Related papers: Efficient Parallel and Out of Core Algorithms for …
We study graph connectivity problem in MPC model. On an undirected graph with $n$ nodes and $m$ edges, $O(\log n)$ round connectivity algorithms have been known for over 35 years. However, no algorithms with better complexity bounds were…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
Cycles are one of the fundamental subgraph patterns and being able to enumerate them in graphs enables important applications in a wide variety of fields, including finance, biology, chemistry, and network science. However, to enable cycle…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
One of the simplest problems on directed graphs is that of identifying the set of vertices reachable from a designated source vertex. This problem can be solved easily sequentially by performing a graph search, but efficient parallel…
Graph clustering has many important applications in computing, but due to growing sizes of graphs, even traditionally fast clustering methods such as spectral partitioning can be computationally expensive for real-world graphs of interest.…
Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many…
The binary-forking model is a parallel computation model, formally defined by Blelloch et al. very recently, in which a thread can fork a concurrent child thread, recursively and asynchronously. The model incurs a cost of $\Theta(\log n)$…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…
We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of…
We develop an efficient parallel algorithm for answering shortest-path queries in planar graphs and implement it on a multi-node CPU/GPU clusters. The algorithm uses a divide-and-conquer approach for decomposing the input graph into small…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
Many of the classic graph problems cannot be solved in the Massively Parallel Computation setting (MPC) with strongly sublinear space per machine and $o(\log n)$ rounds, unless the 1-vs-2 cycles conjecture is false. This is true even on…
Graphs are fundamental objects that find widespread applications across computer science and beyond. Graph Theory has yielded deep insights about structural properties of various families of graphs, which are leveraged in the design and…
The problem of finding dense components of a graph is a widely explored area in data analysis, with diverse applications in fields and branches of study including community mining, spam detection, computer security and bioinformatics. This…
Graph algorithms and techniques are increasingly being used in scientific and commercial applications to express relations and explore large data sets. Although conventional or commodity computer architectures, like CPU or GPU, can compute…
The subgraph enumeration problem asks us to find all subgraphs of a target graph that are isomorphic to a given pattern graph. Determining whether even one such isomorphic subgraph exists is NP-complete---and therefore finding all such…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
We present an efficient distributed memory parallel algorithm for computing connected components in undirected graphs based on Shiloach-Vishkin's PRAM approach. We discuss multiple optimization techniques that reduce communication volume as…
We developed a flexible parallel algorithm for graph summarization based on vertex-centric programming and parameterized message passing. The base algorithm supports infinitely many structural graph summary models defined in a formal…