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1. Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants

   https://doi.org/10.1186/s13015-024-00262-6  

   Qiu, Yutong; Shen, Yihang; Kingsford, Carl (December 2024, Algorithms for Molecular Biology)

   Abstract The graph traversal edit distance (GTED), introduced by Ebrahimpour Boroojeny et al. (2018), is an elegant distance measure defined as the minimum edit distance between strings reconstructed from Eulerian trails in two edge-labeled graphs. GTED can be used to infer evolutionary relationships between species by comparing de Bruijn graphs directly without the computationally costly and error-prone process of genome assembly. Ebrahimpour Boroojeny et al. (2018) propose two ILP formulations for GTED and claim that GTED is polynomially solvable because the linear programming relaxation of one of the ILPs always yields optimal integer solutions. The claim that GTED is polynomially solvable is contradictory to the complexity results of existing string-to-graph matching problems. We resolve this conflict in complexity results by proving that GTED is NP-complete and showing that the ILPs proposed by Ebrahimpour Boroojeny et al. do not solve GTED but instead solve for a lower bound of GTED and are not solvable in polynomial time. In addition, we provide the first two, correct ILP formulations of GTED and evaluate their empirical efficiency. These results provide solid algorithmic foundations for comparing genome graphs and point to the direction of heuristics. The source code to reproduce experimental results is available athttps://github.com/Kingsford-Group/gtednewilp/. 

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2. An O(n5/4) Time ∊-Approximation Algorithm for RMS Matching in a Plane

   https://doi.org/10.1137/1.9781611976465.55  

   Lahn, Nathaniel; Raghvendra, Sharath (January 2021, Proceedings of the Annual ACMSIAM Symposium on Discrete Algorithms)

   null (Ed.)

   The 2-Wasserstein distance (or RMS distance) is a useful measure of similarity between probability distributions with exciting applications in machine learning. For discrete distributions, the problem of computing this distance can be expressed in terms of finding a minimum-cost perfect matching on a complete bipartite graph given by two multisets of points A, B ⊂ ℝ2, with |A| = |B| = n, where the ground distance between any two points is the squared Euclidean distance between them. Although there is a near-linear time relative ∊-approximation algorithm for the case where the ground distance is Euclidean (Sharathkumar and Agarwal, JACM 2020), all existing relative ∊-approximation algorithms for the RMS distance take Ω(n3/2) time. This is primarily because, unlike Euclidean distance, squared Euclidean distance is not a metric. In this paper, for the RMS distance, we present a new ∊-approximation algorithm that runs in O(n^5/4 poly{log n, 1/∊}) time. Our algorithm is inspired by a recent approach for finding a minimum-cost perfect matching in bipartite planar graphs (Asathulla et al, TALG 2020). Their algorithm depends heavily on the existence of sublinear sized vertex separators as well as shortest path data structures that require planarity. Surprisingly, we are able to design a similar algorithm for a complete geometric graph that is far from planar and does not have any vertex separators. Central components of our algorithm include a quadtree-based distance that approximates the squared Euclidean distance and a data structure that supports both Hungarian search and augmentation in sublinear time. 

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3. Separating the NP-Hardness of the Grothendieck Problem from the Little-Grothendieck Problem

   https://doi.org/10.4230/LIPIcs.ITCS.2022.22  

   Bhattiprolu, Vijay and (January 2022, Leibniz international proceedings in informatics)

   Braverman, Mark (Ed.)

   Grothendieck’s inequality [Grothendieck, 1953] states that there is an absolute constant K > 1 such that for any n× n matrix A, ‖A‖_{∞→1} := max_{s,t ∈ {± 1}ⁿ}∑_{i,j} A[i,j]⋅s(i)⋅t(j) ≥ 1/K ⋅ max_{u_i,v_j ∈ S^{n-1}}∑_{i,j} A[i,j]⋅⟨u_i,v_j⟩. In addition to having a tremendous impact on Banach space theory, this inequality has found applications in several unrelated fields like quantum information, regularity partitioning, communication complexity, etc. Let K_G (known as Grothendieck’s constant) denote the smallest constant K above. Grothendieck’s inequality implies that a natural semidefinite programming relaxation obtains a constant factor approximation to ‖A‖_{∞ → 1}. The exact value of K_G is yet unknown with the best lower bound (1.67…) being due to Reeds and the best upper bound (1.78…) being due to Braverman, Makarychev, Makarychev and Naor [Braverman et al., 2013]. In contrast, the little Grothendieck inequality states that under the assumption that A is PSD the constant K above can be improved to π/2 and moreover this is tight. The inapproximability of ‖A‖_{∞ → 1} has been studied in several papers culminating in a tight UGC-based hardness result due to Raghavendra and Steurer (remarkably they achieve this without knowing the value of K_G). Briet, Regev and Saket [Briët et al., 2015] proved tight NP-hardness of approximating the little Grothendieck problem within π/2, based on a framework by Guruswami, Raghavendra, Saket and Wu [Guruswami et al., 2016] for bypassing UGC for geometric problems. This also remained the best known NP-hardness for the general Grothendieck problem due to the nature of the Guruswami et al. framework, which utilized a projection operator onto the degree-1 Fourier coefficients of long code encodings, which naturally yielded a PSD matrix A. We show how to extend the above framework to go beyond the degree-1 Fourier coefficients, using the global structure of optimal solutions to the Grothendieck problem. As a result, we obtain a separation between the NP-hardness results for the two problems, obtaining an inapproximability result for the Grothendieck problem, of a factor π/2 + ε₀ for a fixed constant ε₀ > 0. 

