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Volume

LIPIcs, Volume 129

35th International Symposium on Computational Geometry (SoCG 2019)

SoCG 2019, June 18-21, 2019, Portland, Oregon, USA

Editors: Gill Barequet and Yusu Wang

Document

DOI: 10.4230/LIPIcs.ESA.2025.42

(Multivariate) k-SUM as Barrier to Succinct Computation

Authors: Geri Gokaj, Marvin Künnemann, Sabine Storandt, and Carina Truschel

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract

How does the time complexity of a problem change when the input is given succinctly rather than explicitly? We study this question for several geometric problems defined on a set X of N points in ℤ^d. As succinct representation, we choose a sumset (or Minkowski sum) representation: Instead of receiving X explicitly, we are given sets A,B of n points that define X as A+B = {a+b∣ a ∈ A,b ∈ B}. We investigate the fine-grained complexity of this succinct version for several Õ(N)-time computable geometric primitives. Remarkably, we can tie their complexity tightly to the complexity of corresponding k-SUM problems. Specifically, we introduce as All-ints 3-SUM(n,n,k) the following multivariate, multi-output variant of 3-SUM: given sets A,B of size n and set C of size k, determine for all c ∈ C whether there are a ∈ A and b ∈ B with a+b = c. We obtain the following results: 1) Succinct closest L_∞-pair requires time N^{1-o(1)} under the 3-SUM hypothesis, while succinct furthest L_∞-pair can be solved in time Õ(n). 2) Succinct bichromatic closest L_∞-Pair requires time N^{1-o(1)} iff the 4-SUM hypothesis holds. 3) The following problems are fine-grained equivalent to All-ints 3-SUM(n,n,k): succinct skyline computation in 2D with output size k and succinct batched orthogonal range search with k given ranges. This establishes conditionally tight Õ(min{nk, N})-time algorithms for these problems. We obtain further connections with All-ints 3-SUM(n,n,k) for succinctly computing independent sets in unit interval graphs. Thus, (Multivariate) k-SUM problems precisely capture the barrier for enabling sumset-succinct computation for various geometric primitives.

Cite as

Geri Gokaj, Marvin Künnemann, Sabine Storandt, and Carina Truschel. (Multivariate) k-SUM as Barrier to Succinct Computation. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 42:1-42:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gokaj_et_al:LIPIcs.ESA.2025.42,
  author =	{Gokaj, Geri and K\"{u}nnemann, Marvin and Storandt, Sabine and Truschel, Carina},
  title =	{{(Multivariate) k-SUM as Barrier to Succinct Computation}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{42:1--42:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.42},
  URN =		{urn:nbn:de:0030-drops-245101},
  doi =		{10.4230/LIPIcs.ESA.2025.42},
  annote =	{Keywords: Fine-grained complexity theory, sumsets, additive combinatorics, succinct inputs, computational geometry}
}

Document

DOI: 10.4230/LIPIcs.ESA.2025.37

Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology

Authors: Henrique Ennes and Clément Maria

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract

Quantum invariants in low-dimensional topology offer a wide variety of valuable invariants about knots and 3-manifolds, presented by explicit formulas that are readily computable. Their computational complexity has been actively studied and is tightly connected to topological quantum computing. In this article, we prove that for any 3-manifold quantum invariant in the Reshetikhin-Turaev model, there is a deterministic polynomial time algorithm that, given as input an arbitrary closed 3-manifold M, outputs a closed 3-manifold M' with the same quantum invariant, such that M' is hyperbolic, contains no low genus embedded incompressible surface, and is presented by a strongly irreducible Heegaard diagram. Our construction relies on properties of Heegaard splittings and the Hempel distance. At the level of computational complexity, this proves that the hardness of computing a given quantum invariant of 3-manifolds is preserved even when severely restricting the topology and the combinatorics of the input. This positively answers a question raised by Samperton [Samperton, 2023].

