Online Pattern Matching for String Edit Distance with Moves

Edit distance with moves (EDM) is a string-to-string distance measure that includes substring moves in addition to ordinal editing operations to turn one string to the other. Although optimizing EDM is intractable, it has many applications especially in error detections. Edit sensitive parsing (ESP) is an efficient parsing algorithm that guarantees an upper bound of parsing discrepancies between different appearances of the same substrings in a string. ESP can be used for computing an approximate EDM as the L1 distance between characteristic vectors built by node labels in parsing trees. However, ESP is not applicable to a streaming text data where a whole text is unknown in advance. We present an online ESP (OESP) that enables an online pattern matching for EDM. OESP builds a parse tree for a streaming text and computes the L1 distance between characteristic vectors in an online manner. For the space-efficient computation of EDM, OESP directly encodes the parse tree into a succinct representation by leveraging the idea behind recent results of a dynamic succinct tree. We experimentally test OESP on the ability to compute EDM in an online manner on benchmark datasets, and we show OESP's efficiency.Comment: This paper has been accepted to the 21st edition of the International Symposium on String Processing and Information Retrieval (SPIRE2014

Entangled Quantum States Generated by Shor's Factoring Algorithm

The intermediate quantum states of multiple qubits, generated during the operation of Shor's factoring algorithm are analyzed. Their entanglement is evaluated using the Groverian measure. It is found that the entanglement is generated during the pre-processing stage of the algorithm and remains nearly constant during the quantum Fourier transform stage. The entanglement is found to be correlated with the speedup achieved by the quantum algorithm compared to classical algorithms.Comment: 7 pages, 4 figures submitted to Phys. Rev.

Algebraic analysis of quantum search with pure and mixed states

An algebraic analysis of Grover's quantum search algorithm is presented for the case in which the initial state is an arbitrary pure quantum state of n qubits. This approach reveals the geometrical structure of the quantum search process, which turns out to be confined to a four-dimensional subspace of the Hilbert space. This work unifies and generalizes earlier results on the time evolution of the amplitudes during the quantum search, the optimal number of iterations and the success probability. Furthermore, it enables a direct generalization to the case in which the initial state is a mixed state, providing an exact formula for the success probability.Comment: 13 page

Characterization of pure quantum states of multiple qubits using the Groverian entanglement measure

The Groverian entanglement measure, G(psi), is applied to characterize a variety of pure quantum states |psi> of multiple qubits. The Groverian measure is calculated analytically for certain states of high symmetry, while for arbitrary states it is evaluated using a numerical procedure. In particular, it is calculated for the class of Greenberger-Horne-Zeilinger states, the W states as well as for random pure states of n qubits. The entanglement generated by Grover's algorithm is evaluated by calculating G(psi) for the intermediate states that are obtained after t Grover iterations, for various initial states and for different sets of the marked states.Comment: 28 pages, 5 figure

A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Surface states in nearly modulated systems

A Landau model is used to study the phase behavior of the surface layer for magnetic and cholesteric liquid crystal systems that are at or near a Lifshitz point marking the boundary between modulated and homogeneous bulk phases. The model incorporates surface and bulk fields and includes a term in the free energy proportional to the square of the second derivative of the order parameter in addition to the usual term involving the square of the first derivative. In the limit of vanishing bulk field, three distinct types of surface ordering are possible: a wetting layer, a non-wet layer having a small deviation from bulk order, and a different non-wet layer with a large deviation from bulk order which decays non-monotonically as distance from the wall increases. In particular the large deviation non-wet layer is a feature of systems at the Lifshitz point and also those having only homogeneous bulk phases.Comment: 6 pages, 7 figures, submitted to Phys. Rev.

Magnetization steps in a diluted Heisenberg antiferromagnetic chain: Theory and experiments on TMMC:Cd

A theory for the equilibrium low-temperature magnetization M of a diluted Heisenberg antiferromagnetic chain is presented. The magnetization curve, M versus B, is calculated using the exact contributions of finite chains with 1 to 5 spins, and the "rise and ramp approximation" for longer chains. Some non-equilibrium effects that occur in a rapidly changing B, are also considered. Specific non-equilibrium models based on earlier treatments of the phonon bottleneck, and of spin flips associated with cross relaxation and with level crossings, are discussed. Magnetization data on powders of TMMC diluted with cadmium [i.e., (CH_3)_4NMn_xCd_(1-x)Cl_3, with 0.16<=x<=0.50 were measured at 0.55 K in 18 T superconducting magnets. The field B_1 at the first MST from pairs is used to determine the NN exchange constant, J, which changes from -5.9 K to -6.5 K as x increases from 0.16 to 0.50. The magnetization curves obtained in the superconducting magnets are compared with simulations based on the equilibrium theory. Data for the differential susceptibility, dM/dB, were taken in pulsed magnetic fields (7.4 ms duration) up to 50 T, with the powder samples in a 1.5 K liquid-helium bath. Non-equilibrium effects, which became more severe as x decreased, were observed. The non-equilibrium effects are tentatively interpreted using the "Inadequate Heat Flow Scenario," or to cross-relaxation, and crossings of energy levels, including those of excited states.Comment: 16 pages, 14 figure