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4. Cryptographic Hardness Under Projections for Time-Bounded Kolmogorov Complexity

   https://doi.org/10.4230/LIPIcs.ISAAC.2021.54  

   Allender, Eric; Gouwar, John; Hirahara, Shuichi; Robelle, Caleb (November 2021, Leibniz international proceedings in informatics)

   Ahn, Hee-Kap; Sadakane, Kunihiko (Ed.)

   A version of time-bounded Kolmogorov complexity, denoted KT, has received attention in the past several years, due to its close connection to circuit complexity and to the Minimum Circuit Size Problem MCSP. Essentially all results about the complexity of MCSP hold also for MKTP (the problem of computing the KT complexity of a string). Both MKTP and MCSP are hard for SZK (Statistical Zero Knowledge) under BPP-Turing reductions; neither is known to be NP-complete. Recently, some hardness results for MKTP were proved that are not (yet) known to hold for MCSP. In particular, MKTP is hard for DET (a subclass of P) under nonuniform ≤^{NC^0}_m reductions. In this paper, we improve this, to show that the complement of MKTP is hard for the (apparently larger) class NISZK_L under not only ≤^{NC^0}_m reductions but even under projections. Also, the complement of MKTP is hard for NISZK under ≤^{P/poly}_m reductions. Here, NISZK is the class of problems with non-interactive zero-knowledge proofs, and NISZK_L is the non-interactive version of the class SZK_L that was studied by Dvir et al. As an application, we provide several improved worst-case to average-case reductions to problems in NP, and we obtain a new lower bound on MKTP (which is currently not known to hold for MCSP). 

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5. Bipartite Matching in Nearly-linear Time on Moderately Dense Graphs

   https://doi.org/10.1109/FOCS46700.2020.00090  

   van den Brand, Jan; Lee, Yin-Tat; Nanongkai, Danupon; Peng, Richard; Saranurak, Thatchaphol; Sidford, Aaron; Song, Zhao; Wang, Di (November 2020, 61st IEEE Annual Symposium on Foundations of Computer Science, FOCS 2020, Durham, NC, USA, November 16-19, 2020)

   null (Ed.)

   We present an $$\tilde O(m+n^{1.5})$$-time randomized algorithm for maximum cardinality bipartite matching and related problems (e.g. transshipment, negative-weight shortest paths, and optimal transport) on $$m$$-edge, $$n$$-node graphs. For maximum cardinality bipartite matching on moderately dense graphs, i.e. $$m = \Omega(n^{1.5})$$, our algorithm runs in time nearly linear in the input size and constitutes the first improvement over the classic $$O(m\sqrt{n})$$-time [Dinic 1970; Hopcroft-Karp 1971; Karzanov 1973] and $$\tilde O(n^\omega)$$-time algorithms [Ibarra-Moran 1981] (where currently $$\omega\approx 2.373$$). On sparser graphs, i.e. when $$m = n^{9/8 + \delta}$$ for any constant $$\delta>0$$, our result improves upon the recent advances of [Madry 2013] and [Liu-Sidford 2020b, 2020a] which achieve an $$\tilde O(m^{4/3+o(1)})$$ runtime. We obtain these results by combining and advancing recent lines of research in interior point methods (IPMs) and dynamic graph algorithms. First, we simplify and improve the IPM of [v.d.Brand-Lee-Sidford-Song 2020], providing a general primal-dual IPM framework and new sampling-based techniques for handling infeasibility induced by approximate linear system solvers. Second, we provide a simple sublinear-time algorithm for detecting and sampling high-energy edges in electric flows on expanders and show that when combined with recent advances in dynamic expander decompositions, this yields efficient data structures for maintaining the iterates of both [v.d.Brand~et~al.] and our new IPMs. Combining this general machinery yields a simpler $$\tilde O(n \sqrt{m})$$ time algorithm for matching based on the logarithmic barrier function, and our state-of-the-art $$\tilde O(m+n^{1.5})$$ time algorithm for matching based on the [Lee-Sidford 2014] barrier (as regularized in [v.d.Brand~et~al.]). 

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