Approximation Algorithms for Steiner Tree Problems Based on Universal Solution Frameworks

This paper summarizes the work on implementing few solutions for the Steiner Tree problem which we undertook in the PAAL project. The main focus of the project is the development of generic implementations of approximation algorithms together with universal solution frameworks. In particular, we have implemented Zelikovsky 11/6-approximation using local search framework, and 1.39-approximation by Byrka et al. using iterative rounding framework. These two algorithms are experimentally compared with greedy 2-approximation, with exact but exponential time Dreyfus-Wagner algorithm, as well as with results given by a state-of-the-art local search techniques by Uchoa and Werneck. The results of this paper are twofold. On one hand, we demonstrate that high level algorithmic concepts can be designed and efficiently used in C++. On the other hand, we show that the above algorithms with good theoretical guarantees, give decent results in practice, but are inferior to state-of-the-art heuristical approaches

A Note on the Practicality of Maximal Planar Subgraph Algorithms

Given a graph $G$, the NP-hard Maximum Planar Subgraph problem (MPS) asks for a planar subgraph of $G$ with the maximum number of edges. There are several heuristic, approximative, and exact algorithms to tackle the problem, but---to the best of our knowledge---they have never been compared competitively in practice. We report on an exploratory study on the relative merits of the diverse approaches, focusing on practical runtime, solution quality, and implementation complexity. Surprisingly, a seemingly only theoretically strong approximation forms the building block of the strongest choice.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

A Survey on Approximation in Parameterized Complexity: Hardness and Algorithms

Parameterization and approximation are two popular ways of coping with NP-hard problems. More recently, the two have also been combined to derive many interesting results. We survey developments in the area both from the algorithmic and hardness perspectives, with emphasis on new techniques and potential future research directions

A Unified PTAS for Prize Collecting TSP and Steiner Tree Problem in Doubling Metrics

We present a unified (randomized) polynomial-time approximation scheme (PTAS) for the prize collecting traveling salesman problem (PCTSP) and the prize collecting Steiner tree problem (PCSTP) in doubling metrics. Given a metric space and a penalty function on a subset of points known as terminals, a solution is a subgraph on points in the metric space, whose cost is the weight of its edges plus the penalty due to terminals not covered by the subgraph. Under our unified framework, the solution subgraph needs to be Eulerian for PCTSP, while it needs to be a tree for PCSTP. Before our work, even a QPTAS for the problems in doubling metrics is not known. Our unified PTAS is based on the previous dynamic programming frameworks proposed in [Talwar STOC 2004] and [Bartal, Gottlieb, Krauthgamer STOC 2012]. However, since it is unknown which part of the optimal cost is due to edge lengths and which part is due to penalties of uncovered terminals, we need to develop new techniques to apply previous divide-and-conquer strategies and sparse instance decompositions

ETH Tight Algorithms for Geometric Intersection Graphs: Now in Polynomial Space

De Berg et al. in [SICOMP 2020] gave an algorithmic framework for subexponential algorithms on geometric graphs with tight (up to ETH) running times. This framework is based on dynamic programming on graphs of weighted treewidth resulting in algorithms that use super-polynomial space. We introduce the notion of weighted treedepth and use it to refine the framework of de Berg et al. for obtaining polynomial space (with tight running times) on geometric graphs. As a result, we prove that for any fixed dimension d ≥ 2 on intersection graphs of similarly-sized fat objects many well-known graph problems including Independent Set, r-Dominating Set for constant r, Cycle Cover, Hamiltonian Cycle, Hamiltonian Path, Steiner Tree, Connected Vertex Cover, Feedback Vertex Set, and (Connected) Odd Cycle Transversal are solvable in time 2^(n^{1-1/d}) and within polynomial space.publishedVersio

