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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
Hardness of RNA Folding Problem with Four Symbols
Yi-Jun Chang · 2015-11-16 · via cs.DS updates on arXiv.org

An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA sequence. The problem is central in bioinformatics and has received much attention over the years. Abboud, Backurs, and Williams (FOCS 2015) demonstrated a conditional lower bound for a generalized version of the RNA folding problem based on a conjectured hardness of the $k$-clique problem. Their lower bound requires the RNA sequence to have at least 36 types of symbols, making the result not applicable to the RNA folding problem in real life (i.e., alphabet size 4). In this paper, we present an improved lower bound that works for the alphabet size 4 case. We also investigate the Dyck edit distance problem, which is a string problem closely related to RNA folding. We demonstrate a reduction from RNA folding to Dyck edit distance with alphabet size 10. This leads to a much simpler proof of the conditional lower bound for Dyck edit distance problem given by Abboud, Backurs, and Williams (FOCS 2015), and lowers the alphabet size requirement.