Cite as

Henrique Ennes and Clément Maria. Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 37:1-37:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ennes_et_al:LIPIcs.ESA.2025.37,
  author =	{Ennes, Henrique and Maria, Cl\'{e}ment},
  title =	{{Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{37:1--37:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.37},
  URN =		{urn:nbn:de:0030-drops-245057},
  doi =		{10.4230/LIPIcs.ESA.2025.37},
  annote =	{Keywords: 3-manifold, Heegaard splitting, Hempel distance, Quantum invariant, polynomial time reduction}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2025.31

A Linear Time Algorithm for the Maximum Overlap of Two Convex Polygons Under Translation

Authors: Timothy M. Chan and Isaac M. Hair

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract

Given two convex polygons P and Q with n and m edges, the maximum overlap problem is to find a translation of P that maximizes the area of its intersection with Q. We give the first randomized algorithm for this problem with linear running time. Our result improves the previous two-and-a-half-decades-old algorithm by de Berg, Cheong, Devillers, van Kreveld, and Teillaud (1998), which ran in O((n+m)log(n+m)) time, as well as multiple recent algorithms given for special cases of the problem.

Cite as

Timothy M. Chan and Isaac M. Hair. A Linear Time Algorithm for the Maximum Overlap of Two Convex Polygons Under Translation. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 31:1-31:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chan_et_al:LIPIcs.SoCG.2025.31,
  author =	{Chan, Timothy M. and Hair, Isaac M.},
  title =	{{A Linear Time Algorithm for the Maximum Overlap of Two Convex Polygons Under Translation}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{31:1--31:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.31},
  URN =		{urn:nbn:de:0030-drops-231832},
  doi =		{10.4230/LIPIcs.SoCG.2025.31},
  annote =	{Keywords: Convex polygons, shape matching, prune-and-search, parametric search}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2025.6

A Sparse Multicover Bifiltration of Linear Size

Authors: Ángel Javier Alonso

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract

The k-cover of a point cloud X of ℝ^d at radius r is the set of all those points within distance r of at least k points of X. By varying r and k we obtain a two-parameter filtration known as the multicover bifiltration. This bifiltration has received attention recently due to being choice-free and robust to outliers. However, it is hard to compute: the smallest known equivalent simplicial bifiltration has O(|X|^{d+1}) simplices. In this paper we introduce a (1+ε)-approximation of the multicover bifiltration of linear size O(|X|), for fixed d and ε. The methods also apply to the subdivision Rips bifiltration on metric spaces of bounded doubling dimension yielding analogous results.

Cite as

Ángel Javier Alonso. A Sparse Multicover Bifiltration of Linear Size. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{alonso:LIPIcs.SoCG.2025.6,
  author =	{Alonso, \'{A}ngel Javier},
  title =	{{A Sparse Multicover Bifiltration of Linear Size}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.6},
  URN =		{urn:nbn:de:0030-drops-231587},
  doi =		{10.4230/LIPIcs.SoCG.2025.6},
  annote =	{Keywords: Multicover, Approximation, Sparsification, Multiparameter persistence}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2025.12

Higher-Order Color Voronoi Diagrams and the Colorful Clarkson-Shor Framework

Authors: Sang Won Bae, Nicolau Oliver, and Evanthia Papadopoulou

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract

Given a set S of n colored sites, each s ∈ S associated with a distance-to-site function δ_s : ℝ² → ℝ, we consider two distance-to-color functions for each color: one takes the minimum of δ_s for sites s ∈ S in that color and the other takes the maximum. These two sets of distance functions induce two families of higher-order Voronoi diagrams for colors in the plane, namely, the minimal and maximal order-k color Voronoi diagrams, which include various well-studied Voronoi diagrams as special cases. In this paper, we derive an exact upper bound 4k(n-k)-2n on the total number of vertices in both the minimal and maximal order-k color diagrams for a wide class of distance functions δ_s that satisfy certain conditions, including the case of point sites S under convex distance functions and the L_p metric for any 1 ≤ p ≤ ∞. For the L_1 (or, L_∞) metric, and other convex polygonal metrics, we show that the order-k minimal diagram of point sites has O(min{k(n-k), (n-k)²}) complexity, while its maximal counterpart has O(min{k(n-k), k²}) complexity. To obtain these combinatorial results, we extend the Clarkson-Shor framework to colored objects, and demonstrate its application to several fundamental geometric structures, including higher-order color Voronoi diagrams, colored j-facets, and levels in the arrangements of piecewise linear/algebraic curves/surfaces. We also present iterative algorithms to compute higher-order color Voronoi diagrams.

