Optimal Computation of Avoided Words

The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $\rho$-avoided word in $x$ if $std(w) \leq \rho$, for a given threshold $\rho < 0$. Notice that such a word may be completely absent from $x$. Hence computing all such words na\"{\i}vely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $\rho$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(\sigma n)$-time and $O(\sigma n)$-space algorithm to compute all $\rho$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $\sigma$. Furthermore, we provide a tight asymptotic upper bound for the number of $\rho$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation

Fault-Tolerant Error Correction with Efficient Quantum Codes

We exhibit a simple, systematic procedure for detecting and correcting errors using any of the recently reported quantum error-correcting codes. The procedure is shown explicitly for a code in which one qubit is mapped into five. The quantum networks obtained are fault tolerant, that is, they can function successfully even if errors occur during the error correction. Our construction is derived using a recently introduced group-theoretic framework for unifying all known quantum codes.Comment: 12 pages REVTeX, 1 ps figure included. Minor additions and revision

Atomic and molecular complex resonances from real eigenvalues using standard (hermitian) electronic structure calculations

Complex eigenvalues, resonances, play an important role in large variety of fields in physics and chemistry. For example, in cold molecular collision experiments and electron scattering experiments, autoionizing and pre-dissociative metastable resonances are generated. However, the computation of complex resonance eigenvalues is difficult, since it requires severe modifications of standard electronic structure codes and methods. Here we show how resonance eigenvalues, positions and widths, can be calculated using the standard, widely used, electronic-structure packages. Our method enables the calculations of the complex resonance eigenvalues by using analytical continuation procedures (such as Pad\'{e}). The key point in our approach is the existence of narrow analytical passages from the real axis to the complex energy plane. In fact, the existence of these analytical passages relies on using finite basis sets. These passages become narrower as the basis set becomes more complete, whereas in the exact limit, these passages to the complex plane are closed. As illustrative numerical examples we calculated the autoionization resonances of helium, hydrogen anion and hydrogen molecule. We show that our results are in an excellent agreement with the results obtained by other theoretical methods and with available experimental results

An improved connectionist activation function for energy minimization

Symmetric networks that are based on energy minimization, such as Boltzmann machines or Hopfield nets, are used extensively for optimization, constraint satisfaction, and approximation of NP-hard problems. Nevertheless, finding a global minimum for the energy function is not guaranteed, and even a local minimum may take an exponential number of steps. We propose an improvement to the standard activation function used for such networks. The improved algorithm guarantees that a global minimum is found in linear time for tree-like subnetworks. The algorithm is uniform and does not assume that the network is a tree. It performs no worse than the standard algorithms for any network topology. In the case where there are trees growing from a cyclic subnetwork, the new algorithm performs better than the standard algorithms by avoiding local minima along the trees and by optimizing the free energy of these trees in linear time. The algorithm is self-stabilizing for trees (cycle-free undirected graphs) and remains correct under various scheduling demons. However, no uniform protocol exists to optimize trees under a pure distributed demon and no such protocol exists for cyclic networks under central demon

Efficient Path Interpolation and Speed Profile Computation for Nonholonomic Mobile Robots

This paper studies path synthesis for nonholonomic mobile robots moving in two-dimensional space. We first address the problem of interpolating paths expressed as sequences of straight line segments, such as those produced by some planning algorithms, into smooth curves that can be followed without stopping. Our solution has the advantage of being simpler than other existing approaches, and has a low computational cost that allows a real-time implementation. It produces discretized paths on which curvature and variation of curvature are bounded at all points, and preserves obstacle clearance. Then, we consider the problem of computing a time-optimal speed profile for such paths. We introduce an algorithm that solves this problem in linear time, and that is able to take into account a broader class of physical constraints than other solutions. Our contributions have been implemented and evaluated in the framework of the Eurobot contest