Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2402.13920

Practical algorithms for Hierarchical overlap graphs

Saumya Talera·Parth Bansal·Shabnam Khan·Shahbaz Khan
View original source ↗Read source document ↗Export metadata ↓

Abstract

Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute the source string efficiently, having a tradeoff between scalability and avoiding information loss. The scalable de Bruijn graphs come at the price of losing crucial overlap information. The complete overlap information is stored in overlap graphs using quadratic space. Hierarchical overlap graphs [IPL20] (HOG) overcome these limitations, avoiding information loss despite using linear space. After a series of suboptimal improvements, Khan and Park et al. simultaneously presented two optimal algorithms [CPM2021], where only the former was seemingly practical. We empirically analyze all the algorithms for computing Hierarchical overlap graphs, where the optimal algorithm~[CPM2021] outperforms the previous algorithms as expected. However, it is still based on relatively complex arguments for its formal proof and uses relatively complex data structures for its implementation. We present an intuitive algorithm, using only elementary arrays, which is also optimal. Our algorithm empirically proves even better for both time and memory over all the algorithms, highlighting its significance in both theory and practice. We further explore the applications of hierarchical overlap graphs to solve variants of suffix-prefix queries on a set of strings, recently studied by Loukides et al.~[CPM2023]. They presented state-of-the-art algorithms requiring complex black-box data structures, making them seemingly impractical. Our algorithms, despite failing to match their theoretical bounds, answer queries in $0.002$-$100~ms$ for datasets having around a billion characters.

Explore related subjects

cs.DS

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Saumya Talera, Parth Bansal, Shabnam Khan, Shahbaz Khan. 2024-09-23. Practical algorithms for Hierarchical overlap graphs. https://arxiv.org/abs/2402.13920

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Independent Set Reconfiguration via Dilworth Decompositions

The Token Jumping and Sliding Token problems are fundamental reconfiguration problems defined on the independent sets of an undirected graph. Given two independent sets $I$ and $J$, each of size $k$, these problems ask whether there exists a sequence of elementary operations transforming $I$ into $J$ such that every intermediate configuration is also an independent set of size $k$. Suppose a token is placed on each vertex of $I$: in Sliding Token, an operation moves a token from a vertex $u \in I$ to an adjacent vertex $v \notin I$; in Token Jumping, the token may instead move to any vertex $v \notin I$. While both problems are $\mathsf{PSPACE}$-complete on general graphs, polynomial-time algorithms for one or both variants have been developed for several graph classes, including trees, block graphs, bipartite permutation graphs, cographs, $P_4$-tidy graphs, and interval graphs. In this paper, we prove that both problems are solvable in polynomial time on threshold signed graphs, also known as Dilworth-2 graphs. A graph $G=(V,E)$ is a threshold signed graph if there exist a mapping $a:V\to\mathbb{R}$ and positive real constants $S,T>0$ such that $|a(v)|< \min\{S,T\}$ for all $v \in V$, and for any distinct vertices $u,v\in V$, $\{u,v\}\in E$ if and only if $|a(u)+a(v)|\ge S$ or $|a(u)-a(v)|\ge T$. More generally, we also show that Token Jumping can be solved in time $n^{O(\mathcal{D}(G))}$, where $\mathcal{D}(G)$ denotes the Dilworth number of $G$. Thus, Token Jumping belongs to $\mathsf{XP}$ when parameterised by the Dilworth number. This graph class is a subclass of permutation graphs, for which the complexity of these problems remains open, and is incomparable with the class of bipartite permutation graphs studied by Fox-Epstein et al. (ISAAC, 2015).

cs.DS↗
arXiv2026

Matrix Spencer: Eight Standard Deviations Suffice and an Almost-Linear Time Algorithm for Dense Input

The Matrix Spencer conjecture asserts that for all symmetric matrices $A_1,\ldots,A_n\in\mathbb{R}^{n\times n}$ with $\|A_i\|\le1$ there are signs $\varepsilon_1,\ldots,\varepsilon_n\in\{-1,1\}$ with $\|\sum_{i=1}^n\varepsilon_iA_i\|=O(\sqrt n)$. We prove it: a signing of discrepancy below $8\sqrt n$ always exists. We also give a randomized algorithm that finds a signing of discrepancy below $12\sqrt n$ with failure probability at most $p$. The algorithm uses $n^{3+o(1)}\operatorname{polylog}(1/p)$ arithmetic operations in the real-arithmetic model. This matches the size $n^3$ of the dense input up to subpolynomial factors. In the other direction, we prove that for every $n$ there are collections of symmetric matrices such that every signing has discrepancy at least $(2-o(1))\sqrt{n}$. We present three different proofs of the matrix Spencer conjecture. The key to every proof is a hereditary small-ball estimate. This is a lower bound on the Gaussian measure of the spectral body $\{x\in \mathbb{R}^n:\|\sum_ix_iA_i\|\le R\}$ that holds for every subfamily of the matrices. The other ingredient turns that Gaussian measure into a partial signing. We give three approaches to obtain such a signing. The first one covers the cube by partially signed faces through Gaussian concentration with a constant $7\cdot10^9$. The second proof replaces the covering by a projection lemma with explicit parameters for a constant $156000$. The third proof turns Gaussian measure into signs by a lossless coding, with no union bound. It proves the estimate at the right radius with smooth spectral barriers and certified coefficients. It gives a constant below $7.88$. For algorithms, the main idea is to project Gaussian points onto a smoothed spectral body. The $n^{3+o(1)}$ time algorithm tracks the Gibbs matrix of that body across coordinate-descent steps with sketched increments and random refreshes.

cs.DS↗
arXiv2026

On Deterministically Computing Total Variation Distance via Zonotope Compression

We study deterministic relative approximation of the total variation distance between high-dimensional distributions given by succinct descriptions. We develop an abstract deterministic approximation framework based on representing the total variation distance as a support function of a low-dimensional zonotope. As applications, we obtain FPTASs for several models. Given two mixtures of product distributions over $[q]^n$ with a total of $K$ component distributions, our algorithm approximates their TV-distance within a factor of $1+\varepsilon$ in time $\widetilde O_K(nq(n/\varepsilon)^{2K})$. We also give an FPTAS for mixtures of $n$-step Markov chains over $[q]^n$ with a total of $K$ component distributions, with running time $\widetilde O_K(nq^2(n/\varepsilon)^{2K})$. Finally, for two latent-tree Ising models with the same underlying tree topology, we give an FPTAS for the TV-distance between their leaf marginals in time $O(|V|^{13}\varepsilon^{-12})$.

cs.DS↗