The streaming kk-mismatch problem

We consider the streaming complexity of a fundamental task in approximate pattern matching: the $k$-mismatch problem. It asks to compute Hamming distances between a pattern of length $n$ and all length-$n$ substrings of a text for which the Hamming distance does not exceed a given threshold $k$. In our problem formulation, we report not only the Hamming distance but also, on demand, the full \emph{mismatch information}, that is the list of mismatched pairs of symbols and their indices. The twin challenges of streaming pattern matching derive from the need both to achieve small working space and also to guarantee that every arriving input symbol is processed quickly. We present a streaming algorithm for the $k$-mismatch problem which uses $O(k\log{n}\log\frac{n}{k})$ bits of space and spends \ourcomplexity time on each symbol of the input stream, which consists of the pattern followed by the text. The running time almost matches the classic offline solution and the space usage is within a logarithmic factor of optimal. Our new algorithm therefore effectively resolves and also extends an open problem first posed in FOCS'09. En route to this solution, we also give a deterministic $O( k (\log \frac{n}{k} + \log |\Sigma|) )$-bit encoding of all the alignments with Hamming distance at most $k$ of a length-$n$ pattern within a text of length $O(n)$. This secondary result provides an optimal solution to a natural communication complexity problem which may be of independent interest.Comment: 27 page

A Dialogue of Multipoles: Matched Asymptotic Expansion for Caged Black Holes

No analytic solution is known to date for a black hole in a compact dimension. We develop an analytic perturbation theory where the small parameter is the size of the black hole relative to the size of the compact dimension. We set up a general procedure for an arbitrary order in the perturbation series based on an asymptotic matched expansion between two coordinate patches: the near horizon zone and the asymptotic zone. The procedure is ordinary perturbation expansion in each zone, where additionally some boundary data comes from the other zone, and so the procedure alternates between the zones. It can be viewed as a dialogue of multipoles where the black hole changes its shape (mass multipoles) in response to the field (multipoles) created by its periodic "mirrors", and that in turn changes its field and so on. We present the leading correction to the full metric including the first correction to the area-temperature relation, the leading term for black hole eccentricity and the "Archimedes effect". The next order corrections will appear in a sequel. On the way we determine independently the static perturbations of the Schwarzschild black hole in dimension d>=5, where the system of equations can be reduced to "a master equation" - a single ordinary differential equation. The solutions are hypergeometric functions which in some cases reduce to polynomials.Comment: 47 pages, 12 figures, minor corrections described at the end of the introductio

The Factorized S-Matrix of CFT/AdS

We argue that the recently discovered integrability in the large-N CFT/AdS system is equivalent to diffractionless scattering of the corresponding hidden elementary excitations. This suggests that, perhaps, the key tool for finding the spectrum of this system is neither the gauge theory's dilatation operator nor the string sigma model's quantum Hamiltonian, but instead the respective factorized S-matrix. To illustrate the idea, we focus on the closed fermionic su(1|1) sector of the N=4 gauge theory. We introduce a new technique, the perturbative asymptotic Bethe ansatz, and use it to extract this sector's three-loop S-matrix from Beisert's involved algebraic work on the three-loop su(2|3) sector. We then show that the current knowledge about semiclassical and near-plane-wave quantum strings in the su(2), su(1|1) and sl(2) sectors of AdS_5 x S^5 is fully consistent with the existence of a factorized S-matrix. Analyzing the available information, we find an intriguing relation between the three associated S-matrices. Assuming that the relation also holds in gauge theory, we derive the three-loop S-matrix of the sl(2) sector even though this sector's dilatation operator is not yet known beyond one loop. The resulting Bethe ansatz reproduces the three-loop anomalous dimensions of twist-two operators recently conjectured by Kotikov, Lipatov, Onishchenko and Velizhanin, whose work is based on a highly complex QCD computation of Moch, Vermaseren and Vogt.Comment: 38 pages, LaTeX, JHEP3.cl

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Inferring Algebraic Effects

We present a complete polymorphic effect inference algorithm for an ML-style language with handlers of not only exceptions, but of any other algebraic effect such as input & output, mutable references and many others. Our main aim is to offer the programmer a useful insight into the effectful behaviour of programs. Handlers help here by cutting down possible effects and the resulting lengthy output that often plagues precise effect systems. Additionally, we present a set of methods that further simplify the displayed types, some even by deliberately hiding inferred information from the programmer

One-loop quantization of rigid spinning strings in AdS3×S3×T4AdS_3 \times S^3 \times T^4 with mixed flux

We compute the one-loop correction to the classical dispersion relation of rigid closed spinning strings with two equal angular momenta in the $AdS_3 \times S^3 \times T^4$ background supported with a mixture of R-R and NS-NS three-form fluxes. This analysis is extended to the case of two arbitrary angular momenta in the pure NS-NS limit. We perform this computation by means of two different methods. The first method relies on the Euler-Lagrange equations for the quadratic fluctuations around the classical solution, while the second one exploits the underlying integrability of the problem through the finite-gap equations. We find that the one-loop correction vanishes in the pure NS-NS limit.Comment: 35 pages. v2: Minor changes and references updated. v3: Published versio