Cite as

Sang Won Bae, Nicolau Oliver, and Evanthia Papadopoulou. Higher-Order Color Voronoi Diagrams and the Colorful Clarkson-Shor Framework. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 12:1-12:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bae_et_al:LIPIcs.SoCG.2025.12,
  author =	{Bae, Sang Won and Oliver, Nicolau and Papadopoulou, Evanthia},
  title =	{{Higher-Order Color Voronoi Diagrams and the Colorful Clarkson-Shor Framework}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{12:1--12:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.12},
  URN =		{urn:nbn:de:0030-drops-231647},
  doi =		{10.4230/LIPIcs.SoCG.2025.12},
  annote =	{Keywords: higher-order Voronoi diagrams, color Voronoi diagrams, Hausdorff Voronoi diagrams, colored j-facets, arrangements, Clarkson-Shor technique}
}

Document

DOI: 10.4230/LIPIcs.ISAAC.2019.62

Unbounded Regions of High-Order Voronoi Diagrams of Lines and Segments in Higher Dimensions

Authors: Gill Barequet, Evanthia Papadopoulou, and Martin Suderland

Published in: LIPIcs, Volume 149, 30th International Symposium on Algorithms and Computation (ISAAC 2019)

Abstract

We study the behavior at infinity of the farthest and the higher-order Voronoi diagram of n line segments or lines in a d-dimensional Euclidean space. The unbounded parts of these diagrams can be encoded by a Gaussian map on the sphere of directions S^(d-1). We show that the combinatorial complexity of the Gaussian map for the order-k Voronoi diagram of n line segments or lines is O(min{k,n-k} n^(d-1)), which is tight for n-k = O(1). All the d-dimensional cells of the farthest Voronoi diagram are unbounded, its (d-1)-skeleton is connected, and it does not have tunnels. A d-cell of the Voronoi diagram is called a tunnel if the set of its unbounded directions, represented as points on its Gaussian map, is not connected. In a three-dimensional space, the farthest Voronoi diagram of lines has exactly n^2-n three-dimensional cells, when n >= 2. The Gaussian map of the farthest Voronoi diagram of line segments or lines can be constructed in O(n^(d-1) alpha(n)) time, while if d=3, the time drops to worst-case optimal O(n^2).

Cite as

Gill Barequet, Evanthia Papadopoulou, and Martin Suderland. Unbounded Regions of High-Order Voronoi Diagrams of Lines and Segments in Higher Dimensions. In 30th International Symposium on Algorithms and Computation (ISAAC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 149, pp. 62:1-62:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{barequet_et_al:LIPIcs.ISAAC.2019.62,
  author =	{Barequet, Gill and Papadopoulou, Evanthia and Suderland, Martin},
  title =	{{Unbounded Regions of High-Order Voronoi Diagrams of Lines and Segments in Higher Dimensions}},
  booktitle =	{30th International Symposium on Algorithms and Computation (ISAAC 2019)},
  pages =	{62:1--62:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-130-6},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{149},
  editor =	{Lu, Pinyan and Zhang, Guochuan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2019.62},
  URN =		{urn:nbn:de:0030-drops-115582},
  doi =		{10.4230/LIPIcs.ISAAC.2019.62},
  annote =	{Keywords: Voronoi diagram, lines, line segments, higher-order, order-k, unbounded, hypersphere arrangement, great hyperspheres}
}

Document

Complete Volume

DOI: 10.4230/LIPIcs.SoCG.2019

LIPIcs, Volume 129, SoCG'19, Complete Volume

Authors: Gill Barequet and Yusu Wang

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

LIPIcs, Volume 129, SoCG'19, Complete Volume

Cite as

35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@Proceedings{barequet_et_al:LIPIcs.SoCG.2019,
  title =	{{LIPIcs, Volume 129, SoCG'19, Complete Volume}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019},
  URN =		{urn:nbn:de:0030-drops-105562},
  doi =		{10.4230/LIPIcs.SoCG.2019},
  annote =	{Keywords: Theory of computation, Computational geometry, Design and analysis of algorithms, Mathematics of computing, Combinatorics, Graph algortihms}
}

