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cs.DS updates on arXiv.org

PAC Learning with Bandit Feedback: Sharp Sample Complexity in the Realizable Setting Algorithms with Polynomially-Improved Approximation Factors for the $2 \rightarrow q$ Norm, and Applications A computational phase transition for learning-to-sample from Ising models Covering vertices by sequential stars Fermi-Dirac machines as quantizations of neurons A Comprehensive Evaluation of Vertex Elimination Algorithms for Algorithmic Differentiation A Tight Bound on Localization of Electrical Flows Optimal Dimension-Free Sampling for Regularized Classification Reducing the Randomness in Partition Oracles for Bounded Degree Minor-Free Graphs Beyond the Half-Approximation: Fair and Efficient Online Class Matching Efficient Uniform Sampling of Surjections via their Profiles Tractable Maximization of Budgeted Phylogenetic Diversity on Networks Utilizing Node Scanwidth Fairness in Aggregation: Optimal Top-$k$ and Improved Full Ranking Learning-Augmented Online Scheduling with Parsimonious Preemption Entropy Equivalence Testing Lumberjack: Better Differentially Private Random Forests through Heavy Hitter Detection in Trees The Secretary Problem with a Stochastic Precursor Polynomial-Time Robust Multiclass Linear Classification under Gaussian Marginals Efficient Banzhaf-Based Data Valuation for $k$-Nearest Neighbors Classification Block-Sphere Vector Quantization An Approximation Algorithm for Graph Label Selection Iterative Chow Filtering for Learning with Distribution Shift Complexity of Non-Log-Concave Sampling in Fisher Information Stochastic Matching via Local Sparsification Finite Sample Bounds for Learning with Score Matching What is Learnable in Valiant's Theory of the Learnable? Provable Quantization with Randomized Hadamard Transform Min-Max Optimization Requires Exponentially Many Queries Fast and Compact Graph Cuts for the Boykov-Kolmogorov Algorithm A proximal gradient algorithm for composite log-concave sampling
Space-Efficient Construction of Compressed Suffix Trees
Nicola Prezza, Giovanna Rosone · 2019-08-12 · via cs.DS updates on arXiv.org

We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $σ$ be the alphabet size. We first provide two algorithms that enumerate all LCP values and suffix tree intervals in $O(n\logσ)$ time using just $o(n\logσ)$ bits of working space on top of the input BWT. Using these algorithms as building blocks, for any parameter $0 < ε\leq 1$ we show how to build the PLCP bitvector and the balanced parentheses representation of the suffix tree topology in $O\left(n(\logσ+ ε^{-1}\cdot \log\log n)\right)$ time using at most $n\logσ\cdot(ε+ o(1))$ bits of working space on top of the input BWT and the output. In particular, this implies that we can build a compressed suffix tree from the BWT using just succinct working space (i.e. $o(n\logσ)$ bits) and any time in $Θ(n\logσ) + ω(n\log\log n)$. This improves the previous most space-efficient algorithms, which worked in $O(n)$ bits and $O(n\log n)$ time. We also consider the problem of merging BWTs of string collections, and provide a solution running in $O(n\logσ)$ time and using just $o(n\logσ)$ bits of working space. An efficient implementation of our LCP construction and BWT merge algorithms use (in RAM) as few as $n$ bits on top of a packed representation of the input/output and process data as fast as $2.92$ megabases per second.