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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
Nucleotide String Indexing using Range Matching
Alon Rashelbach, Ori Rottensterich, Mark Silberstien · 2023-08-06 · via cs.DS updates on arXiv.org

The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both memory efficient and fast. We observe that nucleotide sequences can be represented as integer ranges and leverage a range-matching algorithm based on neural networks to perform the lookup. We prototype Ranger in software and integrate it into the popular Minimap2 tool. Ranger achieves almost identical end-to-end performance as the original Minimap2, while occupying 1.7$\times$ and 1.2$\times$ less memory for short- and long-reads, respectively. With a limited memory capacity, Ranger achieves up to 4.3$\times$ speedup for short reads compared to FM-Index, and up to 4.2$\times$ and 1.8$\times$ speedups for short- and long-reads, compared to hash-tables. Ranger opens up new opportunities in the context of hardware acceleration by reducing the memory footprint of long-seed indexes used in state-of-the-art alignment accelerators by up to 23$\times$ which results with 3$\times$ faster alignment and negligible accuracy degradation. Moreover, its worst case memory bandwidth and latency can be bounded in advance without the need to inflate DRAM capacity.