Document

Front Matter

DOI: 10.4230/LIPIcs.SoCG.2019.0

Front Matter, Table of Contents, Preface, Conference Organization

Authors: Gill Barequet and Yusu Wang

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

Front Matter, Table of Contents, Preface, Conference Organization

Cite as

35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{barequet_et_al:LIPIcs.SoCG.2019.0,
  author =	{Barequet, Gill and Wang, Yusu},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{0:i--0:xvi},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.0},
  URN =		{urn:nbn:de:0030-drops-104047},
  doi =		{10.4230/LIPIcs.SoCG.2019.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}

Document

Invited Talk

DOI: 10.4230/LIPIcs.SoCG.2019.1

A Geometric Data Structure from Neuroscience (Invited Talk)

Authors: Sanjoy Dasgupta

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

An intriguing geometric primitive, "expand-and-sparsify", has been found in the olfactory system of the fly and several other organisms. It maps an input vector to a much higher-dimensional sparse representation, using a random linear transformation followed by winner-take-all thresholding. I will show that this representation has a variety of formal properties, such as locality preservation, that make it an attractive data structure for algorithms and machine learning. In particular, mimicking the fly’s circuitry yields algorithms for similarity search and for novelty detection that have provable guarantees as well as having practical performance that is competitive with state-of-the-art methods. This talk is based on work with Saket Navlakha (Salk Institute), Chuck Stevens (Salk Institute), and Chris Tosh (Columbia).

Cite as

Sanjoy Dasgupta. A Geometric Data Structure from Neuroscience (Invited Talk). In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, p. 1:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{dasgupta:LIPIcs.SoCG.2019.1,
  author =	{Dasgupta, Sanjoy},
  title =	{{A Geometric Data Structure from Neuroscience}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{1:1--1:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.1},
  URN =		{urn:nbn:de:0030-drops-104055},
  doi =		{10.4230/LIPIcs.SoCG.2019.1},
  annote =	{Keywords: Geometric data structure, algorithm design, neuroscience}
}

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Invited Talk

DOI: 10.4230/LIPIcs.SoCG.2019.2

Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk)

Authors: Bruce R. Donald

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

Computational protein design is a transformative field with exciting prospects for advancing both basic science and translational medical research. New algorithms blend discrete and continuous geometry to address the challenges of creating designer proteins. I will discuss recent progress in this area and some interesting open problems. I will motivate this talk by discussing how, by using continuous geometric representations within a discrete optimization framework, broadly-neutralizing anti-HIV-1 antibodies were computationally designed that are now being tested in humans - the designed antibodies are currently in eight clinical trials, one of which is Phase 2a (NCT03721510). These continuous representations model the flexibility and dynamics of biological macromolecules, which are an important structural determinant of function. However, reconstruction of biomolecular dynamics from experimental observables requires the determination of a conformational probability distribution. These distributions are not fully constrained by the limited geometric information from experiments, making the problem ill-posed in the sense of Hadamard. The ill-posed nature of the problem comes from the fact that it has no unique solution. Multiple or even an infinite number of solutions may exist. To avoid the ill-posed nature, the problem must be regularized by making (hopefully reasonable) assumptions. I will present new ways to both represent and visualize correlated inter-domain protein motions. We use Bingham distributions, based on a quaternion fit to circular moments of a physics-based quadratic form. To find the optimal solution for the distribution, we designed an efficient, provable branch-and-bound algorithm that exploits the structure of analytical solutions to the trigonometric moment problem. Hence, continuous conformational PDFs can be determined directly from NMR measurements. The representation works especially well for multi-domain systems with broad conformational distributions. For more information please see Y. Qi et al. Jour. Mol. Biol. 2018; 430(18 Pt B):3412-3426. doi: 10.1016/j.jmb.2018.06.022. Ultimately, this method has parallels to other branches of geometric computing that balance discrete and continuous representations, including physical geometric algorithms, robotics, computational geometry, and robust optimization. I will advocate for using continuous distributions for protein modeling, and describe future work and open problems.

