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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
Computing Maximal Unique Matches with the r-index
Sara Giuliani, Giuseppe Romana, Massimiliano Rossi · 2022-05-03 · via cs.DS updates on arXiv.org

In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique Matches (MUMs) have proven themselves to be useful in multiple bioinformatic contexts, for example short-read alignment and multiple-genome alignment. However, standard techniques using suffix trees and FM-indexes do not scale to a pangenomic level. Recently, Gagie et al. [JACM 20] introduced the $r$-index that is a Burrows-Wheeler Transform (BWT)-based index able to handle hundreds of human genomes. Later, Rossi et al. [JCB 22] enabled the computation of MEMs using the $r$-index, and Boucher et al. [DCC 21] showed how to compute them in a streaming fashion. In this paper, we show how to augment Boucher et al.'s approach to enable the computation of MUMs on the $r$-index, while preserving the space and time bounds. We add additional $O(r)$ samples of the longest common prefix (LCP) array, where $r$ is the number of equal-letter runs of the BWT, that permits the computation of the second longest match of the pattern suffix with respect to the input text, which in turn allows the computation of candidate MUMs. We implemented a proof-of-concept of our approach, that we call mum-phinder, and tested on real-world datasets. We compared our approach with competing methods that are able to compute MUMs. We observe that our method is up to 8 times smaller, while up to 19 times slower when the dataset is not highly repetitive, while on highly repetitive data, our method is up to 6.5 times slower and uses up to 25 times less memory.