An Efficient Data Structure for Dynamic Two-Dimensional Reconfiguration

In the presence of dynamic insertions and deletions into a partially reconfigurable FPGA, fragmentation is unavoidable. This poses the challenge of developing efficient approaches to dynamic defragmentation and reallocation. One key aspect is to develop efficient algorithms and data structures that exploit the two-dimensional geometry of a chip, instead of just one. We propose a new method for this task, based on the fractal structure of a quadtree, which allows dynamic segmentation of the chip area, along with dynamically adjusting the necessary communication infrastructure. We describe a number of algorithmic aspects, and present different solutions. We also provide a number of basic simulations that indicate that the theoretical worst-case bound may be pessimistic.Comment: 11 pages, 12 figures; full version of extended abstract that appeared in ARCS 201

Computing the Longest Unbordered Substring

International audienceA substring of a string is unbordered if its only border is the empty string. The study of unbordered substrings goes back to the paper of Ehrenfeucht and Silberger [7]. The main focus of [7] and of subsequent papers was to elucidate the relationship between the longest unbordered substring and the minimal period of strings. In this paper, we consider the algorithmic problem of computing the longest unbordered substring of a string. The problem was introduced recently in [12], where the authors showed that the average-case running time of the simple, border-array based algorithm can be bounded by O(n 2 /σ 4) for σ being the size of the alphabet. (The worst-case running time remained O(n 2).) Here we propose two algorithms, both presenting substantial theoretical improvements to the result of [12]. The first algorithm has O(n log n) average-case running time and O(n 2) worst-case running time, and the second algorithm has O(n 1.5) worst-case running time

A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Faster algorithms for 1-mappability of a sequence

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y. We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n). We present two algorithms that require worst-case time O(mn) and O(n log^2 n), respectively, and space O(n), thus greatly improving the state of the art. Moreover, we present an algorithm that requires average-case time and space O(n) for integer alphabets if m = {\Omega}(log n/ log {\sigma}), where {\sigma} is the alphabet size

A general lower bound for collaborative tree exploration

We consider collaborative graph exploration with a set of $k$ agents. All agents start at a common vertex of an initially unknown graph and need to collectively visit all other vertices. We assume agents are deterministic, vertices are distinguishable, moves are simultaneous, and we allow agents to communicate globally. For this setting, we give the first non-trivial lower bounds that bridge the gap between small ($k \leq \sqrt n$) and large ($k \geq n$) teams of agents. Remarkably, our bounds tightly connect to existing results in both domains. First, we significantly extend a lower bound of $\Omega(\log k / \log\log k)$ by Dynia et al. on the competitive ratio of a collaborative tree exploration strategy to the range $k \leq n \log^c n$ for any $c \in \mathbb{N}$. Second, we provide a tight lower bound on the number of agents needed for any competitive exploration algorithm. In particular, we show that any collaborative tree exploration algorithm with $k = Dn^{1+o(1)}$ agents has a competitive ratio of $\omega(1)$, while Dereniowski et al. gave an algorithm with $k = Dn^{1+\varepsilon}$ agents and competitive ratio $O(1)$, for any $\varepsilon > 0$ and with $D$ denoting the diameter of the graph. Lastly, we show that, for any exploration algorithm using $k = n$ agents, there exist trees of arbitrarily large height $D$ that require $\Omega(D^2)$ rounds, and we provide a simple algorithm that matches this bound for all trees

Identification of the first surrogate agonists for the G protein-coupled receptor GPR132

We report the first pharmacological tool agonist for in vitro characterization of the orphan receptor GPR132, preliminary structure–activity relationships based on 32 analogs and a suggested binding mode from docking.M.A.S. was supported by a research scholarship from the Drug Research Academy and Novo Nordisk A/S. D.E.G. and H.B.-O. gratefully acknowledge financial support by the Carlsberg Foundation. D.E.G. and D.S.P. gratefully acknowledges financial support by the Lundbeck Foundation. Nils Nyberg is acknowledged for help with NMR spectroscopy. NMR equipment used in this work was purchased via a grant from The Lundbeck Foundation (R77-A6742).This is the accepted manuscript. The final version is available at http://pubs.rsc.org/en/Content/ArticleLanding/2015/RA/c5ra04804d#!divAbstract

