Related papers: A memory-efficient data structure representing exa…
We study the knapsack problem with graph theoretic constraints. That is, we assume that there exists a graph structure on the set of items of knapsack and the solution also needs to satisfy certain graph theoretic properties on top of…
Given a source of iid samples of edges of an input graph $G$ with $n$ vertices and $m$ edges, how many samples does one need to compute a constant factor approximation to the maximum matching size in $G$? Moreover, is it possible to obtain…
The (Perfect) Matching Cut problem is to decide if a connected graph has a (perfect) matching that is also an edge cut. The Disconnected Perfect Matching problem is to decide if a connected graph has a perfect matching that contains a…
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
In a graph, a matching cut is an edge cut that is a matching. Matching Cut is the problem of deciding whether or not a given graph has a matching cut, which is known to be NP-complete even when restricted to bipartite graphs. It has been…
Finding a maximum-cardinality or maximum-weight matching in (edge-weighted) undirected graphs is among the most prominent problems of algorithmic graph theory. For $n$-vertex and $m$-edge graphs, the best known algorithms run in…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
In the Survivable Network Design Problem (SNDP), the input is an edge-weighted (di)graph $G$ and an integer $r_{uv}$ for every pair of vertices $u,v\in V(G)$. The objective is to construct a subgraph $H$ of minimum weight which contains…
A graph $G = (V,E)$ can be described by the characteristic function of the edge set $\chi_E$ which maps a pair of binary encoded nodes to 1 iff the nodes are adjacent. Using \emph{Ordered Binary Decision Diagrams} (OBDDs) to store $\chi_E$…
Finding dense subgraphs is a core problem in graph mining with many applications in diverse domains. At the same time many real-world networks vary over time, that is, the dataset can be represented as a sequence of graph snapshots. Hence,…
Temporal graphs are graphs whose topology is subject to discrete changes over time. Given a static underlying graph $G$, a temporal graph is represented by assigning a set of integer time-labels to every edge $e$ of $G$, indicating the…
Maximal clique enumeration (MCE) is a fundamental problem in graph theory and is used in many applications, such as social network analysis, bioinformatics, intelligent agent systems, cyber security, etc. Most existing MCE algorithms focus…
Past studies on the local limit of maximal weight matchings in edge-weighted large random graphs rely fundamentally on the assumption that the weights are atomless, which ensures that the maximal weight matching is unique. This excludes de…
This paper shows the weighted matching problem on general graphs can be solved in time $O(n(m + n\log n))$ for $n$ and $m$ the number of vertices and edges, respectively. This was previously known only for bipartite graphs. The crux is a…
Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…
The discovery and analysis of network patterns are central to the scientific enterprise. In the present work, we developed and evaluated a new approach that learns the building blocks of graphs that can be used to understand and generate…
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the…
We propose Slim Graph: the first programming model and framework for practical lossy graph compression that facilitates high-performance approximate graph processing, storage, and analytics. Slim Graph enables the developer to express…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…