An Optimal Algorithm for the Maximum-Density Segment Problem

We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers $w_{\min}$ and $w_{\max}$ and a sequence $S$ of $n$ number pairs $(a_i,w_i)$ with $w_i>0$. Let {\em segment} $S(i,j)$ of $S$ be the consecutive subsequence of $S$ between indices $i$ and $j$. The {\em density} of $S(i,j)$ is $d(i,j)=(a_i+a_{i+1}+...+a_j)/(w_i+w_{i+1}+...+w_j)$. The {\em maximum-density segment problem} is to find a maximum-density segment over all segments $S(i,j)$ with $w_{\min}\leq w_i+w_{i+1}+...+w_j \leq w_{\max}$. The best previously known algorithm for the problem, due to Goldwasser, Kao, and Lu, runs in $O(n\log(w_{\max}-w_{\min}+1))$ time. In the present paper, we solve the problem in O(n) time. Our approach bypasses the complicated {\em right-skew decomposition}, introduced by Lin, Jiang, and Chao. As a result, our algorithm has the capability to process the input sequence in an online manner, which is an important feature for dealing with genome-scale sequences. Moreover, for a type of input sequences $S$ representable in $O(m)$ space, we show how to exploit the sparsity of $S$ and solve the maximum-density segment problem for $S$ in $O(m)$ time.Comment: 15 pages, 12 figures, an early version of this paper was presented at 11th Annual European Symposium on Algorithms (ESA 2003), Budapest, Hungary, September 15-20, 200

A Center Transversal Theorem for Hyperplanes and Applications to Graph Drawing

Motivated by an open problem from graph drawing, we study several partitioning problems for line and hyperplane arrangements. We prove a ham-sandwich cut theorem: given two sets of n lines in R^2, there is a line l such that in both line sets, for both halfplanes delimited by l, there are n^{1/2} lines which pairwise intersect in that halfplane, and this bound is tight; a centerpoint theorem: for any set of n lines there is a point such that for any halfplane containing that point there are (n/3)^{1/2} of the lines which pairwise intersect in that halfplane. We generalize those results in higher dimension and obtain a center transversal theorem, a same-type lemma, and a positive portion Erdos-Szekeres theorem for hyperplane arrangements. This is done by formulating a generalization of the center transversal theorem which applies to set functions that are much more general than measures. Back to Graph Drawing (and in the plane), we completely solve the open problem that motivated our search: there is no set of n labelled lines that are universal for all n-vertex labelled planar graphs. As a side note, we prove that every set of n (unlabelled) lines is universal for all n-vertex (unlabelled) planar graphs

Algorithms for the Problems of Length-Constrained Heaviest Segments

We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a sequence of n real numbers and two real parameters L and U (L <= U), the maximum sum segment problem is to find a consecutive subsequence, called a segment, of length at least L and at most U such that the sum of the numbers in the subsequence is maximum. The maximum density segment problem is to find a segment of length at least L and at most U such that the density of the numbers in the subsequence is the maximum. For the first problem with non-uniform width there is an algorithm with time and space complexities in O(n). We present an algorithm with time complexity in O(n) and space complexity in O(U). For the second problem with non-uniform width there is a combinatorial solution with time complexity in O(n) and space complexity in O(U). We present a simple geometric algorithm with the same time and space complexities. We extend our algorithms to respectively solve the length-constrained k maximum sum segments problem in O(n+k) time and O(max{U, k}) space, and the length-constrained $k$ maximum density segments problem in O(n min{k, U-L}) time and O(U+k) space. We present extensions of our algorithms to find all the length-constrained segments having user specified sum and density in O(n+m) and O(nlog (U-L)+m) times respectively, where m is the number of output. Previously, there was no known algorithm with non-trivial result for these problems. We indicate the extensions of our algorithms to higher dimensions. All the algorithms can be extended in a straight forward way to solve the problems with non-uniform width and non-uniform weight.Comment: 21 pages, 12 figure

Regression Depth and Center Points

We show that, for any set of n points in d dimensions, there exists a hyperplane with regression depth at least ceiling(n/(d+1)). as had been conjectured by Rousseeuw and Hubert. Dually, for any arrangement of n hyperplanes in d dimensions there exists a point that cannot escape to infinity without crossing at least ceiling(n/(d+1)) hyperplanes. We also apply our approach to related questions on the existence of partitions of the data into subsets such that a common plane has nonzero regression depth in each subset, and to the computational complexity of regression depth problems.Comment: 14 pages, 3 figure

Model-based probing strategies for convex polygons

AbstractWe prove that n+4 finger probes are sufficient to determine the shape of a convex n-gon from a finite collection of models, improving the previous result of 2n+1. Further, we show that n−1 are necessary, proving this is optimal to within an additive constant. For line probes, we show that 2n+4 probes are sufficient and 2n−3 necessary. The difference between these results is particularly interesting in light of the duality relationship between finger and line probes

Partial-Matching and Hausdorff RMS Distance Under Translation: Combinatorics and Algorithms

We consider the RMS distance (sum of squared distances between pairs of points) under translation between two point sets in the plane, in two different setups. In the partial-matching setup, each point in the smaller set is matched to a distinct point in the bigger set. Although the problem is not known to be polynomial, we establish several structural properties of the underlying subdivision of the plane and derive improved bounds on its complexity. These results lead to the best known algorithm for finding a translation for which the partial-matching RMS distance between the point sets is minimized. In addition, we show how to compute a local minimum of the partial-matching RMS distance under translation, in polynomial time. In the Hausdorff setup, each point is paired to its nearest neighbor in the other set. We develop algorithms for finding a local minimum of the Hausdorff RMS distance in nearly linear time on the line, and in nearly quadratic time in the plane. These improve substantially the worst-case behavior of the popular ICP heuristics for solving this problem.Comment: 31 pages, 6 figure

Minimum Partial-Matching and Hausdorff RMS-Distance under Translation: Combinatorics and Algorithms

We consider the RMS-distance (sum of squared distances between pairs of points) under translation between two point sets in the plane. In the Hausdorff setup, each point is paired to its nearest neighbor in the other set. We develop algorithms for finding a local minimum in near-linear time on the line, and in nearly quadratic time in the plane. These improve substantially the worst-case behavior of the popular ICP heuristics for solving this problem. In the partial-matching setup, each point in the smaller set is matched to a distinct point in the bigger set. Although the problem is not known to be polynomial, we establish several structural properties of the underlying subdivision of the plane and derive improved bounds on its complexity. In addition, we show how to compute a local minimum of the partial-matching RMS-distance under translation, in polynomial time