Increasing vertical resolution in US models to improve track forecasts of Hurricane Joaquin with HWRF as an example

The atmosphere−ocean coupled Hurricane Weather Research and Forecast model (HWRF) developed at the National Centers for Environmental Prediction (NCEP) is used as an example to illustrate the impact of model vertical resolution on track forecasts of tropical cyclones. A number of HWRF forecasting experiments were carried out at different vertical resolutions for Hurricane Joaquin, which occurred from September 27 to October 8, 2015, in the Atlantic Basin. The results show that the track prediction for Hurricane Joaquin is much more accurate with higher vertical resolution. The positive impacts of higher vertical resolution on hurricane track forecasts suggest that National Oceanic and Atmospheric Administration/NCEP should upgrade both HWRF and the Global Forecast System to have more vertical levels

Fast Label Extraction in the CDAWG

The compact directed acyclic word graph (CDAWG) of a string $T$ of length $n$ takes space proportional just to the number $e$ of right extensions of the maximal repeats of $T$, and it is thus an appealing index for highly repetitive datasets, like collections of genomes from similar species, in which $e$ grows significantly more slowly than $n$. We reduce from $O(m\log{\log{n}})$ to $O(m)$ the time needed to count the number of occurrences of a pattern of length $m$, using an existing data structure that takes an amount of space proportional to the size of the CDAWG. This implies a reduction from $O(m\log{\log{n}}+\mathtt{occ})$ to $O(m+\mathtt{occ})$ in the time needed to locate all the $\mathtt{occ}$ occurrences of the pattern. We also reduce from $O(k\log{\log{n}})$ to $O(k)$ the time needed to read the $k$ characters of the label of an edge of the suffix tree of $T$, and we reduce from $O(m\log{\log{n}})$ to $O(m)$ the time needed to compute the matching statistics between a query of length $m$ and $T$, using an existing representation of the suffix tree based on the CDAWG. All such improvements derive from extracting the label of a vertex or of an arc of the CDAWG using a straight-line program induced by the reversed CDAWG.Comment: 16 pages, 1 figure. In proceedings of the 24th International Symposium on String Processing and Information Retrieval (SPIRE 2017). arXiv admin note: text overlap with arXiv:1705.0864

Quantum four-body system in D dimensions

By the method of generalized spherical harmonic polynomials, the Schr\"{o}dinger equation for a four-body system in $D$-dimensional space is reduced to the generalized radial equations where only six internal variables are involved. The problem on separating the rotational degrees of freedom from the internal ones for a quantum $N$-body system in $D$ dimensions is generally discussed.Comment: 19 pages, no figure, RevTex, Submitted to J. Math. Phy

Dynamical Measurements of Black Hole Masses in Four Brightest Cluster Galaxies at 100 Mpc

We present stellar kinematics and orbit superposition models for the central regions of four Brightest Cluster Galaxies (BCGs), based upon integral-field spectroscopy at Gemini, Keck, and McDonald Observatories. Our integral-field data span radii from < 100 pc to tens of kpc. We report black hole masses, M_BH, of 2.1 +/- 1.6 x 10^10 M_Sun for NGC 4889, 9.7 + 3.0 - 2.6 x 10^9 M_Sun for NGC 3842, and 1.3 + 0.5 - 0.4 x 10^9 M_Sun for NGC 7768. For NGC 2832 we report an upper limit of M_BH < 9 x 10^9 M_Sun. Stellar orbits near the center of each galaxy are tangentially biased, on comparable spatial scales to the galaxies' photometric cores. We find possible photometric and kinematic evidence for an eccentric torus of stars in NGC 4889, with a radius of nearly 1 kpc. We compare our measurements of M_BH to the predicted black hole masses from various fits to the relations between M_BH and stellar velocity dispersion, luminosity, or stellar mass. The black holes in NGC 4889 and NGC 3842 are significantly more massive than all dispersion-based predictions and most luminosity-based predictions. The black hole in NGC 7768 is consistent with a broader range of predictions.Comment: 24 pages, 18 figures. Accepted for publication in Ap