Related papers: Space efficient merging of de Bruijn graphs and Wh…
A recent surprising result in the implementation of worst-case-optimal (wco) multijoins in graph databases (specifically, basic graph patterns) is that they can be supported on graph representations that take even less space than a plain…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
We call a graph $G$ separable if a balanced separator can be computed for $G$ of size $O(n^c)$ with $c<1$. Many real-world graphs are separable such as graphs of bounded genus, graphs of constant treewidth, and graphs excluding a fixed…
Graph partitioning schedules parallel calculations like sparse matrix-vector multiply (SpMV). We consider contiguous partitions, where the $m$ rows (or columns) of a sparse matrix with $N$ nonzeros are split into $K$ parts without…
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…
With the development of cheap image sensors, the amount of available image data have increased enormously, and the possibility of using crowdsourced collection methods has emerged. This calls for development of ways to handle all these…
We spot a hole in the area of succinct data structures for graph classes from a universe of size at most $n^n$. Very often, the input graph is labeled by the user in an arbitrary and easy-to-use way, and the data structure for the graph…
Analysing Web graphs has applications in determining page ranks, fighting Web spam, detecting communities and mirror sites, and more. This study is however hampered by the necessity of storing a major part of huge graphs in the external…
This paper presents a novel meta algorithm, Partition-Merge (PM), which takes existing centralized algorithms for graph computation and makes them distributed and faster. In a nutshell, PM divides the graph into small subgraphs using our…
We consider the problem of designing a succinct data structure for {\it path graphs} (which are a proper subclass of chordal graphs and a proper superclass of interval graphs) on $n$ vertices while supporting degree, adjacency, and…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
This work addresses the challenge of using a deep learning model to prune graphs and the ability of this method to integrate explainability into spatio-temporal problems through a new approach. Instead of applying explainability to the…
We propose a weighted common subgraph (WCS) matching algorithm to find the most similar subgraphs in two labeled weighted graphs. WCS matching, as a natural generalization of the equal-sized graph matching or subgraph matching, finds wide…
In practical machine learning systems, graph based data representation has been widely used in various learning paradigms, ranging from unsupervised clustering to supervised classification. Besides those applications with natural graph or…
We develop a novel parallel decomposition strategy for unweighted, undirected graphs, based on growing disjoint connected clusters from batches of centers progressively selected from yet uncovered nodes. With respect to similar previous…
In this paper we show how to combine two algorithmic techniques to obtain linear time algorithms for various optimization problems on graphs, and present a subroutine which will be useful in doing so. The first technique is iterative…
A common way of partitioning graphs is through minimum cuts. One drawback of classical minimum cut methods is that they tend to produce small groups, which is why more balanced variants such as normalized and ratio cuts have seen more…
We consider the problem of designing succinct data structures for interval graphs with $n$ vertices while supporting degree, adjacency, neighborhood and shortest path queries in optimal time in the $\Theta(\log n)$-bit word RAM model. The…
Merging two sorted arrays is a prominent building block for sorting and other functions. Its efficient parallelization requires balancing the load among compute cores, minimizing the extra work brought about by parallelization, and…
Spectral clustering approaches have led to well-accepted algorithms for finding accurate clusters in a given dataset. However, their application to large-scale datasets has been hindered by computational complexity of eigenvalue…