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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
Probabilistic RNA Designability via Interpretable Ensembl...
Tianshuo Zhou, David H. Mathews, Liang Huang · 2026-02-14 · via cs.DS updates on arXiv.org

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have focused primarily on minimum free energy (MFE)-based criteria, while ensemble-based notions of designability remain largely underexplored. To address this gap, we introduce a theory of ensemble approximation and a probability decomposition framework for bounding the folding probabilities of RNA structures in an explainable way. We further develop a linear-time dynamic programming algorithm that efficiently searches over exponentially many decompositions and identifies the optimal one that yields the tightest probabilistic bound for a given structure. Results: Applying our methods to both native and artificial RNA structures in the ArchiveII and Eterna100 benchmarks, we obtained probability bounds that are much tighter than prior approaches. In addition, our methods further provide anatomical tools for analyzing RNA structures and understanding the sources of design difficulty at the motif level. Availability: Source code and data are available at https://github.com/shanry/RNA-Undesign. Supplementary information: Supplementary text and data are available in a separate PDF.