arXiv subjects

Ljiljana Brankovic

Publications and source records attributed to Ljiljana Brankovic.

4 recordsLinked to original sources

arXiv2015

Linear-Time Superbubble Identification Algorithm for Genome Assembly

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce masses of data in the form of short sequences known as reads. Assembling these reads into a whole genome constitutes a major algorithmic challenge. Most assembly algorithms utilize de Bruijn graphs constructed from reads for this purpose. A critical step of these algorithms is to detect typical motif structures in the graph caused by sequencing errors and genome repeats, and filter them out; one such complex subgraph class is a so-called superbubble. In this paper, we propose an O(n+m)-time algorithm to detect all superbubbles in a directed acyclic graph with n nodes and m (directed) edges, improving the best-known O(m log m)-time algorithm by Sung et al.

cs.DS↗

arXiv2015

Algorithmic Aspects of Upper Domination

In this paper we study combinatorial and algorithmic resp. complexity questions of upper domination, i.e., the maximum cardinality of a minimal dominating set in a graph. We give a full classification of the related maximisation and minimisation problems, as well as the related parameterised problems, on general graphs and on graphs of bounded degree, and we also study planar graphs.

cs.CC↗

arXiv2014

Quantifying Privacy: A Novel Entropy-Based Measure of Disclosure Risk

It is well recognised that data mining and statistical analysis pose a serious treat to privacy. This is true for financial, medical, criminal and marketing research. Numerous techniques have been proposed to protect privacy, including restriction and data modification. Recently proposed privacy models such as differential privacy and k-anonymity received a lot of attention and for the latter there are now several improvements of the original scheme, each removing some security shortcomings of the previous one. However, the challenge lies in evaluating and comparing privacy provided by various techniques. In this paper we propose a novel entropy based security measure that can be applied to any generalisation, restriction or data modification technique. We use our measure to empirically evaluate and compare a few popular methods, namely query restriction, sampling and noise addition.

cs.CR↗

arXiv2009

Breaking the 2^n-Barrier for Irredundance: A Parameterized Route to Solving Exact Puzzles

The lower and the upper irredundance numbers of a graph $G$, denoted $ir(G)$ and $IR(G)$ respectively, are conceptually linked to domination and independence numbers and have numerous relations to other graph parameters. It is a long-standing open question whether determining these numbers for a graph $G$ on $n$ vertices admits exact algorithms running in time less than the trivial $Ω(2^n)$ enumeration barrier. We solve these open problems by devising parameterized algorithms for the dual of the natural parameterizations of the problems with running times faster than $O^*(4^{k})$. For example, we present an algorithm running in time $O^*(3.069^{k})$ for determining whether $IR(G)$ is at least $n-k$. Although the corresponding problem has been known to be in FPT by kernelization techniques, this paper offers the first parameterized algorithms with an exponential dependency on the parameter in the running time. Additionally, our work also appears to be the first example of a parameterized approach leading to a solution to a problem in exponential time algorithmics where the natural interpretation as an exact exponential-time algorithm fails.

cs.DS↗