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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
Faster PBWT prefix-array access via batching
Travis Gagie · 2026-05-15 · via cs.DS updates on arXiv.org

The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes in a panel. There are generally two steps in this process: first we find the maximal substrings of the query that occur in the same positions in haplotypes in the panel and then, for each such substring, report the haplotypes in the panel in which the substring occurs in the same position as in the query. Very recently, Bonizzoni, Gagie and Gao (2026) gave two time-space tradeoffs for the second step: they use either $O ((r + h) \log n)$ bits and $O (\log \log \min (h, \ell) + k)$ time to report $k$ haplotypes in the panel, or $O (r \log h + h \log n)$ bits and $O (k \log \log h)$ time, where $r$ is the number of runs in the panel's PBWT and $h$, $\ell$ and $n = h \ell$ are the panel's height, length and size, respectively. We observe here that if we can batch queries until we have found $r \lg (h) / \lg r$ such substrings and we report an average of at least $\lg (r) / \lg h$ haplotypes in the panel per substring, for example, then for the second step we can easily use $O (r \log h)$ bits and constant time to report each haplotype. Our approach is based on an algorithm for constructing the prefix arrays quickly from the PBWT, which may be of independent interest.