Optimality program in segment and string graphs

Planar graphs are known to allow subexponential algorithms running in time $2^{O(\sqrt n)}$ or $2^{O(\sqrt n \log n)}$ for most of the paradigmatic problems, while the brute-force time $2^{\Theta(n)}$ is very likely to be asymptotically best on general graphs. Intrigued by an algorithm packing curves in $2^{O(n^{2/3}\log n)}$ by Fox and Pach [SODA'11], we investigate which problems have subexponential algorithms on the intersection graphs of curves (string graphs) or segments (segment intersection graphs) and which problems have no such algorithms under the ETH (Exponential Time Hypothesis). Among our results, we show that, quite surprisingly, 3-Coloring can also be solved in time $2^{O(n^{2/3}\log^{O(1)}n)}$ on string graphs while an algorithm running in time $2^{o(n)}$ for 4-Coloring even on axis-parallel segments (of unbounded length) would disprove the ETH. For 4-Coloring of unit segments, we show a weaker ETH lower bound of $2^{o(n^{2/3})}$ which exploits the celebrated Erd\H{o}s-Szekeres theorem. The subexponential running time also carries over to Min Feedback Vertex Set but not to Min Dominating Set and Min Independent Dominating Set.Comment: 19 pages, 15 figure

Locked and Unlocked Polygonal Chains in 3D

In this paper, we study movements of simple polygonal chains in 3D. We say that an open, simple polygonal chain can be straightened if it can be continuously reconfigured to a straight sequence of segments in such a manner that both the length of each link and the simplicity of the chain are maintained throughout the movement. The analogous concept for closed chains is convexification: reconfiguration to a planar convex polygon. Chains that cannot be straightened or convexified are called locked. While there are open chains in 3D that are locked, we show that if an open chain has a simple orthogonal projection onto some plane, it can be straightened. For closed chains, we show that there are unknotted but locked closed chains, and we provide an algorithm for convexifying a planar simple polygon in 3D with a polynomial number of moves.Comment: To appear in Proc. 10th ACM-SIAM Sympos. Discrete Algorithms, Jan. 199

Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract)

We consider a model of algorithmic self-assembly of geometric shapes out of square Wang tiles studied in SODA 2010, in which there are two types of tiles (e.g., constructed out of DNA and RNA material) and one operation that destroys all tiles of a particular type (e.g., an RNAse enzyme destroys all RNA tiles). We show that a single use of this destruction operation enables much more efficient construction of arbitrary shapes. In particular, an arbitrary shape can be constructed using an asymptotically optimal number of distinct tile types (related to the shape's Kolmogorov complexity), after scaling the shape by only a logarithmic factor. By contrast, without the destruction operation, the best such result has a scale factor at least linear in the size of the shape, and is connected only by a spanning tree of the scaled tiles. We also characterize a large collection of shapes that can be constructed efficiently without any scaling

Signal Transmission Across Tile Assemblies: 3D Static Tiles Simulate Active Self-Assembly by 2D Signal-Passing Tiles

The 2-Handed Assembly Model (2HAM) is a tile-based self-assembly model in which, typically beginning from single tiles, arbitrarily large aggregations of static tiles combine in pairs to form structures. The Signal-passing Tile Assembly Model (STAM) is an extension of the 2HAM in which the tiles are dynamically changing components which are able to alter their binding domains as they bind together. For our first result, we demonstrate useful techniques and transformations for converting an arbitrarily complex STAM$^+$ tile set into an STAM$^+$ tile set where every tile has a constant, low amount of complexity, in terms of the number and types of ``signals'' they can send, with a trade off in scale factor. Using these simplifications, we prove that for each temperature $\tau>1$ there exists a 3D tile set in the 2HAM which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $\tau$ (where the STAM$^+$ does not make use of the STAM's power of glue deactivation and assembly breaking, as the tile components of the 2HAM are static and unable to change or break bonds). This means that there is a single tile set $U$ in the 3D 2HAM which can, for an arbitrarily complex STAM$^+$ system $S$, be configured with a single input configuration which causes $U$ to exactly simulate $S$ at a scale factor dependent upon $S$. Furthermore, this simulation uses only two planes of the third dimension. This implies that there exists a 3D tile set at temperature $2$ in the 2HAM which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $1$. Moreover, we show that for each temperature $\tau>1$ there exists an STAM$^+$ tile set which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $\tau$, including the case where $\tau = 1$.Comment: A condensed version of this paper will appear in a special issue of Natural Computing for papers from DNA 19. This full version contains proofs not seen in the published versio

Beyond Worst-Case Analysis for Joins with Minesweeper

We describe a new algorithm, Minesweeper, that is able to satisfy stronger runtime guarantees than previous join algorithms (colloquially, `beyond worst-case guarantees') for data in indexed search trees. Our first contribution is developing a framework to measure this stronger notion of complexity, which we call {\it certificate complexity}, that extends notions of Barbay et al. and Demaine et al.; a certificate is a set of propositional formulae that certifies that the output is correct. This notion captures a natural class of join algorithms. In addition, the certificate allows us to define a strictly stronger notion of runtime complexity than traditional worst-case guarantees. Our second contribution is to develop a dichotomy theorem for the certificate-based notion of complexity. Roughly, we show that Minesweeper evaluates $\beta$-acyclic queries in time linear in the certificate plus the output size, while for any $\beta$-cyclic query there is some instance that takes superlinear time in the certificate (and for which the output is no larger than the certificate size). We also extend our certificate-complexity analysis to queries with bounded treewidth and the triangle query.Comment: [This is the full version of our PODS'2014 paper.

