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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
Large-Scale Pattern Search Using Reduced-Space On-Disk Su...
Simon Gog, Alistair Moffat, J. Shane Culpepper, Andrew Turpin, A · 2013-03-26 · via cs.DS updates on arXiv.org

The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix pointers. In this paper we describe a new two-level suffix array-based index structure that requires significantly less disk space than previous approaches. Key to the saving is the use of disk blocks that are based on prefixes rather than the more usual uniform-sampling approach, allowing reductions between blocks and subparts of other blocks. We also describe a new in-memory structure based on a condensed BWT string, and show that it allows common patterns to be resolved without access to the text. Experiments using 64 GB of English web text and a laptop computer with just 4 GB of main memory demonstrate the speed and versatility of the new approach. For this data the index is around one- third the size of previous two-level mechanisms; and the memory footprint of as little as 1% of the text size means that queries can be processed more quickly than is possible with a compact FM-INDEX.