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The suffix array $SA[1..n]$ of a text $T$ of length $n$ is a permutation of $\{1,\ldots,n\}$ describing the lexicographical ordering of suffixes of $T$, and it is considered to be among of the most important data structures in string algorithms, with dozens of applications in data compression, bioinformatics, and information retrieval. One of the biggest drawbacks of the suffix array is that it is very difficult to maintain under text updates: even a single character substitution can completely change the contents of the suffix array. Thus, the suffix array of a dynamic text is modelled using suffix array queries, which return the value $SA[i]$ given any $i\in[1..n]$. Prior to this work, the fastest dynamic suffix array implementations were by Amir and Boneh. At ISAAC 2020, they showed how to answer suffix array queries in $\tilde{O}(k)$ time, where $k\in[1..n]$ is a trade-off parameter, with $\tilde{O}(\frac{n}{k})$-time text updates. In a very recent preprint [2021], they also provided a solution with $O(\log^5 n)$-time queries and $\tilde{O}(n^{2/3})$-time updates. We propose the first data structure that supports both suffix array queries and text updates in $O({\rm polylog}\,n)$ time (achieving $O(\log^4 n)$ and $O(\log^{3+o(1)} n)$ time, respectively). Our data structure is deterministic and the running times for all operations are worst-case. In addition to the standard single-character edits (character insertions, deletions, and substitutions), we support (also in $O(\log^{3+o(1)} n)$ time) the "cut-paste" operation that moves any (arbitrarily long) substring of $T$ to any place in $T$. We complement our structure by a hardness result: unless the Online Matrix-Vector Multiplication (OMv) Conjecture fails, no data structure with $O({\rm polylog}\,n)$-time suffix array queries can support the "copy-paste" operation in $O(n^{1-\epsilon})$ time for any $\epsilon>0$.

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Explanation:生物(wu)信息學。 Publisher:Oxford University Press。 SIT:

We study reinforcement learning for two-player zero-sum Markov games with simultaneous moves in the finite-horizon setting, where the transition kernel of the underlying Markov games can be parameterized by a linear function over the current state, both players' actions and the next state. In particular, we assume that we can control both players and aim to find the Nash Equilibrium by minimizing the duality gap. We propose an algorithm Nash-UCRL based on the principle "Optimism-in-Face-of-Uncertainty". Our algorithm only needs to find a Coarse Correlated Equilibrium (CCE), which is computationally efficient. Specifically, we show that Nash-UCRL can provably achieve an $\tilde{O}(dH\sqrt{T})$ regret, where $d$ is the linear function dimension, $H$ is the length of the game and $T$ is the total number of steps in the game. To assess the optimality of our algorithm, we also prove an $\tilde{\Omega}( dH\sqrt{T})$ lower bound on the regret. Our upper bound matches the lower bound up to logarithmic factors, which suggests the optimality of our algorithm.

We describe a polynomial-time algorithm which, given a graph $G$ with treewidth $t$, approximates the pathwidth of $G$ to within a ratio of $O(t\sqrt{\log t})$. This is the first algorithm to achieve an $f(t)$-approximation for some function $f$. Our approach builds on the following key insight: every graph with large pathwidth has large treewidth or contains a subdivision of a large complete binary tree. Specifically, we show that every graph with pathwidth at least $th+2$ has treewidth at least $t$ or contains a subdivision of a complete binary tree of height $h+1$. The bound $th+2$ is best possible up to a multiplicative constant. This result was motivated by, and implies (with $c=2$), the following conjecture of Kawarabayashi and Rossman (SODA'18): there exists a universal constant $c$ such that every graph with pathwidth $\Omega(k^c)$ has treewidth at least $k$ or contains a subdivision of a complete binary tree of height $k$. Our main technical algorithm takes a graph $G$ and some (not necessarily optimal) tree decomposition of $G$ of width $t'$ in the input, and it computes in polynomial time an integer $h$, a certificate that $G$ has pathwidth at least $h$, and a path decomposition of $G$ of width at most $(t'+1)h+1$. The certificate is closely related to (and implies) the existence of a subdivision of a complete binary tree of height $h$. The approximation algorithm for pathwidth is then obtained by combining this algorithm with the approximation algorithm of Feige, Hajiaghayi, and Lee (STOC'05) for treewidth.

