Longest Common Subsequence on Weighted Sequences

We consider the general problem of the Longest Common Subsequence (LCS) on weighted sequences. Weighted sequences are an extension of classical strings, where in each position every letter of the alphabet may occur with some probability. Previous results presented a PTAS and noticed that no FPTAS is possible unless P=NP. In this paper we essentially close the gap between upper and lower bounds by improving both. First of all, we provide an EPTAS for bounded alphabets (which is the most natural case), and prove that there does not exist any EPTAS for unbounded alphabets unless FPT=W[1]. Furthermore, under the Exponential Time Hypothesis, we provide a lower bound which shows that no significantly better PTAS can exist for unbounded alphabets. As a side note, we prove that it is sufficient to work with only one threshold in the general variant of the problem

Unifying Sparsest Cut, Cluster Deletion, and Modularity Clustering Objectives with Correlation Clustering

Graph clustering, or community detection, is the task of identifying groups of closely related objects in a large network. In this paper we introduce a new community-detection framework called LambdaCC that is based on a specially weighted version of correlation clustering. A key component in our methodology is a clustering resolution parameter, $\lambda$, which implicitly controls the size and structure of clusters formed by our framework. We show that, by increasing this parameter, our objective effectively interpolates between two different strategies in graph clustering: finding a sparse cut and forming dense subgraphs. Our methodology unifies and generalizes a number of other important clustering quality functions including modularity, sparsest cut, and cluster deletion, and places them all within the context of an optimization problem that has been well studied from the perspective of approximation algorithms. Our approach is particularly relevant in the regime of finding dense clusters, as it leads to a 2-approximation for the cluster deletion problem. We use our approach to cluster several graphs, including large collaboration networks and social networks

Resilient Level Ancestor, Bottleneck, and Lowest Common Ancestor Queries in Dynamic Trees

We study the problem of designing a resilient data structure maintaining a tree under the Faulty-RAM model [Finocchi and Italiano, STOC\u2704] in which up to ? memory words can be corrupted by an adversary. Our data structure stores a rooted dynamic tree that can be updated via the addition of new leaves, requires linear size, and supports resilient (weighted) level ancestor queries, lowest common ancestor queries, and bottleneck vertex queries in O(?) worst-case time per operation

Self-Evaluation Applied Mathematics 2003-2008 University of Twente

This report contains the self-study for the research assessment of the Department of Applied Mathematics (AM) of the Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) at the University of Twente (UT). The report provides the information for the Research Assessment Committee for Applied Mathematics, dealing with mathematical sciences at the three universities of technology in the Netherlands. It describes the state of affairs pertaining to the period 1 January 2003 to 31 December 2008

Separate, measure and conquer: faster polynomial-space algorithms for Max 2-CSP and counting dominating sets

We show a method resulting in the improvement of several polynomial-space, exponential-time algorithms. The method capitalizes on the existence of small balanced separators for sparse graphs, which can be exploited for branching to disconnect an instance into independent components. For this algorithm design paradigm, the challenge to date has been to obtain improvements in worst-case analyses of algorithms, compared with algorithms that are analyzed with advanced methods, notably Measure and Conquer. Our contribution is the design of a general method to integrate the advantage from the separator-branching into Measure and Conquer, for a more precise and improved running time analysi