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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
Optimal Computation of Avoided Words
Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas · 2016-04-29 · via cs.DS updates on arXiv.org

The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $ρ$-avoided word in $x$ if $std(w) \leq ρ$, for a given threshold $ρ< 0$. Notice that such a word may be completely absent from $x$. Hence computing all such words naïvely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $ρ$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(σn)$-time and $O(σn)$-space algorithm to compute all $ρ$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $σ$. Furthermore, we provide a tight asymptotic upper bound for the number of $ρ$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation.