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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
Fast Iteration of Spaced k-mers
Lucas Czech · 2026-03-26 · via cs.DS updates on arXiv.org

Background: Short sequence substrings of a fixed length k, called k-mers, are a ubiquitous computational primitive in bioinformatics, used across sequence indexing, read mapping, genome assembly, metagenomic classification, and comparative genomics. Spaced k-mers generalize this concept by selecting only a subset of positions within a k-mer, improving robustness to mismatches and sequencing errors. While k-mers are computationally highly efficient, spaced k-mers require additional work to be extracted from a sequence, which has slowed down existing methods. Results: We present a collection of efficient algorithms for extracting spaced k-mers from nucleotide sequences, optimized for different hardware architectures. They are based on bit manipulation instructions at CPU level, making them both simpler to implement and up to an order of magnitude faster than existing methods. We further evaluate common pitfalls in k-mer processing, which can cause substantial inefficiencies. Conclusions: Our approaches allow the utilization of spaced k-mers in high-performance bioinformatics applications without major performance degradation compared to regular k-mers, achieving a throughput of up to 750MB of sequence data per second per core. Availability: The implementation in C++20 is published under the MIT license, and freely available at https://github.com/lczech/fisk