siEDM: an efficient string index and search algorithm for edit distance with moves

Although several self-indexes for highly repetitive text collections exist, developing an index and search algorithm with editing operations remains a challenge. 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 into another. Although the problem of computing EDM is intractable, it has a wide range of potential applications, especially in approximate string retrieval. Despite the importance of computing EDM, there has been no efficient method for indexing and searching large text collections based on the EDM measure. We propose the first algorithm, named string index for edit distance with moves (siEDM), for indexing and searching strings with EDM. The siEDM algorithm builds an index structure by leveraging the idea behind the edit sensitive parsing (ESP), an efficient algorithm enabling approximately computing EDM with guarantees of upper and lower bounds for the exact EDM. siEDM efficiently prunes the space for searching query strings by the proposed method, which enables fast query searches with the same guarantee as ESP. We experimentally tested the ability of siEDM to index and search strings on benchmark datasets, and we showed siEDM's efficiency.Comment: 23 page

Improving the accuracy and efficiency of time-resolved electronic spectra calculations: Cellular dephasing representation with a prefactor

Time-resolved electronic spectra can be obtained as the Fourier transform of a special type of time correlation function known as fidelity amplitude, which, in turn, can be evaluated approximately and efficiently with the dephasing representation. Here we improve both the accuracy of this approximation---with an amplitude correction derived from the phase-space propagator---and its efficiency---with an improved cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. We demonstrate the advantages of the new methodology by computing dispersed time-resolved stimulated emission spectra in the harmonic potential, pyrazine, and the NCO molecule. In contrast, we show that in strongly chaotic systems such as the quartic oscillator the original dephasing representation is more appropriate than either the cellular or prefactor-corrected methods.Comment: submitte

Approximation Algorithms for Route Planning with Nonlinear Objectives

We consider optimal route planning when the objective function is a general nonlinear and non-monotonic function. Such an objective models user behavior more accurately, for example, when a user is risk-averse, or the utility function needs to capture a penalty for early arrival. It is known that as nonlinearity arises, the problem becomes NP-hard and little is known about computing optimal solutions when in addition there is no monotonicity guarantee. We show that an approximately optimal non-simple path can be efficiently computed under some natural constraints. In particular, we provide a fully polynomial approximation scheme under hop constraints. Our approximation algorithm can extend to run in pseudo-polynomial time under a more general linear constraint that sometimes is useful. As a by-product, we show that our algorithm can be applied to the problem of finding a path that is most likely to be on time for a given deadline.Comment: 9 pages, 2 figures, main part of this paper is to be appear in AAAI'1

Faster all-pairs shortest paths via circuit complexity

We present a new randomized method for computing the min-plus product (a.k.a., tropical product) of two $n \times n$ matrices, yielding a faster algorithm for solving the all-pairs shortest path problem (APSP) in dense $n$-node directed graphs with arbitrary edge weights. On the real RAM, where additions and comparisons of reals are unit cost (but all other operations have typical logarithmic cost), the algorithm runs in time $$\frac{n^3}{2^{\Omega(\log n)^{1/2}}}$$ and is correct with high probability. On the word RAM, the algorithm runs in $n^3/2^{\Omega(\log n)^{1/2}} + n^{2+o(1)}\log M$ time for edge weights in $([0,M] \cap {\mathbb Z})\cup\{\infty\}$. Prior algorithms used either $n^3/(\log^c n)$ time for various $c \leq 2$, or $O(M^{\alpha}n^{\beta})$ time for various $\alpha > 0$ and $\beta > 2$. The new algorithm applies a tool from circuit complexity, namely the Razborov-Smolensky polynomials for approximately representing ${\sf AC}^0[p]$ circuits, to efficiently reduce a matrix product over the $(\min,+)$ algebra to a relatively small number of rectangular matrix products over ${\mathbb F}_2$, each of which are computable using a particularly efficient method due to Coppersmith. We also give a deterministic version of the algorithm running in $n^3/2^{\log^{\delta} n}$ time for some $\delta > 0$, which utilizes the Yao-Beigel-Tarui translation of ${\sf AC}^0[m]$ circuits into "nice" depth-two circuits.Comment: 24 pages. Updated version now has slightly faster running time. To appear in ACM Symposium on Theory of Computing (STOC), 201