Probability and Problems in Euclidean Combinatorial Optimization

This article summarizes the current status of several streams of research that deal with the probability theory of problems of combinatorial optimization. There is a particular emphasis on functionals of finite point sets. The most famous example of such functionals is the length associated with the Euclidean traveling salesman problem (TSP), but closely related problems include the minimal spanning tree problem, minimal matching problems and others. Progress is also surveyed on (1) the approximation and determination of constants whose existence is known by subadditive methods, (2) the central limit problems for several functionals closely related to Euclidean functionals, and (3) analogies in the asymptotic behavior between worst-case and expected-case behavior of Euclidean problems. No attempt has been made in this survey to cover the many important applications of probability to linear programming, arrangement searching or other problems that focus on lines or planes

Routing congestion analysis and reduction in deep sub-micron VLSI design

Congestion is one of the main optimization objectives in global routing. However, the optimization performance is constrained because the cells are already fixed at this stage. Therefore, designer can save substantial time and resources by detecting and reducing congested regions during the planning stages. An efficient and yet accurate congestion estimation model is crucial to be included in the inner loop of floorplanning and placement design. In this dissertation, we mainly focus on routing congestion modeling and reduction during floorplanning and placement

Equidistribution of Point Sets for the Traveling Salesman and Related Problems

Given a set S of n points in the unit square [0, 1)2, an optimal traveling salesman tour of S is a tour of S that is of minimum length. A worst-case point set for the Traveling Salesman Problem in the unit square is a point set S(n) whose optimal traveling salesman tour achieves the maximum possible length among all point sets S C [0, 1)2, where JSI = n. An open problem is to determine the structure of S(n). We show that for any rectangle R contained in [0, 1 F, the number of points in S(n) n R is asymptotic to n times the area of R. One corollary of this result is an 0( n log n) approximation algorithm for the worst-case Euclidean TSP. Analogous results are proved for the minimum spanning tree, minimum-weight matching, and rectilinear Steiner minimum tree. These equidistribution theorems are the first results concerning the structure of worst-case point sets like S(n)

Robustness Evaluation for Phylogenetic Reconstruction Methods and Evolutionary Models Reconstruction of Tumor Progression

During evolutionary history, genomes evolve by DNA mutation, genome rearrangement, duplication and gene loss events. There has been endless effort to the phylogenetic and ancestral genome inference study. Due to the great development of various technology, the information about genomes is exponentially increasing, which make it possible figure the problem out. The problem has been shown so interesting that a great number of algorithms have been developed rigorously over the past decades in attempts to tackle these problems following different kind of principles. However, difficulties and limits in performance and capacity, and also low consistency largely prevent us from confidently statement that the problem is solved. To know the detailed evolutionary history, we need to infer the phylogeny of the evolutionary history (Big Phylogeny Problem) and also infer the internal nodes information (Small Phylogeny Problem). The work presented in this thesis focuses on assessing methods designed for attacking Small Phylogeny Problem and algorithms and models design for genome evolution history inference from FISH data for cancer data. During the recent decades, a number of evolutionary models and related algorithms have been designed to infer ancestral genome sequences or gene orders. Due to the difficulty of knowing the true scenario of the ancestral genomes, there must be some tools used to test the robustness of the adjacencies found by various methods. When it comes to methods for Big Phylogeny Problem, to test the confidence rate of the inferred branches, previous work has tested bootstrapping, jackknifing, and isolating and found them good resampling tools to corresponding phylogenetic inference methods. However, till now there is still no system work done to try and tackle this problem for small phylogeny. We tested the earlier resampling schemes and a new method inversion on different ancestral genome reconstruction methods and showed different resampling methods are appropriate for their corresponding methods. Cancer is famous for its heterogeneity, which is developed by an evolutionary process driven by mutations in tumor cells. Rapid, simultaneous linear and branching evolution has been observed and analyzed by earlier research. Such process can be modeled by a phylogenetic tree using different methods. Previous phylogenetic research used various kinds of dataset, such as FISH data, genome sequence, and gene order. FISH data is quite clean for the reason that it comes form single cells and shown to be enough to infer evolutionary process for cancer development. RSMT was shown to be a good model for phylogenetic analysis by using FISH cell count pattern data, but it need efficient heuristics because it is a NP-hard problem. To attack this problem, we proposed an iterative approach to approximate solutions to the steiner tree in the small phylogeny tree. It is shown to give better results comparing to earlier method on both real and simulation data. In this thesis, we continued the investigation on designing new method to better approximate evolutionary process of tumor and applying our method to other kinds of data such as information using high-throughput technology. Our thesis work can be divided into two parts. First, we designed new algorithms which can give the same parsimony tree as exact method in most situation and modified it to be a general phylogeny building tool. Second, we applied our methods to different kinds data such as copy number variation information inferred form next generation sequencing technology and predict key changes during evolution