Cite as

Bruce R. Donald. Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk). In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 2:1-2:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{donald:LIPIcs.SoCG.2019.2,
  author =	{Donald, Bruce R.},
  title =	{{Some Geometric and Computational Challenges Arising in Structural Molecular Biology}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{2:1--2:2},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.2},
  URN =		{urn:nbn:de:0030-drops-104065},
  doi =		{10.4230/LIPIcs.SoCG.2019.2},
  annote =	{Keywords: Geometric computing, combutational biology, Continuous Interdomain Orientation Distributions of Protein Conformations}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2019.3

A New Lower Bound for Semigroup Orthogonal Range Searching

Authors: Peyman Afshani

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

We report the first improvement in the space-time trade-off of lower bounds for the orthogonal range searching problem in the semigroup model, since Chazelle’s result from 1990. This is one of the very fundamental problems in range searching with a long history. Previously, Andrew Yao’s influential result had shown that the problem is already non-trivial in one dimension [Yao, 1982]: using m units of space, the query time Q(n) must be Omega(alpha(m,n) + n/(m-n+1)) where alpha(*,*) is the inverse Ackermann’s function, a very slowly growing function. In d dimensions, Bernard Chazelle [Chazelle, 1990] proved that the query time must be Q(n) = Omega((log_beta n)^{d-1}) where beta = 2m/n. Chazelle’s lower bound is known to be tight for when space consumption is "high" i.e., m = Omega(n log^{d+epsilon}n). We have two main results. The first is a lower bound that shows Chazelle’s lower bound was not tight for "low space": we prove that we must have m Q(n) = Omega(n (log n log log n)^{d-1}). Our lower bound does not close the gap to the existing data structures, however, our second result is that our analysis is tight. Thus, we believe the gap is in fact natural since lower bounds are proven for idempotent semigroups while the data structures are built for general semigroups and thus they cannot assume (and use) the properties of an idempotent semigroup. As a result, we believe to close the gap one must study lower bounds for non-idempotent semigroups or building data structures for idempotent semigroups. We develope significantly new ideas for both of our results that could be useful in pursuing either of these directions.

Cite as

Peyman Afshani. A New Lower Bound for Semigroup Orthogonal Range Searching. In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 3:1-3:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{afshani:LIPIcs.SoCG.2019.3,
  author =	{Afshani, Peyman},
  title =	{{A New Lower Bound for Semigroup Orthogonal Range Searching}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{3:1--3:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.3},
  URN =		{urn:nbn:de:0030-drops-104075},
  doi =		{10.4230/LIPIcs.SoCG.2019.3},
  annote =	{Keywords: Data Structures, Range Searching, Lower bounds}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2019.4

Independent Range Sampling, Revisited Again

Authors: Peyman Afshani and Jeff M. Phillips

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

We revisit the range sampling problem: the input is a set of points where each point is associated with a real-valued weight. The goal is to store them in a structure such that given a query range and an integer k, we can extract k independent random samples from the points inside the query range, where the probability of sampling a point is proportional to its weight. This line of work was initiated in 2014 by Hu, Qiao, and Tao and it was later followed up by Afshani and Wei. The first line of work mostly studied unweighted but dynamic version of the problem in one dimension whereas the second result considered the static weighted problem in one dimension as well as the unweighted problem in 3D for halfspace queries. We offer three main results and some interesting insights that were missed by the previous work: We show that it is possible to build efficient data structures for range sampling queries if we allow the query time to hold in expectation (the first result), or obtain efficient worst-case query bounds by allowing the sampling probability to be approximately proportional to the weight (the second result). The third result is a conditional lower bound that shows essentially one of the previous two concessions is needed. For instance, for the 3D range sampling queries, the first two results give efficient data structures with near-linear space and polylogarithmic query time whereas the lower bound shows with near-linear space the worst-case query time must be close to n^{2/3}, ignoring polylogarithmic factors. Up to our knowledge, this is the first such major gap between the expected and worst-case query time of a range searching problem.