This paper establishes the asymptotic independence between the quadratic form and maximum of a sequence of independent random variables. Based on this theoretical result, we find the asymptotic joint distribution for the quadratic form and maximum, which can be applied into the high-dimensional testing problems. By combining the sum-type test and the max-type test, we propose the Fisher's combination tests for the one-sample mean test and two-sample mean test. Under this novel general framework, several strong assumptions in existing literature have been relaxed. Monte Carlo simulation has been done which shows that our proposed tests are strongly robust to both sparse and dense data.

We extend the Deep Galerkin Method (DGM) introduced in Sirignano and Spiliopoulos (2018)} to solve a number of partial differential equations (PDEs) that arise in the context of optimal stochastic control and mean field games. First, we consider PDEs where the function is constrained to be positive and integrate to unity, as is the case with Fokker-Planck equations. Our approach involves reparameterizing the solution as the exponential of a neural network appropriately normalized to ensure both requirements are satisfied. This then gives rise to nonlinear a partial integro-differential equation (PIDE) where the integral appearing in the equation is handled by a novel application of importance sampling. Secondly, we tackle a number of Hamilton-Jacobi-Bellman (HJB) equations that appear in stochastic optimal control problems. The key contribution is that these equations are approached in their unsimplified primal form which includes an optimization problem as part of the equation. We extend the DGM algorithm to solve for the value function and the optimal control \simultaneously by characterizing both as deep neural networks. Training the networks is performed by taking alternating stochastic gradient descent steps for the two functions, a technique inspired by the policy improvement algorithms (PIA).

Many existing algorithms for streaming geometric data analysis have been plagued by exponential dependencies in the space complexity, which are undesirable for processing high-dimensional data sets. In particular, once $d\geq\log n$, there are no known non-trivial streaming algorithms for problems such as maintaining convex hulls and L\"owner-John ellipsoids of $n$ points, despite a long line of work in streaming computational geometry since [AHV04]. We simultaneously improve these results to $\mathrm{poly}(d,\log n)$ bits of space by trading off with a $\mathrm{poly}(d,\log n)$ factor distortion. We achieve these results in a unified manner, by designing the first streaming algorithm for maintaining a coreset for $\ell_\infty$ subspace embeddings with $\mathrm{poly}(d,\log n)$ space and $\mathrm{poly}(d,\log n)$ distortion. Our algorithm also gives similar guarantees in the \emph{online coreset} model. Along the way, we sharpen results for online numerical linear algebra by replacing a log condition number dependence with a $\log n$ dependence, answering a question of [BDM+20]. Our techniques provide a novel connection between leverage scores, a fundamental object in numerical linear algebra, and computational geometry. For $\ell_p$ subspace embeddings, we give nearly optimal trade-offs between space and distortion for one-pass streaming algorithms. For instance, we give a deterministic coreset using $O(d^2\log n)$ space and $O((d\log n)^{1/2-1/p})$ distortion for $p>2$, whereas previous deterministic algorithms incurred a $\mathrm{poly}(n)$ factor in the space or the distortion [CDW18]. Our techniques have implications in the offline setting, where we give optimal trade-offs between the space complexity and distortion of subspace sketch data structures. To do this, we give an elementary proof of a "change of density" theorem of [LT80] and make it algorithmic.

Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the counting of such substrings, and the second problem being the problem of listing all such substrings. In this paper, we describe linear-time, linear-space suffix tree-based algorithms for both problems. More specifically, we describe an $O(|T| + |P|)$ time algorithm for the counting problem, and an $O(|T| + |P| + \#(ans))$ time algorithm for the listing problem, where $\#(ans)$ refers to the number of strings being listed in total, and $|P|$ refers to the total length of the strings in $P$. We also consider the reversed version of the problems, where one prefix condition string and multiple suffix condition strings are given instead, and similarly describe linear-time, linear-space algorithms to solve them.