Optimal competitiveness for Symmetric Rectilinear Steiner Arborescence and related problems

We present optimal competitive algorithms for two interrelated known problems involving Steiner Arborescence. One is the continuous problem of the Symmetric Rectilinear Steiner Arborescence (SRSA), studied by Berman and Coulston. A very related, but discrete problem (studied separately in the past) is the online Multimedia Content Delivery (MCD) problem on line networks, presented originally by Papadimitriu, Ramanathan, and Rangan. An efficient content delivery was modeled as a low cost Steiner arborescence in a grid of network*time they defined. We study here the version studied by Charikar, Halperin, and Motwani (who used the same problem definitions, but removed some constraints on the inputs). The bounds on the competitive ratios introduced separately in the above papers are similar for the two problems: O(log N) for the continuous problem and O(log n) for the network problem, where N was the number of terminals to serve, and n was the size of the network. The lower bounds were Omega(sqrt{log N}) and Omega(sqrt{log n}) correspondingly. Berman and Coulston conjectured that both the upper bound and the lower bound could be improved. We disprove this conjecture and close these quadratic gaps for both problems. We first present an O(sqrt{log n}) deterministic competitive algorithm for MCD on the line, matching the lower bound. We then translate this algorithm to become a competitive optimal algorithm O(sqrt{log N}) for SRSA. Finally, we translate the latter back to solve MCD problem, this time competitive optimally even in the case that the number of requests is small (that is, O(min{sqrt{log n},sqrt{log N}})). We also present a Omega(sqrt[3]{log n}) lower bound on the competitiveness of any randomized algorithm. Some of the techniques may be useful in other contexts

Subadditive Euclidean Functionals and Nonlinear Growth in Geometric Probability

A limit theorem is established for a class of random processes (called here subadditive Euclidean functionals) which arise in problems of geometric probability. Particular examples include the length of shortest path through a random sample, the length of a rectilinear Steiner tree spanned by a sample, and the length of a minimal matching. Also, a uniform convergence theorem is proved which is needed in Karp\u27s probabilistic algorithm for the traveling salesman problem

Rectilinear Steiner Trees in Narrow Strips

A rectilinear Steiner tree for a set $P$ of points in $\mathbb{R}^2$ is a tree that connects the points in $P$ using horizontal and vertical line segments. The goal of Minimal Rectilinear Steiner Tree is to find a rectilinear Steiner tree with minimal total length. We investigate how the complexity of Minimal Rectilinear Steiner Tree for point sets $P$ inside the strip $(-\infty,+\infty)\times [0,\delta]$ depends on the strip width $\delta$. We obtain two main results. 1) We present an algorithm with running time $n^{O(\sqrt{\delta})}$ for sparse point sets, that is, point sets where each $1\times\delta$ rectangle inside the strip contains $O(1)$ points. 2) For random point sets, where the points are chosen randomly inside a rectangle of height $\delta$ and expected width $n$, we present an algorithm that is fixed-parameter tractable with respect to $\delta$ and linear in $n$. It has an expected running time of $2^{O(\delta \sqrt{\delta})} n$.Comment: 21 pages, 13 figure