Locked and Unlocked Polygonal Chains in Three Dimensions

This paper studies movements of polygonal chains in three dimensions whose links are not allowed to cross or change length. Our main result is an algorithmic proof that any simple closed chain that initially takes the form of a planar polygon can be made convex in three dimensions. Other results include an algorithm for straightening open chains having a simple orthogonal projection onto some plane, and an algorithm for making convex any open chain initially configured on the surface of a polytope. All our algorithms require only O (n) basic moves.

A PTAS for planar group Steiner tree via spanner bootstrapping and prize collecting

We present the first polynomial-time approximation scheme (PTAS), i.e., (1 + ϵ)-approximation algorithm for any constant ϵ > 0, for the planar group Steiner tree problem (in which each group lies on a boundary of a face). This result improves on the best previous approximation factor of O(logn(loglogn)O(1)). We achieve this result via a novel and powerful technique called spanner bootstrapping, which allows one to bootstrap from a superconstant approximation factor (even superpolynomial in the input size) all the way down to a PTAS. This is in contrast with the popular existing approach for planar PTASs of constructing lightweight spanners in one iteration, which notably requires a constant-factor approximate solution to start from. Spanner bootstrapping removes one of the main barriers for designing PTASs for problems which have no known constant-factor approximation (even on planar graphs), and thus can be used to obtain PTASs for several difficult-to-approximate problems. Our second major contribution required for the planar group Steiner tree PTAS is a spanner construction, which reduces the graph to have total weight within a factor of the optimal solution while approximately preserving the optimal solution. This is particularly challenging because group Steiner tree requires deciding which terminal in each group to connect by the tree, making it much harder than recent previous approaches to construct spanners for planar TSP by Klein [SIAM J. Computing 2008], subset TSP by Klein [STOC 2006], Steiner tree by Borradaile, Klein, and Mathieu [ACM Trans. Algorithms 2009], and Steiner forest by Bateni, Hajiaghayi, and Marx [J. ACM 2011] (and its improvement to an efficient PTAS by Eisenstat, Klein, and Mathieu [SODA 2012]. The main conceptual contribution here is realizing that selecting which terminals may be relevant is essentially a complicated prize-collecting process: we have to carefully weigh the cost and benefits of reaching or avoiding certain terminals in the spanner. Via a sequence of involved prize-collecting procedures, we can construct a spanner that reaches a set of terminals that is sufficient for an almost-optimal solution. Our PTAS for planar group Steiner tree implies the first PTAS for geometric Euclidean group Steiner tree with obstacles, as well as a (2 + ϵ)-approximation algorithm for group TSP with obstacles, improving over the best previous constant-factor approximation algorithms. By contrast, we show that planar group Steiner forest, a slight generalization of planar group Steiner tree, is APX-hard on planar graphs of treewidth 3, even if the groups are pairwise disjoint and every group is a vertex or an edge

Collaborative Delivery with Energy-Constrained Mobile Robots

We consider the problem of collectively delivering some message from a specified source to a designated target location in a graph, using multiple mobile agents. Each agent has a limited energy which constrains the distance it can move. Hence multiple agents need to collaborate to move the message, each agent handing over the message to the next agent to carry it forward. Given the positions of the agents in the graph and their respective budgets, the problem of finding a feasible movement schedule for the agents can be challenging. We consider two variants of the problem: in non-returning delivery, the agents can stop anywhere; whereas in returning delivery, each agent needs to return to its starting location, a variant which has not been studied before. We first provide a polynomial-time algorithm for returning delivery on trees, which is in contrast to the known (weak) NP-hardness of the non-returning version. In addition, we give resource-augmented algorithms for returning delivery in general graphs. Finally, we give tight lower bounds on the required resource augmentation for both variants of the problem. In this sense, our results close the gap left by previous research.Comment: 19 pages. An extended abstract of this paper was published at the 23rd International Colloquium on Structural Information and Communication Complexity 2016, SIROCCO'1

(Total) Vector Domination for Graphs with Bounded Branchwidth

Given a graph $G=(V,E)$ of order $n$ and an $n$-dimensional non-negative vector $d=(d(1),d(2),\ldots,d(n))$, called demand vector, the vector domination (resp., total vector domination) is the problem of finding a minimum $S\subseteq V$ such that every vertex $v$ in $V\setminus S$ (resp., in $V$) has at least $d(v)$ neighbors in $S$. The (total) vector domination is a generalization of many dominating set type problems, e.g., the dominating set problem, the $k$-tuple dominating set problem (this $k$ is different from the solution size), and so on, and its approximability and inapproximability have been studied under this general framework. In this paper, we show that a (total) vector domination of graphs with bounded branchwidth can be solved in polynomial time. This implies that the problem is polynomially solvable also for graphs with bounded treewidth. Consequently, the (total) vector domination problem for a planar graph is subexponential fixed-parameter tractable with respectto $k$, where $k$ is the size of solution.Comment: 16 page

Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM

We study the difference between the standard seeded model (aTAM) of tile self-assembly, and the "seedless" two-handed model of tile self-assembly (2HAM). Most of our results suggest that the two-handed model is more powerful. In particular, we show how to simulate any seeded system with a two-handed system that is essentially just a constant factor larger. We exhibit finite shapes with a busy-beaver separation in the number of distinct tiles required by seeded versus two-handed, and exhibit an infinite shape that can be constructed two-handed but not seeded. Finally, we show that verifying whether a given system uniquely assembles a desired supertile is co-NP-complete in the two-handed model, while it was known to be polynomially solvable in the seeded model.National Science Foundation (U.S.) (NSF grant CDI-0941538