Computing a dense subgraph is a fundamental problem in graph mining, with a diverse set of applications ranging from electronic commerce to community detection in social networks. In many of these applications, the underlying context is better modelled as a weighted hypergraph that keeps evolving with time. This motivates the problem of maintaining the densest subhypergraph of a weighted hypergraph in a {\em dynamic setting}, where the input keeps changing via a sequence of updates (hyperedge insertions/deletions). Previously, the only known algorithm for this problem was due to Hu et al. [HWC17]. This algorithm worked only on unweighted hypergraphs, and had an approximation ratio of $(1+\epsilon)r^2$ and an update time of $O(\text{poly} (r, \log n))$, where $r$ denotes the maximum rank of the input across all the updates. We obtain a new algorithm for this problem, which works even when the input hypergraph is weighted. Our algorithm has a significantly improved (near-optimal) approximation ratio of $(1+\epsilon)$ that is independent of $r$, and a similar update time of $O(\text{poly} (r, \log n))$. It is the first $(1+\epsilon)$-approximation algorithm even for the special case of weighted simple graphs. To complement our theoretical analysis, we perform experiments with our dynamic algorithm on large-scale, real-world data-sets. Our algorithm significantly outperforms the state of the art [HWC17] both in terms of accuracy and efficiency.

For any small positive real $\varepsilon$ and integer $t > \frac{1}{\varepsilon}$, we build a graph with a vertex deletion set of size $t$ to a tree, and twin-width greater than $2^{(1-\varepsilon) t}$. In particular, this shows that the twin-width is sometimes exponential in the treewidth, in the so-called oriented twin-width and grid number, and that adding an apex may multiply the twin-width by at least $2-\varepsilon$. Except for the one in oriented twin-width, these lower bounds are essentially tight.

Dynamic Linear Models (DLMs) are commonly employed for time series analysis due to their versatile structure, simple recursive updating, ability to handle missing data, and probabilistic forecasting. However, the options for count time series are limited: Gaussian DLMs require continuous data, while Poisson-based alternatives often lack sufficient modeling flexibility. We introduce a novel semiparametric methodology for count time series by warping a Gaussian DLM. The warping function has two components: a (nonparametric) transformation operator that provides distributional flexibility and a rounding operator that ensures the correct support for the discrete data-generating process. We develop conjugate inference for the warped DLM, which enables analytic and recursive updates for the state space filtering and smoothing distributions. We leverage these results to produce customized and efficient algorithms for inference and forecasting, including Monte Carlo simulation for offline analysis and an optimal particle filter for online inference. This framework unifies and extends a variety of discrete time series models and is valid for natural counts, rounded values, and multivariate observations. Simulation studies illustrate the excellent forecasting capabilities of the warped DLM. The proposed approach is applied to a multivariate time series of daily overdose counts and demonstrates both modeling and computational successes.

A palindromic substring $T[i.. j]$ of a string $T$ is said to be a shortest unique palindromic substring (SUPS) in $T$ for an interval $[p, q]$ if $T[i.. j]$ is a shortest one such that $T[i.. j]$ occurs only once in $T$, and $[i, j]$ contains $[p, q]$. The SUPS problem is, given a string $T$ of length $n$, to construct a data structure that can compute all the SUPSs for any given query interval. It is known that any SUPS query can be answered in $O(\alpha)$ time after $O(n)$-time preprocessing, where $\alpha$ is the number of SUPSs to output [Inoue et al., 2018]. In this paper, we first show that $\alpha$ is at most $4$, and the upper bound is tight. Also, we present an algorithm to solve the SUPS problem for a sliding window that can answer any query in $O(\log\log W)$ time and update data structures in amortized $O(\log\sigma)$ time, where $W$ is the size of the window, and $\sigma$ is the alphabet size. Furthermore, we consider the SUPS problem in the after-edit model and present an efficient algorithm. Namely, we present an algorithm that uses $O(n)$ time for preprocessing and answers any $k$ SUPS queries in $O(\log n\log\log n + k\log\log n)$ time after single character substitution. As a by-product, we propose a fully-dynamic data structure for range minimum queries (RmQs) with a constraint where the width of each query range is limited to polylogarithmic. The constrained RmQ data structure can answer such a query in constant time and support a single-element edit operation in amortized constant time.

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