Cite as

Peyman Afshani and Jeff M. Phillips. Independent Range Sampling, Revisited Again. In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{afshani_et_al:LIPIcs.SoCG.2019.4,
  author =	{Afshani, Peyman and Phillips, Jeff M.},
  title =	{{Independent Range Sampling, Revisited Again}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{4:1--4:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.4},
  URN =		{urn:nbn:de:0030-drops-104088},
  doi =		{10.4230/LIPIcs.SoCG.2019.4},
  annote =	{Keywords: Range Searching, Data Structures, Sampling}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2019.5

An Efficient Algorithm for Generalized Polynomial Partitioning and Its Applications

Authors: Pankaj K. Agarwal, Boris Aronov, Esther Ezra, and Joshua Zahl

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

In 2015, Guth proved that if S is a collection of n g-dimensional semi-algebraic sets in R^d and if D >= 1 is an integer, then there is a d-variate polynomial P of degree at most D so that each connected component of R^d \ Z(P) intersects O(n/D^{d-g}) sets from S. Such a polynomial is called a generalized partitioning polynomial. We present a randomized algorithm that computes such polynomials efficiently - the expected running time of our algorithm is linear in |S|. Our approach exploits the technique of quantifier elimination combined with that of epsilon-samples. We present four applications of our result. The first is a data structure for answering point-enclosure queries among a family of semi-algebraic sets in R^d in O(log n) time, with storage complexity and expected preprocessing time of O(n^{d+epsilon}). The second is a data structure for answering range search queries with semi-algebraic ranges in O(log n) time, with O(n^{t+epsilon}) storage and expected preprocessing time, where t > 0 is an integer that depends on d and the description complexity of the ranges. The third is a data structure for answering vertical ray-shooting queries among semi-algebraic sets in R^{d} in O(log^2 n) time, with O(n^{d+epsilon}) storage and expected preprocessing time. The fourth is an efficient algorithm for cutting algebraic planar curves into pseudo-segments.

Cite as

Pankaj K. Agarwal, Boris Aronov, Esther Ezra, and Joshua Zahl. An Efficient Algorithm for Generalized Polynomial Partitioning and Its Applications. In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 5:1-5:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{agarwal_et_al:LIPIcs.SoCG.2019.5,
  author =	{Agarwal, Pankaj K. and Aronov, Boris and Ezra, Esther and Zahl, Joshua},
  title =	{{An Efficient Algorithm for Generalized Polynomial Partitioning and Its Applications}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{5:1--5:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.5},
  URN =		{urn:nbn:de:0030-drops-104096},
  doi =		{10.4230/LIPIcs.SoCG.2019.5},
  annote =	{Keywords: Polynomial partitioning, quantifier elimination, semi-algebraic range spaces, epsilon-samples}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2019.6

Efficient Algorithms for Geometric Partial Matching

Authors: Pankaj K. Agarwal, Hsien-Chih Chang, and Allen Xiao

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)

Abstract

Let A and B be two point sets in the plane of sizes r and n respectively (assume r <= n), and let k be a parameter. A matching between A and B is a family of pairs in A x B so that any point of A cup B appears in at most one pair. Given two positive integers p and q, we define the cost of matching M to be c(M) = sum_{(a, b) in M}||a-b||_p^q where ||*||_p is the L_p-norm. The geometric partial matching problem asks to find the minimum-cost size-k matching between A and B. We present efficient algorithms for geometric partial matching problem that work for any powers of L_p-norm matching objective: An exact algorithm that runs in O((n + k^2)polylog n) time, and a (1 + epsilon)-approximation algorithm that runs in O((n + k sqrt{k})polylog n * log epsilon^{-1}) time. Both algorithms are based on the primal-dual flow augmentation scheme; the main improvements involve using dynamic data structures to achieve efficient flow augmentations. With similar techniques, we give an exact algorithm for the planar transportation problem running in O(min{n^2, rn^{3/2}}polylog n) time.

Cite as

Pankaj K. Agarwal, Hsien-Chih Chang, and Allen Xiao. Efficient Algorithms for Geometric Partial Matching. In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 6:1-6:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{agarwal_et_al:LIPIcs.SoCG.2019.6,
  author =	{Agarwal, Pankaj K. and Chang, Hsien-Chih and Xiao, Allen},
  title =	{{Efficient Algorithms for Geometric Partial Matching}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{6:1--6:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.6},
  URN =		{urn:nbn:de:0030-drops-104109},
  doi =		{10.4230/LIPIcs.SoCG.2019.6},
  annote =	{Keywords: partial matching, transportation, optimal transport, minimum-cost flow, bichromatic closest pair}
}

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