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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
R-enum Revisited: Speedup and Extension for Context-Sensi...
Kotaro Kimura, Tomohiro I · 2025-11-14 · via cs.DS updates on arXiv.org

Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the number of runs in the Burrows-Wheeler transform (BWT) of $T$. Given the run-length encoded BWT (RLBWT) of $T$, r-enum runs in $O(n \log \log_{w} (n/r))$ time in addition to the time linear to the number of output strings, where $w = Θ(\log n)$ is the word size. In this paper, we first improve the $O(n \log \log_{w} (n/r))$ term to $O(n)$. We next extend r-enum to compute other context-sensitive repeats such as near-supermaximal repeats (NSMRs) and supermaximal repeats, as well as the context diversity for every maximal repeat in the same complexities. Furthermore, we study net occurrences: An occurrence of a repeat is called a net occurrence if it is not covered by another repeat, and the net frequency of a repeat is the number of its net occurrences. With this terminology, an NSMR is a repeat with a positive net frequency. Given the RLBWT of $T$, we show how to compute the set $S^{nsmr}$ of all NSMRs in $T$ together with their net frequency/occurrences in $O(n)$ time and $O(r)$ space. We also show that an $O(r)$-space data structure can be built from the RLBWT to compute the net frequency/occurrences of any pattern in optimal time. The data structure is built in $O(r)$ space and in $O(n)$ time with high probability or deterministic $O(n + |S^{nsmr}| \log \log \min(σ, |S^{nsmr}|))$ time, where $σ\le r$ is the alphabet size of $T$. To achieve this, we prove that the total number of net occurrences is less than $2r$. With the duality between net occurrences and \emph{minimal unique substrings (MUSs)}, we get a new upper bound $2r$ of the number of MUSs in $T$, which may be of independent interest.