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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
On Minimizers of Minimum Density
Arseny Shur · 2025-06-06 · via cs.DS updates on arXiv.org

Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $σ$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $ρ$ on strings of length $k$ (also called $k$-mers). A string is processed by a sliding window algorithm that chooses, in each window of length $w+k-1$, its minimal $k$-mer with respect to $ρ$. A key characteristic of the minimizer is its density, which is the expected frequency of chosen $k$-mers among all $k$-mers in a random infinite $σ$-ary string. Minimizers of smaller density are preferred as they produce smaller samples with the same guarantee: each window is represented by a $k$-mer. The problem of finding a minimizer of minimum density for given input parameters $(σ,k,w)$ has a huge search space of $(σ^k)!$ and is representable by an ILP of size $\tildeΘ(σ^{k+w})$, which has worst-case solution time that is doubly-exponential in $(k+w)$ under standard complexity assumptions. We solve this problem in $w\cdot 2^{σ^k+O(k)}$ time and provide several additional tricks reducing the practical runtime and search space. As a by-product, we describe an algorithm computing the average density of a minimizer within the same time bound. Then we propose a novel method of studying minimizers via regular languages and show how to find, via the eigenvalue/eigenvector analysis over finite automata, minimizers with the minimal density in the asymptotic case $w\to\infty$. Implementing our algorithms, we compute the minimum density minimizers for $(σ,k)\in\{(2,2),(2,3),(2,4),(2,5),(4,2)\}$ and \textbf{all} $w\ge 2$. The obtained densities are compared against the average density and the theoretical lower bounds, including the new bound presented in this paper.