Networking - A Statistical Physics Perspective

Efficient networking has a substantial economic and societal impact in a broad range of areas including transportation systems, wired and wireless communications and a range of Internet applications. As transportation and communication networks become increasingly more complex, the ever increasing demand for congestion control, higher traffic capacity, quality of service, robustness and reduced energy consumption require new tools and methods to meet these conflicting requirements. The new methodology should serve for gaining better understanding of the properties of networking systems at the macroscopic level, as well as for the development of new principled optimization and management algorithms at the microscopic level. Methods of statistical physics seem best placed to provide new approaches as they have been developed specifically to deal with non-linear large scale systems. This paper aims at presenting an overview of tools and methods that have been developed within the statistical physics community and that can be readily applied to address the emerging problems in networking. These include diffusion processes, methods from disordered systems and polymer physics, probabilistic inference, which have direct relevance to network routing, file and frequency distribution, the exploration of network structures and vulnerability, and various other practical networking applications.Comment: (Review article) 71 pages, 14 figure

Approximation Algorithms for Distributionally Robust Stochastic Optimization

Two-stage stochastic optimization is a widely used framework for modeling uncertainty, where we have a probability distribution over possible realizations of the data, called scenarios, and decisions are taken in two stages: we take first-stage actions knowing only the underlying distribution and before a scenario is realized, and may take additional second-stage recourse actions after a scenario is realized. The goal is typically to minimize the total expected cost. A common criticism levied at this model is that the underlying probability distribution is itself often imprecise. To address this, an approach that is quite versatile and has gained popularity in the stochastic-optimization literature is the two-stage distributionally robust stochastic model: given a collection D of probability distributions, our goal now is to minimize the maximum expected total cost with respect to a distribution in D. There has been almost no prior work however on developing approximation algorithms for distributionally robust problems where the underlying scenario collection is discrete, as is the case with discrete-optimization problems. We provide frameworks for designing approximation algorithms in such settings when the collection D is a ball around a central distribution, defined relative to two notions of distance between probability distributions: Wasserstein metrics (which include the L_1 metric) and the L_infinity metric. Our frameworks yield efficient algorithms even in settings with an exponential number of scenarios, where the central distribution may only be accessed via a sampling oracle. For distributionally robust optimization under a Wasserstein ball, we first show that one can utilize the sample average approximation (SAA) method (solve the distributionally robust problem with an empirical estimate of the central distribution) to reduce the problem to the case where the central distribution has a polynomial-size support, and is represented explicitly. This follows because we argue that a distributionally robust problem can be reduced in a novel way to a standard two-stage stochastic problem with bounded inflation factor, which enables one to use the SAA machinery developed for two-stage stochastic problems. Complementing this, we show how to approximately solve a fractional relaxation of the SAA problem (i.e., the distributionally robust problem obtained by replacing the original central distribution with its empirical estimate). Unlike in two-stage {stochastic, robust} optimization with polynomially many scenarios, this turns out to be quite challenging. We utilize a variant of the ellipsoid method for convex optimization in conjunction with several new ideas to show that the SAA problem can be approximately solved provided that we have an (approximation) algorithm for a certain max-min problem that is akin to, and generalizes, the k-max-min problem (find the worst-case scenario consisting of at most k elements) encountered in two-stage robust optimization. We obtain such an algorithm for various discrete-optimization problems; by complementing this via rounding algorithms that provide local (i.e., per-scenario) approximation guarantees, we obtain the first approximation algorithms for the distributionally robust versions of a variety of discrete-optimization problems including set cover, vertex cover, edge cover, facility location, and Steiner tree, with guarantees that are, except for set cover, within O(1)-factors of the guarantees known for the deterministic version of the problem. For distributionally robust optimization under an L_infinity ball, we consider a fractional relaxation of the problem, and replace its objective function with a proxy function that is pointwise close to the true objective function (within a factor of 2). We then show that we can efficiently compute approximate subgradients of the proxy function, provided that we have an algorithm for the problem of computing the t worst scenarios under a given first-stage decision, given an integer t. We can then approximately minimize the proxy function via a variant of the ellipsoid method, and thus obtain an approximate solution for the fractional relaxation of the distributionally robust problem. Complementing this via rounding algorithms with local guarantees, we obtain approximation algorithms for distributionally robust versions of various covering problems, including set cover, vertex cover, edge cover, and facility location, with guarantees that are within O(1)-factors of the guarantees known for their deterministic versions

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia