—DC testing of parametric faults in non-linear analog circuits based on a new transformation, entitled, V-Transform acting on polynomial coefficient expansion of the circuit function is presented. V-Transform serves the dual purpose of monotonizing polynomial coefficients of circuit function expansion and increasing the sensitivity of these coefficients to circuit parameters. The sensitivity of V-Transform Coefficients (VTC) to circuit parameters is up to 3x-5x more than sensitivity of polynomial coefficients. As a case study, we consider a benchmark elliptic filter to validate our method. The technique is shown to uncover hitherto untestable parametric faults whose sizes are smaller than 10 % of the nominal values. I.

Performance analysis of a fluid queue with random service rate in discrete time

We consider a fluid queue in discrete time with random service rate. Such a queue has been used in several recent studies on wireless networks where the packets can be arbitrarily fragmented. We provide conditions on finiteness of moments of stationary delay, its Laplace-Stieltjes transform and various approximations under heavy traffic. Results are extended to the case where the wireless link can transmit in only a few slots during a frame.