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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 Adaptive Multi-Round Allocation with Stochastic Arrivals The tractability landscape of diffusion alignment: regularization, rewards, and computational primitives Mistake-Bounded Language Generation Positional LSH: Binary Block Matrix Approximation for Attention with Linear Biases Learning-Augmented Scalable Linear Assignment Problem Optimization via Neural Dual Warm-Starts A Note on Non-Negative $L_1$-Approximating Polynomials Curvature Beyond Positivity: Greedy Guarantees for Arbitrary Submodular Functions Convex Optimization with Nested Evolving Feasible Sets On the Complexity of the Matching Problem of Regular Expressions with Backreferences Simple KNN-Based Outlier Detection Achieves Robust Clustering Online Allocation with Unknown Shared Supply Equivalence of Coarse and Fine-Grained Models for Learning with Distribution Shift Accelerated Relax-and-Round for Concave Coverage Problems Contrastive Identification and Generation in the Limit Quantizing With Randomized Hadamard Transforms: Efficient Heuristic Now Proven Nearly Optimal Attention Coresets On Computing Total Variation Distance Between Mixtures of Product Distributions Exact and Approximate Algorithms for Polytree Learning Provable Accuracy Collapse in Embedding-Based Representations under Dimensionality Mismatch New Bounds for Kernel Sums via Fast Spherical Embeddings Unlearning Offline Stochastic Multi-Armed Bandits Matroid Algorithms Under Size-Sensitive Independence Oracles On the Learning Curves of Revenue Maximization Asymptotically Robust Learning-Augmented Algorithms for Preemptive FIFO Buffer Management Flashback: A Reversible Bilateral Run-Peeling Decomposition of Strings Incremental Strongly Connected Components with Predictions Characterizing Admissible Objective Functions for Hierarchical Clustering Well-Conditioned Oblivious Perturbations in Linear Space Mathematical Foundations for Peer-to-Peer Lattice Computation Graph Neural Network-Informed Predictive Flows for Faster Ford-Fulkerson and PAC-Learnability A weighted angle distance on strings Towards Universal Convergence of Backward Error in Linear System Solvers Constant-Factor Approximations for Doubly Constrained Fair k-Center, k-Median and k-Means Tight Bounds for Learning Polyhedra with a Margin Efficiency of Proportional Mechanisms in Online Auto-Bidding Advertising Skyline-First Traversal as a Control Mechanism for Multi-Criteria Graph Search Constant-Factor Approximation for the Uniform Decision Tree Limited Perfect Monotonical Surrogates constructed using low-cost recursive linkage discovery with guaranteed output Query Lower Bounds for Diffusion Sampling Early Pruning for Public Transport Routing Adapting Dijkstra for Buffers and Unlimited Transfers Exploiting Low-Rank Structure in Max-K-Cut Problems Partial Optimality in the Preordering Problem High-accuracy log-concave sampling with stochastic queries Learning to Approximate Uniform Facility Location via Graph Neural Networks Linear Regression with Unknown Truncation Beyond Gaussian Features Adaptive Power Iteration Method for Differentially Private PCA Finite and Corruption-Robust Regret Bounds in Online Inverse Linear Optimization under M-Convex Action Sets Learning Mixture Models via Efficient High-dimensional Sparse Fourier Transforms Variance Computation for Weighted Model Counting with Knowledge Compilation Approach Deterministic Coreset for Lp Subspace Online Algorithms for Repeated Optimal Stopping: Balancing Baseline Guarantees and Regret Learned Static Function Data Structures Optimal hypersurface decision trees A Perfectly Truthful Calibration Measure The Geometry of LLM Quantization: GPTQ as Babai's Nearest Plane Algorithm Best Agent Identification for General Game Playing A Faster Generalized Two-Stage Approximate Top-K Fast and Simple Densest Subgraph with Predictions Smoothed Analysis of Learning from Positive Samples Ineffectiveness for Search and Undecidability of PCSP Meta-Problems Sample-Efficient Optimization over Generative Priors via Coarse Learnability Efficient distributional regression trees learning algorithms for calibrated non-parametric probabilistic forecasts Testing Noise Assumptions of Learning Algorithms Testing Support Size More Efficiently Than Learning Histograms Sharper Bounds for Chebyshev Moment Matching, with Applications Expander Hierarchies for Normalized Cuts on Graphs Multilayer Correlation Clustering Efficient Parameter Estimation of Truncated Boolean Product Distributions Faster Hamiltonian Monte Carlo by Learning Leapfrog Scale: a self-calibrated randomized solution
Parallelism and Time in Hierarchical Self-Assembly
Ho-Lin Chen, David Doty · 2011-04-28 · via cs.DS updates on arXiv.org

We study the role that parallelism plays in time complexity of Winfree's abstract Tile Assembly Model (aTAM), a model of molecular algorithmic self-assembly. In the "hierarchical" aTAM, two assemblies, both consisting of multiple tiles, are allowed to aggregate together, whereas in the "seeded" aTAM, tiles attach one at a time to a growing assembly. Adleman, Cheng, Goel, and Huang ("Running Time and Program Size for Self-Assembled Squares", STOC 2001) showed how to assemble an n x n square in O(n) time in the seeded aTAM using O(log n / log log n) unique tile types, where both of these parameters are optimal. They asked whether the hierarchical aTAM could allow a tile system to use the ability to form large assemblies in parallel before they attach to break the Omega(n) lower bound for assembly time. We show that there is a tile system with the optimal O(log n / log log n) tile types that assembles an n x n square using O(log^2 n) parallel "stages", which is close to the optimal Omega(log n) stages, forming the final n x n square from four n/2 x n/2 squares, which are themselves recursively formed from n/4 x n/4 squares, etc. However, despite this nearly maximal parallelism, the system requires superlinear time to assemble the square. We extend the definition of *partial order tile systems* studied by Adleman et al. in a natural way to hierarchical assembly and show that no hierarchical partial order tile system can build any shape with diameter N in less than time Omega(N), demonstrating that in this case the hierarchical model affords no speedup whatsoever over the seeded model. We strengthen the Omega(N) time lower bound for deterministic seeded systems of Adleman et al. to nondeterministic seeded systems. Finally, we show that for infinitely many n, a tile system can assemble an n x n' rectangle, with n > n', in time O(n^{4/5} log n), breaking the linear-time lower bound.