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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
Local Decodability of the Burrows-Wheeler Transform
Sandip Sinha, Omri Weinstein · 2018-08-13 · via cs.DS updates on arXiv.org

The Burrows-Wheeler Transform (BWT) is among the most influential discoveries in text compression and DNA storage. It is a reversible preprocessing step that rearranges an $n$-letter string into runs of identical characters (by exploiting context regularities), resulting in highly compressible strings, and is the basis of the \texttt{bzip} compression program. Alas, the decoding process of BWT is inherently sequential and requires $Ω(n)$ time even to retrieve a \emph{single} character. We study the succinct data structure problem of locally decoding short substrings of a given text under its \emph{compressed} BWT, i.e., with small additive redundancy $r$ over the \emph{Move-To-Front} (\texttt{bzip}) compression. The celebrated BWT-based FM-index (FOCS '00), as well as other related literature, yield a trade-off of $r=\tilde{O}(n/\sqrt{t})$ bits, when a single character is to be decoded in $O(t)$ time. We give a near-quadratic improvement $r=\tilde{O}(n\lg(t)/t)$. As a by-product, we obtain an \emph{exponential} (in $t$) improvement on the redundancy of the FM-index for counting pattern-matches on compressed text. In the interesting regime where the text compresses to $n^{1-o(1)}$ bits, these results provide an $\exp(t)$ \emph{overall} space reduction. For the local decoding problem of BWT, we also prove an $Ω(n/t^2)$ cell-probe lower bound for "symmetric" data structures. We achieve our main result by designing a compressed partial-sums (Rank) data structure over BWT. The key component is a \emph{locally-decodable} Move-to-Front (MTF) code: with only $O(1)$ extra bits per block of length $n^{Ω(1)}$, the decoding time of a single character can be decreased from $Ω(n)$ to $O(\lg n)$. This result is of independent interest in algorithmic information theory.