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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
Approximating LCS and Alignment Distance over Multiple Se...
Debarati Das, Barna Saha · 2021-10-24 · via cs.DS updates on arXiv.org

We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the alignment distance (AD)). Multiple sequence alignment is a well-studied problem in bioinformatics and is used to identify regions of similarity among DNA, RNA, or protein sequences to detect functional, structural, or evolutionary relationships among them. It is known that exact computation of LCS or AD of $m$ sequences each of length $n$ requires $Θ(n^m)$ time unless the Strong Exponential Time Hypothesis is false. In this paper, we provide several results to approximate LCS and AD of multiple sequences. If the LCS of $m$ sequences each of length $n$ is $λn$ for some $λ\in [0,1]$, then in $\tilde{O}_m(n^{\lfloor\frac{m}{2}\rfloor+1})$ time, we can return a common subsequence of length at least $\frac{λ^2 n}{2+ε}$ for any arbitrary constant $ε>0$. It is possible to approximate the AD within a factor of two in time $\tilde{O}_m(n^{\lceil\frac{m}{2}\rceil})$. However, going below-2 approximation requires breaking the triangle inequality barrier which is a major challenge in this area. No such algorithm with a running time of $O(n^{αm})$ for any $α< 1$ is known. If the AD is $θn$, then we design an algorithm that approximates the AD within an approximation factor of $\left(2-\frac{3θ}{16}+ε\right)$ in $\tilde{O}_m(n^{\lfloor\frac{m}{2}\rfloor+2})$ time. Thus, if $θ$ is a constant, we get a below-two approximation in $\tilde{O}_m(n^{\lfloor\frac{m}{2}\rfloor+2})$ time. Moreover, we show if just one out of $m$ sequences is $(p,B)$-pseudorandom then, we get a below-2 approximation in $\tilde{O}_m(nB^{m-1}+n^{\lfloor \frac{m}{2}\rfloor+3})$ time irrespective of $θ$.